bluuebunny/crossref_metadata_2025_split huggingface dataset:
Azoospermia factor and male infertility
Authors: Koh Eitetsu , Sin Ho‐Su , Fukushima Masato , Namiki Mikio 
Published: June 2010

AbstractRecently, work has shown that azoospermia factor (AZF) microdeletions result from homologous recombination between almost identical blocks in this gene region. These microdeletions in the Y chromosome are a common molecular genetic cause of spermatogenetic failure leading to male infertility. After completion of the sequencing of the Y chromosome, the classical definition of AZFa, AZFb, and AZFc was modified to five regions, namely AZFa, P5/proximal‐P1, P5/distal‐P1, P4/distal‐P1, and AZFc, as a result of the determination of Y chromosomal structure. Moreover, partial AZFc deletions have also been reported, resulting from recombination in their sub‐ampliconic identical pair sequences. These deletions are also implicated in a possible association with Y chromosome haplogroups. In this review, we address Y chromosomal complexity and the modified categories of the AZF deletions. Recognition of the association of Y deletions with male infertility has implications for the diagnosis, treatment, and genetic counseling of infertile men, in particular candidates for intracytoplasmic sperm injection.
Tyrosine requirement during the rapid catch-up growth phase of recovery from severe childhood undernutrition
Authors: Badaloo Asha , Hsu Jean W.-C. , Taylor-Bryan Carolyn , Reid Marvin , Forrester Terrence , Jahoor Farook 
Published: June 2010

The requirement for aromatic amino acids during the rapid catch-up in weight phase of recovery from severe childhood undernutrition (SCU) is not clearly established. As a first step, the present study aimed to estimate the tyrosine requirement of children with SCU during the catch-up growth phase of nutritional rehabilitation using a diet enriched in energy and proteins. Tyrosine requirement was calculated from the rate of excretion of 13CO2 (F 13CO2) during [13C]phenylalanine infusion in thirteen children with SCU, five females and eight males, at about 19 d after admission when the subjects were considered to have entered their rapid catch-up growth phase and were consuming 627·3 kJ and about 3·5 g protein/kg per d. Measurements of F 13CO2 during [13C]phenylalanine infusion were made on two separate days with a 1 d interval. Three measurements at tyrosine intakes of 48, 71 and 95 mg/kg per d were performed on experimental day 1 and measurements at tyrosine intakes of 148, 195 and 241 mg/kg per d were performed on experimental day 2. An estimate of the mean requirement was derived by breakpoint analysis with a two-phase linear regression cross-over model. The breakpoint, which represents an estimate of the mean tyrosine requirement, is a value of 99 mg/kg per d when the children were growing at about 15 g/kg per d. The result indicates that the mean requirement for tyrosine during the catch-up growth phase of SCU is about 99 mg/kg per d under similar conditions to the present study.
Spatial variation in gender-biased parasitism: host-related, parasite-related and environment-related effects
Authors: KRASNOV BORIS R. , MATTHEE SONJA 
Published: June 2010

SUMMARYThe gender-biased pattern of parasite infestation has been shown to be a complicated phenomenon that cannot be explained by a single mechanism but rather involves several different mechanisms. We asked what are the factors that affect the manifestation and extent of gender-biased parasitism and studied the relationship between parasite-related (mean abundance, mean species richness and total species richness of all parasites), host-related (rodent density and proportion of reproductive males and females both separately and together) and environment-related (mean daily maximal and minimal temperatures, rainfall and relative humidity) factors and the magnitude of gender-biased infestation of a South African rodent Rhabdomys pumilio by ixodid ticks, gamasid mites, lice and fleas. We found that spatial variation in gender differences in parasite infestation was affected by parasite-, host- and environment-related factors, although the set of factors affecting gender differences in infestation differed among higher taxa of ectoparasites. Gender differences in infestation by fleas and lice were affected mainly by parasite-related factors, whereas gender differences in infestation by ticks and, in part, by mites were affected mainly by host-related and environmental factors. In addition, spatial variation in most measures of gender difference in mite infestation remained unexplained.
Comparative analysis of two fatty acid binding proteins fromFasciola gigantica
Authors: CHUNCHOB SUPATRA , GRAMS RUDI , VIYANANT VITHOON , SMOOKER PETER M. , VICHASRI-GRAMS SUKSIRI 
Published: June 2010

SUMMARYFatty acid binding proteins are considered to be promising vaccine candidates against trematodiasis. In order to provide additional information about their function inFasciola giganticawe performed a comparative analysis of FgFABP1 and FgFABP3, two isoforms with quite different isoelectric points of 4·9 and 9·9 and 67% sequence identity. Both are expressed in the juvenile and adult parasite but differ in their tissue-specific distribution. In addition, the sequence of FABP3 is identical inF. hepaticaandF. giganticaindicating the protein's functional importance in this genus. Immune sera produced against soluble recombinant FgFABPs reacted with 14 kDa antigens in crude worm, soluble egg, cirrus sac extracts, and excretion/secretion product. Both FgFABPs were located in the parenchyma of the parasite but in addition, FgFABP1 was abundant in testes and spermatozoa while FgFABP3 was abundant in vitelline cells, eggs, and caecal epithelium. Mass spectrometry identified FgFABP1 and FgFABP3 in the ES product whereas only FgFABP3 was identified in egg extract. Serum samples of an experimentally infected rabbit reacted from week 6 post-infection with FgFABP3 and from week 12 with FgFABP1 while sera of infected sheep were not reactive. The results suggest differences in the biological functions of these 2 isoforms and differences in the host/parasite interaction that should be considered for their potential as vaccines against fascioliasis.
Personal debt and suicidal ideation
Authors: Meltzer H. , Bebbington P. , Brugha T. , Jenkins R. , McManus S. , Dennis M. S. 
Published: June 2010

BackgroundPersonal debt is one of many factors associated with anxiety, depression and suicidality. The aim of this study was to examine the relationship between personal debt and suicidal ideation in the context of sociodemographic factors, employment and income, lifestyle behaviours, and recently experienced traumatic events.MethodInterviews were conducted with a random probability sample comprising 7461 respondents for the third national survey of psychiatric morbidity of adults in England. Fieldwork was carried out throughout 2007. The prevalence of suicidal thoughts in the past week, past year and lifetime was assessed and current sources of debt were recorded.ResultsIn 2007, 4.3% of adults in England had thought about taking their own life in the past 12 months, ranging from 1.8% of men aged ⩾55 years to 7.0% of women aged 35–54 years. Those in debt were twice as likely to think about suicide after controlling for sociodemographic, economic, social and lifestyle factors. Difficulty in making hire purchase or mail order repayments and paying off credit card debt, in addition to housing-related debt (rent and mortgage arrears), was strongly associated with suicidal thoughts. Feelings of hopelessness partially mediated the relationship between debt and suicidal ideation.ConclusionsThe number of debts, source of the debt and reasons for debt are key correlates of suicidal ideation. Individuals experiencing difficulties in repaying their debts because they are unemployed or have had a relationship breakdown or have heavy caring responsibilities may require psychiatric evaluation in addition to debt counselling.
‘If you're gonna have a hit’: intratextual mixes and edits of pop recordings
Authors: Everett Walter 
Published: June 2010

AbstractThis essay reviews alternate mixes and edited versions produced for numerous purposes over the past half-century for stock singles, promotional singles, albums and reissues of all sorts, all evidencing a form of literary intertextuality of uniquely central importance to the record industry that has not previously been covered systematically. These multiple texts resulting from different manipulations of a single tape source exhibit what is termed intratextuality, leading to variations in composition, arranging and engineering. In addition, much of the essay's discussion will document for scholars as well as for fans a number of recordings whose continuing availability has been jeopardized by never having been reissued in CD format.
Hits and misses: crafting a pop single for the top-40 market in the 1960s
Authors: Toft Robert 
Published: June 2010

AbstractThe art of crafting successful pop singles can be a hit and miss affair, and this essay addresses the notion of hits and misses through a consideration of ‘(They Long to Be) Close to You’ by Burt Bacharach and Hal David. In September 1963, Bacharach produced the first version of the song with Richard Chamberlain, but the recording was, and still is, considered an artistic failure, as was the version Bacharach produced with Dionne Warwick a year later. It was not until Richard and Karen Carpenter recorded the song in 1970, without input from Bacharach, that the full potential of ‘Close to You’ was realised. But what made the two Bacharach versions miss the mark, while the Carpenters, to use Bacharach's words, ‘nailed it’? If one identifies the elements of a recording's sonic surface that contribute to its success, the deficiencies of Bacharach's misses become as readily apparent as the strategies The Carpenters employed to score a hit. Specifically, this essay considers how groove, instrumentation, melodic style, tempo, manner of performance (both vocal and instrumental), and the disposition of the song's sections (verses and bridge) generate an expressive flow that either enhances (The Carpenters) or diminishes (Bacharach) the emotional impact of the story told in the lyrics.
REFLECTION AND MORALITY
Authors: Larmore Charles 
Published: June 2010

AbstractOur capacity for impersonal reflection, for looking at our own perspective from without, as part of a world that exists independently of us, is our most distinctive trait as human beings. It finds its most striking expression in our moral thinking. For we are moral beings insofar as we stand back from our individual concerns and see in the good of others, in and of itself, a reason for action on our part. It is not, to be sure, in morality alone that we exercise this power of impersonal reflection. We do so too, whenever we set about weighing the evidence for some belief without regard for what we would like to be true or for what common opinion would say. Yet nowhere does this self-transcendence show forth more vividly than when we turn our attention from our own happiness to that of another, taking the same immediate interest in that person's good—just because it is his or hers—as we naturally harbor for our own. In this essay, I explore the way that the moral point of view is shaped by the nature of impersonal reflection and thus constitutes a signal expression of our humanity.
SUBJECTIVE RIGHTNESS
Authors: Smith Holly M. 
Published: June 2010

AbstractTwentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of (i) what is best for an agent to do in light of the actual circumstances in which she acts and (ii) what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who may be uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance.
MAKING ROOM FOR OPTIONS: MORAL REASONS, IMPERFECT DUTIES, AND CHOICE
Authors: Greenspan Patricia 
Published: June 2010

AbstractAn imperfect duty such as the duty to aid those in need is supposed to leave leeway for choice as to how to satisfy it, but if our reason for a certain way of satisfying it is our strongest, that leeway would seem to be eliminated. This paper defends a conception of practical reasons designed to preserve it, without slighting the binding force of moral requirements, though it allows us to discount certain moral reasons. Only reasons that offer criticism of alternatives can yield requirements, but our reasons for particular ways of satisfying imperfect duties merely count in favor of the acts in question.When the state is authorized to take over charitable obligations, it should not be seen as enforcing fulfillment of our imperfect duties, but rather as forcing us to help fulfill collective duties that may be substantially modified by transfer to the state, replacing imperfect duties with perfect. Besides the cost to us in freedom of choice there is a moral cost to replacing the virtuous motives of charity with those that tend to accompany paying taxes. However, a compensating feature of state involvement is the fact that its more precise demands come with limits.
THE OBLIGATION TO BE VIRTUOUS: KANT'S CONCEPTION OF THETUGENDVERPFLICHTUNG
Authors: Guyer Paul 
Published: June 2010

AbstractIn theMetaphysics of Morals, Kant makes a distinction betweenduties of virtue and the obligation to be virtuous. For a number of reasons, it may seem as if the latter does not actually require any actions of us not already required by the former. This essay argues that Kant does succeed in describing obligations that we have to prepare for virtuous conduct that are different from simply fulfilling specific duties of virtue, and that in so doing he describes an important element of the moral life.
Farmer-developed vegetable intercropping systems in southern Hebei, China
Authors: Feike Til , Chen Qing , Graeff-Hönninger Simone , Pfenning Judit , Claupein Wilhelm 
Published: June 2010

AbstractThe expansion of intensive vegetable production systems exacerbates ongoing resource degradation in China's Hebei province. There is an urgent need to develop and disseminate more sustainable vegetable production systems. Intercropping, the simultaneous cultivation of two or more crops on the same field, is widely practiced in the region. Intercropping can use environmental resources more efficiently and is therefore considered to generate high and stable yields with lower inputs. Until now, scientific literature on vegetable intercropping in China is non-existent. To identify prevailing vegetable intercropping systems, a qualitative inquiry was conducted in southern Hebei province. Researchers, extensionists and farmers were interviewed on the occurrence, methods, potentials and constraints of vegetable intercropping. Furthermore, semi-structured in-depth interviews were conducted to examine the farmers' underlying motives and concepts and to determine the origin and distribution of the systems. The investigations revealed a huge variety of sophisticated systems being practiced in southern Hebei. Apart from pure vegetable intercropping systems such as spinach–garlic, especially maize–vegetable and cotton–vegetable systems are widespread. The systems are developed by the farmers themselves and disseminated by the state extension service. Apart from the benefits of plant health, the optimal use of limited land resources is the main reason for farmers to exercise intercropping. However, with the ongoing mechanization and labor force reduction in the agricultural sector, a great part of the intercropping systems, which demand a high input of manual labor, are prone to extinction in the long run. Recent research in China focused purely on agronomic advantages of intercropping, neglecting the linkages between the socio-economic developments and farmers' decisions in the field. To overcome this dilemma and to maintain the traditional and sustainable intercropping systems, we conclude that only an integrative research approach that involves various stakeholders from the beginning is able to adjust the intercropping systems to future demands.
ViewDock TDW: high-throughput visualization of virtual screening results
Authors: Lau Christopher D. , Levesque Marshall J. , Chien Shu , Date Susumu , Haga Jason H. 
Published: June 2010

Abstract
Summary: ViewDock TDW is a modification of the pre-existing ViewDock Chimera extension (http://www.cgl.ucsf.edu/chimera/) used to visualize results of virtual screening experiments. By combing TDW hardware and an enhanced ViewDock interface, dozens of ligand–protein complexes are rendered simultaneously to parallelize the analysis of candidate ligands. The ViewDock TDW GUI allows the user to easily and interactively manipulate the molecules on the TDW as an entire set, a selected subset or a single ligand–protein complex and preserves all Chimera functionality.
Availability and Implementation: ViewDock TDW is an open source software; freely available on the web at http://www.tdw-prime.webs.com. Chimera UCSF is also available, free of charge, at http://www.cgl.ucsf.edu/chimera/
Contact: jhaga@bioeng.ucsd.edu
JAMIE: joint analysis of multiple ChIP-chip experiments
Authors: Wu Hao , Ji Hongkai 
Published: June 2010

AbstractMotivation: Chromatin immunoprecipitation followed by genome tiling array hybridization (ChIP-chip) is a powerful approach to identify transcription factor binding sites (TFBSs) in target genomes. When multiple related ChIP-chip datasets are available, analyzing them jointly allows one to borrow information across datasets to improve peak detection. This is particularly useful for analyzing noisy datasets.Results: We propose a hierarchical mixture model and develop an R package JAMIE to perform the joint analysis. The genome is assumed to consist of background and potential binding regions (PBRs). PBRs have context-dependent probabilities to become bona fide binding sites in individual datasets. This model captures the correlation among datasets, which provides basis for sharing information across experiments. Real data tests illustrate the advantage of JAMIE over a strategy that analyzes individual datasets separately.Availability: JAMIE is freely available from http://www.biostat.jhsph.edu/∼hji/jamieContact: hji@jhsph.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood
Authors: Csűös Miklós 
Published: June 2010

AbstractSummary: Count is a software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is suited to study any other integer-valued evolutionary characters. Count performs ancestral reconstruction, and infers family- and lineage-specific characteristics along the evolutionary tree. It implements popular methods employed in gene content analysis such as Dollo and Wagner parsimony, propensity for gene loss, as well as probabilistic methods involving a phylogenetic birth-and-death model.Availability: Count is available as a stand-alone Java application, as well as an application bundle for MacOS X, at the web site http://www.iro.umontreal.ca/∼csuros/gene_content/count.html. It can also be launched using Java Webstart from the same site. The software is distributed under a BSD-style license. Source code is available upon request from the author.Contact: csuros@iro.umontreal.ca
Molecular signatures-based prediction of enzyme promiscuity
Authors: Carbonell Pablo , Faulon Jean-Loup 
Published: June 2010

AbstractMotivation: Enzyme promiscuity, a property with practical applications in biotechnology and synthetic biology, has been related to the evolvability of enzymes. At the molecular level, several structural mechanisms have been linked to enzyme promiscuity in enzyme families. However, it is at present unclear to what extent these observations can be generalized. Here, we introduce for the first time a method for predicting catalytic and substrate promiscuity using a graph-based representation known as molecular signature.Results: Our method, which has an accuracy of 85% for the non-redundant KEGG database, is also a powerful analytical tool for characterizing structural determinants of protein promiscuity. Namely, we found that signatures with higher contribution to the prediction of promiscuity are uniformly distributed in the protein structure of promiscuous enzymes. In contrast, those signatures that act as promiscuity determinants are significantly depleted around non-promiscuous catalytic sites. In addition, we present the study of the enolase and aminotransferase superfamilies as illustrative examples of characterization of promiscuous enzymes within a superfamily and achievement of enzyme promiscuity by protein reverse engineering. Recognizing the role of enzyme promiscuity in the process of natural evolution of enzymatic function can provide useful hints in the design of directed evolution experiments. We have developed a method with potential applications in the guided discovery and enhancement of latent catalytic capabilities surviving in modern enzymes.Availability: http://www.issb.genopole.fr∼faulonContact: pcarbonell@issb.genopole.frSupplementary information: Supplementary data are available at Bioinformatics online.