bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple Sequence Repeats in the Human Genome: Evolution
Authors: Riley Donald E , Krieger John N 
Published: October 2009

Abstract
Recent evolutionary findings suggest important functions for even‐numbered, simple sequence repeats (SRs). During evolution, weak‐folding SRs whose single‐stranded forms were incapable of forming classically paired duplex stems, replaced other weak‐folding repeats. Strong‐folding repeats replaced other strong‐folding repeats. Among untranslated regions, SRs were associated with genes encoding membrane‐related functions and genes encoding transcription factors. Among all possible SR sequences, evolution selected primarily weak‐folding repeats. The evolution of many of the differences comparing human SR usage with other mammals can now be mapped using publically available genome sequences. Human SR sites evolved by a variety of pathways.
Ultraconserved
DNA
Sequence Elements in the Human Genome
Authors: Lee Alison P , Venkatesh B 
Published: October 2009

Abstract

Ultraconserved elements are
deoxyribonucleic acid
(DNA) sequences at least 200 base pairs in length and perfectly conserved in human, mouse and rat genomes. These elements are under extreme purifying selection and are implicated in functions such as transcriptional enhancers, exons of noncoding ribonucleic acid (RNA) transcripts and alternatively spliced ‘poison cassette exons’ that regulate the expression of certain classes of proteins.
Mitochondrial Genome Sequences and Their Phylogeographic Interpretation
Authors: Macaulay Vincent , Richards Martin 
Published: October 2009

Abstract

The strong phylogenetic signal provided by complete mitochondrial
deoxyribonucleic acid
(mtDNA) sequences within species is being exploited to reconstruct the maternal genealogy and anchor it in space and time. This is the starting point for interpretations of the processes in population history that led to those patterns, as illustrated here for humans.
Comparison of Rates and Patterns of Meiotic Recombination between Humans and Chimpanzees
Authors: Freudenberg Jan 
Published: October 2009

Abstract
Meiotic recombination events were found to be concentrated in relatively small genomic regions that were termed recombination hotspots. Surprisingly, the genomic locations of recombination hotspots are hardly conserved between human and chimpanzee, rendering individual hotspots as evolutionarily transient features. Based on the theoretical advantages of recombination one may thus hypothesize coevolution of gene sequences and recombination modifiers. Consistently, human recombination hotspot predictions were found enriched at central nervous system (CNS) gene loci and those regions that showed accelerated sequence evolution in hominids.
Evolution of Microsatellite DNA
Authors: Vargas Jentzsch Iris M , Bagshaw Andrew , Buschiazzo Emmanuel , Merkel Angelika , Gemmell Neil J 
Published: October 2009

AbstractMicrosatellites are highly mutable tandemly repeated sequences that are ubiquitously distributed in bacterial and eukaryotic genomes. Microsatellites became the preferred molecular marker for a variety of applications under the basic assumption that they are selectively neutral. However, the simplicity of this assumption contrasts with the observed variability of mutation rates across microsatellite loci and with the increasing evidence supporting microsatellite functionality. The evolutionary importance of microsatellites is only recently being uncovered with the intense study of their impact on the regulation of gene expression and the interaction among genomic structures.
Identifying Regions of the Human Genome that Exhibit Evidence for Positive Selection
Authors: Kimura Ryosuke , Ohashi Jun 
Published: October 2009

AbstractThe recent availability of human genomic data has driven genome‐wide scans for natural selection with different approaches based on comparative genetics and population genetics. Such studies have provided many candidates for targets of positive selection in the human genome, but the results should be interpreted with caution because of the inevitability of false positives. Here, approaches for identifying positive selection in the human genome are reviewed, and, especially, an up‐to‐date approach based on haplotype variation and linkage disequilibrium is explained in detail.
Indels in the Evolution of the Human and Chimpanzee Genomes
Authors: Wetterbom Anna , Cavelier Lucia , Bergström Tomas F 
Published: October 2009

AbstractMutations in thedeoxyribonucleic acid(DNA) cause genomic divergence between species and provide a starting point for evolutionary change. There are several sources of sequence variation and here we will focus on insertions and deletions (indels). Such events occur frequently in genomic alignments of humans and chimpanzees and the indel divergence is estimated to 3–5%. In this article, we will discuss some causes behind indels and the possible impact of indels on the evolution of primate genomes. In addition, we will provide some examples of indels that may affect protein function as well as alternative splicing.
Spectrum of Mutations in the Human Genome Inferred by Single Nucleotide Polymorphisms
Authors: Zhongming Zhao 
Published: October 2009

Abstract
The spectrum of mutations in the human genome inferred by single nucleotide polymorphisms (SNPs) may be measured by three approaches: directly observed frequencies of nucleotide changes, relative frequencies of nucleotide changes by normalizing the nucleotide content and frequencies of nucleotide changes after excluding the CpG effect. The spectrum of mutations indicates that point mutation does not occur randomly in the human genome and varies between the categorized genomic regions.
Modelling Cancer in
Drosophila
Authors: Brumby Anthony M , Richardson Helena E 
Published: October 2009

Abstract

Ever since the discovery of neoplastic and metastatic overgrowths in
Drosophila melanogaster
, the fly has been recognized as an excellent model organism for studying tumorigenesis. Recently, however, its relevance has become even more pronounced with the modelling of neoplasias in somatic clones of tissue using cooperative interactions between tumour suppressors and homologues of known mammalian oncogenes. The realization that many
Drosophila
neoplasias can be understood with respect to aberrant differentiation of stem cell progeny, together with the growing trend to postulate a stem cell origin of mammalian cancers, further highlight the enormous potential of fly cancer models to greatly increase our understanding of how human cancers develop.
Micro
RNAs
in Development and Disease
Authors: Staton Alison A , Giraldez Antonio J 
Published: October 2009

Abstract

Micro
ribonucleic acids
(miRNAs) are small RNAs responsible for selective repression and degradation of mRNAs. Regulation by miRNAs during development facilitates the transition from one stage to the next and can control specialized characteristics of mature cells. When this regulation is disrupted, cancer can result through increases in proliferation and defects in differentiation.
Methods for Live Microscopy ofDrosophilaSpermatocytes
Authors: Savoian Matthew S , Glover David M 
Published: October 2009

AbstractDrosophilais a genetically tractable system well suited for cell cycle investigations. The combination of live cell imaging and the variety of different cell types available, in particular, the easily cultured, exceptionally large and flat, primary spermatocyte, offer powerful tools for studying dynamic cell division events.
Evolutionary History and Impact of Human
DNA
Transposons
Authors: Feschotte Cédric 
Published: October 2009

Abstract

Deoxyribonucleic acid
(DNA) transposons are mobile elements that move via a DNA intermediate. The human genome harbours over 300 000 DNA transposon copies, accounting for approximately 3% of the total genomic DNA. Nearly one‐third of these elements are specific to the primate lineage, but there is no evidence for transposition activity within the last 40 million years. However, there is growing evidence that DNA transposons have contributed in shaping the current genome architecture of humans and have been a recurrent source of new regulatory and coding DNA throughout mammalian evolution.
Human‐specific Changes of Genome Structure
Authors: Harris R Alan , Milosavljevic Aleksandar 
Published: October 2009

Abstract
Genomic changes occur along a size continuum ranging from small‐scale base substitutions to large‐scale cytogenetically detectable chromosome rearrangements. Intermediate‐scale changes between these two extremes are the least studied group of genomic changes. The genomic triangulation method was developed to detect intermediate‐scale changes by integrating genomic sequence and mapping data from human, chimpanzee and rhesus macaque. Human‐specific genomic changes associate with segmental duplications (SDs), involve numerous genes and may result in human‐specific phenotypic traits.
Chromatin Structure and Human Genome Evolution
Authors: Semple Colin AM 
Published: October 2009

Abstract
Functional and comparative genomics have provided data on the evolution and function of the human genome, but we still know relatively little about its spatial organization. What is the three‐dimensional structure of the genome? How and when does this structure vary? It has long been suspected that the structural organization of the genome might impose constraints on its evolution. Recent genome‐wide data on chromatin structure have revealed the complex physical landscape of the human genome, and have yielded unexpected insights into the evolution of chromosome architecture, gene order and patterns of mutation and selection.
Evolution of Skin Pigmentation Differences in Humans
Authors: Norton Heather L 
Published: October 2009

Abstract
The distribution of human skin pigmentation variation is highly correlated with the intensity of ultraviolet radiation (UVR). Several hypotheses propose that this strong relationship between skin colour and UVR is best explained by natural selection. The identification of a large number of genes involved in the pigmentary system now enables researchers to test these hypotheses within an evolutionary genetics framework. Genetic data indicate that the light pigmentation that characterizes populations in Europe and East Asia has evolved independently through positive selection, and that functional variation in pigmentation genes in high UVR populations has likely been subject to purifying selection.
Comparing the Human and Fish Genomes
Authors: Nakatani Yoichiro , Morishita Shinichi 
Published: October 2009

Abstract
How have the genomes of vertebrates evolved over the last 600 million years? In 1970, based on limited observations, Ohno postulated that whole genome duplication events took place in early vertebrates and were essential to increasing complexity of vertebrates. This issue, however, remains a biological quandary. Recent rapid progress in sequencing the genomes of many vertebrates has revealed fundamental insights into the evolutionary process, and the comparative genomics of the fish and human genomes is indispensable for providing conclusive support to Ohno's hypothesis.
Evolutionarily Conserved Intronic Splicing Regulatory Elements in the Human Genome
Authors: Van Nostrand Eric L , Yeo Gene W 
Published: October 2009

Abstract

Splicing is the process by which introns are removed from premature messenger
ribonucleic acid
(pre‐mRNA), and exons are ligated to form mature mRNA before translation into protein products. Aside from the consensus splice signals such as the branch point, acceptor and donor splice sites, additional
cis
‐regulatory elements embedded within the exons and introns control the recognition of exonic (approximately 150 bases) from intronic sequence (approximately 100–100 000 bases). Intronic splicing elements that are evolutionarily conserved across multiple species play important roles in the regulation of constitutive splicing, where a single mRNA is produced, and alternative splicing, where multiple mRNA isoforms are generated.
Evolution of Imprinting: Imprinted Gene Function in Human Disease
Authors: Dickins Benjamin JA , Kelsey Gavin 
Published: October 2009

AbstractA subset of genes in mammals, known as imprinted genes, show a conditional expression strategy in which transcription depends on an allele's parental origin. Several explanations have been advanced to explain this phenomenon and these, with varying levels of success, predict the functions of imprinted genes. After outlining these explanations, we summarize what is known about human genetic disorders involving abnormal expression of imprinted genes and ask what this can tell us about the evolution of imprinting.
Gene Inactivation and Tissue‐specific Metabolism
Authors: Flowers Matthew T , Ntambi James M 
Published: October 2009

Abstract

The application of gene inactivation strategies targeting genes with various metabolic functions has greatly advanced our understanding of metabolism at both the cellular and physiological level. Whole‐body genomic ablation of a gene of interest may be achieved using transgenic methods to introduce a null allele. Alternatively, the Cre‐loxP recombinase system allows for the generation of animals harbouring a tissue‐specific gene inactivation. Another approach is to alter the messenger
ribonucleic acid
(mRNA) abundance of the target gene using RNA interference (RNAi) or antisense oligonucleotide (ASO) methods. Together, these strategies help elucidate gene function through association of metabolic phenotypes with gene inactivation at a defined genetic locus.
Membrane Rafts and Caveolae
Authors: Thomas Candice M , Smart Eric J 
Published: October 2009

AbstractThe plasma membrane does more than serve as a barrier between the contents of the cell and the extracellular space. It is a highly organized structure which contains fatty acids, cholesterol and a variety of proteins and is functionally important in trafficking cellular signals. The concept of organized structures or domains within the plasma membrane has proven invaluable to understanding how the plasma membrane interacts with the surrounding environment. One class of these domains is lipid rafts which have been shown to organize and regulate signalling platforms. Caveolae are a subset of lipid rafts which contain specific proteins and lipids that aid in the regulation of signalling processes differently from other domains. Purification techniques have made it possible to study the biochemistry of lipid rafts and caveolae and to gain a better understanding of their roles in signal transduction.
Ficolins
Authors: Takahashi Kazue 
Published: October 2009

Abstract

Ficolins are soluble pattern‐recognition molecules of the innate immunity. Ficolins consist of a collagen‐like domain, a neck region and a fibrinogen‐like domain that binds specific molecular structures of pathogens and the body's own damaged cells by preferably recognizing acetylated compounds. Humans have three homologous proteins,
H‐ficolin
(or
ficolin‐3
),
L‐ficolin
(or
ficolin‐2
) and
M‐ficolin
(or
ficolin‐1
). The first two ficolins are circulating in blood whereas ficolin‐1 is locally secreted. Ficolins activates the lectin complement pathway, which results in neutralization of pathogens, thus ficolins play important roles in innate immunity, both to protect from infection as well as to maintain tissue health.
Molecular Genetics of Polygenic Hypertension
Authors: Deng Alan Y 
Published: October 2009

AbstractContrasting to rare monogenic forms of hypertension, essential hypertension is the most clinically diagnosed ailment leading to high morbidity and mortality; however, its underlying mechanisms continue to be undeciphered. To assist this endeavor, investigations utilizing rodent models have revealed multiplex genetic architecture for quantitative trait loci (QTLs), for blood pressure (BP), elaborate QTL–QTL interactions and efficacious genome regulations of QTL functions. Although BP is a quantitatively measured trait manifesting in a continuous variation, each QTL governing it appears to behave as an independent and ‘monogenic’ Mendelian determinant. Some QTLs are functionally modularized by epistasis that implies a common pathway or cascade; whereas others belong to parallel epistatic modules. These insights suggest that similar genetic mechanisms probably shepherd the genetic architecture for essential hypertension. Translation of gene discovery to therapeutic targets and diagnostic tools will require a consolidation of functional validation of genes in animal models with association studies in targeted human populations.Key ConceptsThe quantitative governance of blood pressure variations is realized by several genes or quantitative trait loci (QTLs). Each QTL can operate autonomously and comports in a ‘monogenic’ pattern. Those QTLs that occur to mutually conceal their BP effects can be epistatically modularized, consequently, solving the conundrum of overabundant QTLs in the genome. Despite the puissance of QTLs, potent genome regulations can disallow QTLs to influence blood pressure (BP). In both human and animal association/linkage studies, population‐dependence and the influence of genome heterogeneity on exhibiting the amplitude of BP effect are frequently observed occurrences.
Work‐related carpal tunnel syndrome in Washington State workers' compensation: Utilization of surgery and the duration of lost work
Authors: Daniell William E. , Fulton‐Kehoe Deborah , Franklin Gary M. 
Published: October 2009

AbstractBackgroundWork‐related carpal tunnel syndrome (CTS) is a leading cause of lengthy disability.MethodsThis population‐based retrospective cohort study used Washington State workers' compensation claims for CTS to characterize associations between utilization of CTS surgery and duration of lost work. The sample included all claims (n = 8,224) filed during 1990–1994 (followed through 2000) and receiving lost‐work compensation.ResultsSixty‐four percent of studied workers had CTS surgery. Among workers with >1 month of lost work, the total duration was much shorter when workers had surgery, versus those who did not (median 4.3 and 6.2 months, respectively; P < 0.001); there was no difference when disability extended >6 months. When workers had surgery, disability was less likely to end before 6 months if non‐CTS conditions were present, surgery occurred >3 months after claim filing, or employment was in an industry with high incidence of CTS; disability was more likely to end if the diagnosing provider and operating surgeon had higher CTS claims volume. Physical and rehabilitation medicine services were associated with lower probability of returning to work, with or without surgery.ConclusionsThere is a need to scrutinize the role of surgery and physical‐rehabilitation medicine modalities in the management of CTS covered by workers' compensation. The findings suggest disability can be minimized by establishing the CTS diagnosis as early as possible and, if surgery is appropriate, conducting surgery without substantial delay and maximizing post‐operative efforts to facilitate return to work. Use of surgery >6 months after filing should be considered with great caution. Am. J. Ind. Med. 52:931–942, 2009. © 2009 Wiley‐Liss, Inc.
Incidence of tuberculosis and HIV and progression of silicosis and lung function impairment among former basotho gold miners
Authors: Park Harriet H. , Girdler‐Brown Brendan V. , Churchyard Gavin J. , White Neil W. , Ehrlich Rodney I. 
Published: October 2009

AbstractBackgroundPulmonary tuberculosis and HIV incidence, mortality, and the progression of silicosis and lung function impairment are described over a 1‐year period in migrant ex‐gold miners from Lesotho.MethodsSeven hundred seventy‐nine Basotho miners were followed for 1 year starting 18 months after lay‐off from a South African gold mine in 1998. At baseline and follow‐up, they underwent a respiratory symptom interview, physical examination, HIV test, chest radiograph, and spirometry.ResultsFive hundred thirteen of 779 (65.9%) participants attended both baseline and follow‐up visits. HIV incidence was 5.4/100 person‐years (95% CI: 3.4–8.2). Prevalence of silicosis (ILO score ≥1/1) was 26.6% at baseline and 27.0% at follow‐up. Active tuberculosis diagnosed at baseline was a strong predictor of radiological progression of silicosis. Lung function as measured by FEV1 declined an average of 91 ml between visits (95% CI: 67–116 ml). Calculated minimum incidence of tuberculosis was 3,085/100,000/years (95% CI: 1,797–4,940) at follow‐up. Of those seen at baseline, 18 died before their scheduled follow‐up visit (mean age: 51 years).ConclusionsHigh rates of mortality and of HIV infection and pulmonary tuberculosis were found in this cohort after leaving the South African goldmines. Continuing lung function loss was also apparent. A partnership between the South African mining industry and governments in labor‐sending areas of Southern Africa is needed to provide continuity of care and access to HIV and tuberculosis treatment and prevention services. Active silicosis surveillance and an improved statutory compensation system are also needed. These findings can serve as a baseline against which the impact of such interventions can be assessed. Am. J. Ind. Med. 52:901–908, 2009. © 2009 Wiley‐Liss, Inc.
Free vibration of symmetric planar frames via the force method and canonical forms
Authors: Kaveh A. , Aalizadeh Arvanaq R. 
Published: October 2009

AbstractIn this paper, the method recently developed for the free vibration of symmetric frames using canonical forms of stiffness matrices is extended to the flexibility matrices. Weighted graphs are associated with the flexibility and mass matrices of the frame structures. Using graph symmetry, the models are decomposed into submodels and a healing process is employed, such that the union of the eigenvalue of the matrices corresponding to the healed submodels contains the eigenvalues of the entire model. This two‐step process is termed as the factorization of a weighted graph. The presented method is illustrated through simple examples having different symmetries. Copyright © 2009 John Wiley & Sons, Ltd.
Solvothermal Synthesis and Characterization of Chalcopyrite CuInSe2 Nanoparticles
Authors: Chen Huiyu , Yu Seong-Man , Shin Dong-Wook , Yoo Ji-Beom 
Published: October 2009

Abstract
The ternary I-III-VI2 semiconductor of CuInSe2 nanoparticles with controllable size was synthesized via a simple solvothermal method by the reaction of elemental selenium powder and CuCl as well as InCl3 directly in the presence of anhydrous ethylenediamine as solvent. X-ray diffraction patterns and scanning electron microscopy characterization confirmed that CuInSe2 nanoparticles with high purity were obtained at different temperatures by varying solvothermal time, and the optimal temperature for preparing CuInSe2 nanoparticles was found to be between 180 and 220 °C. Indium selenide was detected as the intermediate state at the initial stage during the formation of pure ternary compound, and the formation of copper-related binary phase was completely deterred in that the more stable complex [Cu(C2H8N2)2]+ was produced by the strong N-chelation of ethylenediamine with Cu+. These CuInSe2 nanoparticles possess a band gap of 1.05 eV calculated from UV–vis spectrum, and maybe can be applicable to the solar cell devices.
Synovial cyst of the fifth digit in a cat
Authors: Hittmair Katharina M. , Maedl Irene , Reifinger Martin , Mayrhofer Elisabeth 
Published: October 2009

A synovial cyst of the fifth digit of the left forelimb in a 15-year-old cat was diagnosed. Radiographs showed severe osteoarthritis of the interphalangeal and metacarpophalangeal joints with soft tissue swelling. An ultrasound examination of the digit revealed a cystic structure. Following amputation of the digit, the cyst recurred 3 months later palmar to the carpus and metacarpus. The aetiology of synovial cysts is discussed.