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Java Web Services Development Pack
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Java Web Services Development Pack
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The Java Web Services Development Pack (JWSDP) is a free software development kit (SDK) for developing Web Services, Web applications and Java applications with the newest technologies for Java.
Oracle replaced JWSDP with GlassFish. All components of JWSDP are part of GlassFish and WSIT and several are in Java SE 6 ("Mustang"). The source is available under the Open Source Initiative-approved CDDL license.
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Java Web Services Development Pack
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Java APIs
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These are the components and APIs available in the JWSDP 1.6: Java API for XML Processing (JAXP), v 1.3 Java API for XML Registries (JAXR) Java Architecture for XML Binding (JAXB), v 1.0 and 2.0 JAX-RPC v 1.1 JAX-WS v 2.0 SAAJ (SOAP with Attachments API for Java) Web Services RegistryStarting with JWSDP 1.6, the JAX-RPC and JAX-WS implementations support the Fast Infoset standard for the binary encoding of the XML infoset. Earlier versions of JWSDP also included Java Servlet JavaServer Pages JavaServer Faces
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Java Web Services Development Pack
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Related technologies
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There are many other Java implementations of Web Services or XML processors. Some of them support the Java standards, some support other standards or non-standard features. Related technologies include: Eclipse Metro - web services stack from GlassFish Apache Axis - web services framework XINS - RPC/web services framework xmlenc - XML output library JBossWS - web services stack from JBoss
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Eileen Southgate
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Eileen Southgate
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Eileen Southgate is a British biologist who mapped the complete nervous system of the roundworm Caenorhabditis elegans (C. elegans), together with John White, Nichol Thomson, and Sydney Brenner. The work, done largely by hand-tracing thousands of serial section electron micrographs, was the first complete nervous system map of any animal and it helped establish C. elegans as a model organism. Among other projects carried out as a laboratory assistant at the Medical Research Council Laboratory of Molecular Biology (MRC-LMB), Southgate contributed to work on solving the structure of hemoglobin with Max Perutz and John Kendrew, and investigating the causes of sickle cell disease with Vernon Ingram.
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Eileen Southgate
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Career
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Southgate spent her entire career as a laboratory technician at the Medical Research Council Laboratory of Molecular Biology (MRC LMB). She began working there in 1956, at the age of 16, after being given the option by a career officer who came to her school.Southgate initially worked for Max Perutz and John Kendrew studying hemoglobin, the protein responsible for carrying oxygen throughout the bloodstream, and the related protein myoglobin. Among other jobs, she was tasked with helping prepare hemoglobin and myoglobin for x-ray crystallography, a technique used to determine the structures of crystallized molecules such as proteins, based on how they interact with x-ray beams to produce a diffraction pattern. Thanks in part to Southgate's assistance, Perutz and Kendrew solved crystal structures of hemoglobin and myoglobin, winning them the 1962 Nobel Prize in chemistry for “for being the first to successfully identify the structures of complex proteins.” Southgate carried out additional research on hemoglobin with Vernon Ingram, assisting with his research on sickle cell disease, a genetic disease in which a mutation in hemoglobin causes it to form chains (polymerize) and block blood vessels.In 1962, Southgate briefly worked with Reuben Lebermen on his studies of plant viruses; she grew the plants, which were then infected by viruses he wanted to study, then she harvested them and purified out the viral particles. She then went to work for Tony Stretton, where after initial work involved helping him investigate β-galactosidase, she aided in his exploration of the nervous system of the parasitic nematode Ascaris lumbricoides using light microscopy. When Stretton left for the University of Wisconsin in 1971, Southgate went to work with John White, who was then a PhD student under Sydney Brenner.Brenner was interested in establishing C. elegans as a model organism at MRC LMB, and using it to study the nervous system and its connection to genetics. In pursuit of this goal, he wanted to obtain a complete map of the C. elegans nervous system, and Southgate was tasked with helping John White and electron microscopist Nichol Thomas achieve this. C. elegans is around 100 times smaller than Ascaris (~1mm compared to ~10 cm), so they had to use a higher-resolution imaging technique, electron microscopy. Nichol Thomson helped prepare thousands of serial transverse sections of C. elegans worms, which Southgate imaged, printed out, and traced. She labeled the cell bodies, processes, and connections in each image and worked with John White to trace each neuron's journey through the worm. The process took close to 15 years and culminated in a 340-page-long paper published in 1986 in the Philosophical Transactions of the Royal Society B. Officially titled “The structure of the nervous system of the nematode Caenorhabditis elegans,” it is commonly referred to by its running title, “The Mind of a Worm.” They identified 302 neurons in the hermaphrodite C. elegans worm, which they grouped into 118 classes, and they discovered that the layout and connections were virtually the same in genetically-identical worms. They found close to 8,000 total synapses (cell to cell connections) which included around 2000 neuromuscular junctions, 5000 chemical synapses & 600 gap junctions (where communication is through electrical signals). Having the map helped establish C. elegans as a model organism and allowed for further research into neural circuitry and the genes involved in establishing C. elegans' neural layout. Additionally, it aided researchers in studying analogous nerves other nematodes, including Ascaris, which, due to its larger size, is more amenable to electrophysiological investigation. Southgate retired in 1993.
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Tanabe–Sugano diagram
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Tanabe–Sugano diagram
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In coordination chemistry, Tanabe–Sugano diagrams are used to predict absorptions in the ultraviolet (UV), visible and infrared (IR) electromagnetic spectrum of coordination compounds. The results from a Tanabe–Sugano diagram analysis of a metal complex can also be compared to experimental spectroscopic data. They are qualitatively useful and can be used to approximate the value of 10Dq, the ligand field splitting energy. Tanabe–Sugano diagrams can be used for both high spin and low spin complexes, unlike Orgel diagrams, which apply only to high spin complexes. Tanabe–Sugano diagrams can also be used to predict the size of the ligand field necessary to cause high-spin to low-spin transitions.
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Tanabe–Sugano diagram
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Tanabe–Sugano diagram
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In a Tanabe–Sugano diagram, the ground state is used as a constant reference, in contrast to Orgel diagrams. The energy of the ground state is taken to be zero for all field strengths, and the energies of all other terms and their components are plotted with respect to the ground term.
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Tanabe–Sugano diagram
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Background
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Until Yukito Tanabe and Satoru Sugano published their paper "On the absorption spectra of complex ions", in 1954, little was known about the excited electronic states of complex metal ions. They used Hans Bethe's crystal field theory and Giulio Racah's linear combinations of Slater integrals, now called Racah parameters, to explain the absorption spectra of octahedral complex ions in a more quantitative way than had been achieved previously. Many spectroscopic experiments later, they estimated the values for two of Racah's parameters, B and C, for each d-electron configuration based on the trends in the absorption spectra of isoelectronic first-row transition metals. The plots of the energies calculated for the electronic states of each electron configuration are now known as Tanabe–Sugano diagrams.
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Tanabe–Sugano diagram
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Background
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Number must be fit for each octahedral coordination complex because the C/B can deviate strongly from the theoretical value of 4.0. This ratio changes the relative energies of the levels in the Tanabe–Sugano diagrams, and thus the diagrams may vary slightly between sources depending on what C/B ratio was selected when plotting.
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Tanabe–Sugano diagram
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Parameters
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The x-axis of a Tanabe–Sugano diagram is expressed in terms of the ligand field splitting parameter, Δ, or Dq (for "differential of quanta"), divided by the Racah parameter B. The y-axis is in terms of energy, E, also scaled by B. Three Racah parameters exist, A, B, and C, which describe various aspects of interelectronic repulsion. A is an average total interelectron repulsion. B and C correspond with individual d-electron repulsions. A is constant among d-electron configuration, and it is not necessary for calculating relative energies, hence its absence from Tanabe and Sugano's studies of complex ions. C is necessary only in certain cases. B is the most important of Racah's parameters in this case. One line corresponds to each electronic state. The bending of certain lines is due to the mixing of terms with the same symmetry. Although electronic transitions are only "allowed" if the spin multiplicity remains the same (i.e. electrons do not change from spin up to spin down or vice versa when moving from one energy level to another), energy levels for "spin-forbidden" electronic states are included in the diagrams, which are also not included in Orgel diagrams. Each state is given its molecular-symmetry label (e.g. A1g, T2g, etc.), but "g" and "u" subscripts are usually left off because it is understood that all the states are gerade. Labels for each state are usually written on the right side of the table, though for more complicated diagrams (e.g. d6) labels may be written in other locations for clarity. Term symbols (e.g. 3P, 1S, etc.) for a specific dn free ion are listed, in order of increasing energy, on the y-axis of the diagram. The relative order of energies is determined using Hund's rules. For an octahedral complex, the spherical, free ion term symbols split accordingly: Certain Tanabe–Sugano diagrams (d4, d5, d6, and d7) also have a vertical line drawn at a specific Dq/B value, which is accompanied by a discontinuity in the slopes of the excited states' energy levels. This pucker in the lines occurs when the identity of the ground state changes, shown in the diagram below. The left depicts the relative energies of the d7 ion states as functions of crystal field strength (Dq), showing an intersection of the 4T1 and the 2E states near Dq/B ~ 2.1. Subtracting the ground state energy produces the standard Tanabe–Sugano diagram shown on the right. This change in identity generally happens when the spin pairing energy, P, is equal to the ligand field splitting energy, Dq. Complexes to the left of this line (lower Dq/B values) are high-spin, while complexes to the right (higher Dq/B values) are low-spin. There is no low-spin or high-spin designation for d2, d3, or d8 because none of the states cross at reasonable crystal field energies.
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Tanabe–Sugano diagram
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Tanabe–Sugano diagrams
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The seven Tanabe–Sugano diagrams for octahedral complexes are shown below.
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Tanabe–Sugano diagram
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Unnecessary diagrams: d1, d9 and d10
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d1 There is no electron repulsion in a d1 complex, and the single electron resides in the t2g orbital ground state. A d1 octahedral metal complex, such as [Ti(H2O)6]3+, shows a single absorption band in a UV-vis experiment. The term symbol for d1 is 2D, which splits into the 2T2g and 2Eg states. The t2g orbital set holds the single electron and has a 2T2g state energy of -4Dq. When that electron is promoted to an eg orbital, it is excited to the 2Eg state energy, +6Dq. This is in accordance with the single absorption band in a UV-vis experiment. The prominent shoulder in this absorption band is due to a Jahn–Teller distortion which removes the degeneracy of the two 2Eg states. However, since these two transitions overlap in a UV-vis spectrum, this transition from 2T2g to 2Eg does not require a Tanabe–Sugano diagram.
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Tanabe–Sugano diagram
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Unnecessary diagrams: d1, d9 and d10
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d9 Similar to d1 metal complexes, d9 octahedral metal complexes have 2D spectral term. The transition is from the (t2g)6(eg)3 configuration (2Eg state) to the (t2g)5(eg)4 configuration (2T2g state). This could also be described as a positive "hole" that moves from the eg to the t2g orbital set. The sign of Dq is opposite that for d1, with a 2Eg ground state and a 2T2g excited state. Like the d1 case, d9 octahedral complexes do not require the Tanabe–Sugano diagram to predict their absorption spectra.
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Tanabe–Sugano diagram
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Unnecessary diagrams: d1, d9 and d10
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d10 There are no d-d electron transitions in d10 metal complexes because the d orbitals are completely filled. Thus, UV-vis absorption bands are not observed and a Tanabe–Sugano diagram does not exist.
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Tanabe–Sugano diagram
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Diagrams for tetrahedral symmetry
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Tetrahedral Tanabe–Sugano diagrams are generally not found in textbooks because the diagram for a dn tetrahedral will be similar to that for d(10-n) octahedral, remembering that ΔT for tetrahedral complexes is approximately 4/9 of ΔO for an octahedral complex. A consequence of the much smaller size of ΔT results in (almost) all tetrahedral complexes being high spin and therefore the change in the ground state term seen on the X-axis for octahedral d4-d7 diagrams is not required for interpreting spectra of tetrahedral complexes.
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Tanabe–Sugano diagram
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Advantages over Orgel diagrams
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In Orgel diagrams, the magnitude of the splitting energy exerted by the ligands on d orbitals, as a free ion approach a ligand field, is compared to the electron-repulsion energy, which are both sufficient at providing the placement of electrons. However, if the ligand field splitting energy, 10Dq, is greater than the electron-repulsion energy, then Orgel diagrams fail in determining electron placement. In this case, Orgel diagrams are restricted to only high spin complexes.Tanabe–Sugano diagrams do not have this restriction, and can be applied to situations when 10Dq is significantly greater than electron repulsion. Thus, Tanabe–Sugano diagrams are utilized in determining electron placements for high spin and low spin metal complexes. However, they are limited in that they have only qualitative significance. Even so, Tanabe–Sugano diagrams are useful in interpreting UV-vis spectra and determining the value of 10Dq.
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Tanabe–Sugano diagram
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Applications as a qualitative tool
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In a centrosymmetric ligand field, such as in octahedral complexes of transition metals, the arrangement of electrons in the d-orbital is not only limited by electron repulsion energy, but it is also related to the splitting of the orbitals due to the ligand field. This leads to many more electron configuration states than is the case for the free ion. The relative energy of the repulsion energy and splitting energy defines the high-spin and low-spin states.
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Tanabe–Sugano diagram
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Applications as a qualitative tool
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Considering both weak and strong ligand fields, a Tanabe–Sugano diagram shows the energy splitting of the spectral terms with the increase of the ligand field strength. It is possible for us to understand how the energy of the different configuration states is distributed at certain ligand strengths. The restriction of the spin selection rule makes it even easier to predict the possible transitions and their relative intensity. Although they are qualitative, Tanabe–Sugano diagrams are very useful tools for analyzing UV-vis spectra: they are used to assign bands and calculate Dq values for ligand field splitting.
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Tanabe–Sugano diagram
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Applications as a qualitative tool
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Examples Manganese(II) hexahydrate In the [Mn(H2O)6]2+ metal complex, manganese has an oxidation state of +2, thus it is a d5 ion. H2O is a weak field ligand (spectrum shown below), and according to the Tanabe–Sugano diagram for d5 ions, the ground state is 6A1. Note that there is no sextet spin multiplicity in any excited state, hence the transitions from this ground state are expected to be spin-forbidden and the band intensities should be low. From the spectra, only very low intensity bands are observed (low molar absorptivity (ε) values on y-axis).
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Tanabe–Sugano diagram
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Applications as a qualitative tool
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Cobalt(II) hexahydrate Another example is [Co(H2O)6]2+. Note that the ligand is the same as the last example. Here the cobalt ion has the oxidation state of +2, and it is a d7 ion. From the high-spin (left) side of the d7 Tanabe–Sugano diagram, the ground state is 4T1(F), and the spin multiplicity is a quartet. The diagram shows that there are three quartet excited states: 4T2, 4A2, and 4T1(P). From the diagram one can predict that there are three spin-allowed transitions. However, the spectra of [Co(H2O)6]2+ does not show three distinct peaks that correspond to the three predicted excited states. Instead, the spectrum has a broad peak (spectrum shown below). Based on the T–S diagram, the lowest energy transition is 4T1 to 4T2, which is seen in the near IR and is not observed in the visible spectrum. The main peak is the energy transition 4T1(F) to 4T1(P), and the slightly higher energy transition (the shoulder) is predicted to be 4T1 to 4A2. The small energy difference leads to the overlap of the two peaks, which explains the broad peak observed in the visible spectrum.
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Chemosis
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Chemosis
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Chemosis is the swelling (or edema) of the conjunctiva. The term derives from the Greek words cheme and -osis, cheme meaning cockleshell due to the swollen conjunctiva resembling it, and -osis meaning condition. The swelling is due to the oozing of exudate from abnormally permeable capillaries. In general, chemosis is a nonspecific sign of eye irritation. The outer surface covering appears to have fluid in it. The conjunctiva becomes swollen and gelatinous in appearance. Often, the eye area swells so much that the eyes become difficult or impossible to close fully. Sometimes, it may also appear as if the eyeball has moved slightly backwards from the white part of the eye due to the fluid filled in the conjunctiva all over the eyes except the iris. The iris is not covered by this fluid and so it appears to be moved slightly inwards.
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Chemosis
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Causes
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It is usually caused by allergies or viral infections, often inciting excessive eye rubbing. Chemosis is also included in the Chandler Classification system of orbital infections.
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Chemosis
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Causes
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If chemosis has occurred due to excessive rubbing of the eye, the first aid to be given is a cold water wash for eyes.Other causes of chemosis include: Superior vena cava obstruction, accompanied by facial oedema Hyperthyroidism, associated with exophthalmos, periorbital puffiness, lid retraction, and lid lag Cavernous sinus thrombosis, associated with infection of the paranasal sinuses, proptosis, periorbital oedema, retinal haemorrhages, papilledema, extraocular movement abnormalities, and trigeminal nerve sensory loss Carotid-cavernous fistula - classic triad of chemosis, pulsatile proptosis, and ocular bruit Cluster headache Trichinellosis Systemic lupus erythematosus (SLE) Angioedema Acute glaucoma Panophthalmitis Orbital cellulitis Gonorrheal conjunctivitis Dacryocystitis Spitting cobra venom to the eye High concentrations of phenacyl chloride in chemical mace spray Urticaria Trauma HSV Keratitis Post surgical Mucor Rhabdomyosarcoma of the orbit
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Chemosis
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Diagnosis
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An eye doctor may most often diagnose chemosis by doing a physical examination of the affected area. They can also ask questions about the severity and length of other symptoms.
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Chemosis
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Treatment
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Treatment depends on the cause of the chemosis.
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Viral evolution
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Viral evolution
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Viral evolution is a subfield of evolutionary biology and virology that is specifically concerned with the evolution of viruses. Viruses have short generation times, and many—in particular RNA viruses—have relatively high mutation rates (on the order of one point mutation or more per genome per round of replication). Although most viral mutations confer no benefit and often even prove deleterious to viruses, the rapid rate of viral mutation combined with natural selection allows viruses to quickly adapt to changes in their host environment. In addition, because viruses typically produce many copies in an infected host, mutated genes can be passed on to many offspring quickly. Although the chance of mutations and evolution can change depending on the type of virus (e.g., double stranded DNA, double stranded RNA, single strand DNA), viruses overall have high chances for mutations.
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Viral evolution
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Viral evolution
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Viral evolution is an important aspect of the epidemiology of viral diseases such as influenza (influenza virus), AIDS (HIV), and hepatitis (e.g. HCV). The rapidity of viral mutation also causes problems in the development of successful vaccines and antiviral drugs, as resistant mutations often appear within weeks or months after the beginning of a treatment. One of the main theoretical models applied to viral evolution is the quasispecies model, which defines a viral quasispecies as a group of closely related viral strains competing within an environment.
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Viral evolution
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Origins
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Three classical hypotheses Viruses are ancient. Studies at the molecular level have revealed relationships between viruses infecting organisms from each of the three domains of life, suggesting viral proteins that pre-date the divergence of life and thus infecting the last universal common ancestor. This indicates that some viruses emerged early in the evolution of life, and that they have probably arisen multiple times. It has been suggested that new groups of viruses have repeatedly emerged at all stages of evolution, often through the displacement of ancestral structural and genome replication genes.There are three classical hypotheses on the origins of viruses and how they evolved: Virus-first hypothesis: Viruses evolved from complex molecules of protein and nucleic acid before cells first appeared on earth. By this hypothesis, viruses contributed to the rise of cellular life. This is supported by the idea that all viral genomes encode proteins that do not have cellular homologs. The virus-first hypothesis has been dismissed by some scientists because it violates the definition of viruses, in that they require a host cell to replicate.
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Viral evolution
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Origins
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Reduction hypothesis (degeneracy hypothesis): Viruses were once small cells that parasitized larger cells. This is supported by the discovery of giant viruses with similar genetic material to parasitic bacteria. However, the hypothesis does not explain why even the smallest of cellular parasites do not resemble viruses in any way.
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Viral evolution
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Origins
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Escape hypothesis (vagrancy hypothesis): Some viruses evolved from bits of DNA or RNA that "escaped" from the genes of larger organisms. This does not explain the structures that are unique to viruses and are not seen anywhere in cells. It also does not explain the complex capsids and other structures of virus particles.Virologists are in the process of re-evaluating these hypotheses.
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Viral evolution
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Origins
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Later hypotheses Coevolution hypothesis (Bubble Theory): At the beginning of life, a community of early replicons (pieces of genetic information capable of self-replication) existed in proximity to a food source such as a hot spring or hydrothermal vent. This food source also produced lipid-like molecules self-assembling into vesicles that could enclose replicons. Close to the food source replicons thrived, but further away the only non-diluted resources would be inside vesicles. Therefore, evolutionary pressure could push replicons along two paths of development: merging with a vesicle, giving rise to cells; and entering the vesicle, using its resources, multiplying and leaving for another vesicle, giving rise to viruses.
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Viral evolution
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Origins
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Chimeric-origins hypothesis: Based on the analyses of the evolution of the replicative and structural modules of viruses, a chimeric scenario for the origin of viruses was proposed in 2019. According to this hypothesis, the replication modules of viruses originated from the primordial genetic pool, although the long course of their subsequent evolution involved many displacements by replicative genes from their cellular hosts. By contrast, the genes encoding major structural proteins evolved from functionally diverse host proteins throughout the evolution of the virosphere. This scenario is distinct from each of the three traditional scenarios but combines features of the Virus-first and Escape hypotheses.One of the problems for studying viral origins and evolution is the high rate of viral mutation, particularly the case in RNA retroviruses like HIV/AIDS. A recent study based on comparisons of viral protein folding structures, however, is offering some new evidence. Fold Super Families (FSFs) are proteins that show similar folding structures independent of the actual sequence of amino acids, and have been found to show evidence of viral phylogeny. The proteome of a virus, the viral proteome, still contains traces of ancient evolutionary history that can be studied today. The study of protein FSFs suggests the existence of ancient cellular lineages common to both cells and viruses before the appearance of the 'last universal cellular ancestor' that gave rise to modern cells. Evolutionary pressure to reduce genome and particle size may have eventually reduced viro-cells into modern viruses, whereas other coexisting cellular lineages eventually evolved into modern cells. Furthermore, the long genetic distance between RNA and DNA FSFs suggests that the RNA world hypothesis may have new experimental evidence, with a long intermediary period in the evolution of cellular life.
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Viral evolution
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Origins
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Definitive exclusion of a hypothesis on the origin of viruses is difficult to make on Earth given the ubiquitous interactions between viruses and cells, and the lack of availability of rocks that are old enough to reveal traces of the earliest viruses on the planet. From an astrobiological perspective, it has therefore been proposed that on celestial bodies such as Mars not only cells but also traces of former virions or viroids should be actively searched for: possible findings of traces of virions in the apparent absence of cells could provide support for the virus-first hypothesis.
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Viral evolution
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Evolution
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Viruses do not form fossils in the traditional sense, because they are much smaller than the finest colloidal fragments forming sedimentary rocks that fossilize plants and animals. However, the genomes of many organisms contain endogenous viral elements (EVEs). These DNA sequences are the remnants of ancient virus genes and genomes that ancestrally 'invaded' the host germline. For example, the genomes of most vertebrate species contain hundreds to thousands of sequences derived from ancient retroviruses. These sequences are a valuable source of retrospective evidence about the evolutionary history of viruses, and have given birth to the science of paleovirology.The evolutionary history of viruses can to some extent be inferred from analysis of contemporary viral genomes. The mutation rates for many viruses have been measured, and application of a molecular clock allows dates of divergence to be inferred.Viruses evolve through changes in their RNA (or DNA), some quite rapidly, and the best adapted mutants quickly outnumber their less fit counterparts. In this sense their evolution is Darwinian. The way viruses reproduce in their host cells makes them particularly susceptible to the genetic changes that help to drive their evolution. The RNA viruses are especially prone to mutations. In host cells there are mechanisms for correcting mistakes when DNA replicates and these kick in whenever cells divide. These important mechanisms prevent potentially lethal mutations from being passed on to offspring. But these mechanisms do not work for RNA and when an RNA virus replicates in its host cell, changes in their genes are occasionally introduced in error, some of which are lethal. One virus particle can produce millions of progeny viruses in just one cycle of replication, therefore the production of a few "dud" viruses is not a problem. Most mutations are "silent" and do not result in any obvious changes to the progeny viruses, but others confer advantages that increase the fitness of the viruses in the environment. These could be changes to the virus particles that disguise them so they are not identified by the cells of the immune system or changes that make antiviral drugs less effective. Both of these changes occur frequently with HIV.
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Viral evolution
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Evolution
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Many viruses (for example, influenza A virus) can "shuffle" their genes with other viruses when two similar strains infect the same cell. This phenomenon is called genetic shift, and is often the cause of new and more virulent strains appearing. Other viruses change more slowly as mutations in their genes gradually accumulate over time, a process known as antigenic drift.Through these mechanisms new viruses are constantly emerging and present a continuing challenge in attempts to control the diseases they cause. Most species of viruses are now known to have common ancestors, and although the "virus first" hypothesis has yet to gain full acceptance, there is little doubt that the thousands of species of modern viruses have evolved from less numerous ancient ones. The morbilliviruses, for example, are a group of closely related, but distinct viruses that infect a broad range of animals. The group includes measles virus, which infects humans and primates; canine distemper virus, which infects many animals including dogs, cats, bears, weasels and hyaenas; rinderpest, which infected cattle and buffalo; and other viruses of seals, porpoises and dolphins. Although it is not possible to prove which of these rapidly evolving viruses is the earliest, for such a closely related group of viruses to be found in such diverse hosts suggests the possibility that their common ancestor is ancient.
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Viral evolution
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Evolution
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Bacteriophage Escherichia virus T4 (phage T4) is a species of bacteriophage that infects Escherichia coli bacteria. It is a double-stranded DNA virus in the family Myoviridae. Phage T4 is an obligate intracellular parasite that reproduces within the host bacterial cell and its progeny are released when the host is destroyed by lysis. The complete genome sequence of phage T4 encodes about 300 gene products. These virulent viruses are among the largest, most complex viruses that are known and one of the best studied model organisms. They have played a key role in the development of virology and molecular biology. The numbers of reported genetic homologies between phage T4 and bacteria and between phage T4 and eukaryotes are similar suggesting that phage T4 shares ancestry with both bacteria and eukaryotes and has about equal similarity to each. Phage T4 may have diverged in evolution from a common ancestor of bacteria and eukaryotes or from an early evolved member of either lineage. Most of the phage genes showing homology with bacteria and eukaryotes encode enzymes acting in the ubiquitous processes of DNA replication, DNA repair, recombination and nucleotide synthesis. These processes likely evolved very early. The adaptive features of the enzymes catalyzing these early processes may have been maintained in the phage T4, bacterial, and eukaryotic lineages because they were established well-tested solutions to basic functional problems by the time these lineages diverged.
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Viral evolution
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Transmission
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Viruses have been able to continue their infectious existence due to evolution. Their rapid mutation rates and natural selection has given viruses the advantage to continue to spread. One way that viruses have been able to spread is with the evolution of virus transmission. The virus can find a new host through: Droplet transmission- passed on through body fluids (sneezing on someone) An example is the influenza virus Airborne transmission- passed on through the air (brought in by breathing) An example would be how viral meningitis is passed on Vector transmission- picked up by a carrier and brought to a new host An example is viral encephalitis Waterborne transmission- leaving a host, infecting the water, and being consumed in a new host Poliovirus is an example for this Sit-and-wait-transmission- the virus is living outside a host for long periods of time The smallpox virus is also an example for thisVirulence, or the harm that the virus does on its host, depends on various factors. In particular, the method of transmission tends to affect how the level of virulence will change over time. Viruses that transmit through vertical transmission (transmission to the offspring of the host) will evolve to have lower levels of virulence. Viruses that transmit through horizontal transmission (transmission between members of the same species that don't have a parent-child relationship) will usually evolve to have a higher virulence.
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Mountainboarding
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Mountainboarding
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Mountainboarding, also known as dirtboarding, offroad boarding, and All-Terrain Boarding (ATB), is a well-established but little-known action sport, derived from snowboarding. The sport was initially pioneered by James Stanley during a visit to the Matterhorn in the 1990's, where snow was not available. A mountainboard is made up of components including a deck, bindings (to secure the rider to the deck), four wheels with pneumatic tires, and two steering mechanisms known as trucks. Mountainboarders, also known as riders, ride specifically designed boardercross tracks, slopestyle parks, grass hills, woodlands, gravel tracks, streets, skateparks, ski resorts, BMX courses, and mountain bike trails. It is this ability to ride such a variety of terrain that makes mountainboarding unique from other board sports.
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Mountainboarding
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History
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Origins Morton Hellig's 'Supercruiser Inc.' was the first company to manufacture and retail the 'All Terrain Dirtboard', patented in 1989.
Mountainboarding (name coined by Jason Lee) began in the UK, the United States and Australia in 1992. Unknown to each other, riders from other boardsports started to design, build, and eventually manufacture boards that could be ridden off-road. This desire to expand the possible terrain that a boarder can ride created the sport of Mountainboarding.
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Mountainboarding
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History
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United Kingdom Dave and Pete Tatham, Joe Inglis and Jim Aveline, whilst looking for an off-season alternative to surfing and snowboarding, began designing boards that could be ridden down hills. Inglis developed initial prototypes, and in 1992 noSno was started. Extensive research and development produced the noSno truck system which enabled the boards to be steered and remain stable at high speeds. NoSno boards utilized snowboard bindings and boots, with large tyres for rough ground, and the option for a hand-operated hydraulic disc brake.
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Mountainboarding
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History
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United States In 1992, after having snowboarded at Heavenly Valley Resort in Northern California, friends Jason Lee, Patrick McConnell and Joel Lee went looking for an alternative for the summer season. Not finding anything suitable they co-founded Mountain Board Sports (MBS) in 1993 to build boards that they could use to carve down hills. The original MBS boards, known as 'Frame Boards' had a small wooden deck metal posts to hold the rider's feet, a tubular metal frame connecting trucks which used springs to enable steering and thus create the carving sensation that the MBS co-founders were looking for.
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Mountainboarding
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History
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The first recorded mountainboarding act occurred in the summer of 1978, when local skateboarder Mike Motta residing in Medford Massachusetts navigated down a hill known as Seven Bumps in Malden Massachusetts on a bet, using a standard Franklin skateboard.
Australia John Milne developed a three-wheeled version of a mountainboard in 1992 in his spare time during periods of very poor surf. It used a unique steering system to emulate surfing on land. It had three wheels and a skate-style deck with no bindings.
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Mountainboarding
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History
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Mid-to-late nineties From the early days of invention there has always been a competitive element in mountainboarding. Encompassing racing, freestyle and downhill, competitions have been organized in the USA since 1993 and in the UK since 1997. In the same year the ATBA-UK (All Terrain Boarding Association), the national governing body for mountainboarding in the UK was born. As a non-profit making organization it represented and promoted the sport by putting riders interests first, promoting safety, sanctioning events, providing training, and sourcing funding to put on the ATBA-UK National Series, an annual series of competitions. The competitions did much to promote the sport and in 1998 mountainboarding had an estimated participation of over 1 million athletes worldwide. The components evolved, and the sport continued to grow. MBS developed the open heel binding, the channel truck, the "eggshock" and the reverse V Brake system and sold boards in around 30 countries worldwide. In 1998 Maxtrack started distributing MBS mountainboards in the UK and Europe.
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Mountainboarding
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History
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Future As of recent there have been some powered mountain boards gaining traction in the board enthusiast world. Small gas or electric motors attached to allow for mountainboarding to be done on flat ground or to climb hills rather than just going downhill. Many DIY electric mountainboard builders are constantly developing new drivetrains for their boards with electric motors, rivaling the power of small motorcycles, becoming the norm.
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Mountainboarding
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Equipment
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Board components Deck Mountainboard decks are the part that most of the components are attached to, and provide the base for the rider to stand on. They are generally from 90–110 cm in length, and can be made from a range of construction methods and materials. For example, high specification boards may be made from composite carbon and glass reinforced plastics, possibly with a wooden core, similarly made to a snowboard deck. Basic decks are generally made using laminated wood pressed into shape, comparable to a longboard deck with larger dimensions and a different shape. There are variable characteristics such as flex, weight, shape, length and tip angle that can be catered for in custom or stock boards from a variety of manufacturers.
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Mountainboarding
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Equipment
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Trucks Trucks are the components made up of a hanger, damping and/or spring system, and axles which attach the wheels to the deck. They also have the mechanisms required to allow the board to turn.
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Mountainboarding
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Equipment
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Skate trucks Skate trucks have a rigid axle and a top hanger, with a single bolt and bushings, also called rubbers or grommets, that provide the cushion mechanism for turning the mountainboard. The bushings cushion the truck when it turns. The stiffer the bushings, the more resistant the mountainboard is to turning. The softer the bushings, the easier it is to turn. A bolt called a kingpin holds these parts together and fits inside the bushings. Thus by tightening or loosening the kingpin nut, the trucks can be adjusted loosely for better turning and tighter for more control. Skate-style mountainboard trucks are similar to skateboard trucks but more robust and with a longer axle.
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Mountainboarding
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Equipment
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Channel trucks Channel trucks are common on mountainboards, and are made up of an axles mounted to the truck bottom piece, which is suspended from a top hanger by a kingpin. They are mounted to the deck using nuts and bolts through the hanger part, on an angle, (usually 35°). When the board is tilted laterally the axles turn together to angle the wheels in the direction of the turn. Two polyurethane dampers sometimes known as "egg shocks" are mounted between the hanger and the axle housing on each truck to provide resistance to the lean of the rider during turning. Springs are mounted in the same place with the dampers inside them.
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Mountainboarding
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Equipment
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The 'shocks' present in channel trucks are there to dampen the turning system, and help reduce the oscillations of the trucks on the board commonly described as speed wobble. The springs are there to return the deck to centre after a turn has been performed, neither are there to provide suspension between the deck and axles. They have a kingpin that can't move vertically which prevents this.
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Mountainboarding
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Equipment
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Also, the effectiveness of springs as employed in current (2009) channel truck designs is open to debate.
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Mountainboarding
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Equipment
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In a "Coil over Oil" shock, the extension of the spring is dampened as well as contraction. In a channel truck design, this is not the case as the damper sits freely inside the spring—therefore only contraction is dampened, not extension. This means that when a spring ceases to be under load and extends, it can extend past the equilibrium point.
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Mountainboarding
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Equipment
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NoSno trucks NoSno trucks use two 'kingpin'-type bolts to create a floating pivot, an axle with a plate into which the bolts go, an angled base plate that attaches to the deck, and polyurethane bushings to dampen the turn. The amount of turn available in the trucks can be adjusted by tightening the bolts or by using bushings of different hardness. A similar design was adopted by Howla Mountainboards for the limited time that they manufactured boards.
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Mountainboarding
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Equipment
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Bindings Bindings involve adjustable straps that hold the rider on to the board while allowing room to move their feet.
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Mountainboarding
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Equipment
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Snowboard bindings Ratchet-strap bindings Velcro Bindings Bar-Bindings Heelstraps Wheels Wheels are made up of plastic or metal hubs and pneumatic tires ranging in size of 8–13 inches. The 8" wheel has evolved into the best choice for freestyle riding, and also an all purpose wheel for general riding. Larger wheels (generally 9" and 10") are more useful to the downhill rider; granting the rider access to high-speed runs and more stability when travelling at speed.
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Mountainboarding
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Equipment
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Tyres Various tyres have been made available by different mountainboard manufacturers, giving riders a choice of tire specifications. For example, the thickness of the tyre is variable between tyres, usually either 2 or 4 ply. 2 ply tyres are lighter, but more susceptible to punctures than 4 ply tyres. There is a variety of tread patterns available, ranging from street slicks to deep tread designed for maximum grip with split center beads to channel water away. Width and diameter is also variable.
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Mountainboarding
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Equipment
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Brakes Brakes are generally reserved for big mountain riding where riders need an increased ability to control their speed over long runs. The brakes are most usually attached to both front wheels of the mountainboard rather than the rear to give greater braking efficiency and reduce the chances of the rear wheels locking up and skidding. They are operated via a hand-held lever which when pulled causes both brake mechanisms to work simultaneously. There are four types of brakes used on mountainboards: Mechanical drum brakes Those brakes use brake drums attached to the wheel with the 5 wheel-screws (Scrub). They are cheap and brake rigidly but get extremely hot and tend to melt the plastic hub. Good emergency brakes only, not any good for long steep hills. There is currently no heat resistant hub where they would attach to, which could however be easily made of e.g. alloy.Hydraulic Disc Brakes Hydraulic disc brakes use rotors attached to the hubs with hydraulically operated brake mechanisms that force ceramic pads against the rotors to effect braking. Advantages include high braking power and reliability. Disadvantages include cost, vulnerability of the discs, heat build up, and weight.Hydraulic Rim Brakes Hydraulic Rim Brakes use the hub, or preferably, a bolt on metal disc as the braking surface for hydraulically operated brake mechanisms that push polyurethane blocks against the braking surface. Advantages include good braking power, and good modulation. Disadvantages include possible damage to bearings.Cable-pull 'V' Brakes Cable-pull 'V' Brakes also use the hub or metal discs as a braking surface. The hand operated lever pulls a metal cable to push polyurethane blocks against the braking surface. Advantages include low cost, low weight, and easy installation and maintenance. Disadvantages include low braking power, and the need to be regularly adjusted.
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Mountainboarding
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Equipment
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Protections Mountainboarders wear a range of protective equipment while riding.
Helmets - are designed to protect the wearer's head from falls and damage to the brain. There are two types; full-face, which provides more protection to the wearer, and open face, which provides greater visibility for the wearer.
Wristguards - are designed to protect the wearer's wrists from impacts. They come in two types, gloves and wrap-arounds, but both include plastic splints which prevent the wearers wrists from bending backwards during a fall and protect the palms against cuts and grazes.
Elbow pads - are designed to protect the wearer's elbows from impact during falls. Sometimes forearm guards are incorporated into the elbow pads.
Knee pads - are designed to protect the wearer's knees from impact during falls.
Padded Shorts - are designed to protect the wearer's hips, coccyx, and buttocks from impact during falls.
Body Armour - is designed to protect the wearer's upper body, arms, shoulders and back from impact during falls.
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Mountainboarding
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Disciplines
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Mountainboarding consists of four main disciplines: Downhill (DH) Timed one-man descents. Usually relatively long courses (1 km+) in the mountains. Sometimes referred to as big mountain.
Boardercross (BoarderX, BX) Two to four-man racing on a specifically designed track.
Freestyle (FS) Slopestyle: Performing tricks on a slopestyle course consisting of multiple jumps, rails and innovative features.
Big Air: Performing tricks including grabs, spins and inverts over jumps.
Jibbing: Similar to Slopestyle except with the focus on smaller more technical features such as rails, quarterpipes, drops and smaller kickers.
Freeriding (FR) Non-competitive riding over a range of natural terrain including woodland.
Similar Sports Similar all terrain boardsports include Dirtsurfing and Kiteboarding.
Crossover Sports Skateboarding Streetboarding Surfing Snowboarding Wakeboarding Mountain biking Sandboarding Dirtsurfing Grassboarding Kite landboarding
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Mountainboarding
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Media
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The following are some of the numerous publications Mountain Boarding has had in various news media outlets and other media, including for the annual Mountain Board US Open in Snowmass and the Twighlight Showdown Mountainboard Championships.
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Mountainboarding
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Media
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Historical Magazines Off-Road Boarding Magazine founded in '99 with its editor Brian Bishop and other dedicated riders. It ran numerous pictorials, US riding spots, rider profiles and carried virtually no ads. It started small, and was given away at comps and shops. The last issue of the mag was printed in full color and a new name "Mountainboard Magazine". The new title was later adopted by a UK publisher.
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Mountainboarding
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Media
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All Terrain Boarding Magazine aka ATBMag: The longest running, 4 years, and only Mountainboard magazine to make it onto mainstream newsagent shelves. Distributed worldwide it ran to 39 copies and one photo album featuring the work of Paul Taylor. ATBMag was also responsible for the creation of the World Freestyle Championships, running it for the first 2 years. It also created the World Series, taking place in 12 countries. ATBmag sponsored a team of riders, who were later sponsored by EXIT. The team featured Tom Kirkman, Laurie Kaye, Alex Downie, Oli Morrison, Arno Van Den Vejver, Ig Wilkinson, Jack Chew and Tuai Lovejoy. 2005 saw the team take to Europe and ride in 7 countries following the World Series Tour. In 2006 the magazine made its final issue.
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Mountainboarding
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Media
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Scuz Mountainboarding Zine was first published in July 2004 as a paid-for magazine, however subsequent issues were published and distributed for free both as a printed hardcopy version and on the internet as a downloadable PDF. It was announced in October 2006 that issue twelve would be the final issue.
Mountainboard Magazine was produced by the same people who created scuz, and it was re-branded to suit changing trends in mountainboarding, and a cover charge was introduced to help pay for the costs involved in producing the magazine as the advertising featured was sufficient. Only one issue was ever printed.
Mountainboarding Video Magazine (MVM) The only video mag to showcase mountain boarding from around the world. This publication only made nine issues, co-produced and edited by Justin Rhodes, Van DeWitt, and Brett Dooley.
UKATB ran for 6 years between 2000 and 2006 and was the first website to feature in-depth advice and tips from board maintenance to ramp building and trick tips. At its peak the site attracted over 10 000 unique visitors a month.
Movies Johnny Kapahala: Back on Board is the 70th Disney Channel Original Movie and is the sequel to the 1999 film Johnny Tsunami. Its popularity encouraged people to take interest in the extreme sport.
TV Mountainboard Aux Saisies TV coverage of the 2009 noSno World Downhill Championships, from the French TV channel Savoie ACTU.
History Channel. The history of extreme sport on the History Channel. Featuring Mountainboarding and many other board sports.
They Think It's All Over. Pete and Dave Tatham from noSno taking part in "Guess the sportsman" on BBC's sports comedy program "They think it's all over" Park City TV: What is Mountainboarding? The Utah DirtStar Army team on Park City TV in late 2005.
Good Morning Utah. The DirtStar Army live on Good Morning Utah 2005.
US Open Mountainboard Championships 2006, held in Snowmass, Colorado. JSP TV talks with the youth division winner and the director of the Dirt Dogs.
Toasted TV. Interview with Munroboards team rider Ryan Slater on the Channel 10 show toasted TV.
Domino's Pizza. "That was Puff" commercial featuring mountainboarders: Ryan Slater, Clint Farqhuar, Markus Lubitz, Adam Zemunic.
Horizon TV. Willingen D-MAX World Series Mountainboard 2007.
Rockon. TV report on WDR on the mountain board park opening in Winterberg.
At Your Leisure: The DirtStar Army. TV report on Utah's DSA mountain board team ripping up the Park City dirt jumps.
Top Gear. TV item showing a staged race between Tom Kirkman and a Mitsubishi Evo rally car and Bowler Wildcat.
Friday Download. Kids TV report on mountain boarding (2012).
Newspapers & Magazines The Guardian. What do snowboarders do when faced with the perennially powderless slopes of the UK? They find the nearest verdant hill and hurtle down it. Tim Moore and son go gung-ho in Surrey.
The Telegraph. Jonny Beardsall loses balance and bottle as he faces a 40 mph slalom on a mountain board.
Men's Health. Fancy traveling at speeds of 60 mph on a board down a mountain? Read on…Chad Harding features in Stroud news and journal about his win in the under 14s UK championship freestyle.
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Mountainboarding
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Public service/Community (online)
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Atboarders. UK based mountainboarding badasses who reignite the hype. Always Fresh. Always A Ting The Dirt. US based mountainboard blog & news site.
Surfing Dirt. International mountainboarders community forum.
Remolition. Free mountainboard webzine with regular features.
MountainboardingUK. Beginner mountainboard-riders website (free advice)
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Mountainboarding
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Competitions
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World Freestyle Championships From 2005 to 2008 was named Fat Face Night Air WFC From 2009 to 2010 was named Battle of Bugs 2004 (Weston Super X Arena, Weston Super Mare, UK) - Leon Robbins, USA 2005 (SWMBC, Bideford, UK) - Tom Kirkman, UK 2006 (SWMBC, Bideford, UK) - Alex Downie, UK 2007 (SWMBC, Bideford, UK) - Arno VDV, Belgium 2008 (Bugs Boarding, Gloucester, UK) - Renny Myles, UK 2009 (Bugs Boarding, Gloucester, UK) - Tom Kirkman, UK 2012 (Luzhniki, Moscow, Russia) - Matt Brind, UK 2017 (Venette, France) - Matt Brind, UK; Natasha Chernikova, RUS 2018 (Kranj, Slovenia) - Matt Brind, UK; Simona Petrò, ITA 2019 (Moszczenica, Poland) - Nicolas Geerse, NLD; Maja Bilik, POLWorld Downhill Championships 2009 (Les Saisies, France) - Pete Tatham, UK 2010 (Bardonecchia, Italy) - Pete Tatham, UK 2011 (Bardonecchia, Italy) - Pete Tatham, UK 2012 (Les Saisies, France) - Jonathan Charles, UKWorld Boardercross Championships 2013 (Bukovac, Novi Sad, Serbia) - Kody Stewart USA; Martina Lippolis, ITA 2014 (Bukovac, Novi Sad, Serbia) - Matt Brind, UK; Martina Lippolis, ITA 2015 (Großerlach, Germany) - Matt Brind, UK; Simona Petro, ITA 2016 (Bukovac, Novi Sad, Serbia) - Matt Brind, UK; Sonya Nicolau, ROM 2017 (Venette, France) - Matt Brind, UK; Senka Bajić, SRB 2018 (Kranj, Slovenia) - Kody Stewart USA; Senka Bajić, SRB 2019 (Bukovac, Novi Sad, Serbia) - Matt Brind, UK; Vanja Rakovic, SRBOverall World Champions 2017 (Venette, France) - Matt Brind, UK; Ola Tomalczyk, POL 2018 (Kranj, Slovenia) - Matt Brind, UK; Simona Petrò, ITA 2019 (Moszczenica, Poland; Bukovac, Novi Sad, Serbia) - Matt Brind, UKEuropean Downhill Championships 2009 (Bardonecchia, Italy) - Pete Tatham, UK 2010 (Bardonecchia, Italy) - Jonathan Charles, UK 2014 (Monte Penice, Italy) - Matt Brind, UKEuropean Mountainboard Tour 2010 - Arno VDV, Belgium 2014 - Matt Brind, UKEuropean Mountainboard Challenge 2010 (Bukovac, Novi Sad, Serbia) - Marcin Staszczyk, POL; Senka Bajić, SRB 2011 (Bukovac, Novi Sad, Serbia) - Marcin Staszczyk, POL; Senka Bajić, SRB 2012 (Bukovac, Novi Sad, Serbia) - James Wanklyn, UK; Sonya Nicolau, ROM 2015 (Kranj, Slovenia) - Dawid Rzaca, POL; Senka Bajić, SRB 2016 (Kranj, Slovenia) - Matteo Andreassi, ITA; Senka Bajić, SRB 2017 (Kranj, Slovenia) - Nicolas Geerse, NED; Senka Bajić, SRB
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Stubble burning
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Stubble burning
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Stubble burning is the practice of intentionally setting fire to the straw stubble that remains after grains, such as rice and wheat, have been harvested. The technique is still widespread today.
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Stubble burning
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Effects
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The burning of stubble has both positive and negative consequences.
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Stubble burning
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Effects
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Generally helpful effects Cheaper and easier than other removal methods Helps to combat pests and weeds Can reduce nitrogen tie-up Generally harmful effects Loss of nutrients Pollution from smoke. Including greenhouse gases and others that damage the ozone layer Damage to electrical and electronic equipment from floating threads of conductive waste Risk of fires spreading out of control Alternative to stubble burning Agriculture residues can have other uses, such as in particle board and biofuel, though these uses can still cause problems like erosion and nutrient loss.
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Stubble burning
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Effects
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Spraying an enzyme, which decomposes the stubble into useful fertiliser, improves the soil, avoids air pollution and prevents carbon dioxide emissions.Several companies worldwide use leftover agricultural waste to make new products. Agricultural waste can serve as raw materials for new applications, such as paper and board, bio-based oils, leather, catering disposables, fuel and plastic.
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Stubble burning
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Attitudes toward stubble burning
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Stubble burning has been effectively prohibited since 1993 in the United Kingdom. A perceived increase in blackgrass, and particularly herbicide resistant blackgrass, has led to a campaign by some arable farmers for its return.
In Australia stubble burning is "not the preferred option for the majority of farmers" but is permitted and recommended in some circumstances. Farmers are advised to rake and burn windrows, and leave a fire break of 3 metres around any burn off.
In the United States, fires are fairly common in mid-western states, but some states such as Oregon and Idaho regulate the practice.
In the European Union, the Common Agricultural Policy strongly discourages stubble burning.
In China, there is a government ban on stubble burning; however the practice remains fairly common.
In northern India, despite a ban by the Punjab Pollution Control Board, stubble burning is still practiced since the 1980s. Authorities are starting to enforce this ban more proactively, and to research alternatives.
Stubble burning is allowed by permit in some Canadian provinces, including Manitoba where 5% of farmers were estimated to do it in 2007.
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Stubble burning
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Attitudes toward stubble burning
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India Stubble burning in Punjab, Haryana, and Uttar Pradesh in north India has been cited as a major cause of air pollution in Delhi since 1980. Consequently, the government is considering implementation of the 1,600 km long and 5 km wide Great Green Wall of Aravalli. From April to May and October to November each year, farmers mainly in Punjab, Haryana, and Uttar Pradesh burn an estimated 35 million tons of crop waste from their wheat and paddy fields after harvesting as a low-cost straw-disposal practice to reduce the turnaround time between harvesting and sowing for the first (summer) crop and the second (winter) crop. Smoke from this burning produces a cloud of particulates visible from space and has produced what has been described as a "toxic cloud" in New Delhi, resulting in declarations of an air-pollution emergency. For this, the NGT (National Green Tribunal) instituted a fine of ₹2 lakh on the Delhi Government for failing to file an action plan providing incentives and infrastructural assistance to farmers to stop them from burning crop residue to prevent air pollution.Although harvesters such as the Indian-manufactured "Happy Seeder" that shred the crop residues into small pieces and uniformly spread them across the field are available as an alternative to burning stubble, and crops such as millets and maize can be grown as an sustainable alternative to rice and wheat in order to conserve water, some farmers complain that the cost of these machines is a significant financial burden, with the crops not incurred under MSP prices when compared to burning the fields and purchasing crops that are produced under MSP prices.The Indian Agricultural Research Institute, developed an enzyme bio-decomposer solution, that can be sprayed after the harvest, to increase organic carbon in the soil and maintain overall soil health. In 2021, they began licensing its use to various companies.
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Stubble burning
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Attitudes toward stubble burning
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In May 2022, the Government of Punjab announced they will purchase maize, bajra, sunflower and moong crops at MSP, encouraging farmers to adopt less water consuming options as a sustainable alternative to paddy and wheat in the wake of fast-depleting groundwater. Stubble burning has increased 160% now in Rajasthan in India claims a minister. [1]
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PATRIC
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PATRIC
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PATRIC (Pathosystems Resource Integration Center) is a bacterial bioinformatics website from the Bioinformatics Resource Center. It is an information system integrating databases with various types of data about bacterial pathogens (transcriptomic, proteomic, structural, biochemical) together with analysis tools. It is designed to support the biomedical research community's work on bacterial infectious diseases via these integrations of various pieces of pathogen information.
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PATRIC
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Description
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PATRIC is a project of Virginia Tech's Cyberinfrastructure Division, and is funded by the National Institutes of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH). PATRIC centralize available bacterial phylogenomic data, proteomic and other various experiment pieces of data linked to specific pathogens from numerous sources. The PATRIC platform provides an interface comprehensive comparative genomics.
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PATRIC
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Bacterial Organisms Covered in the PATRIC Database
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Bacillus Bartonella Borrelia Brucella Burkholderia Campylobacter Chlamydophila Clostridium Coxiella Ehrlichia Escherichia Francisella Helicobacter Listeria Mycobacterium Rickettsia Salmonella Shigella Staphylococcus Vibrio Yersinia Other Bacteria
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PATRIC
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About Cyberinfrastructure Division and VBI
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The CyberInfrastructure Division at VBI develops methods, infrastructure, and resources to help enable scientific discoveries in infectious disease research. The group applies the principles of cyberinfrastructure to integrate data, computational infrastructure, and people. CyberInfrastructure Division has developed public resources for curated, diverse molecular and literature data from various infectious disease systems, and implemented the processes, systems, and databases required to support them. It also conducts research by applying its methods and data to make new discoveries of its own.
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PATRIC
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About Cyberinfrastructure Division and VBI
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The Virginia Bioinformatics Institute (VBI) at Virginia Tech has a research platform centered on understanding the "disease triangle" of host-pathogen-environment interactions in plants, humans and other animals.
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Basal metabolic rate
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Basal metabolic rate
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Basal metabolic rate (BMR) is the rate of energy expenditure per unit time by endothermic animals at rest. It is reported in energy units per unit time ranging from watt (joule/second) to ml O2/min or joule per hour per kg body mass J/(h·kg). Proper measurement requires a strict set of criteria to be met. These criteria include being in a physically and psychologically undisturbed state and being in a thermally neutral environment while in the post-absorptive state (i.e., not actively digesting food). In bradymetabolic animals, such as fish and reptiles, the equivalent term standard metabolic rate (SMR) applies. It follows the same criteria as BMR, but requires the documentation of the temperature at which the metabolic rate was measured. This makes BMR a variant of standard metabolic rate measurement that excludes the temperature data, a practice that has led to problems in defining "standard" rates of metabolism for many mammals.Metabolism comprises the processes that the body needs to function. Basal metabolic rate is the amount of energy per unit of time that a person needs to keep the body functioning at rest. Some of those processes are breathing, blood circulation, controlling body temperature, cell growth, brain and nerve function, and contraction of muscles. Basal metabolic rate affects the rate that a person burns calories and ultimately whether that individual maintains, gains, or loses weight. The basal metabolic rate accounts for about 60 to 75% of the daily calorie expenditure by individuals. It is influenced by several factors. In humans, BMR typically declines by 1–2% per decade after age 20, mostly due to loss of fat-free mass, although the variability between individuals is high.
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Basal metabolic rate
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Description
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The body's generation of heat is known as thermogenesis and it can be measured to determine the amount of energy expended. BMR generally decreases with age, and with the decrease in lean body mass (as may happen with aging). Increasing muscle mass has the effect of increasing BMR. Aerobic (resistance) fitness level, a product of cardiovascular exercise, while previously thought to have effect on BMR, has been shown in the 1990s not to correlate with BMR when adjusted for fat-free body mass. But anaerobic exercise does increase resting energy consumption (see "aerobic vs. anaerobic exercise"). Illness, previously consumed food and beverages, environmental temperature, and stress levels can affect one's overall energy expenditure as well as one's BMR.
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Basal metabolic rate
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Description
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BMR is measured under very restrictive circumstances when a person is awake. An accurate BMR measurement requires that the person's sympathetic nervous system not be stimulated, a condition which requires complete rest. A more common measurement, which uses less strict criteria, is resting metabolic rate (RMR).BMR may be measured by gas analysis through either direct or indirect calorimetry, though a rough estimation can be acquired through an equation using age, sex, height, and weight. Studies of energy metabolism using both methods provide convincing evidence for the validity of the respiratory quotient (RQ), which measures the inherent composition and utilization of carbohydrates, fats and proteins as they are converted to energy substrate units that can be used by the body as energy.
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Basal metabolic rate
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Phenotypic flexibility
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BMR is a flexible trait (it can be reversibly adjusted within individuals), with, for example, lower temperatures generally resulting in higher basal metabolic rates for both birds and rodents. There are two models to explain how BMR changes in response to temperature: the variable maximum model (VMM) and variable fraction model (VFM). The VMM states that the summit metabolism (or the maximum metabolic rate in response to the cold) increases during the winter, and that the sustained metabolism (or the metabolic rate that can be indefinitely sustained) remains a constant fraction of the former. The VFM says that the summit metabolism does not change, but that the sustained metabolism is a larger fraction of it. The VMM is supported in mammals, and, when using whole-body rates, passerine birds. The VFM is supported in studies of passerine birds using mass-specific metabolic rates (or metabolic rates per unit of mass). This latter measurement has been criticized by Eric Liknes, Sarah Scott, and David Swanson, who say that mass-specific metabolic rates are inconsistent seasonally.In addition to adjusting to temperature, BMR also may adjust before annual migration cycles. The red knot (ssp. islandica) increases its BMR by about 40% before migrating northward. This is because of the energetic demand of long-distance flights. The increase is likely primarily due to increased mass in organs related to flight. The end destination of migrants affects their BMR: yellow-rumped warblers migrating northward were found to have a 31% higher BMR than those migrating southward.In humans, BMR is directly proportional to a person's lean body mass. In other words, the more lean body mass a person has, the higher their BMR; but BMR is also affected by acute illnesses and increases with conditions like burns, fractures, infections, fevers, etc. In menstruating females, BMR varies to some extent with the phases of their menstrual cycle. Due to the increase in progesterone, BMR rises at the start of the luteal phase and stays at its highest until this phase ends. There are different findings in research how much of an increase usually occurs. Small sample, early studies, found various figures, such as; a 6% higher postovulatory sleep metabolism, a 7% to 15% higher 24 hour expenditure following ovulation, and an increase and a luteal phase BMR increase by up to 12%. A study by the American Society of Clinical Nutrition found that an experimental group of female volunteers had an 11.5% average increase in 24 hour energy expenditure in the two weeks following ovulation, with a range of 8% to 16%. This group was measured via simultaneously direct and indirect calorimetry and had standardized daily meals and sedentary schedule in order to prevent the increase from being manipulated by change in food intake or activity level. A 2011 study conducted by the Mandya Institute of Medical Sciences found that during a woman's follicular phase and menstrual cycle is no significant difference in BMR, however the calories burned per hour is significantly higher, up to 18%, during the luteal phase. Increased state anxiety (stress level) also temporarily increased BMR.
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Basal metabolic rate
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Physiology
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The early work of the scientists J. Arthur Harris and Francis G. Benedict showed that approximate values for BMR could be derived using body surface area (computed from height and weight), age, and sex, along with the oxygen and carbon dioxide measures taken from calorimetry. Studies also showed that by eliminating the sex differences that occur with the accumulation of adipose tissue by expressing metabolic rate per unit of "fat-free" or lean body mass, the values between sexes for basal metabolism are essentially the same. Exercise physiology textbooks have tables to show the conversion of height and body surface area as they relate to weight and basal metabolic values.
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Basal metabolic rate
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Physiology
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The primary organ responsible for regulating metabolism is the hypothalamus. The hypothalamus is located on the diencephalon and forms the floor and part of the lateral walls of the third ventricle of the cerebrum. The chief functions of the hypothalamus are: control and integration of activities of the autonomic nervous system (ANS) The ANS regulates contraction of smooth muscle and cardiac muscle, along with secretions of many endocrine organs such as the thyroid gland (associated with many metabolic disorders).
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Basal metabolic rate
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Physiology
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Through the ANS, the hypothalamus is the main regulator of visceral activities, such as heart rate, movement of food through the gastrointestinal tract, and contraction of the urinary bladder.
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Basal metabolic rate
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Physiology
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production and regulation of feelings of rage and aggression regulation of body temperature regulation of food intake, through two centers: The feeding center or hunger center is responsible for the sensations that cause us to seek food. When sufficient food or substrates have been received and leptin is high, then the satiety center is stimulated and sends impulses that inhibit the feeding center. When insufficient food is present in the stomach and ghrelin levels are high, receptors in the hypothalamus initiate the sense of hunger.
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Basal metabolic rate
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Physiology
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The thirst center operates similarly when certain cells in the hypothalamus are stimulated by the rising osmotic pressure of the extracellular fluid. If thirst is satisfied, osmotic pressure decreases.All of these functions taken together form a survival mechanism that causes us to sustain the body processes that BMR measures.
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Basal metabolic rate
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Physiology
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BMR estimation formulas Several equations to predict the number of calories required by humans have been published from the early 20th–21st centuries. In each of the formulas below: P is total heat production at complete rest, m is mass (kg), h is height (cm), a is age (years).The original Harris–Benedict equationHistorically, the most notable formula was the Harris–Benedict equation, which was published in 1919: for men, 13.7516 kg 5.0033 cm 6.7550 year 66.4730 kcal day , for women, 9.5634 kg 1.8496 cm 4.6756 year 655.0955 kcal day .
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Basal metabolic rate
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Physiology
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The difference in BMR for men and women is mainly due to differences in body mass. For example, a 55-year-old woman weighing 130 pounds (59 kg) and 66 inches (170 cm) tall would have a BMR of 1,272 kilocalories (5,320 kJ) per day.
The revised Harris–Benedict equationIn 1984, the original Harris–Benedict equations were revised using new data. In comparisons with actual expenditure, the revised equations were found to be more accurate: for men, 13.397 kg 4.799 cm 5.677 year 88.362 kcal day , for women, 9.247 kg 3.098 cm 4.330 year 447.593 kcal day .
It was the best prediction equation until 1990, when Mifflin et al. introduced the equation: The Mifflin St Jeor equation 10.0 kg 6.25 cm 5.0 year kcal day , where s is +5 for males and −161 for females.
According to this formula, the woman in the example above has a BMR of 1,204 kilocalories (5,040 kJ) per day.
During the last 100 years, lifestyles have changed, and Frankenfield et al. showed it to be about 5% more accurate.
These formulas are based on body mass, which does not take into account the difference in metabolic activity between lean body mass and body fat. Other formulas exist which take into account lean body mass, two of which are the Katch–McArdle formula and Cunningham formula.
The Katch–McArdle formula (resting daily energy expenditure)The Katch–McArdle formula is used to predict resting daily energy expenditure (RDEE).
The Cunningham formula is commonly cited to predict RMR instead of BMR; however, the formulas provided by Katch–McArdle and Cunningham are the same.
370 21.6 ⋅ℓ, where ℓ is the lean body mass (LBM in kg): 100 ), where f is the body fat percentage.
According to this formula, if the woman in the example has a body fat percentage of 30%, her resting daily energy expenditure (the authors use the term of basal and resting metabolism interchangeably) would be 1262 kcal per day.
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Basal metabolic rate
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Physiology
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Research on individual differences in BMR The basic metabolic rate varies between individuals. One study of 150 adults representative of the population in Scotland reported basal metabolic rates from as low as 1,027 kilocalories (4,300 kJ) per day to as high as 2,499 kilocalories (10,460 kJ); with a mean BMR of 1,500 kilocalories (6,300 kJ) per day. Statistically, the researchers calculated that 62% of this variation was explained by differences in fat free mass. Other factors explaining the variation included fat mass (7%), age (2%), and experimental error including within-subject difference (2%). The rest of the variation (27%) was unexplained. This remaining difference was not explained by sex nor by differing tissue size of highly energetic organs such as the brain.A cross-sectional study of more than 1400 subjects in Europe and the US showed that once adjusted for differences in body composition (lean and fat mass) and age, BMR has fallen over the past 35 years. The decline was also observed in a meta-analysis of more than 150 studies dating back to the early 1920s, translating into a decline in total energy expenditure of about 6%.
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Basal metabolic rate
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Biochemistry
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About 70% of a human's total energy expenditure is due to the basal life processes taking place in the organs of the body (see table). About 20% of one's energy expenditure comes from physical activity and another 10% from thermogenesis, or digestion of food (postprandial thermogenesis). All of these processes require an intake of oxygen along with coenzymes to provide energy for survival (usually from macronutrients like carbohydrates, fats, and proteins) and expel carbon dioxide, due to processing by the Krebs cycle.
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Basal metabolic rate
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Biochemistry
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For the BMR, most of the energy is consumed in maintaining fluid levels in tissues through osmoregulation, and only about one-tenth is consumed for mechanical work, such as digestion, heartbeat, and breathing.What enables the Krebs cycle to perform metabolic changes to fats, carbohydrates, and proteins is energy, which can be defined as the ability or capacity to do work. The breakdown of large molecules into smaller molecules—associated with release of energy—is catabolism. The building up process is termed anabolism. The breakdown of proteins into amino acids is an example of catabolism, while the formation of proteins from amino acids is an anabolic process.
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Basal metabolic rate
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Biochemistry
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Exergonic reactions are energy-releasing reactions and are generally catabolic. Endergonic reactions require energy and include anabolic reactions and the contraction of muscle. Metabolism is the total of all catabolic, exergonic, anabolic, endergonic reactions.
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Basal metabolic rate
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Biochemistry
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Adenosine triphosphate (ATP) is the intermediate molecule that drives the exergonic transfer of energy to switch to endergonic anabolic reactions used in muscle contraction. This is what causes muscles to work which can require a breakdown, and also to build in the rest period, which occurs during the strengthening phase associated with muscular contraction. ATP is composed of adenine, a nitrogen containing base, ribose, a five carbon sugar (collectively called adenosine), and three phosphate groups. ATP is a high energy molecule because it stores large amounts of energy in the chemical bonds of the two terminal phosphate groups. The breaking of these chemical bonds in the Krebs Cycle provides the energy needed for muscular contraction.
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Basal metabolic rate
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Biochemistry
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Glucose Because the ratio of hydrogen to oxygen atoms in all carbohydrates is always the same as that in water—that is, 2 to 1—all of the oxygen consumed by the cells is used to oxidize the carbon in the carbohydrate molecule to form carbon dioxide. Consequently, during the complete oxidation of a glucose molecule, six molecules of carbon dioxide and six molecules of water are produced and six molecules of oxygen are consumed.
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Basal metabolic rate
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Biochemistry
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The overall equation for this reaction is 12 CO 2+6H2O (30–32 ATP molecules produced depending on type of mitochondrial shuttle, 5–5.33 ATP molecules per molecule of oxygen.) Because the gas exchange in this reaction is equal, the respiratory quotient (R.Q.) for carbohydrate is unity or 1.0: R.Q.
CO 1.0.
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Basal metabolic rate
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Biochemistry
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Fats The chemical composition for fats differs from that of carbohydrates in that fats contain considerably fewer oxygen atoms in proportion to atoms of carbon and hydrogen. When listed on nutritional information tables, fats are generally divided into six categories: total fats, saturated fatty acid, polyunsaturated fatty acid, monounsaturated fatty acid, dietary cholesterol, and trans fatty acid. From a basal metabolic or resting metabolic perspective, more energy is needed to burn a saturated fatty acid than an unsaturated fatty acid. The fatty acid molecule is broken down and categorized based on the number of carbon atoms in its molecular structure. The chemical equation for metabolism of the twelve to sixteen carbon atoms in a saturated fatty acid molecule shows the difference between metabolism of carbohydrates and fatty acids. Palmitic acid is a commonly studied example of the saturated fatty acid molecule.
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Basal metabolic rate
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Biochemistry
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The overall equation for the substrate utilization of palmitic acid is 16 32 23 16 CO 16 H2O (106 ATP molecules produced, 4.61 ATP molecules per molecule of oxygen.) Thus the R.Q. for palmitic acid is 0.696: R.Q.
16 CO 23 0.696.
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Basal metabolic rate
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Biochemistry
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Proteins Proteins are composed of carbon, hydrogen, oxygen, and nitrogen arranged in a variety of ways to form a large combination of amino acids. Unlike fat the body has no storage deposits of protein. All of it is contained in the body as important parts of tissues, blood hormones, and enzymes. The structural components of the body that contain these amino acids are continually undergoing a process of breakdown and replacement. The respiratory quotient for protein metabolism can be demonstrated by the chemical equation for oxidation of albumin: 72 112 18 22 77 63 CO 38 SO CO NH 2)2 The R.Q. for albumin is 0.818: R.Q.
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Basal metabolic rate
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Biochemistry
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The reason this is important in the process of understanding protein metabolism is that the body can blend the three macronutrients and based on the mitochondrial density, a preferred ratio can be established which determines how much fuel is utilized in which packets for work accomplished by the muscles. Protein catabolism (breakdown) has been estimated to supply 10% to 15% of the total energy requirement during a two-hour aerobic training session. This process could severely degrade the protein structures needed to maintain survival such as contractile properties of proteins in the heart, cellular mitochondria, myoglobin storage, and metabolic enzymes within muscles.
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Basal metabolic rate
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Biochemistry
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The oxidative system (aerobic) is the primary source of ATP supplied to the body at rest and during low intensity activities and uses primarily carbohydrates and fats as substrates. Protein is not normally metabolized significantly, except during long term starvation and long bouts of exercise (greater than 90 minutes.) At rest approximately 70% of the ATP produced is derived from fats and 30% from carbohydrates. Following the onset of activity, as the intensity of the exercise increases, there is a shift in substrate preference from fats to carbohydrates. During high intensity aerobic exercise, almost 100% of the energy is derived from carbohydrates, if an adequate supply is available.
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Basal metabolic rate
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Biochemistry
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Aerobic vs. anaerobic exercise Studies published in 1992 and 1997 indicate that the level of aerobic fitness of an individual does not have any correlation with the level of resting metabolism. Both studies find that aerobic fitness levels do not improve the predictive power of fat free mass for resting metabolic rate.
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