bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Profile of Fallers with Femoral Neck Fractures
Authors: Tsur Atzmon , Eluz Dana , Itah Dorit , Segal Zvi , Shakeer Nael , Galin Arkady 
Published: November 2013

ObjectiveTo describe the most common characteristics of elderly people who fell and fractured their femoral neck and who were admitted to our rehabilitation setting after surgery by an orthopedic surgeon.SettingA rehabilitation department in a general regional hospital.ParticipantsA cohort of 100 patients, 37 men and 63 women, hospitalized for rehabilitation after surgery for a fracture in the femoral neck.MethodsAll the patients were interviewed by a physician from the rehabilitation department about the circumstances of their fall injuries, examined by an ophthalmologist for ocular problems, and evaluated by an occupational therapist for cognitive function. Data about background diseases were retrieved from the patients' medical records.Main Outcome MeasurementsAge of the patients, place and time of the fall, the circumstances of the fall event, the footwear used at the time of the fall, ophthalmic problems, cognitive disorders, eyeglasses use, walking aids use, medication used that may affect the central nervous system, and the presence of diseases that may influence patients' equilibrium.ResultsThe mean age of the patients was 78 years, with a mean weight of 69 kg. Seventy‐eight percent had 1‐5 diseases that could influence their balance during weight bearing; 67% had an ophthalmic disease. For 70% of the patients, the cause of the fall appeared to be intrinsic (personal). Seventy‐two percent wore socks or slippers, or were barefoot at the time of the fall. Sixty‐four percent of the patients who used a walking aid did not use it during the fall event. Seventy‐one percent of falls occurred indoors and 29% outdoors. Fifty‐five percent of the patients were with another person when they fell. Fifty‐one percent were taking tranquilizers or medications for sleep disorders. Sixty‐eight percent fell during the daylight hours, between 6 AM and 6 PM. Of the patients who wore eyeglasses, 77.6% were not wearing them when they fell. Seventy percent had a short‐term memory disorder, 57% had a concentration disorder, and 49% had an orientation disorder.ConclusionsCharacteristics common to patients who fell and fractured their femoral neck included age older than 78 years, cognitive impairment, nonuse of eyeglasses that were prescribed, and inappropriate footwear.
High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing
Authors: Lou Dianne I. , Hussmann Jeffrey A. , McBee Ross M. , Acevedo Ashley , Andino Raul , Press William H. , Sawyer Sara L. 
Published: November 2013

Significance
This paper presents a library preparation method that dramatically improves the error rate associated with high-throughput DNA sequencing and is substantially more cost-effective than existing error-correction methods. In this strategy, DNA templates are circularized, copied multiple times in tandem with a rolling circle polymerase, and then sequenced on any high-throughput sequencing machine. Each read produced is computationally processed to obtain a consensus sequence of all linked copies of the original molecule. Because it efficiently reduces sequencing error, this method will be broadly enabling in projects where high-throughput sequencing is applied to detect variation in complex samples such as tumors, microbial populations, and environmental communities.
Applying a multidimensional, register-sensitive approach to visualize normalization in translated and non-translated Dutch
Authors: Delaere Isabelle , De Sutter Gert 
Published: November 2013

In this paper we investigate the differences in risk-averse behavior in translated versus non-translated texts by comparing lexical normalization in various registers of translated and non-translated Dutch. We want to verify: (i) to what extent normalization is register dependent; (ii) whether normalizing behavior is similar in translated and non-translated texts of the same register, and (iii) to what extent normalization is source-language dependent. We relied on the Dutch Parallel Corpus to investigate the dispersion of 10 profiles, i.e. sets of synonymous lexical alternatives consisting of a Standard Dutch and a Belgian Standard Dutch alternative. Using an exploratory, multivariate technique we visualized and measured the degrees to which a number of registers of translated and non-translated Dutch conform to linguistic norms.
Eye-tracking and ERPs in multi-word expression research
Authors: Siyanova-Chanturia Anna 
Published: November 2013

In recent years, there has been growing interest in the mechanisms that underlie online processing (comprehension and production) of units above the word level, known as multi-word expressions (MWEs). MWEs are a heterogeneous family of expressions that vary greatly in their linguistic properties but are perceived as highly conventional by native speakers. Extensive behavioural research has demonstrated that, due to their frequency and predictability, MWEs are processed differently from novel strings of language. At the very least, MWEs have been shown to be processed faster than matched control phrases. However, behavioural measures are limited in what they can tell us about MWE processing in the brain above and beyond the speed of processing. The present paper argues in favour of two powerful psycho- and neurolinguistic techniques — eye-tracking and event-related brain potentials (ERPs) — and presents a case for why these techniques are particularly suited for the investigation of phrasal frequency and predictive linguistic mechanisms. A number of studies that have drawn on these methods in their exploration of MWEs are reviewed, with a particular emphasis on the unique role of the method and its ability to tap into the underlying mechanisms implicated in MWE processing. It is argued that the two techniques complement, rather than duplicate each other, providing an ever richer account of the (psycho)linguistic phenomenon that MWEs are.
From hacker spirit to collaborative terminology
Authors: Rico Celia 
Published: November 2013

Whether dealing with social work, humanitarian assistance, solidarity or cooperation, the multilingual linguistic resources necessary for supporting social mediators within the domain of humanitarian work are significantly lacking. Institutional infrastructures which could be capable of fulfilling these needs end up being excessively rigid and sluggish in responding to the complex linguistic situations in which people in vulnerable circumstances find themselves immersed. As such, in times of need and of assistance following a natural disaster, or as a consequence of armed conflict or due to reasons of social injustice, the traditional, linear and hierarchical processes of terminology production prove inadequate when the tools critical for dealing with urgent situations must be provided.
Unlike the methods typically used in industrial societies, the “network society” proposes new models of collaborative work patterned on virtual communities. This article takes as its premise that the hacker spirit, a key aspect of the “network society” (Castells 2011), is an exceptional point of reference around which new processes for terminology work can be developed. The goal of the article is to explore this terrain and show how these ideas have actually been implemented in practice through the creation of the collaborative platform Humanterm.
ASSIST: a fast versatile local structural comparison tool
Authors: Caprari Silvia , Toti Daniele , Viet Hung Le , Di Stefano Maurizio , Polticelli Fabio 
Published: November 2013

Abstract
Motivation: Structural genomics initiatives are increasingly leading to the determination of the 3D structure of target proteins whose catalytic function is not known. The aim of this work was that of developing a novel versatile tool for searching structural similarity, which allows to predict the catalytic function, if any, of these proteins.
Results: The algorithm implemented by the tool is based on local structural comparison to find the largest subset of similar residues between an input protein and known functional sites. The method uses a geometric hashing approach where information related to residue pairs from the input structures is stored in a hash table and then is quickly retrieved during the comparison step. Tests on proteins belonging to different functional classes, done using the Catalytic Site Atlas entries as targets, indicate that the algorithm is able to identify the correct functional class of the input protein in the vast majority of the cases.
Availability and implementation: The application was developed in Java SE 6, with a Java Swing Graphic User Interface (GUI). The system can be run locally on any operating system (OS) equipped with a suitable Java Virtual Machine, and is available at the following URL: http://www.computationalbiology.it/software/ASSISTv1.zip.
Contact: polticel@uniroma3.it
Supplementary information: Supplementary data are available at Bioinformatics online.
Apoptotic cell death and altered calcium homeostasis caused by frataxin depletion in dorsal root ganglia neurons can be prevented by BH4 domain of Bcl-xL protein
Authors: Mincheva-Tasheva Stefka , Obis Elia , Tamarit Jordi , Ros Joaquim 
Published: November 2013

Abstract
Friedreich ataxia (FRDA) is a neurodegenerative disease characterized by a decreased expression of the mitochondrial protein frataxin. Major neurological symptoms of the disease are due to degeneration of dorsal root ganglion (DRG) sensory neurons. In this study we have explored the neurodegenerative events occurring by frataxin depletion on primary cultures of neurons obtained from rat DRGs. Reduction of 80% of frataxin levels in these cells was achieved by transduction with lentivirus containing shRNA silencing sequences. Frataxin depletion caused mitochondrial membrane potential decrease, neurite degeneration and apoptotic cell death. A marked increase of free intracellular Ca2+ levels and alteration in Ca2+-mediated signaling pathways was also observed, thus suggesting that altered calcium homeostasis can play a pivotal role in neurodegeneration caused by frataxin deficiency. These deleterious effects were reverted by the addition of a cell-penetrant TAT peptide coupled to the BH4, the anti-apoptotic domain of Bcl-xL. Treatment of cultured frataxin-depleted neurons with TAT-BH4 was able to restore the free intracellular Ca2+ levels and protect the neurons from degeneration. These observations open the possibility of new therapies of FRDA based on modulating the Ca2+ signaling and prevent apoptotic process to protect DRG neurons from neurodegeneration.
Sex- and age-interacting eQTLs in human complex diseases
Authors: Yao Chen , Joehanes Roby , Johnson Andrew D. , Huan Tianxiao , Esko Tõnu , Ying Saixia , Freedman Jane E. , Murabito Joanne , Lunetta Kathryn L. , Metspalu Andres , Munson Peter J. , Levy Daniel 
Published: November 2013

Abstract
Many complex human diseases exhibit sex or age differences in gene expression. However, the presence and the extent of genotype-specific variations in gene regulation are largely unknown. Here, we report results of a comprehensive analysis of expression regulation of genetic variation related to 11 672 complex disease-associated SNPs as a function of sex and age in whole-blood-derived RNA from 5254 individuals. At false discovery rate &lt;0.05, we identified 14 sex- and 10 age-interacting expression quantitative trait loci (eQTLs). We show that these eQTLs are also associated with many sex- or age-associated traits. These findings provide important context regarding the regulation of phenotypes by genotype–environment interaction.
Modelling the likely impacts of climate-driven changes in cod-capelin overlap in the Barents Sea
Authors: Howell Daniel , Filin Anatoly A. 
Published: November 2013

Abstract
Howell, D., and Filin, A. A. Modelling the likely impacts of climate-driven changes in cod-capelin overlap in the Barents Sea. – ICES Journal of Marine Science, 71: . Recent observations have indicated that the cod distribution within the Barents Sea is expanding towards the northeast. The area into which the cod are expanding has historically been an area with large stocks of polar cod and capelin. It can be expected that the continued expansion of cod into this region would lead to greater availability of these forage fish for cod predation and have a direct impact on the forage fish stock. The distributional shift may also reduce the level of cod cannibalism. Such changes have implications for the management of both cod and capelin fisheries. In this paper, we use two different models (Gadget and STOCOBAR) to examine the effects of the changing overlap on cod and capelin. The results from the two models are compared to reduce uncertainty due to model formulation and exploit the different strengths of the two approaches. Although there are many uncertainties around the ongoing changes, the results indicate that the increased spatial overlap could contribute to modest rises by up to 20% in the average cod stock biomass, but with an increase in the impact of cannibalism, and hence an increased variability in the cod stock size.
Dual role of transcription and transcript stability in the regulation of gene expression inEscherichia colicells cultured on glucose at different growth rates
Authors: Esquerré Thomas , Laguerre Sandrine , Turlan Catherine , Carpousis Agamemnon J. , Girbal Laurence , Cocaign-Bousquet Muriel 
Published: November 2013

AbstractMicroorganisms extensively reorganize gene expression to adjust growth rate to changes in growth conditions. At the genomic scale, we measured the contribution of both transcription and transcript stability to regulating messenger RNA (mRNA) concentration in Escherichia coli. Transcriptional control was the dominant regulatory process. Between growth rates of 0.10 and 0.63 h−1, there was a generic increase in the bulk mRNA transcription. However, many transcripts became less stable and the median mRNA half-life decreased from 4.2 to 2.8 min. This is the first evidence that mRNA turnover is slower at extremely low-growth rates. The destabilization of many, but not all, transcripts at high-growth rate correlated with transcriptional upregulation of genes encoding the mRNA degradation machinery. We identified five classes of growth-rate regulation ranging from mainly transcriptional to mainly degradational. In general, differential stability within polycistronic messages encoded by operons does not appear to be affected by growth rate. We show here that the substantial reorganization of gene expression involving downregulation of tricarboxylic acid cycle genes and acetyl-CoA synthetase at high-growth rates is controlled mainly by transcript stability. Overall, our results demonstrate that the control of transcript stability has an important role in fine-tuning mRNA concentration during changes in growth rate.
Modification of picornavirus genomic RNA using ‘click’ chemistry shows that unlinking of the VPg peptide is dispensable for translation and replication of the incoming viral RNA
Authors: Langereis Martijn A. , Feng Qian , Nelissen Frank H. T. , Virgen-Slane Richard , van der Heden van Noort Gerbrand J. , Maciejewski Sonia , Filippov Dmitri V. , Semler Bert L. , van Delft Floris L. , van Kuppeveld Frank J.M. 
Published: November 2013

AbstractPicornaviruses constitute a large group of viruses comprising medically and economically important pathogens such as poliovirus, coxsackievirus, rhinovirus, enterovirus 71 and foot-and-mouth disease virus. A unique characteristic of these viruses is the use of a viral peptide (VPg) as primer for viral RNA synthesis. As a consequence, all newly formed viral RNA molecules possess a covalently linked VPg peptide. It is known that VPg is enzymatically released from the incoming viral RNA by a host protein, called TDP2, but it is still unclear whether the release of VPg is necessary to initiate RNA translation. To study the possible requirement of VPg release for RNA translation, we developed a novel method to modify the genomic viral RNA with VPg linked via a ‘non-cleavable’ bond. We coupled an azide-modified VPg peptide to an RNA primer harboring a cyclooctyne [bicyclo[6.1.0]nonyne (BCN)] by a copper-free ‘click’ reaction, leading to a VPg-triazole-RNA construct that was ‘non-cleavable’ by TDP2. We successfully ligated the VPg-RNA complex to the viral genomic RNA, directed by base pairing. We show that the lack of VPg unlinkase does not influence RNA translation or replication. Thus, the release of the VPg from the incoming viral RNA is not a prerequisite for RNA translation or replication.
Conserved Changes in the Dynamics of Metabolic Processes during Fruit Development and Ripening across Species
Authors: Klie Sebastian , Osorio Sonia , Tohge Takayuki , Drincovich María F. , Fait Aaron , Giovannoni James J. , Fernie Alisdair R. , Nikoloski Zoran 
Published: November 2013

AbstractComputational analyses of molecular phenotypes traditionally aim at identifying biochemical components that exhibit differential expression under various scenarios (e.g. environmental and internal perturbations) in a single species. High-throughput metabolomics technologies allow the quantification of (relative) metabolite levels across developmental stages in different tissues, organs, and species. Novel methods for analyzing the resulting multiple data tables could reveal preserved dynamics of metabolic processes across species. The problem we address in this study is 2-fold. (1) We derive a single data table, referred to as a compromise, which captures information common to the investigated set of multiple tables containing data on different fruit development and ripening stages in three climacteric (i.e. peach [Prunus persica] and two tomato [Solanum lycopersicum] cultivars, Ailsa Craig and M82) and two nonclimacteric (i.e. strawberry [Fragaria × ananassa] and pepper [Capsicum chilense]) fruits; in addition, we demonstrate the power of the method to discern similarities and differences between multiple tables by analyzing publicly available metabolomics data from three tomato ripening mutants together with two tomato cultivars. (2) We identify the conserved dynamics of metabolic processes, reflected in the data profiles of the corresponding metabolites that contribute most to the determined compromise. Our analysis is based on an extension to principal component analysis, called STATIS, in combination with pathway overenrichment analysis. Based on publicly available metabolic profiles for the investigated species, we demonstrate that STATIS can be used to identify the metabolic processes whose behavior is similarly affected during fruit development and ripening. These findings ultimately provide insights into the pathways that are essential during fruit development and ripening across species.
A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms
Authors: Ariyadasa Ruvini , Mascher Martin , Nussbaumer Thomas , Schulte Daniela , Frenkel Zeev , Poursarebani Naser , Zhou Ruonan , Steuernagel Burkhard , Gundlach Heidrun , Taudien Stefan , Felder Marius , Platzer Matthias , Himmelbach Axel , Schmutzer Thomas , Hedley Pete E. , Muehlbauer Gary J. , Scholz Uwe , Korol Abraham , Mayer Klaus F.X. , Waugh Robbie , Langridge Peter , Graner Andreas , Stein Nils 
Published: November 2013

AbstractBarley (Hordeum vulgare) is an important cereal crop and a model species for Triticeae genomics. To lay the foundation for hierarchical map-based sequencing, a genome-wide physical map of its large and complex 5.1 billion-bp genome was constructed by high-information content fingerprinting of almost 600,000 bacterial artificial chromosomes representing 14-fold haploid genome coverage. The resultant physical map comprises 9,265 contigs with a cumulative size of 4.9 Gb representing 96% of the physical length of the barley genome. The reliability of the map was verified through extensive genetic marker information and the analysis of topological networks of clone overlaps. A minimum tiling path of 66,772 minimally overlapping clones was defined that will serve as a template for hierarchical clone-by-clone map-based shotgun sequencing. We integrated whole-genome shotgun sequence data from the individuals of two mapping populations with published bacterial artificial chromosome survey sequence information to genetically anchor the physical map. This novel approach in combination with the comprehensive whole-genome shotgun sequence data sets allowed us to independently validate and improve a previously reported physical and genetic framework. The resources developed in this study will underpin fine-mapping and cloning of agronomically important genes and the assembly of a draft genome sequence.
Is there a proctor in the house?
Authors: McMullen Anthony 
Published: November 2013

PurposeThis article aims to provide insights into issues encountered in maintaining library technologies and technology‐based services on a limited budget and with limited personnel.Design/methodology/approachThe article uses real world experiences to provide commentary on protocols and practices as they relate to providing library services under increasingly tight budget constraints.FindingsThe rapid growth in online education has brought about many changes to library services. Librarians must make conscious efforts to not only adapt accordingly, but also to stay true to the mission and core values in the face of this rapidly changing landscape.Originality/valueThe paper uses real‐world examples to provide critical commentary on the librarian service ethic as it relates to staying true to the mission as opposed to overreaching in the name of service for all.
Adequacy or inadequacy of budgets for University of Malawi Libraries (UML)
Authors: Mapulanga Patrick 
Published: November 2013

PurposeThe purpose of this paper is to look at adequacy or inadequacy of budgets for University of Malawi Libraries (UML) from financial years 2004 to 2009.Design/methodology/approachA case study design was used to collect quantitative data. University budget estimate from 2003/2004 to 2009/2010 financial years were used.FindingsThe results of the study show that of five constituent colleges of the University of Malawi, four (80 per cent) of their college libraries are inadequately funded below 6 per cent. The average funding as a percentage of the total college funding for the five UML in the six‐year financial period from 2004 to 2010 are as follows: Bunda College Library 2.7 per cent; Chancellor College Library 3.72 per cent; College of Medicine Library 3.52 per cent; Kamuzu College of Nursing Library 6.27 per cent; and the Polytechnic Library 3.43 per cent. Only Kamuzu College of Nursing Library received a minimum average of 6 per cent of the total college funding.Practical implicationsThe study recommends that college librarians should lobby for increased budgets for UML. College librarians should also consider income‐generating activities as a means to supplement funding through government subvention.Originality/valueThere is very little researched information on inadequacy or adequacy of budgeting and funding on UML. This research adds some information on UML budgeting and financing.