bluuebunny/crossref_metadata_2025_split huggingface dataset:
The past and future of geriatric day hospitals
Authors: Beynon JH , Padiachy D 
Published: July 2009

SummaryThe status of the geriatric day hospital within the National Health Service (NHS) in the UK has changed significantly over the past fifty years. We conducted a literature review starting from the inception of the geriatric day hospital, when it was viewed as the ‘shop front for geriatric services’ and was subsequently replicated in many western health systems, to the present uncertainty surrounding the model in terms of outcomes and cost effectiveness. The article also highlights the input of the Royal College of Physicians and the British Geriatric Society to the management and development of day hospitals. The geriatric day hospital has become one of the many service models under the umbrella of intermediate care services, offering comprehensive geriatric assessment and care to older people in the community. However, with the current practices of commissioning of services and ‘payment by results’, the future of this precious health resource remains uncertain.
Differential item functioning of the Boston Naming Test in cognitively normal African American and Caucasian older adults
Authors: PEDRAZA OTTO , GRAFF-RADFORD NEILL R. , SMITH GLENN E. , IVNIK ROBERT J. , WILLIS FLOYD B. , PETERSEN RONALD C. , LUCAS JOHN A. 
Published: July 2009

AbstractScores on the Boston Naming Test (BNT) are frequently lower for African American when compared with Caucasian adults. Although demographically based norms can mitigate the impact of this discrepancy on the likelihood of erroneous diagnostic impressions, a growing consensus suggests that group norms do not sufficiently address or advance our understanding of the underlying psychometric and sociocultural factors that lead to between-group score discrepancies. Using item response theory and methods to detect differential item functioning (DIF), the current investigation moves beyond comparisons of the summed total score to examine whether the conditional probability of responding correctly to individual BNT items differs between African American and Caucasian adults. Participants included 670 adults age 52 and older who took part in Mayo’s Older Americans and Older African Americans Normative Studies. Under a two-parameter logistic item response theory framework and after correction for the false discovery rate, 12 items where shown to demonstrate DIF. Of these 12 items, 6 (“dominoes,” “escalator,” “muzzle,” “latch,” “tripod,” and “palette”) were also identified in additional analyses using hierarchical logistic regression models and represent the strongest evidence for race/ethnicity-based DIF. These findings afford a finer characterization of the psychometric properties of the BNT and expand our understanding of between-group performance. (JINS, 2009,15, 758–768.)
Efficient description logic reasoning in Prolog: The DLog system
Authors: LUKÁCSY GERGELY , SZEREDI PÉTER 
Published: July 2009

AbstractTraditional algorithms for description logic (DL) instance retrieval are inefficient for large amounts of underlying data. As DL is becoming more and more popular in areas such as the Semantic Web and information integration, it is very important to have systems which can reason efficiently over large data sets. In this paper we present an approach to transform DL axioms, formalised in the$\mathcal{SHIQ}$DL language, into a Prolog program under the unique name assumption. This transformation is performed with no knowledge about particular individuals: they are accessed dynamically during the normal Prolog execution of the generated program. This technique, together with the top-down Prolog execution, implies that only those pieces of data are accessed that are indeed important for answering the query. This makes it possible to store the individuals in a database instead of memory, which results in better scalability and helps in using DL ontologies directly on top of existing information sources. The transformation process consists of two steps: (1) the DL axioms are converted to first-order clauses of a restricted form, and (2) a Prolog program is generated from these clauses. Step (2), which is the focus of the present paper, actually works on more general clauses than those obtainable by applying step (1) to a$\mathcal{SHIQ}$knowledge base. We first present a base transformation, the output of which can be either executed using a simple interpreter or further extended to executable Prolog code. We then discuss several optimisation techniques, applicable to the output of the base transformation. Some of these techniques are specific to our approach, while others are general enough to be interesting for DL reasoner implementors not using Prolog. We give an overview ofDLog, a DL reasoner in Prolog, which is an implementation of the techniques outlined above. We evaluate the performance of DLog and compare it to some widely used DL reasoners, such as RacerPro, Pellet and KAON2.
Financial innovation and climate change: the case of renewable energy certificates and the role of the GATS
Authors: DELIMATSIS PANAGIOTIS 
Published: July 2009

AbstractEnergy has come to the forefront of the public debate in the past decade for two main reasons: the first relates to the lack of a secure, continuous, and unconditional energy supply in the importing countries, mostly developed and transition economies, which are still dependent on non-renewable carbon-based fossil fuels. The second reason is that uncontrolled production, distribution, and use of conventional energy may lead to environmental degradation and global warming. Renewable energy certificates (RECs) are instruments that allow countries to promote energy generation from renewables and form part of domestic policies aimed at climate change mitigation and adaptation. Since RECs can be traded in secondary markets, this paper discusses issues raised by the nature of and the trade in RECs which can be of concern for the General Agreement on Trade in Services (GATS) and the multilateral regulation of trade in financial services, notably in the case where World Trade Organisation (WTO) Members undertook sweeping commitments in financial services which equally apply to trade in RECs.
Earthquake hazards program reauthorization
Authors: Showstack Randy 
Published: July 2009

With the U.S. National Earthquake Hazards Reduction Program (NEHRP) coming up for reauthorization and with funding for the program expiring at the end of fiscal year (FY) 2009, a subcommittee of the House of Representatives Committee on Science and Technology held an 11 June hearing to examine the program and question whether it should be focused solely on earthquakes or be broadened to include other hazards as well.Subcommittee chair David Wu (D‐Oreg.) told Eos that in drafting reauthorization legislation, he is leaning toward a multihazard approach for NEHRP. ‘As we discuss the successes in earthquake mitigation and priorities moving forward, we must note that research for other hazards has yet to produce the same advances. This lag may exist because wind, fire, and tsunami mitigation do not have the same federal [research and development] structure that has produced our many advances on the seismic front,” he noted at the hearing.
Architectural differentiation reflects bacterial community structure in stream biofilms
Authors: Besemer Katharina , Hödl Iris , Singer Gabriel , Battin Tom J 
Published: July 2009

Abstract
Laboratory studies have documented the extensive architectural differentiation of biofilms into complex structures, including filamentous streamers generated by turbulent flow. Still, it remains elusive whether this spatial organization of natural biofilms is reflected in the community structure. We analyzed bacterial community differentiation between the base and streamers (filamentous structures floating in the water) of stream biofilms under various flow conditions using denaturing gradient gel electrophoresis (DGGE) and sequencing. Fourth-corner analysis showed pronounced deviation from random community structure suggesting that streamers constitute a more competitive zone within the biofilm than its base. The same analysis also showed members of the α-Proteobacteria and Gemmatimonadetes to preferentially colonize the biofilm base, whereas β-Proteobacteria and Bacteroidetes were comparatively strong competitors in the streamers. We suggest this micro-scale differentiation as a response to the environmental dynamics in natural ecosystems.
Experimental design and environmental parameters affect Rhodospirillum rubrum S1H response to space flight
Authors: Mastroleo Felice , Van Houdt Rob , Leroy Baptiste , Benotmane M Abderrafi , Janssen Ann , Mergeay Max , Vanhavere Filip , Hendrickx Larissa , Wattiez Ruddy , Leys Natalie 
Published: July 2009

Abstract
In view of long-haul space exploration missions, the European Space Agency initiated the Micro-Ecological Life Support System Alternative (MELiSSA) project targeting the total recycling of organic waste produced by the astronauts into oxygen, water and food using a loop of bacterial and higher plant bioreactors. In that purpose, the α-proteobacterium, Rhodospirillum rubrum S1H, was sent twice to the International Space Station and was analyzed post-flight using a newly developed R. rubrum whole genome oligonucleotide microarray and high throughput gel-free proteomics with Isotope-Coded Protein Label technology. Moreover, in an effort to identify a specific response of R. rubrum S1H to space flight, simulation of microgravity and space-ionizing radiation were performed on Earth under identical culture set-up and growth conditions as encountered during the actual space journeys. Transcriptomic and proteomic data were integrated and permitted to put forward the importance of medium composition and culture set-up on the response of the bacterium to space flight-related environmental conditions. In addition, we showed for the first time that a low dose of ionizing radiation (2 mGy) can induce a significant response at the transcriptomic level, although no change in cell viability and only a few significant differentially expressed proteins were observed. From the MELiSSA perspective, we could argue the effect of microgravity to be minimized, whereas R. rubrum S1H could be more sensitive to ionizing radiation during long-term space exploration mission.
Microbial community gene expression within colonies of the diazotroph, Trichodesmium, from the Southwest Pacific Ocean
Authors: Hewson Ian , Poretsky Rachel S , Dyhrman Sonya T , Zielinski Brian , White Angelicque E , Tripp H James , Montoya Joseph P , Zehr Jonathan P 
Published: July 2009

Abstract
Trichodesmium are responsible for a large fraction of open ocean nitrogen fixation, and are often found in complex consortia of other microorganisms, including viruses, prokaryotes, microbial eukaryotes and metazoa. We applied a community gene expression (metatranscriptomic) approach to study the patterns of microbial gene utilization within colonies of Trichodesmium collected during a bloom in the Southwest Pacific Ocean in April 2007. The survey generated 5711-day and 5385-night putative mRNA reads. The majority of mRNAs were from the co-occurring microorganisms and not Trichodesmium, including other cyanobacteria, heterotrophic bacteria, eukaryotes and phage. Most transcripts did not share homology with proteins from cultivated microorganisms, but were similar to shotgun sequences and unannotated proteins from open ocean metagenomic surveys. Trichodesmium transcripts were mostly expressed photosynthesis, N2 fixation and S-metabolism genes, whereas those in the co-occurring microorganisms were mostly involved in genetic information storage and processing. Detection of Trichodesmium genes involved in P uptake and As detoxification suggest that local enrichment of N through N2 fixation may lead to a P-stress response. Although containing similar dominant transcripts to open ocean metatranscriptomes, the overall pattern of gene expression in Trichodesmium colonies was distinct from free-living pelagic assemblages. The identifiable genes expressed by Trichodesmium and closely associated microorganisms reflect the constraints of life in well-lit and nutrient-poor waters, with biosynthetic investment in nutrient acquisition and cell maintenance, which is in contrast to gene transcription by soil and coastal seawater microbial assemblages. The results provide insight into aggregate microbial communities in contrast to planktonic free-living assemblages that are the focus of other studies.
Isotope array analysis of Rhodocyclales uncovers functional redundancy and versatility in an activated sludge
Authors: Hesselsoe Martin , Füreder Stephanie , Schloter Michael , Bodrossy Levente , Iversen Niels , Roslev Peter , Nielsen Per Halkjær , Wagner Michael , Loy Alexander 
Published: July 2009

Abstract
Extensive physiological analyses of different microbial community members in many samples are difficult because of the restricted number of target populations that can be investigated in reasonable time by standard substrate-mediated isotope-labeling techniques. The diversity and ecophysiology of Rhodocyclales in activated sludge from a full-scale wastewater treatment plant were analyzed following a holistic strategy based on the isotope array approach, which allows for a parallel functional probing of different phylogenetic groups. Initial diagnostic microarray, comparative 16S rRNA gene sequence, and quantitative fluorescence in situ hybridization surveys indicated the presence of a diverse community, consisting of an estimated number of 27 operational taxonomic units that grouped in at least seven main Rhodocyclales lineages. Substrate utilization profiles of probe-defined populations were determined by radioactive isotope array analysis and microautoradiography-fluorescence in situ hybridization of activated sludge samples that were briefly exposed to different substrates under oxic and anoxic, nitrate-reducing conditions. Most detected Rhodocyclales groups were actively involved in nitrogen transformation, but varied in their consumption of propionate, butyrate, or toluene, and thus in their ability to use different carbon sources in activated sludge. This indicates that the functional redundancy of nitrate reduction and the functional versatility of substrate usage are important factors governing niche overlap and differentiation of diverse Rhodocyclales members in this activated sludge.
EMPLOYERS' DEMAND FOR QUALIFICATIONS AND SKILLS
Authors: Dörfler Laura , van de Werfhorst Herman G. 
Published: July 2009

ABSTRACT
The paper attempts to empirically test skill demand on the Austrian labour market between 1985 and 2005 by making use of job advertisements. We analyze job advertisements covering a time span of 20 years. This allows us to examine whether there is a trend towards increased merit selection. Our empirical research is based on a content analysis of 975 newspaper job advertisements. We expand on the operationalization of education by looking at both educational level and field of study. Results indicate that jobs described in advertisements increasingly demanded various types of skill. Besides educational merits, other types of skills are also relevant in modern-day economies: social and personal skills. It is demonstrated that the driving force in changing demands is not only compositional change (with the expansion of high-skill demanding jobs), but also changes within occupational groups.
High-throughput minor histocompatibility antigen prediction
Authors: DeLuca David S. , Eiz-Vesper Britta , Ladas Nektarios , Khattab Barbara Anna-Maria , Blasczyk Rainer 
Published: July 2009

Abstract
Motivation: Minor histocompatibility antigens (mHags) are a diverse collection of MHC-bound peptides that have immunological implications in the context of allogeneic transplantation because of their differential presence in donor and host, and thus play a critical role in the induction of the detrimental graft-versus-host disease (GvHD) or in the development of the beneficial graft-versus-leukemia (GvL) effect. Therefore, the search for mHags has implications not only for preventing GvHD, but also for therapeutic applications involving leukemia-specific T cells. We have created a web-based system, named PeptideCheck, which aims to augment the experimental discovery of mHags using bioinformatic means. Analyzing peptide elution data to search for mHags and predicting mHags from polymorphism and protein databases are the core features.
Results: Comparison with known mHag data reveals that some but not all of the previously known mHags can be reproduced. By applying a system of filtering and ranking, we were able to produce an ordered list of potential mHag candidates in which HA-1, HA-3 and HA-8 occur in the best 0.25%. By combining single nucleotide polymorphism, protein, tissue expression and genotypic frequency data, together with antigen presentation prediction algorithms, we propose a list of the best peptide candidates which could potentially induce the GvL effect without causing GvFD.
Availability: http://www.peptidecheck.org
Contact: blasczyk.rainer@mh-hannover.de
Robustness considerations in selecting efficient two-color microarray designs
Authors: Latif A. H. M. Mahbub , Bretz Frank , Brunner Edgar 
Published: July 2009

AbstractThe main goal of microarray experiments is to select a small subset of genes that are differentially expressed among competing mRNA samples. For a given set of such mRNA samples, it is possible to consider a number of two-color cDNA microarray designs with a fixed number of arrays. Appropriate criteria can be used to select an efficient design from such a set of alternative experimental designs. In practice, however, microarray expression data often contain missing observations and the most efficient design (with complete observations) for a specific setup may not be efficient in the presence of missing observations. In this article, we propose two criteria to address the robustness of microarray designs against missing observations. We demonstrate the simultaneous use of efficiency and robustness criteria to select good microarray designs for both one-factor and multi-factor experiments.Contact: mlatif@isrt.ac.bd
Determining noisy attractors of delayed stochastic gene regulatory networks from multiple data sources
Authors: Dai Xiaofeng , Yli-Harja Olli , Ribeiro Andre S. 
Published: July 2009

AbstractMotivation: Gene regulatory networks (GRNs) are stochastic, thus, do not have attractors, but can remain in confined regions of the state space, i.e. the ‘noisy attractors’, which define the cell type and phenotype.Results: We propose a gamma-Bernoulli mixture model clustering algorithm (ΓBMM), tailored for quantizing states from gamma and Bernoulli distributed data, to determine the noisy attractors of stochastic GRN. ΓBMM uses multiple data sources, naturally selects the number of states and can be extended to other parametric distributions according to the number and type of data sources available. We apply it to protein and RNA levels, and promoter occupancy state of a toggle switch and show that it can be bistable, tristable or monostable depending on its internal noise level. We show that these results are in agreement with the patterns of differentiation of model cells whose pathway choice is driven by the switch. We further apply ΓBMM to a model of the MeKS module of Bacillus subtilis, and the results match experimental data, demonstrating the usability of ΓBMM.Availability: Implementation software is available upon request.Contact: andre.sanchesribeiro@tut.fi; xiaofeng.dai@tut.fiSupplementary information: Supplementary data are available at Bioinformatics online.
HI: haplotype improver using paired-end short reads
Authors: Long Quan , MacArthur Daniel , Ning Zemin , Tyler-Smith Chris 
Published: July 2009

Abstract
Summary: We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable.
Availability: The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI.
Contact: ql2@sanger.ac.uk
Affy exon tissues: exon levels in normal tissues in human, mouse and rat
Authors: Pohl Andrew A. , Sugnet Charles W. , Clark Tyson A. , Smith Kayla , Fujita Pauline A. , Cline Melissa S. 
Published: July 2009

Abstract
Summary: Most genes in human, mouse and rat produce more than one transcript isoform. The Affymetrix Exon Array is a tool for studying the many processes that regulate RNA production, with separate probesets measuring RNA levels at known and putative exons. For insights on how exons levels vary between normal tissues, we constructed the Affy Exon Tissues track from tissue data published by Affymetrix. This track reports exon probeset intensities as log ratios relative to median values across the dataset and renders them as colored heat maps, to yield quick visual identification of exons with intensities that vary between normal tissues.
Availability: Affy Exon Tissues track is freely available under the UCSC Genome Browser (http://genome.ucsc.edu/) for human (hg18), mouse (mm8 and mm9), and rat (rn4).
Contact: cline@soe.ucsc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The fat years: the structure and profitability of the US banking sector in the pre-crisis period
Authors: Tregenna Fiona 
Published: July 2009

Abstract
Bank profitability in the USA was extremely high in the pre-crisis period, yet this did not prevent the current crisis. It has become clear that these profits were on shaky grounds and also that bank profits were not used to buttress banks’ capital bases. This paper analyses the effects of structure on profitability from 1994 to 2005. Bank-level panel data are used to test the effects of concentration, market power, bank size and operational efficiency on profitability. Efficiency is not found to be a strong determinant of profitability, suggesting that banks’ high profits during this period were not ‘earned’ through efficient performance. Robust evidence is found that concentration increases bank profitability. This holds even when the largest banks are excluded from the sample, suggesting that the relationship between concentration and profitability acts in a generalised structural way and that the higher profits arising from concentration are at the expense of the rest of the economy. The analysis points to various policy implications relevant to the current crisis, in particular in terms of the legitimacy of expectations of the restoration of pre-crisis profit rates and the need for much stronger regulation of the banking sector, especially in terms of the structure of the sector, pricing behaviour and use of profits.