bluuebunny/crossref_metadata_2025_split huggingface dataset:
Animal Viruses Pathogenic for Humans
Authors: Nel Louis H , Weyer Jacqueline 
Published: November 2014

Abstract

Diseases and infections that are transmitted between vertebrate animals and man are known as zoonoses. Nearly, two‐thirds of infectious diseases known to affect mankind are zoonotic. Many of these zoonoses are caused by viruses – some of these are rare, but others are of great epidemiological importance based on high mortality and morbidity and global distribution. New viral zoonoses continue to emerge from all parts of the world, particularly as wildlife and humans come into closer contact, given the present‐day dynamics of global development. Human Immunodeficiency virus is one of the most profound examples of zoonosis which through a species jump has established in the human population and has gained worldwide distribution. Important emerging viral zoonotic diseases include Avian Influenza, severe acute respiratory syndrome, West Nile fever and hantavirus infection with pulmonary syndrome.

Key Concepts:

Many viruses can be transmitted from vertebrate animals to humans and cause disease. This is known as zoonoses.

Close to two thirds of infectious diseases that affect mankind are zoonoses.

Most emerging infectious diseases are zoonotic in origin.

Viral pathogens are more likely to emerge as zoonoses due to their propensity to adapt and mutate.

Changes in human ecology contribute to emerging zoonoses from wildlife.
Glycogen, Starch and Sucrose Synthesis
Authors: King Michael W 
Published: November 2014

AbstractGlucose constitutes a universal energy‐providing molecule. It is the primary fuel substance for a wide array of organisms from bacteria to man. Its great utility as an energy source is that it can be oxidised for the production of the high energy molecule,adenosine triphosphate (ATP), even in the absence of oxygen. Within humans, certain tissues, in particular red blood cells, derive all of their energy from the anaerobic oxidation of glucose. The human brain prefers glucose for energy and consumes the largest percentage of glucose on a daily basis. For these reasons the consumption of glucose or glucose containing sugars, such as sucrose, is important for life processes. Given the importance of glucose, it is not surprising that organisms store this carbohydrate for easy access for ATP production. Storage of glucose is in the form of a polymer composed of long linear chains and occasional branched chains termed glycogen in animals and starch in plants. Due to its highly important role in cellular viability, glucose storage and utilisation in humans is stringently controlled by hormones and neurotransmitters.Key Concepts:Glucose represents a key energy molecule for the majority of phyla.Glucose uptake from dietary sources (e.g. starch and sucrose) involves both sodium‐dependent and ‐independent intestinal enterocyte membrane transporters.Ready access to glucose is ensured via its storage as a highly polymeric molecule in plants and animals.Storage and release of glucose, from cellular stores such as glycogen, is highly regulated by hormones and neurotransmitters.Key hormones in the overall regulation of glycogen homeostasis include insulin, glucagon, and epinephrine.Abnormalities in the genes encoding the enzymes that regulate glucose storage and release in humans result in a family of disorders called glycogen storage diseases.
Claude, Albert
Authors: Rasmussen Nicolas 
Published: November 2014

AbstractAlbert Claude (1899–1983) made major contributions to the understanding of the living cell's architecture in the 1940s, and even more importantly, to devising the methodological approach on which the discipline of cell biology is founded. This approach is marked by the coordinated use of independent experimental techniques, especially the separation of cellular components from homogenised tissue by means of high speed centrifugation, so that each of the centrifuge‐isolated cell fractions can be separately studied biochemically, and the use of the electron microscope to locate these components in native cell structure.Key Concepts:The field of cell biology depends upon the coordinated application of several independent experimental methods, especially the use of fractionation biochemistry to characterise the function of cell components and the use of electron microscopy to determine their location in the cell.
Krogh, Schack August Steenberg
Authors: Kragh Helge 
Published: November 2014

Abstract

The Danish zoophysiologist August Krogh (1874–1949) was a pioneer of studies of the gas exchange in living organisms and the function of capillaries in muscles at rest and at work. In 1910, he provided strong evidence that diffusion alone can explain the exchange of oxygen in the lungs, and in 1919 he suggested a mechanism that explained how the capillaries regulate the supply of oxygen to the tissue. Krogh received the Nobel Prize in medicine for 1920. He was instrumental in securing the rights for insulin production in Scandinavia, an initiative with important industrial consequences. From 1908 to his retirement in 1945 he was a professor at the University of Copenhagen.
Tropical Forests
Authors: Corlett Richard T 
Published: November 2014

Abstract

Tropical forests occupy approximately 10% of the world's total land area, but they play a disproportionate role in global carbon and water cycles, and are believed to house more than half of the world's species. Tropical forests occupy a wide range of environments, and the structure and species composition vary with dry season length, altitude above sea level, and the occurrence of extreme soil types or regular inundation by fresh or saline water. Lowland evergreen rain forests are the most diverse ecosystems on Earth, but the processes that generated and maintain this diversity are not fully understood. Forests are under threat throughout the tropics from clearance for agriculture, logging for timber, hunting, fires, climate change and other human impacts. Major conservation priorities include protecting large areas of intact forest ecosystems where still possible, improving the management of logged forests, controlling hunting, and reconnecting isolated forest fragments by restoring forest between them.

Key Concepts:

Tropical forests house the majority of the world's species.

Tropical forests have a large role in global carbon and water cycles.

Distinctive types of tropical forests occur in different climates, on extreme soil types, and in areas subject to flooding by fresh or saline water.

Forests in similar environments but different tropical regions also differ, because the forest communities in each region have different evolutionary histories.

Lowland rain forests are far more diverse than any other terrestrial ecosystem, at least partly because of the age and continuity of warm, wet tropical climates.

The most important commercial product from tropical forests is timber, but these forests also provide many other products and services to local human communities.

The biggest threats to tropical forests and their species are conversion to agriculture, hunting and unsustainable logging.

Legally protected areas are still the cornerstone of tropical forest conservation, but sustainable exploitation for timber and other products offers an alternative in countries with good governance capabilities.
Centre National de la Recherche Scientifique (
CNRS
)
Authors: Guthleben Denis 
Published: November 2014

Abstract

Centre national de la recherche scientifique – National Center for Scientific Research (CNRS) – was created in October 1939, in the early days of World War II, in order to encourage and to coordinate research at the national level in France. If its origins may be traced as early as the 1870s, the conditions of its founding were met in the late 1930s, during and after the Popular Front coalition, at the initiative of physicist and Nobel Prize winner Jean Perrin. After 1945, it has developed in all scientific fields, becoming in the 1960s and 1970s a top‐leading institution for basic research as well as for research related to the needs of society. Today the CNRS has more than 30 000 scientists, engineers and technicians, and 1200 laboratories, brought together in 10 institutes under the direction of its president, chemist Alain Fuchs.

Key Concepts

The CNRS is the largest public research organisation in France and the largest basic science agency in Europe.

The CNRS has contributed to the emergence of a national scientific policy in France.

Valorisation has become a major objective for the CNRS.

The CNRS is designed to encourage interdisciplinary research.

The mission of the CNRS is to evaluate and carry out all research capable of advancing knowledge and bringing social, cultural, and economic benefits for society.
Bioinformatics
Authors: Makałowski Wojciech , Jąkalski Marcin , Makałowska Izabela 
Published: November 2014

Abstract

Molecular biologists generate data at an unparalleled pace, and the demands and opportunities for interpreting such data are expanding more than ever. In this context, bioinformatics has emerged as a strategic frontier involving molecular biology, molecular evolution, information technology and statistics. Bioinformatics may be defined as the research, development, or application of computational tools and approaches for expanding the use of biological data, including those to acquire, store, organise, archive, analyse, or visualise such data. Its goal is to enable biological discovery based on existing data, or in other words to transform biological data into information, and eventually into knowledge.

Key Concepts

Biological data grow faster than Moore's law predicts, which means that information technology might be a bottleneck of the data analyses.

The amount of data produced by biologists triggered a boom of specialized databases.

Nucleotide sequences are read in small stretches that need to be assembled computationally into whole molecules.

Searching sequence databases with the unknown sequence as a query, so‐called similarity search, is most likely the most frequent bioinformatic activity.

Systems biology uses advanced mathematics to build complex models of biological activities.
DNA
Databanks and Genomics Research: Forensic and Military (Ab)Uses
Authors: Williams Robin 
Published: November 2014

Abstract

Efforts to identify criminal suspects, victims of crime, those killed in military conflicts and mass fatality casualties are increasingly supported by the availability of databanks holding
deoxyribonucleic acid (DNA)
profiles obtained from known subjects. The development of these databanks has been made possible by advances in forensic genetic technologies, legislative changes and substantial (usually state) investment. Although there is widespread public support for the criminal justice uses of these innovations in genetic and information technologies, some critics argue that the growth of forensic DNA databanks and their expanding use by police and judicial authorities can also threaten individual and collective human rights. Relevant questions are: what should be the criteria for the inclusion and retention of profiles in forensic DNA databanks; what are the legitimate uses of samples and profiles; and what governance arrangements are appropriate to secure public trust in forensic DNA databank establishment and growth?

Key Concepts

Several substantial research studies have shown that forensic DNA profiling and databanking can play a significant and cost‐effective role in criminal justice outcomes for a wide variety of crime types.

There is a global trend for criminal jurisdictions to adopt forensic DNA profiling and databanking in support of criminal investigations and prosecutions.

DNA profiling and matching is an important resource for the identification of civilian and military casualties in conflict and natural disaster situations.

Public trust in the police and judicial forensic DNA databanks depends on the inclusiveness, transparency and accountability of databank governance arrangements.

Legislation governing criminal and military DNA databanks normally specifies that information cannot be shared between these and medical databanks.

There is increasing interest in the investigative usefulness of automated exchange of forensic DNA profiles between national jurisdictions; new transnational arrangements are emerging – at least within the European Union – to reflect this interest.
Radical
S
‐Adenosylmethionine (
SAM
) Superfamily
Authors: Jarrett Joseph T , Farrar Christine E 
Published: November 2014

Abstract

A large superfamily of enzymes uses
S
‐adenosyl‐
l
‐methionine (SAM) to generate high‐energy carbon radicals as intermediates in a variety of metabolic and biosynthetic reactions. All radical SAM enzymes contain one or more iron‐sulphur clusters, with SAM binding directly to an iron‐sulphur cluster in a manner that facilitates reduction of SAM and generation of a highly reactive 5′‐deoxyadenosyl radical intermediate. This potent intermediate typically initiates the subsequent radical transformations by abstracting a hydrogen atom from the substrate or from a nearby protein residue. Despite the diverse array of reactions catalysed, members of the Radical SAM superfamily share a similar structural topology that facilitates this interaction between SAM and an iron‐sulphur cluster and allows restricted access of substrates to the site of radical generation.

Key Concepts:

The Radical SAM superfamily comprises a diverse array of enzymes that contain a common core structural fold and use
S
‐adenosylmethionine to generate organic radicals.

Radical SAM enzymes contain one or more iron‐sulphur clusters that are essential for catalysis.

S
‐Adenosylmethionine is reduced and cleaved at the sulfonium centre to generate a 5′‐deoxyadenosyl radical.

Radical SAM enzymes typically use a 5′‐deoxyadenosyl radical to abstract a hydrogen atom from the substrate.

Reaction types catalysed by radical SAM enzymes include oxidation, reduction, methylation, methylthiolation, sulfurylation and complex rearrangement reactions.

Radical SAM enzymes are use to introduce several posttranslational and posttranscriptional modifications into proteins and RNA.

Radical SAM enzymes are involved in thousands of uncharacterised bacterial natural product biosynthesis pathways.
Membrane Traffic and Disease
Authors: Cláudio Nuno , Pereira Francisco JC , Barral Duarte C 
Published: November 2014

Abstract

Membrane traffic is a highly regulated process that ensures the communication between membrane‐bound compartments while maintaining their specific protein and lipid composition. It can be divided into four steps: cargo sorting and budding of a vesicle from a donor compartment, transport along the cytoskeleton, tethering and docking to an acceptor compartment, and finally fusion with the acceptor compartment. Importantly, defects in any of these steps can lead to diseases that affect different tissues and organs. At the subcellular level, several of these diseases affect compartments from specialized cell types known as lysosome‐related organelles. Moreover, the dysfunction of membrane traffic processes required ubiquitously can lead to restricted phenotypes, underscoring the redundancy of these processes and/or the sensitivity of certain cell types to their impairment. Thus, the study of the diseases caused by defects in membrane traffic provides an opportunity to understand its role in normal cell physiology and discover novel therapies.

Key Concepts:

Defects in any of the steps of vesicular traffic can lead to disease.

Vesicular traffic regulation shows redundancy.

Defects in ubiquitously‐expressed proteins can result in a tissue‐restricted phenotype.

Lysosome‐related organelles are commonly affected upon impairment of vesicular traffic.

Several diseases are caused by defects in different proteins involved in the same biological process/pathway.
Use of Personalized Genomic Information
Authors: Giovanni Monica A , Murray Michael F 
Published: November 2014

Abstract

Advances in
deoxyribonucleic acid (DNA)
sequencing technologies have driven down the cost of obtaining individualised genomic information, however, interested parties must consider the potential benefits and risks to the individual in applying this data to healthcare. Previously, the cost of genetic testing was such that it was used sparingly to query a small number of genes and only in cases in which there was a high pretest probability of a diagnostic result. It is now possible to receive whole‐genome data for similar costs. While technically feasible, our collective ability to interpret variation observed in the entire genome has not progressed as quickly as the technology. Currently, only a small fraction of observed variation in the human genome is interpretable with certainty. There exists a risk of over‐interpretation of variants of uncertain significance; therefore, individuals with interest in the personalised use of this information should seek consultation with clinical experts.

Key Concepts:

Personalised use of genomic information as a tool in clinical medicine is not a new concept; genomic information has long been used to guide patient care. Traditional clinical genetic and genomic testing has been used in selected patients for decades.

Advances in DNA sequencing technology, namely the advent of next generation sequencing techniques, have improved accuracy, decreased costs, and led to whole genome, whole exome, and multi‐gene panel sequencing as new offerings in clinical molecular testing; these new methods add to traditional approaches of Sanger sequencing, multiplex ligation‐dependent probe amplification (MLPA), array‐based chromosomal analysis and karyotype, among others.

While whole genome sequencing allows for rapid reading of an individual's entire genetic code, the analytic interpretation of this data has not yet met the speed and precision of the sequence acquisition.

Given the current state of technology, whole exome and whole genome sequencing will be best employed in a select subset of patients as a diagnostic test at this point in time.

Widespread application of whole genome sequencing in all patients will eventually be feasible, but at the current time application of these technologies could raise significant uncertainty, in the form of incidental findings, variants of uncertain significance and uninterpretable data. Targeted sequencing or targeted analysis of data can be used with currently available tools to provide useful diagnostic information in some individuals.

High definition clinical genomics (HDCG), where the detailed effects of any DNA sequence variant is understood at the individual nucleotide level, will be achieved sometime in this century and will lead to significantly greater utility in the use of genomic technologies to personalise health management.
NSD

1
,

EZH

2
and

DNMT

3

A

Overgrowth Genes and Their Associated Overgrowth Syndromes
Authors: Tatton‐Brown Katrina 
Published: November 2014

Abstract

Nuclear receptor SET‐domain containing protein 1 (
NSD1
), Enhancer of Zeste, drosophila, Homolog 2 (
EZH2
) and DNA methyltransferase 3A (
DNMT3A
) constitute an emerging family of epigenetic regulatory genes with a dual somatic/germline role in the pathogenesis of haematological malignancies and overgrowth disorders.
NSD1
,
EZH2
and
DNMT3A
all encode components of the epigenetic arsenal and are involved in the regulation of transcription: both NSD1 and EZH2 are histone methyltransferases whilst DNMT3A is a DNA methyltransferase. The three overgrowth disorders caused by germline mutations of
NSD1
,
EZH2
and
DNMT3A
, Sotos syndrome, Weaver syndrome and the DNMT3A overgrowth disorder, respectively, are all characterised by pre‐ and postnatal increased growth, a variable intellectual disability and a distinctive, syndrome‐specific but often subtle facial appearance. However, despite the vast increase in knowledge over the last decade, there are still many questions about this new family of overgrowth genes that remain unanswered and further clinical and molecular studies are underway to try to address these.

Key Concepts:

NSD1
,
EZH2
and
DNMT3A
are all overgrowth genes with a dual somatic/germline role in the pathogenesis of haematological malignancies/overgrowth disorders.

NSD1, EZH2 and DNMT3A all have a role in the regulation of the epigenome.

Germline
NSD1
gene abnormalities causes Sotos syndrome, germline
EZH2
gene abnormalities cause Weaver syndrome and the DNMT3A overgrowth syndrome is caused by germline
DNMT3A
gene abnormalities.

Sotos syndrome, Weaver syndrome and the DNMT3A overgrowth syndrome are all characterised by postnatal overgrowth (height and/or head circumference at least two standard deviations above the mean); a variable learning disability and a distinctive, but often subtle, facial appearance.

Other overgrowth conditions which should be considered in the differential diagnosis of Sotos, Weaver and the DNMT3A overgrowth syndromes include the PTEN hamartoma tumours spectrum, Simpson–Golabi–Behmel syndrome, Beckwith–Wiedemann syndrome and the overgrowth disorder associated with
NFIX
mutations.
Cryo‐Soft X‐ray Tomography of the Cell
Authors: Pereiro Eva , Chichón Francisco J 
Published: November 2014

Abstract

Cryo soft X‐ray tomography (cryo‐SXT) is an emerging X‐ray microscopy technique for three‐dimensional visualisation of cryo‐preserved, whole, unstained cells at a spatial resolution of 30 nm (half‐pitch). It is, therefore, bridging the gap between the low‐resolution visible light imaging techniques that provide dynamic information of specific processes, and the high resolution electron microscopy ones which achieve molecular resolution. As a first‐order approximation, in SXT as in electron tomography, a series of absorption contrast projections of the specimen are collected at different angles to finally compute the 3D absorption maps. In addition to the 3D structural information that can be obtained, the chemical sensitivity of the X‐rays to the atomic elements of the sample can also be exploited to enhance visualisation of these elements or to distinguish different chemical compositions, as well as to extract quantitative information from the data.

Key Concepts:

Tomography allows three‐dimensional visualisation of the sample.

The soft X‐ray water window energy range allows penetrating up to 10 μm of water therefore enabling a full cell to be imaged.

Cryo‐fixation is the only sample preparation step required in soft X‐ray tomography (SXT).

Cryo soft X‐ray tomography data suffers from the limited depth of field of the Fresnel zone plate objective lens which is usually smaller than the thickness of vitreous ice that can be penetrated.

The interpretation of soft X‐ray tomography data is complex and requires complementary information from electron and optical microscopy.
Studies on Palladium‐Catalyzed Synthesis of Dihydrocycloocta‐ [b]indoles and their Thermal Reactivities with Maleimide or Maleic Anhydride
Authors: Zhu Can , Ma Shengming 
Published: November 2014

AbstractA palladium(0)‐catalyzed reaction of 2‐allyl‐3‐indolyl boronates/propargylic carbonates was observed to afford dihydrocycloocta[b]indoles highly efficiently via carbon‐carbon coupling, [1,5]‐hydrogen migration involving dearomatization, and electrocyclization involving rearomatization. Their thermal reactions with the addition of dienophiles involving eletrocyclization and [4+2] cycloaddition have been studied.magnified image