bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Mechanisms Underlying Pathogenic Missense Mutations
Authors: Wu Bohua , Eggert Julia , Alexov Emil 
Published: August 2014

AbstractResearch has identified there is a multiplicity of plausible molecular effects caused by human genetic differences that may lead to human diseases. Although humandeoxyribonucleic acid (DNA)variations and rare mutations may be manifested at different levels and different magnitudes, a single nucleotide polymorphism (SNP) to a missing chromosome or a single amino acid mutation to a truncated protein, the pathological effect is the malfunction of the cell or the corresponding organ. It is pointed out that pathological DNA defects can cause more than one phenotypic change to the wild‐type macromolecular characteristics, for example, alterations of macromolecular stability and a variation in the ability to interact with macromolecular partners. The main obstacles to predicting pathogenic DNA variations are the complexity of biological reactions and the difficulty of assessing the threshold of the change that will make it pathogenic. Although some small deviations from the wild‐type properties of a particular biomolecule or a network may be harmless and result in natural differences between individuals, the deviations of the same magnitude occurring in different molecule or network can be pathogenic. These diverse molecular mechanisms that induce the malfunctions are the primary focus of this review.Key Concepts:Molecular mechanisms of pathogenic mutations refer to the disease‐causing change of the wild‐type properties of the corresponding macromolecules and networks. It could be an effect altering a particular characteristic, for example, stability, but could also be a combination of several factors affecting normal function of the cell.The magnitude of change of the wild‐type characteristics alone cannot be used to predict whether a mutation is pathogenic. In some cases, a small deviation from the wild‐type properties can be deleterious, whereas in others, much larger changes are observed without a disease‐causing effect. Frequently, a detailed knowledge of the biological reactions that are involved is needed to discriminate the pathogenic mutations from harmless variations.Personalised medicine provides personalised or individualized medical care on the basis of an individual's DNA.The knowledge of an individual's DNA is emerging as a powerful tool for selecting the most efficient drug among several alternative drugs available in the market.A DNA defect in a particular gene may not be pathogenic if there is a compensatory mechanism accounting for dysfunctional product and if the dysfunctional product is not toxic for the cell.
Human Embryonic Aneuploidy
Authors: Fragouli Elpida , Wells Dagan 
Published: August 2014

Abstract

Human embryonic aneuploidy can have a meiotic or a mitotic origin. The majority of meiotic chromosome errors arise during oogenesis. Two main aneuploidy‐causing mechanisms have been defined: the first involves the nondisjunction of entire chromosomes and takes place during both meiotic divisions, whereas the second involves the premature division of a chromosome into its two sister chromatids during meiosis I, followed by their random segregation. Mitotic aneuploidy can arise as a consequence of problems such as nondisjunction, endoreduplication and anaphase lag and occurs most often during the first three divisions after fertilisation. The cleavage stage of development is characterised by the highest rates of aneuploidy, after which the incidence of cytogenetic abnormality decreases significantly. A large number of oocytes and embryos have been examined in order to define the spectrum of aneuploidies during the first few days of life and to shed light upon their origins. Various classical and molecular cytogenetic methods have been employed for this purpose, and valuable data of biological and clinical relevance have been obtained.

Key Concepts:

Aneuploidy is the most important genetic cause of human reproductive wastage (i.e. the principal reason for embryo implantation failure and miscarriage).

The outcome of assisted reproductive treatments (e.g.
in vitro
fertilisation (IVF)) and natural reproductive cycles is negatively affected by aneuploidy.

Most meiotically derived abnormalities arise during oogenesis.

There is a strong relationship between advancing female age and increasing aneuploidy rates in oocytes.

Two distinct mechanisms of oocyte chromosome malsegregation have been described, whole chromosome nondisjunction and unbalanced chromatid predivision.

Post‐zygotic aneuploidy usually arises during the first few mitotic divisions and leads to mosaicism in the embryo.

There are three main mechanisms responsible for aneuploidy of mitotic origin: anaphase lag, endoreduplication and mitotic nondisjunction.

The cleavage stage of preimplantation development is associated with the highest aneuploidy rates.

The frequency of chromosome abnormalities and mosaicism declines as embryos progress to the blastocyst stage, presumably due to loss of abnormal cells or demise of affected embryos.
Upstream Open Reading Frames and Human Genetic Disease
Authors: Barbosa Cristina , Onofre Cláudia , Romão Luísa 
Published: August 2014

AbstractIn many eukaryoticmessenger ribonucleic acids (mRNAs)one or more short upstream open reading frames (uORFs) precede the initiation codon of the main coding region. For example, in human cells, uORFs are present in about half of the transcripts. Emerging ribosome profiling and peptidomics analyses have recently shown that these uORFs are translated into polypeptides that seem to serve important biological functions. In addition, very interesting examples have shown that these uORFs arecis‐acting RNA elements that can impact gene expression by repressing translation of the downstream main ORF under control conditions and derepressing it under certain pathophysiological stresses. Furthermore, evidence from genetic and bioinformatic studies implicate disturbed uORF‐mediated translational control in the aetiology of human diseases. Identifying more cases and understanding the aberrant mechanisms of uORF‐mediated translational control, as well as discovering the biological function of the uORF‐encoded polypeptides, is fundamental to advance in diagnosis, prognosis and treatment of many human disorders.Key Concepts:Upstream open reading frames (uORFs) arecis‐acting RNA elements involved in translational regulation, which precede the initiation codon of the main coding region.For a uORF to function as a translational regulatory element, its initiation codon must be recognised, at least at certain times, by the scanning 40S ribosomal subunit and associated translation initiation factors.uORFs can impact gene expression by repressing translation of the downstream main ORF under control conditions, and derepressing it under certain pathophysiological stresses.The impact the uORFs can have on translation depends on variables, such as (1) the distance between the 5′ cap and the uORF, (2) the context in which the uORF AUG (or non‐AUG) is located, (3) the length of the uORF, (4) the sequence and secondary structure of the uORF, (5) the number of uORFs per transcript, (6) the position of the uORF termination codon and (7) the length of the intercistronic sequence(s).uORF‐encoded polypeptides might serve functional roles in cells.Polymorphisms or mutations that introduce/eliminate uORFs or modify the uORF‐encoded peptide can cause human disease.Understanding the mechanisms through which the uORFs regulate gene expression may lead to innovation in diagnosis, prognosis and treatment of many human disorders.
Optical and Electrooptical Properties of Porous‐Silicon/Conjugated‐Polymer Composite Structures
Authors: Nahor Amit , Shalev Itai , Sa'ar Amir , Yitzchaik Shlomo 
Published: August 2014

AbstractWe report on the fabrication and characterization of porous‐silicon/conjugated‐polymer hybrids, created by combining a host columnar matrix of mesoporous silicon and a network of organic nanowires made from poly(N‐vinylcarbazole) (PVK). A uniform and homogeneous filling of the pores by the polymers was accomplished by electrochemical polymerization of organic monomers inside the pores by using cyclic voltammetry. Spectroscopic measurements showed that polymerization inside the confined environment of the nanometric pores results in a tighter and denser packing of the polymer due to a change of the polymerization process from the vinyl groups to the conjugated carbazole groups, giving rise to a redshift of the absorption spectra and better electrical conductivity. Current‐voltage characterization of the hybrids under dark conditions and under illumination were investigated. We demonstrate a simple method to control the band alignment between the organic polymer and the porous silicon, altering it from a type‐I to a type‐II interface by changing the doping polarity of the silicon substrate (from p‐type to n‐type, respectively). An efficient photoinduced charge separation was observed for the type‐II interface (n‐type porous‐silicon–polymer interface), while no such effect was observed for the type‐I organic–inorganic interface.
Redox and Photochemistry of Bis(terpyridine)ruthenium(II) Amino Acids and Their Amide Conjugates – from Understanding to Applications
Authors: Breivogel Aaron , Kreitner Christoph , Heinze Katja 
Published: August 2014

AbstractThe push‐pull‐substituted bis(terpyridine)ruthenium(II) amino acid [Ru(4′‐tpy‐COOH)(4′‐tpy‐NH2)]2+ ([5]2+; tpy = 2,2′;6′,2″‐terpyridine) with carboxylic acid and amino substituents features exceptional chemical and photophysical properties. Its interaction with photons, electrons, and/or protons results in room‐temperature phosphorescence, reversible oxidative and reductive redox chemistry, reversible acid/base chemistry, proton‐coupled electron transfer, photoinduced reductive and oxidative electron transfer, excited‐state proton transfer and energy transfer reactions. These properties can be fine‐tuned by variations of the bis(terpyridine) amino acid motif, namely extension of the π system and expansion of the chelate ring. Furthermore, the chemically orthogonal functional groups enable the incorporation of this metallo amino acid into peptide architectures in a highly selective manner, even by solid‐phase peptide synthesis protocols. Amide‐linked conjugates with other metal complexes [(terpyridine)ruthenium(II), ferrocene, (bipyridine)rhenium(I), (bipyridine)platinum(II)], organic chromophores, or ZnO nanoparticles underscore the versatile synthetic, redox, and photochemistry of this building block. First real‐world applications of [5]2+ and its derivatives include light‐emitting electrochemical cells (LECs) and dye‐sensitized solar cells (DSSCs).
Mixed‐Metal Oxo Clusters Structurally Derived from Ti6O4(OR)8(OOCR′)8
Authors: Artner Christine , Koyun Ayse , Czakler Matthias , Schubert Ulrich 
Published: August 2014

AbstractThe mixed‐metal oxo clusters FeTi5O4(OiPr)4(OMc)10 (OMc = methacrylate), Zn2Ti4O4(OiPr)2(OMc)10, Cd4Ti2O2(OAc)2(OMc)10(HOiPr)2, [Ca2Ti4O4(OAc)2(OMc)10]n, and [Sr2Ti4O4(OMc)12(HOMc)2]n were obtained from the reaction of titanium alkoxides with the corresponding metal acetates and methacrylic acid. Their structures are derived from Ti clusters with the composition Ti6O4(OR)8(OOCR′)8. The Ca and Sr derivatives consist of chains of condensed clusters.
Development of ST:REAM: a reach‐based stream power balance approach for predicting alluvial river channel adjustment
Authors: Parker Chris , Thorne Colin R , Clifford Nicholas J 
Published: August 2014

AbstractRiver channel sediment dynamics are important in integrated catchment management because changes in channel morphology resulting from sediment transfer have important implications for many river functions. However, application of existing approaches that account for catchment‐scale sediment dynamics has been limited, largely due to the difficulty in obtaining data necessary to support them. It is within this context that this study develops a new, reach‐based, stream power balance approach for predicting river channel adjustment.The new approach, named ST:REAM (sediment transport: reach equilibrium assessment method), is based upon calculations of unit bed area stream power (ω) derived from remotely sensed slope, width and discharge datasets. ST:REAM applies a zonation algorithm to values of ω that are spaced every 50 m along the catchment network in order to divide the branches of the network up into relatively homogenous reaches. ST:REAM then compares each reach's ω value with the ω of its upstream neighbour in order to predict whether or not the reach is likely to be either erosion dominated or deposition dominated.The paper describes the application of ST:REAM to the River Taff in South Wales, UK. This test study demonstrated that ST:REAM can be rapidly applied using remotely sensed data that are available across many river catchments and that ST:REAM correctly predicted the status of 87.5% of sites within the Taff catchment that field observations had defined as being either erosion or deposition dominated. However, there are currently a number of factors that limit the usefulness of ST:REAM, including inconsistent performance and the need for additional, resource intensive, data to be collected to both calibrate the model and aid interpretation of its results. Copyright © 2014 John Wiley & Sons, Ltd.
Effects of serial and concurrent training on acquisition and generalization
Authors: Wunderlich Kara L. , Vollmer Timothy R. , Donaldson Jeanne M. , Phillips Cara L. 
Published: August 2014

Despite a large body of research demonstrating that generalization to novel stimuli can be produced by training sufficient exemplars, the methods by which exemplars can be trained remain unclear. The purpose of the current study was to evaluate 2 methods, serial and concurrent presentation of stimuli, to train sufficient exemplars. Five preschool children with developmental delays were taught to identify letters or letter sounds using serial and concurrent presentation. Generalization to untrained exemplars was evaluated for targets trained using each method. Participants reached the mastery criterion in fewer training sessions, on average, using the concurrent method of presentation than the serial method, and the concurrent method also resulted in greater generalization to untrained exemplars.Video Methods
Influence of combined grazing by wild boar and small ruminant on soil and plant nutrient contents in a coppice oak forest
Authors: Parissi Zoi M. , Papaioannou Athanassios , Abraham Eleni M. , Kyriazopoulos Apostolos P. , Sklavou Paraskevi , Tsiouvaras Constantinos N. 
Published: August 2014

AbstractLimited information is available about the impact of grazing on soil and plant nutrient contents in Mediterranean deciduous oak forests grazed by both livestock and wild life. Thus, the main objective of this study was to investigate the effect of wild boar and small ruminants grazing in a coppice oak forest in N Greece. Eight even‐aged stands of similar canopy cover and site quality were selected: four stands with long‐time grazing mainly by wild boar and four stands with long‐time grazing by sheep and goats. A plot of 150 m2in each of the stands was fenced in order to be protected from grazing. A similarly sized plot open to grazing was assigned next to the fenced plot. Species composition was recorded in fenced and grazed plots. Soil samples and individual plants of the dominant palatable grass speciesDactylis glomerata andBrachypodium sylvaticumwere collected in every fenced and grazed plot. These samples were analysed for contents of nutrients. The results indicated that grazing increased organic matter, C, and total N, P and Ca, while it had no effect on the plant nutrients Mg, Na, K and all micronutrients, and pH as well. Wild boar grazing had a significantly negative impact on the concentrations of Na, Fe, Zn, and Mn in the soil. Beside a decrease in K and Mn, grazing had minimal effects on the contents of plant nutrients. Conversely, wild boar grazing increased the contents of several nutrients such as N, Na, Cu and Fe in plant tissue. It seems that species composition was more affected by the topography and management than by the soil features as revealed by RDA analysis. The results of this study indicate that it is important to maintain moderate small ruminant grazing intensity for the sustainable multi‐disciplinary management of coppice oak forests. It is also important to control wild boar population in order to facilitate ecosystem process, soil preservation and forage quality.
Perceptions of Investors and Stockbrokers on Corporate Social Responsibility: A Stakeholder Perspective from India
Authors: Kansal Monika , Joshi Mahesh 
Published: August 2014

This paper aims to understand the perceptions of shareholders and brokers regarding corporate social responsibility (CSR) initiatives by Indian companies. The research, presented in this paper, employs stakeholder theory to examine the perceptions of investors and sharebrokers on CSR in the context of a fast growing country, India. The data has been collected by using semistructured survey instrument. The findings of the study highlight that the respondents in both categories of stakeholder groups agree that CSR‐oriented companies enjoy higher levels of investor confidence, which is reflected in higher stock prices, and leads to enhanced reputation and corporate goodwill. The research demonstrates that Indian companies are in fact implementing CSR initiatives and that stakeholders have a considerable interest in such initiatives. Both the groups expect higher CSR disclosures from large corporations and multinational companies operating in India.Educational initiatives have received maximum attention from the both the groups of stakeholders followed by the environmental issues. Investors are least aware of healthcare and rural development initiatives possibly because of the relatively low penetration of Indian financial markets into the rural areas. This study demonstrates that the stakeholder theory is a useful tool for collecting and evaluating CSR data and explains that the stakeholder perception of CSR performance determines corporate initiatives to a certain level. The findings would help in building consensus on strengthening the implementation and establishing the future CSR framework in emerging economies and other parts of the world. Copyright © 2014 John Wiley & Sons, Ltd.
Data‐driven model reduction for the Bayesian solution of inverse problems
Authors: Cui Tiangang , Marzouk Youssef M. , Willcox Karen E. 
Published: August 2014

SummaryOne of the major challenges in the Bayesian solution of inverse problems governed by partial differential equations (PDEs) is the computational cost of repeatedly evaluating numerical PDE models, as required by Markov chain Monte Carlo (MCMC) methods for posterior sampling. This paper proposes a data‐driven projection‐based model reduction technique to reduce this computational cost. The proposed technique has two distinctive features. First, the model reduction strategy is tailored to inverse problems: the snapshots used to construct the reduced‐order model are computed adaptively from the posterior distribution. Posterior exploration and model reduction are thus pursued simultaneously. Second, to avoid repeated evaluations of the full‐scale numerical model as in a standard MCMC method, we couple the full‐scale model and the reduced‐order model together in the MCMC algorithm. This maintains accurate inference while reducing its overall computational cost. In numerical experiments considering steady‐state flow in a porous medium, the data‐driven reduced‐order model achieves better accuracy than a reduced‐order model constructed using the classical approach. It also improves posterior sampling efficiency by several orders of magnitude compared with a standard MCMC method. Copyright © 2014 John Wiley & Sons, Ltd.
Repetitive Sequences in Plant Nuclear DNA: Types, Distribution, Evolution and Function
Authors: Mehrotra Shweta , Goyal Vinod 
Published: August 2014

Abstract
Repetitive DNA sequences are a major component of eukaryotic genomes and may account for up to 90% of the genome size. They can be divided into minisatellite, microsatellite and satellite sequences. Satellite DNA sequences are considered to be a fast-evolving component of eukaryotic genomes, comprising tandemly-arrayed, highly-repetitive and highly-conserved monomer sequences. The monomer unit of satellite DNA is 150–400 base pairs (bp) in length. Repetitive sequences may be species- or genus-specific, and may be centromeric or subtelomeric in nature. They exhibit cohesive and concerted evolution caused by molecular drive, leading to high sequence homogeneity. Repetitive sequences accumulate variations in sequence and copy number during evolution, hence they are important tools for taxonomic and phylogenetic studies, and are known as “tuning knobs” in the evolution. Therefore, knowledge of repetitive sequences assists our understanding of the organization, evolution and behavior of eukaryotic genomes. Repetitive sequences have cytoplasmic, cellular and developmental effects and play a role in chromosomal recombination. In the post-genomics era, with the introduction of next-generation sequencing technology, it is possible to evaluate complex genomes for analyzing repetitive sequences and deciphering the yet unknown functional potential of repetitive sequences.
Heinrich event 4 and Dansgaard/Oeschger events 5–10 recorded by high-resolution speleothem oxygen isotope data from central China
Authors: Zhou Houyun , Zhao Jian-xin , Feng Yuexing , Chen Qiong , Mi Xiaojian , Shen Chuan-Chou , He Haibo , Yang Liang , Liu Shuhua , Chen Lin , Huang Jiayi , Zhu Liyan 
Published: August 2014

AbstractA 50-yr resolution reconstruction of climate and environment variability during the period 43–14 ka was developed using 26 high-precision U/Th dates and 390 oxygen isotope (δ18O) data of a stalagmite (SJ1) collected from Songjia Cave in central China, which is close to the northwestern boundary of the Asian summer monsoon (ASM). The δ18O record in SJ1 displays significant millennial-scale changes that correlate well in timing and duration with Dansgaard/Oeschger (D/O) events 5–10 and Heinrich event 4 (H4) identified in high-latitude regions of the Northern Hemisphere. Four 230Th dates constrain the H4 event precisely to the period of 39.7 to 38.3 ka. Notable centennial variations of the ASM activity could be observed within the H4 event. The magnitude and duration of D/O event 4.1 recorded in SJ1 are similar to those archived in east China but different from those documented in southwest China, suggesting that the manifestation of this event may be regionally different. The timing, duration and structure of D/O events 5–10 and Heinrich event 4 suggest that temperature changes in both hemispheres have exerted significant influences on the ASM variations in central China.