bluuebunny/crossref_metadata_2025_split huggingface dataset:
Titanium Corrosion by a Hot Perfluoropolyether
Authors: CHANDLER WAYNE L. , LLOYD LINDSAY B. , FARROW MICHAEL M. , BURNHAM ROGER K. , EYRING EDWARD M. 
Published: September 2013

Abstract
The kinetics and mechanism of titanium corrosion by Krytox MLO-71-6 are reported. The rate of corrosion is found to be dependent on the presence of molecular oxygen in the environment. For titanium corrosion to occur, the lubricant chains must first break down into smaller reactive molecules. This degradation process is accelerated by TiF3 corrosion products on the metal surface, thus giving rise to a chain mechanism. The corrosion is not promoted by intense CW laser illumination at λ = 514nm.
Simulation of Coal Conversion Reactor Environments
Authors: COOKE RICHARD A. , DEVEREUX OWEN F. 
Published: September 2013

Abstract
Two models simulating the coal gasifier environment are described; Model 1 comprises coal gas components and a molten sodium salt phase, while Model 2 also includes a solid carbon phase. The use of equilibrium constants to compute the equilibrium state of an open system and the occurrence of multiple equilibrium states are detailed. Representative computations pertaining to the two models are shown in which dependent partial pressures and activity ratios are computed as function of temperature, total pressure, and the partial pressures of hydrogen, carbon monoxide, and hydrogen sulfide. The dominant anion in the liquid phase is mapped as a function of equilibrium gas phase composition.
Effect of Anions and Organic Corrosion Inhibitors on the Rate of Hydrogen Penetration of Iron
Authors: SAITO Y. , NOBE KEN 
Published: September 2013

Abstract
The rates of hydrogen penetration of annealed iron in different acids (pH 0.3), H2SO4, HCl, HClO4, and H3PO4, in the absence and presence of the organic compounds, benzotriazole, methylhydroxypentyne, and thiourea, have been measured. Although the differences in the hydrogen penetration rates of iron in the strong acids are not substantial, the penetration rate of iron in H3PO4 is significantly larger than that measured in the three strong acids. Both Benzotriazole (BTA) and methylhydroxypentyne (MHP) retard hydrogen penetration in all three strong acids. On the other hand, thiourea (TU) substantially accelerates penetration due to the presence of H2S. Anion effects on hydrogen penetration are small in the presence of BTA and MHP, while they are insignificant in the presence of TU.
Lymphocytes: Antigen‐Induced Gene Activation
Authors: Suárez‐Fueyo Abel , Madrenas Joaquín , Criado Gabriel 
Published: September 2013

Abstract

Lymphocytes are activated upon antigen (Ag) recognition by their clonotypic surface Ag receptors, TCR in the case of T cells and BCR in the case of B cells. Lymphocyte activation triggers multiple signalling cascades that converge in the cell nucleus to cause significant changes in the pattern of gene expression that determine the phenotype of activated lymphocytes and, ultimately, the type of immune response. Primary activation in T cells is coupled to rapid T‐cell cycling and progressive epigenetic changes that guide the cell down distinct T‐cell lineages, either effector (T
H
1, T
H
2, T
H
17) or regulatory (Treg), characterised by the expression of specific transcription factors and cytokines. CD8 T cells and B cells also differentiate into cytotoxic thymus‐derived lymphocytes and plasma cells, respectively, driven by specific activation in the context of CD4 T
H
cells (helper) and the cytokine microenvironment.

Key Concepts:

Lymphocyte stimulation leads to the activation of selected transcription factors depending on the type of signals.

Lymphocyte differentiation and function is directed by specific transcription factors that determine the cell lineage.

Interaction and/or collaboration of different transcription factors lead to expression or repression of different genes.

Alterations in the control of TFs activity lead to the development of autoimmune diseases and/or other pathologies.

Some TFs and the molecular pathways that control their activity are targets for the treatment of different diseases.
Relationships of Birds – Molecules versus Morphology
Authors: Torres Christopher , van Tuinen Marcel 
Published: September 2013

AbstractMolecules and morphology frequently point to different phylogenies of modern birds, hence making birds unique models to study reasons for such conflicts. Molecules generally make a less biased tool for phylogenetic inference, but evolutionary interpretation of a phylogeny requires knowledge from both morphology and fossils. In the past decade, considerable progress has been made in reconciling molecular and morphological phylogenies, the examples of which are discussed here. Despite this progress and a wealth of new data now available, key features of the avian phylogenetic tree remain unresolved. This pattern more likely reflects the short time interval during which the majority of modern bird lineages diversified. Much improved insight about the early evolution of modern birds more likely will come from (1) genomic data, provided that biases at this scale are understood and (2) well‐preserved fossils that represent the stem of distinct bird lineages. At present, such data are too incomplete to resolve most key nodes in the diversification of modern birds.Key Concepts:Phylogenies represent the best interpretation of the evolutionary history of a chosen taxon set.At increasing taxonomic level, both DNA sequence‐based and morphological variation are expected to increase.DNA sequence variation at neutral markers is produced and enhanced by the process of random mutation; therefore, it is a function of time.Morphological variation is enhanced by selection for certain phenotypes; therefore, it is a function of the environment.Evolutionary convergence is less likely at the molecular level than at the morphological level.If underlying changes at the molecular/morphological level are modelled appropriately (e.g. alignment, substitution bias and character weighting), reconstruction of phylogeny from either molecular or morphological data should yield the same result.Rampant phylogenetic conflict at the ordinal level in modern birds can be explained by ordinal diversification taking place over a short time interval. During this interval, morphological key innovations were quickly selected for, but augmentation of molecular differences was small.Phylogenetic conflict in modern birds is exacerbated by lack of molecular resolution, imperfect taxonomic sampling, uncertainty about extent of morphological homoplasy and paucity of well‐preserved fossils plesiomorphic for clades Palaeognathae, Neognathae and Neoaves.
Integrins: Signalling and Disease
Authors: Danen Erik HJ 
Published: September 2013

Abstract
Cell‐surface adhesion molecules of the integrin family are not a passive glue, but rather are dynamic molecules that mediate the transfer of information across the membrane in both directions. Integrin‐mediated adhesion can be regulated in response to signals by clustering and conformational changes triggered at their cytoplasmic tails. Vice versa, integrins probe chemical and physical aspects of the extracellular environment and, in concert with growth factor receptors, activate signalling pathways in response. Integrin signalling controls cell survival, cell cycle progression, and differentiation, and the dynamic regulation of integrin‐mediated adhesion structures is critical for many forms of cell migration. Lastly, integrins contribute to the pathogenesis of a diverse array of acquired and hereditary diseases, and hence represent major targets for therapeutic intervention.

Key Concepts:

Integrins are heterodimeric transmembrane receptors that mediate cell adhesion to extracellular matrix proteins and other cells.

Integrins cluster in cell–matrix or cell–cell adhesions where they assemble large multiprotein complexes including actin‐binding proteins.

Integrin‐containing adhesions contain enzymes such as FAK, Src, Rac and many others as well as their upstream activators and downstream effectors allowing local activation of cellular signalling cascades.

Through a series of conformational changes in mechanoresponsive proteins, integrin‐containing adhesions provide mechanical coupling between the environment and the cytoskeletal network.

Signalling through various growth factor receptors is amplified in response to integrin‐mediated adhesion.

The ability of integrins to modulate cellular shape and cytoarchitecture in accordance with environmental stiffness as well as their role in a variety of biochemical signal transduction cascades underlies their critical function in cell proliferation, survival, differentiation and motility.

Defective integrin function underlies several human diseases.

Integrins represent potential drug targets and therapeutic strategies based on interference with integrin‐mediated adhesion have entered clinical trials.
Expression AnalysisIn Vitro
Authors: Colosimo Alfredo 
Published: September 2013

AbstractExpression analysisin vitrois a constantly evolving field, consolidated in the fourth quarter of the last century and essentially based on the use of a template ofribonucleic acid (RNA), for a translation reaction, or ofdeoxyribonucleic acid (DNA), in a coupled transcription–translation system. Traditional applications of expression analysisin vitrocover a wide range of structural and functional studies on proteins and nucleotides using methodologies like yeast one‐, two‐ and three‐hybrid systems, reporter genes, phage display, DNase footprinting, methylation interference assays and gel‐shift assays. Moreover, in the last decadesin‐vitroexpression analyses benefitted from substantial advancements, mostly associated with the use of a number of refined cell‐free protein synthesis methods and of microarrays and nanodevices. The frequency trends of related keywords in a huge database of English books published all over the world and covering a wide, recent time window provide an indirect – although highly suggestive – estimate of their relative importance in the next years.Key Concepts:In‐vitroexpression systems can: (1) be used for the expression of toxic, proteolytically sensitive or unstable proteins; (2) incorporate unnatural amino acids and (3) allow the addition of exogenous factors to study enzymatic activity, and of microsomal membranes to study post‐translational modifications.Application ofin‐vitroexpression systems include: (1) site‐specific methods that utilise tRNA charged with any number of unnatural amino acids; (2) the use of putative DNA‐binding proteins such as transcription factors and (3) improving particular features of preexisting molecules like ultraspecificity, affinity and reaction rate.The intrinsic appealing ofin‐vitroexpression analysis has been reinforced in the last decades thanks to refined cell‐free protein synthesis (CFPS) methods, microarrays (MA) and nanodevices (ND), whose evolution occurred at a remarkably fast pace. The data flow streaming out of the above‐mentioned techniques demands, in any case, massive statistical analyses and systematic cross‐checking of results by independent strategies.
Energy and Biodiversity
Authors: Turner John RG 
Published: September 2013

Abstract

The biodiversity level (number of species) of the Earth declines from the tropics to the poles and is strongly correlated with temperature and water availability. ‘Energy theories’ provide a simple explanation: more energy=more organisms=more species, but the question is more complex, and the empirical evidence equivocal. Theoretical models try to show how energy/climate can influence species birth (speciation), species death (extinction) and species migration; but there is only limited understanding of what controls these parameters, which may further be influenced by planetary area (smaller towards the poles) and the intricate processes of adaptive evolution, which build highly structured communities. The distribution of life is further deeply influenced by long‐ and short‐term climatic change. The three main explanations of the biodiversity gradient are therefore (1) energy theories, (2) area theories, (3) climate change theories and (4) community‐building theories.

Key Concepts:

The latitudinal diversity gradient: Biodiversity (the number of species) declines from the tropics to the poles, and is strongly correlated with climatic temperature and rainfall.

Energy theories attempt to explain how climate influences the rates of speciation, species extinction and species migration.

The water–energy (interim general) model and the metabolic theory of ecology show how energy (and water) could affect biodiversity.

Dante's principle (species are adapted to their local climate) and the favourableness hypothesis propose that there are more species adapted to warmer climates than to cooler climates.

The privileged tropics: Most clades originate in the tropics which are a passport‐free zone for species and have an effectively much greater area and volume than any other part of the planet.

Niche conservatism: Species can adapt to novel conditions and expand their geographic ranges, but seem usually to be unable to do so.

The ‘more individuals hypothesis’ successfully explains how larger populations will produce more species, but is challenged by empirical evidence.

Community structure: Adaptive evolution produces intricate competitive and mutualistic relationships within ecological communities, whose species composition is not simply a random sample from the wider geographical community.

Biodiversity gradients will differ according to the grain of sampling (the quadrat size).

The biological volume of a geographic region is not measured by the simple area on the map, because from the organisms' point of view the area is fractally folded across the surface of the ground and the vegetation.
Molecular Genetics of Aniridia
Authors: Hingorani Melanie 
Published: September 2013

Abstract

Aniridia is a rare congenital disorder of eye development in which the characteristic feature is hypoplastic or absent iris tissue. Further ocular changes affecting the cornea, intraocular pressure, retina and lens can occur as the patient ages, which can lead to progressive visual loss and other changes such as optic nerve malformations may occur. Most typical aniridia cases are associated with dominantly inherited null mutations or deletions of the
PAX6
gene and the missense mutations are usually associated with mild aniridia or other ocular developmental abnormalities such as Peter's anomaly or isolated foveal hypoplasia. Rarely, mutations of other genes such as
FOXC1
can underlie aniridia. Clinical and genetic testing of new sporadic cases aids diagnosis and is crucial to exclude a risk of the malignant Wilms’ tumour. A testing strategy in which deletions are first assessed, followed by sequencing, is suggested as most efficient, particularly for ensuring that a risk of Wilms’ tumour is identified early to ensure screening for this tumour is not delayed in at‐risk individuals. Familial aniridia is much less likely to be associated with Wilms’ tumour risk but there can be marked phenotypic variability amongst family members. Long‐term care includes screening for and management of eye complications such as glaucoma and surgery for cataract, supportive care for visual impairment and long‐term renal monitoring and therapy for those with
WT1
deletions.

Key Concepts:

Aniridia is a rare, sight‐threatening panocular disorder.

The major clinical feature is congenital absence or hypoplasia of the iris; most cases also demonstrate foveal hypoplasia with reduced visual acuity and nystagmus.

Progressive sight‐threatening complications occur later and include keratopathy, cataract and glaucoma.

The
PAX6
gene at 11p13 encodes a highly conserved transcription factor crucial for early ocular development.

In the vast majority of cases, aniridia is caused by loss of function of one copy (haploinsufficiency) of the
PAX6
gene by intragenic mutation or chromosomal rearrangement.

Missense mutations in the
PAX6
paired domain often cause other ocular phenotypes such as Peter's anomaly and foveal hypoplasia but may also cause a mild aniridia phenotype.

Familial aniridia cases show autosomal‐dominant inheritance with high penetrance but considerable phenotypic heterogeneity.

Newborns with sporadic aniridia are at high risk of the malignant Wilms’ tumour if they have a deletion encompassing
PAX6
and the nearby
WT1
gene. Such deletions may manifest as WAGR syndrome.

A genetic testing strategy that assesses for deletions first and then sequencing will ensure the early identification of a high risk for Wilms’ tumour and directs sequencing to those more likely to have intragenic mutations.
Antiviral Resistance Testing
Authors: Mbisa Jean Lutamyo 
Published: September 2013

Abstract

The number of antiviral drugs approved for clinical use has dramatically increased in the past 25 years. However, the use of the drugs may result in the development of resistance mutations in viral genes targeted for therapy. As a result, antiviral resistance testing is commonplace in many molecular diagnostic laboratories and has become a useful tool for the clinical management of viral infections that can be treated with antivirals. Antiviral resistance testing involves identification of the mutations using sequencing methods (genotyping) and determination of their effect on viral drug susceptibility using
in‐vitro
cell‐based assays (phenotyping). For viruses with well characterised resistance mutations, such as human immunodeficiency virus, genotypic methods that are fast and easier to perform are sufficient. However, phenotypic methods or a combination of both methods provide a comprehensive strategy for other viruses.

Key Concepts:

The majority of antiviral drugs target virus‐specific proteins important for viral replication.

Antiviral resistance develops via the emergence of mutations in viral genes targeted for therapy.

There are two main methods for the measurement of antiviral resistance namely, genotypic antiviral resistance testing and phenotypic drug susceptibility testing.

Genotypic antiviral resistance testing identifies mutations associated with drug resistance using sequencing techniques.

Genotypic interpretation systems (GISs) are rule‐based computational tools that rely on a database of sequence, clinical and laboratory information to translate the mutational pattern in amplified sequence into drug susceptibility levels using arbitrary scores.

Phenotypic drug susceptibility testing is a direct measure of the ability of a virus isolate to replicate in the presence of a specific drug using an
in‐vitro
cell culture system.

The clinical significance and utility of detecting minority drug resistance mutations present at less than 20% of the population has yet to be fully determined.
Germline Genomic Copy Number Variation Contribution to Cancer Predisposition
Authors: Silva Amanda Gonçalves , Rodrigues Tatiane Cristina , Pearson Peter Lees , Rosenberg Carla , Krepischi Ana Cristina Victorino 
Published: September 2013

Abstract

The majority of familial cancer remains with unknown genetic aetiology. Issues impairing the discovery of new genes in complex diseases such as cancer include multifactorial origin, incomplete penetrance of the disease and late‐onset. The authors present an outline of the contribution of constitutive
deoxyribonucleic acid
copy number variations (CNVs) in cancer predisposition. Even though the mechanisms by which germline CNVs influence disease are hitherto largely speculative, nowadays it is consensual that they play a major role in a range of human pathologies. Point mutations have been far more commonly described, mainly because sequencing is the first‐tier diagnostic test, but deletions and duplications of known cancer genes have been reported as an alternative mechanism for cancer susceptibility. Additionally, CNV screening in familial cancer cohorts with unknown genetic aetiology has pointed to new candidate genes for high cancer risk. Therefore, this type of genomic variation must be taken into account in the cancer risk assessment.

Key Concepts:

Structural variation, including copy number variation (CNV), is responsible for a large fraction of the genetic diversity of the human genome.

CNVs can be inherited in a Mendelian fashion or occur
de novo
.

Germline CNVs play an important role in a range of human pathologies through several mechanisms, mainly affecting gene dosage or function.

Nearly half of the approximately 100 Mendelian cancer predisposition genes were also reported as rare pathogenic germline CNVs.

Next‐generation sequencing (NGS) combined with automated high throughput data analysis is the most promising approach for elucidating the contribution of both CNVs and point mutations to cancer predisposition.
Genetics of Lipoprotein(a) in Relation to Coronary Heart Disease
Authors: Enkhmaa Byambaa , Anuurad Erdembileg , Zhang Wei , Abbuthalha Adnan , Berglund Lars 
Published: September 2013

Abstract

Lipoprotein(a), Lp(a), a complex between a low‐density lipoprotein‐like lipid moiety containing apolipoprotein (apo) B, and apo(a), a plasminogen‐derived, carbohydrate‐rich, hydrophilic protein, is one of the most genetically regulated cardiovascular risk factors. For any given population, Lp(a) levels are distributed in a skewed fashion and are strongly impacted by polymorphisms of the
LPA
gene. The quantitatively most impactful polymorphism results in a variable number of kringle 4 (K4) units, a key motif of apo(a) that predicts Lp(a) levels and has been associated with cardiovascular risk. In addition, other
LPA
genetic variants impact Lp(a) levels and may contribute to interethnic Lp(a) level variability. Further, it has been suggested that genetic variants beyond the
LPA
gene may affect Lp(a) levels. Recent studies using Mendelian randomisation approaches have documented an association between Lp(a) and cardiovascular disease and are indicative of a causal relationship.

Key Concepts

Lp(a) is a type of plasma lipoprotein synthesised in the liver, and consists of a cholesteryl‐ester‐rich lipid core and one molecule each of two different apolipoproteins, apoB‐100 and apo(a).

LPA
, the gene encoding apo(a) located on chromosome 6, is evolved from the plasminogen gene during primate evolution, and has repeated triloop structures called kringles (K).

Lp(a) levels differ significantly between individuals and ethnicities, and are regulated to a major extent by genetics through the
LPA
gene.

A copy number variation (i.e. apo(a) size polymorphism) in the
LPA
gene plays an important role in Lp(a) regulation, and smaller apo(a) sizes with fewer K repeats, in general, are associated with higher Lp(a) levels.

Additionally, some other single‐nucleotide polymorphisms (SNPs) in the
LPA
gene, as well as in some other non‐
LPA
genes, have been shown to influence Lp(a) levels.

Although the physiological function of Lp(a) is not well understood, its role in the development of atherosclerotic cardiovascular disease is increasingly well documented, and is recognised in clinical guidelines.

Lp(a) levels are not appreciably affected by lifestyle improvements (diet, exercise, etc.); however, some nongenetic factors such as hormones, menopausal status, inflammatory burden and immune status have been shown to impact Lp(a) levels.

Currently, no drug can specifically and effectively lower high Lp(a) levels, but development of this type of treatment is in progress.