bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological Methods
Authors: Henderson Peter Alan 
Published: April 2013

Abstract

Ecological methods cover a wide range of techniques required for studies that range in scale from the individuals on a single flower head to entire ecosystems with thousands of species. Although both the scale and the questions a study is designed to answer can vary greatly, there are certain key components that are always present in a well‐designed ecological study. First, ecological studies involve setting objectives and formulating a sampling programme. Second, there is often a practical component involving measurement and sampling in the field, which frequently includes sorting, identifying and measuring the organisms retrieved. Third, there is data analysis and reporting. The results can be used to derive absolute or relative population abundance measures, construct life tables, probe population dynamics and estimate biodiversity.

Key Concepts:

Ecological methods address a wide range of scales and are concerned with the acquisition of data on individual organisms, single populations and entire ecosystems.

Ecological studies have three key components: programme planning, field data acquisition and data analysis.

Studies can be broadly classified as intensive or extensive. Extensive studies are carried out over larger areas than intensive studies and seek to obtain information on the distribution and abundance of species for conservation and management purposes. Intensive studies involve the repeated observation of a population to gain insight into demographic processes.

Sampling methods can be classified into absolute methods, which give densities per unit area of habitat and relative measures which give an index of abundance.
Dinosaur Growth: Egg to Adult
Authors: Chinsamy‐Turan Anusuya 
Published: April 2013

AbstractThe integrity of the microstructure of fossilised bones generally survives millions of years of fossilisation. Analysis of the preserved bone microstructure of dinosaurs permits a direct assessment of the nature and type of bone that was present in the once living animal. By comparison with the bone microstructure of living vertebrates, deductions pertaining to various aspects of the life history and biology of the dinosaur can be made. Studies of the bone microstructure of dinosaurs suggest that the growth strategies of dinosaurs varied: some dinosaurs grew rapidly and uninterruptedly, whereas others experienced periodic pauses in growth. If growth rings are present in the fossil bones of different sized individuals of a particular taxon, skeletochronology can be applied to deduce the growth trajectory for the dinosaur. Such growth curves suggest that dinosaurs had a unique growth strategy that was faster than that of extant reptiles, but not as fast as similar sized birds and mammals.Key Concepts:Fossilisation generally preserves the integrity of the dinosaur bone microstructure.Bone microstructure of dinosaurs can be directly compared to extant vertebrates.Different types of bone microstructure suggest different rates of bone deposition.Dinosaurs have an abundance of fibro‐lamellar bone.Many dinosaurs have an interrupted (zonal) type of bone tissue.Changes in bone microstructure through ontogeny can be assessed.Growth lines are assumed to be annually formed.Skeletochronology can be applied to many dinosaur taxa to assess age.Growth curves can be deduced for dinosaurs.Growth curves suggest dinosaurs grew faster than similar sized reptiles, but not as fast as similar sized birds and mammals.
Evolutionary Progress: Conceptual Issues
Authors: Shanahan Timothy 
Published: April 2013

AbstractPerhaps no idea has proven more controversial within evolutionary biology than the idea that evolution manifests progress. To some biologists evidence of progress in the history of life has seemed undeniable. From utterly simple beginnings have come organisms of astounding complexity and sophistication. But to others the hazy notion of evolutionary progress appears distinctly unscientific inasmuch as it is thought to require subjective value judgements that have no place in a science based squarely on empirical facts. Debates over evolutionary progress can be substantially, albeit not entirely, resolved by examining some of the assumptions underlying such debates and by attending more carefully to the definition of key concepts such as ‘direction’ and ‘improvement’. Doing so suggests that acceptance of a moderate form of evolutionary progress can accommodate evidence from the history of life while satisfying standards of scientific objectivity.Key Concepts:The concept of ‘progress’ has been controversial within evolutionary biology.Resolving disagreements about evolutionary progress requires careful examination of theoretical, empirical and conceptual issues.Evolutionary progress may be defined as intergenerational directional change embodying improvement in the properties characterising a population of biological entities.A process has a direction over a given time interval if the value of one of its properties increases during that time interval.Directional change, which is an observable fact, must be distinguished from directionality, that is, a tendency to change in a specific direction.It is important to distinguish uniform, net and apex directional change.Critics of the idea of evolutionary progress complain that ‘improvement’ is a value‐laden term that cannot be given an objective scientific definition.Improvement in the evolutionary sense is any directional change that contributes to the solution of a problem facing biological entities in a particular environment.A number of biologists, beginning with Darwin, have argued that evolution manifests progress in the sense defined here.If the ability of organisms in even one lineage to cope with some problem impacting their chances for survival and reproduction has improved over some time interval, then evolutionary progress, at least in this limited sense, is a scientific fact.
History of Enzyme Chemistry
Authors: Cornish‐Bowden Athel 
Published: April 2013

Abstract

Enzymes have been recognized as the catalysts necessary for all physiological processes since the end of the nineteenth century. Before then their study was complicated by arguments over vitalism, which only subsided after Buchner showed that a cell‐free extract from yeast could carry out alcoholic fermentation. This led to the flowering of studies of metabolism, and with it a corresponding increase in studies of enzyme catalysis, which were no longer mainly limited to extracellular enzymes such as
pepsin
. The groundwork for kinetic studies was laid by Henri and by Michaelis and Menten, and understanding of enzyme catalysis was later strengthened when Sumner demonstrated that enzymes could be crystallized. The principal features of three‐dimensional structure became known by the 1950s, by which time hundreds of enzymes had been characterized, making it necessary to create a rational classification of reactions catalysed, the basis of the modern EC system.

Key Concepts:

Nearly all physiological processes are catalysed by proteins known as enzymes.

A few reactions are catalysed by non‐protein enzymes based on
RNA
.

Enzymes are highly specific, with all apart from degradative enzymes extremely restrictive in the reactions they catalyse.

Most enzymes are similar in amino acid sequence to their homologues in other species even between organisms that are phylogenetically very different.

Enzyme catalysis was initially studied primarily by kinetic measurements, but is now based also on three‐dimensional structural information derived from crystallography or NMR.
Collectins
Authors: Thiel Steffen , Takahashi Kazue 
Published: April 2013

Abstract

Collectins are pattern‐recognition molecules of innate immunity and are involved in recognising pathogens and abnormal cells in an antibody‐independent manner. The name collectin is derived from the basic structure, consisting of a collagen‐like domain and a carbohydrate‐recognition domain (CRD), akin to lectins, which recognise sugars. The CRDs bind pathogen‐associated molecular patterns, which are chemical motifs exposed on the surface of pathogens and abnormal cells. Collectins are synthesised in many organs and some are circulating in blood, whereas others are localised to a tissue. Collectin genes are germinally present and therefore, their proteins are expressed at healthy state, affording an instant action. There are also a homologous protein family called ficolins, which are similar to collectins structurally and functionally. Mechanisms of actions include a direct opsonin activity, activation of complement pathways and coagulation, modulation of inflammation and adaptive immunity.

Key Concepts:

Collectins are molecules of innate immunity, which is the first line of host defence and is fully functional throughout the body and the life regardless of health.

Collectins are pattern‐recognition molecules, which are able to identify invading pathogens and abnormal cells and tissues.

Selected genetic mutations affect functions of collectins and are associated with reduced host defence mechanisms and developmental disorder.

Some collectins are disease modifier, as deficiency itself may cause no problem whereas it may have adverse effect depending on type of disease, infection or sterile injury.

Collectins have homology to ficolins structurally and functionally, and may share and substitute functions in host defence.
Post‐copulatory Reproductive Strategies
Authors: Snook Rhonda R , Pizzari Tommaso 
Published: April 2013

Abstract

In most sexually reproducing organisms females obtain sperm from multiple males. Such widespread female promiscuity prolongs the operation of sexual selection after copulation, through the competition of the ejaculates of different males over fertilisation (sperm competition) and mechanisms by which females systematically bias the outcome of sperm competition (cryptic female choice – CFC). Post‐copulatory sexual selection can either consistently favour certain male or ejaculate phenotypes or certain combinations of male and female genotypes. Sperm competition and CFC drive the evolution of a diverse range of post‐copulatory strategies resulting in differential ejaculate allocation by males and differential sperm utilisation by females. The post‐copulatory reproductive strategies of each sex have considerable impact on the fitness of the opposite sex, giving rise to an intimate process of intersexual coevolution. The concept of post‐copulatory sexual selection is therefore a powerful heuristic tool to explain variation in individual fitness and the staggering variation in sexual strategies both across and within species.

Key Concepts:

Sexual selection, or intrasexual competition for mates and fertilisation, can continue after copulation when females mate with multiple males (polyandry).

The post‐copulatory processes of sperm competition and cryptic female choice are equivalent to pre‐copulatory mate competition and female choice.

Molecular and behavioural studies have demonstrated the female multiple mating is nearly ubiquitous and therefore post‐copulatory sexual selection is a major evolutionary force.

Sperm competition occurs when the ejaculates of different males compete to fertilise the same set of eggs, and selects for male adaptations both to prevent and win such competition

A male's relative share of paternity is increased through adaptations of sperm quantity and quality, in addition to behavioural, morphological and physiological adaptations in somatic traits.

Cryptic female choice (CFC) refers to female‐driven biases in the outcome of sperm competition, which are repeatable within females. CFC and sperm competition are often difficult to distinguish because they can interact to bias sperm use.

Females have a wide variety of adaptations that mediate CFC; examples include differential sperm ejection, spermicide, and differential maternal allocation.

Patterns of CFC can either differ between different combinations of male and female genotypes, or be consistent among females sharing similar preferences.

Post‐copulatory sexual selection can foster the maintenance of polymorphism and alternative reproductive strategies within a species.

The post‐copulatory reproductive strategies of one sex can reduce the fitness of the other sex, reflecting sexual conflict over mating and fertilisation. Such conflict can fuel sexually antagonistic coevolution of post‐copulatory traits.
Arecales (Palms)
Authors: Dransfield John 
Published: April 2013

Abstract

Arecales is the order of monocotyledonous angiosperms that includes the single family, Arecaceae, the palms. The family is divisible into five subfamilies, each with very distinctive morphology. Palms are economically very important, providing a huge range of products from food, clothing, construction and basketry material to medicine. They are usually instantly recognisable as palms, having distinctive morphology; in particular, the fan (palmate) or feather (pinnate) leaves are almost unique in development. The fossil record of palms extends from the middle of the late Cretaceous to the present day. Palms are largely confined to the tropics and subtropics, with a very few outliers in temperate regions. Across the tropics the distribution of subfamilies, tribes, subtribes and genera is uneven, reflecting a complex history of evolution and dispersal.

Key Concepts:

The palms are an iconic group of plants that epitomise the tropical world (Figure 1).

Palms boast the largest leaf, the longest unbranched stem and the largest and heaviest seed.

Palms are of immense economic significance.
Severe Acute Respiratory Syndrome (
SARS
)
Authors: Page Carly A , Frieman Matthew B 
Published: April 2013

Abstract

Severe acute respiratory syndrome (SARS) is a disease that caused significant morbidity and mortality during the outbreak in 2002–2003. In early 2003, a novel coronavirus was identified as the aetiological agent of SARS and is currently known as SARS‐CoV. This virus has since been extensively characterised and studied as a model for acute respiratory infection. SARS‐CoV utilises a number of virally encoded proteins to subvert the host immune system and establish infection. The ensuing immune dysregulation often results in prolonged, severe disease and sometimes death that does not always associate with the long‐term presence of virus. In addition to being an important respiratory virus model, SARS‐CoV is also an important model for emerging infectious diseases as it emerged from natural animal reservoirs. Here we review the epidemiology, clinical disease and virology of this disease‐causing virus.

Key Concepts:

Emerging viruses are able to jump from animals to people and cause infections.

Epidemiological controls can slow down respiratory virus epidemics.

Understanding viral pathogenesis aids in our ability to fight current and future virus outbreaks.
Ribosomes and Ribosomal Proteins: More Than Just ‘Housekeeping’
Authors: Chakraborty Anirban , Kenmochi Naoya 
Published: April 2013

AbstractAs the catalyst for protein synthesis, the omnipresent ribosome is essential to all organisms. In mammalian cells, the ribosome is composed of four ribosomalribonucleic acid(RNA) species and 79 differentribosomal proteins. Several hundred copies of the genes encoding the ribosomal RNAs form clusters within the human genome; by contrast, the genes encoding the ribosomal proteins are widely dispersed, although they are functionally related and coordinately expressed. Ribosome biogenesis is a tightly controlled multi‐step process that requires massive cellular energy. Over the past decade, our perception of the ribosome has changed significantly. In the past, ribosomes were considered critical for cellular survival. However, it has now become clear that defects in ribosome biogenesis cause pleiotropic effects that may manifest as specific disease conditions in humans. Ribosomal proteins, which were previously considered to play only a housekeeping role, are now known to have many extraribosomal functions, including the surveillance of ribosomal integrity.Key Concepts:All of the three RNA polymerases, several accessory proteins, and numerous small nucleolar RNAs act in a coordinated manner to ensure that ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) are properly synthesised and assembled into a functionally active ribosome.The numbers of rRNAs and RPs vary between eukaryotes, archaea, and bacteria; however, the functions of ribosomal components have been conserved to a substantial degree throughout evolution.The nucleolus, a sub‐compartment of the nucleus that assembles around the rDNA clusters, is the major site of ribosome production.In general, RPs are basic proteins and exhibit specific affinities for nucleic acids; however, four RPs have acidic pI values.In humans, the genes encoding rRNAs are usually clustered together in multiple copies within the genome; whereas, the genes for the RPs, which are typically encoded by single genes, are scattered through out the genome.Over the past two decades, RPs have been implicated in many cellular activities that are distinct from their primary functions in ribosome biogenesis.The p53 tumour suppressor protein, an important component in the cellular response to a variety of stressors, monitors the fidelity of ribosome biogenesis through a surveillance mechanism that involves several RPs.The disruption of ribosome biogenesis causes ‘nucleolar stress’ that triggers the p53‐signalling pathway, resulting in cell cycle arrest and apoptosis.Haploinsufficiency in RP genes or mutations in genes that encode proteins essential for ribosome biogenesis can lead to a specific class of diseases in humans, called ribosomopathies, which often manifest as prominent tissue‐specific defects with associated pleiotropic anomalies.
Disability: Stigma and Discrimination
Authors: Scully Jackie Leach 
Published: April 2013

AbstractDisability is connected to the contemporary life sciences in obvious and less obvious ways. A key justification for human genetic research is that it will lead to better understanding of the ‘normal’ human genome and thus of genetically based disability. However, there is abundant evidence that people with physical and mental impairments remain stigmatised, and the potential for science to increase the stigma of disability demands a critical examination of our beliefs about disability, normality and diversity. Where the medical model of disability sees disability as originating in the deviation of an individual from a biological or physiological norm, social models see it generated by the interaction of an anomalous body with the physical and attitudinal constraints of society. These are very different approaches to the role of biology in disability. There is concern that the biomedical model today dominates to the extent of excluding other useful approaches to disability. ‘Genetic discrimination’, not all of which can be eliminated by legislation, remains a risk to people with genetically based disabilities.Key Concepts:The potential for advances in genetic medicine to prevent disability provides a key justification for genetic research.There is abundant empirical evidence that people with physical and mental impairments remain stigmatised and discriminated against around the world.The focus on disability as a person's difference from normality is reinforced by the ‘medical model’ of disability. Within this framework, disability is seen as a nominative pathology.Alternative models of disability place less emphasis on the individual's ‘problematic body’. For example, in the strong social model, what defines disabled people as a group is the collective of oppression or exclusion from society.There is concern that the biomedical approach to disability, and genetic models in particular, could reinforce the stigma attached to disability.There is a risk of ‘genetic discrimination’ – discrimination directed against people with particular genotypes. Some forms of genetic discrimination can be prevented by legislation, but others, such as the routine pre‐natal screening for and termination of affected pregnancies, are harder to prevent.Some disability theorists are concerned that the stigma of disability will inevitably lead to information about the human genome is used for eugenic purposes.The rapid accumulation of genetic information through the ‘genome revolution’ challenges us to look more critically at our beliefs about diversity and the value of different kinds of human being. This discussion should include the perspectives of disabled people.
Disability and Genetics: A Disability Critique of Pre‐natal Testing and Pre‐implantation Genetic Diagnosis (PGD)
Authors: Asch Adrienne , Barlevy Dorit 
Published: April 2013

AbstractSelecting against embryos or foetuses on the basis of predicted disability reinforces the belief that disability is inimical to a worthwhile life. The disability critique of pre‐natal testing and pre‐implantation genetic diagnosis (PGD) flows from the belief that life with disability can be valuable to individuals, their families, and society. Disability should be understood as just another form of human variation. Reassessment of the crucial elements of the parent–child relationship is fundamental to create a welcoming society for persons with varying abilities. Reforms should be made to the information provided about the lives of persons with disabilities and their families in order to enhance women and couples’ informed reproductive decision‐making. Additionally, clinicians and genetics professionals need to understand that society contributes significantly to the difficulties that people with disabilities experience in attaining full participation in family and community life.Key Concepts:Neither PGD nor any method of pre‐natal testing can accurately indicate a potential child's quality of life.The expressivist argument is only one type of disability critique, which focuses on the negative message that PGD or pre‐natal testing followed by selective embryo implantation or selective abortion sends to current persons living with disabilities.The disability critique is not primarily expressivist.Most negative facets of life with disability can be attributed to societal attitudes and practices that are open to change, and not to the medical condition itself.Clinicians and professionals should understand that they have a role in ending discrimination against people with disabilities, much as they work to practice their professions without sexism or racism.Disability, like sex, race, and ethnicity, is a legitimate, respectable form of human variation.Preventing the incidence of disability is quite different from preventing the existence of persons with disability.Research indicates that people with disabilities and their families fare relatively the same as the rest of the population.The norms of good parenting include fostering and supporting the uniqueness of individual children, with all their mix of talents, personalities, strengths, and problems.Information about the nonmedical facets of life with disability and connections to disability support groups need to be provided to prospective parents deciding about their reproductive future.