bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling
Authors: Wang Sheng , Peng Jian , Xu Jinbo 
Published: July 2011

Abstract
Motivation: Building an accurate alignment of a large set of distantly related protein structures is still very challenging.
Results: This article presents a novel method 3DCOMB that can generate a multiple structure alignment (MSA) with not only as many conserved cores as possible, but also high-quality pairwise alignments. 3DCOMB is unique in that it makes use of both local and global structure environments, combined by a statistical learning method, to accurately identify highly similar fragment blocks (HSFBs) among all proteins to be aligned. By extending the alignments of these HSFBs, 3DCOMB can quickly generate an accurate MSA without using progressive alignment. 3DCOMB significantly excels others in aligning distantly related proteins. 3DCOMB can also generate correct alignments for functionally similar regions among proteins of very different structures while many other MSA tools fail. 3DCOMB is useful for many real-world applications. In particular, it enables us to find out that there is still large improvement room for multiple template homology modeling while several other MSA tools fail to do so.
Availability: 3DCOMB is available at http://ttic.uchicago.edu/~jinbo/software.htm.
Contact: jinboxu@gmail.com
Supplementary Information: Supplementary data are available at Bioinformatics online.
ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices
Authors: Dang Cuong Cao , Lefort Vincent , Le Vinh Sy , Le Quang Si , Gascuel Olivier 
Published: July 2011

Abstract
Summary: Amino acid replacement rate matrices are an essential basis of protein studies (e.g. in phylogenetics and alignment). A number of general purpose matrices have been proposed (e.g. JTT, WAG, LG) since the seminal work of Margaret Dayhoff and co-workers. However, it has been shown that matrices specific to certain protein groups (e.g. mitochondrial) or life domains (e.g. viruses) differ significantly from general average matrices, and thus perform better when applied to the data to which they are dedicated. This Web server implements the maximum-likelihood estimation procedure that was used to estimate LG, and provides a number of tools and facilities. Users upload a set of multiple protein alignments from their domain of interest and receive the resulting matrix by email, along with statistics and comparisons with other matrices. A non-parametric bootstrap is performed optionally to assess the variability of replacement rate estimates. Maximum-likelihood trees, inferred using the estimated rate matrix, are also computed optionally for each input alignment. Finely tuned procedures and up-to-date ML software (PhyML 3.0, XRATE) are combined to perform all these heavy calculations on our clusters.
Availability: http://www.atgc-montpellier.fr/ReplacementMatrix/
Contact: olivier.gascuel@lirmm.fr
Supplementary information: Supplementary data are available at http://www.atgc-montpellier.fr/ReplacementMatrix/
A dynamic programming algorithm for identification of triplex-forming sequences
Authors: Lexa Matej , Martínek Tomáš , Burgetová Ivana , Kopeček Daniel , Brázdová Marie 
Published: July 2011

Abstract
Motivation: Current methods for identification of potential triplex-forming sequences in genomes and similar sequence sets rely primarily on detecting homopurine and homopyrimidine tracts. Procedures capable of detecting sequences supporting imperfect, but structurally feasible intramolecular triplex structures are needed for better sequence analysis.
Results: We modified an algorithm for detection of approximate palindromes, so as to account for the special nature of triplex DNA structures. From available literature, we conclude that approximate triplexes tolerate two classes of errors. One, analogical to mismatches in duplex DNA, involves nucleotides in triplets that do not readily form Hoogsteen bonds. The other class involves geometrically incompatible neighboring triplets hindering proper alignment of strands for optimal hydrogen bonding and stacking. We tested the statistical properties of the algorithm, as well as its correctness when confronted with known triplex sequences. The proposed algorithm satisfactorily detects sequences with intramolecular triplex-forming potential. Its complexity is directly comparable to palindrome searching.
Availability: Our implementation of the algorithm is available at http://www.fi.muni.cz/lexa/triplex as source code and a web-based search tool. The source code compiles into a library providing searching capability to other programs, as well as into a stand-alone command-line application based on this library.
Contact: lexa@fi.muni.cz
Supplementary Information: Supplementary data are available at Bioinformatics online.
VISTA Region Viewer (RViewer)—a computational system for prioritizing genomic intervals for biomedical studies
Authors: Lukashin Igor , Novichkov Pavel , Boffelli Dario , Paciorkowski Alex R. , Minovitsky Simon , Yang Song , Dubchak Inna 
Published: July 2011

Abstract
Summary: Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human disease makes it very important to develop user-friendly tools for comparing several genomic regions in parallel and prioritizing them based on their functional content. We introduce VISTA Region Viewer (RViewer), an interactive online tool that allows for efficient screening and prioritization of regions of the human genome for follow-up studies. The tool takes as input genetic variation data from different biomedical studies, determines a number of various functional parameters for both coding and non-coding sequences in each region and allows for sorting and searching the results of the analysis in multiple ways.
Availability and implementation: The tool is implemented as a web application and is freely accessible on the Web at http://rviewer.lbl.gov
Contact: rviewer@lbl.gov; ildubchak@lbl.gov
Baseline left ventricular dP/dtmax rather than the acute improvement in dP/dtmax predicts clinical outcome in patients with cardiac resynchronization therapy
Authors: Bogaard Margot D. , Houthuizen Patrick , Bracke Frank A. , Doevendans Pieter A. , Prinzen Frits W. , Meine Mathias , van Gelder Berry M. 
Published: July 2011

AimsThe maximum rate of left ventricular (LV) pressure rise (dP/dtmax) has been used to assess the acute haemodynamic effect of cardiac resynchronization therapy (CRT). We tested the hypothesis that LV dP/dtmax predicts long‐term clinical outcome after initiation of CRT.Methods and resultsThis was a retrospective observational multicentre study in 285 patients in whom dP/dtmax was measured invasively following implantation of a CRT device. The minimum required follow‐up was 1 year. We analysed the relationship between dP/dtmax and time to the composite endpoint, consisting of all‐cause mortality, heart transplantation (HTX), or LV assist device (LVAD) implantation within the first year of CRT. Thirty‐four events occurred after a mean follow‐up of 160 days (range 21–359). Patients with an event had lower dP/dtmax than patients without an event both at baseline (705 ± 194 vs. 800 ± 222 mmHg/s, P= 0.018) and during CRT (894 ± 224 vs. 985 ± 244 mmHg/s, P= 0.033), but the acute increase in dP/dtmax was similar in patients with and without an event (190 ± 133 vs. 185 ± 115 mmHg/s, P= n.s.). Left ventricular dP/dtmax‐level at baseline and during CRT both predicted the clinical outcome after adjustment for gender, aetiology and New York Heart Association class: hazard ratio (HR) 0.791 [95% confidence interval (CI) 0.658–0.950, P= 0.012] and HR 0.846 (95% CI 0.723–0.991, P= 0.038), respectively.ConclusionLeft ventricular dP/dtmax measured at baseline and during CRT are predictors of 1‐year survival free from all‐cause mortality, HTX, or LVAD implantation, but the acute improvement in dP/dtmax is not correlated to clinical outcome.
Essential Role of Tissue-Specific Proline Synthesis and Catabolism in Growth and Redox Balance at Low Water Potential
Authors: Sharma Sandeep , Villamor Joji Grace , Verslues Paul E. 
Published: July 2011

Abstract
To better define the still unclear role of proline (Pro) metabolism in drought resistance, we analyzed Arabidopsis (Arabidopsis thaliana) Ɗ1-pyrroline-5-carboxylate synthetase1 (p5cs1) mutants deficient in stress-induced Pro synthesis as well as proline dehydrogenase (pdh1) mutants blocked in Pro catabolism and found that both Pro synthesis and catabolism were required for optimal growth at low water potential (ψw). The abscisic acid (ABA)-deficient mutant aba2-1 had similar reduction in root elongation as p5cs1 and p5cs1/aba2-1 double mutants. However, the reduced growth of aba2-1 but not p5cs1/aba2-1 could be complemented by exogenous ABA, indicating that Pro metabolism was required for ABA-mediated growth protection at low ψw. PDH1 maintained high expression in the root apex and shoot meristem at low ψw rather than being repressed, as in the bulk of the shoot tissue. This, plus a reduced oxygen consumption and buildup of Pro in the root apex of pdh1-2, indicated that active Pro catabolism was needed to sustain growth at low ψw. Conversely, P5CS1 expression was most highly induced in shoot tissue. Both p5cs1-4 and pdh1-2 had a more reduced NADP/NADPH ratio than the wild type at low ψw. These results indicate a new model of Pro metabolism at low ψw whereby Pro synthesis in the photosynthetic tissue regenerates NADP while Pro catabolism in meristematic and expanding cells is needed to sustain growth. Tissue-specific differences in Pro metabolism and function in maintaining a favorable NADP/NADPH ratio are relevant to understanding metabolic adaptations to drought and efforts to enhance drought resistance.
Effects of a randomized contingency management intervention on opiate abstinence and retention in methadone maintenance treatment in China
Authors: Hser Yih‐Ing , Li Jianhua , Jiang Haifeng , Zhang Ruimin , Du Jiang , Zhang Congbin , Zhang Bo , Evans Elizabeth , Wu Fei , Chang Yen‐Jung , Peng Chinyi , Huang David , Stitzer Maxine L. , Roll John , Zhao Min 
Published: July 2011

ABSTRACTAims  Methadone maintenance treatment has been made available in China in response to the rapid spread of human immunodeficiency virus (HIV), but high rates of dropout and relapse are problematic. The aim of this study was to apply and test if a contingency management (or motivational incentives) intervention can improve treatment retention and reduce drug use.Design  Random assignment to usual care with (n = 160) or without (n = 159) incentives during a 12‐week trial. Incentives participants earned draws for a chance to win prizes on two separate tracks targeting opiate‐negative urine sample or consecutive attendance; the number of draws increased with continuous abstinence or attendance.Setting  Community‐based methadone maintenance clinics in Shanghai and Kunming.Participants   The sample was 23.8% female, mean age was 38, mean years of drug use was 9.4 and 57.8% had injected drugs in the past 30 days.Measurements  Treatment retention and negative drug urine.Findings  Relative to the treatment‐as‐usual (control) group, better retention was observed among the incentive group in Kunming (75% versus 44%), but no difference was found in Shanghai (90% versus 86%). Submission of negative urine samples was more common among the incentive group than the usual care (74% versus 68% in Shanghai, 27% versus 18% in Kunming), as was the longest duration of sustained abstinence (7.7 weeks versus 6.5 in Shanghai, 2.5 versus 1.6 in Kunming). The average total prize amount was 371 Yuan (or $55) per participant (527 for Shanghai versus 216 in Kunming).Conclusions   Contingency management improves treatment retention and drug abstinence in methadone maintenance treatment clinics in China, although there can be considerable site differences in magnitude of effects.
Mortality and causes of death in children with sickle cell disease in the Netherlands, before the introduction of neonatal screening
Authors: van der Plas Evelyn M. , van den Tweel Xandra W. , Geskus Ronald B. , Heijboer Harriët , Biemond Bart J. , Peters Marjolein , Fijnvandraat Karin 
Published: July 2011

SummaryThis study analyzed the mortality and causes of death in sickle cell disease patients in the Netherlands, to provide a baseline for monitoring the effect of the recently introduced neonatal screening programme and to indicate areas of improvement in the care for these patients. All children (<18 years) diagnosed with sickle cell disease in a tertiary hospital from 1985 to 2007 were included. Vital status was determined up to March 2008. A total of 298 children were included: 189 (63%) patients had HbSS, 17 (6%) HbSβ0 thalassaemia, 72 (24%) HbSC and 20 (7%) HbSβ+ thalassaemia. Twelve patients (4%) died during a total follow‐up of 3896 patient years. All known deaths were sickle cell disease‐related. Meningitis/sepsis (n = 4; 33%), stroke (n = 3; 25%) and death during a visit to the country of origin (n = 3; 25%) were the most common causes of death. The overall mortality rate was 0·27 deaths/100 patient years [95% confidence interval (CI): 0·15–0·43]. The estimated survival at the age of 18 years was 97·3% (95% CI: 95–99%). This report confirms that the burden of mortality in sickle cell disease is increasingly shifting to adults. It is recommended that compliance to antibiotic prophylaxis, thorough counselling and support for patients travelling abroad and specialized peri‐operative care should receive continuous attention.
A welcome can of worms? Hypoxia mitigation by an invasive species
Authors: Norkko Joanna , Reed Daniel C. , Timmermann Karen , Norkko Alf , Gustafsson Bo G. , Bonsdorff Erik , Slomp Caroline P. , Carstensen Jacob , Conley Daniel J. 
Published: July 2011

AbstractInvasive species and bottom‐water hypoxia both constitute major global threats to the diversity and integrity of marine ecosystems. These stressors may interact with unexpected consequences, as invasive species that require an initial environmental disturbance to become established can subsequently become important drivers of ecological change. There is recent evidence that improved bottom‐water oxygen conditions in coastal areas of the northern Baltic Sea coincide with increased abundances of the invasive polychaetesMarenzelleriaspp. Using a reactive‐transport model, we demonstrate that the long‐term bioirrigation activities of denseMarenzelleriapopulations have a major impact on sedimentary phosphorus dynamics. This may facilitate the switch from a seasonally hypoxic system back to a normoxic system by reducing the potential for sediment‐induced eutrophication in the upper water column. In contrast to short‐term laboratory experiments, our simulations, which cover a 10‐year period, show thatMarenzelleriahas the potential to enhance long‐term phosphorus retention in muddy sediments. Over time bioirrigation leads to a substantial increase in the iron‐bound phosphorus content of sediments while reducing the concentration of labile organic carbon. As surface sediments are maintained oxic, iron oxyhydroxides are able to persist and age into more refractory forms. The model illustrates mechanisms through whichMarenzelleriacan act as a driver of ecological change, although hypoxic disturbance or natural population declines in native species may be needed for them to initially become established. Invasive species are generally considered to have a negative impact; however, we show here that one of the main recent invaders in the Baltic Sea may provide important ecosystem services. This may be of particular importance in low‐diversity systems, where disturbances may dramatically alter ecosystem services due to low functional redundancy. Thus, an environmental problem in one region may be either exacerbated or alleviated by a single species from another region, with potentially ecosystem‐wide consequences.
The theory‐practice relationship: reflective skills and theoretical knowledge as key factors in bridging the gap between theory and practice in initial nursing education
Authors: Hatlevik Ida Katrine Riksaasen 
Published: July 2011

hatlevik i.k.r. (2011) The theory‐practice relationship: reflective skills and theoretical knowledge as key factors in bridging the gap between theory and practice in initial nursing education. Journal of Advanced Nursing 68(4), 868–877.AbstractAim.  This paper is a report of a correlational study of the relations of nursing students’ acquired reflective skills, practical skills and theoretical knowledge on their perception of coherence between theory and practice.Background.  Reflection is considered a key factor in bridging the gap between theory and practice. However, it is not evident whether reflective skills are primarily generic in nature or whether they develop from a theoretical knowledge base or the acquisition of practical skills.Method.  This study is a secondary analysis of existing data. The data are part of a student survey that was conducted among third‐year nursing students in Norway during the spring of 2007. A total of 446 nursing students participated in this study and the response rate was 71%. Structural equation modelling analyses were performed.Findings.  The results indicate that students’ perception of coherence between theory and practice during initial nursing education is directly influenced by reflective skills and theoretical knowledge. The results also reveal that reflective skills have mediating effects and that practical skills have a fully mediated and theoretical knowledge a partially mediated influence on students’ perception of coherence.Conclusion.  The findings imply that helping students perceive coherence between theory and practice in nursing education, developing students’ reflective skills and strengthening the theoretical components of the initial nursing education programme might be beneficial. The results suggest that reflective thinking is not merely a generic skill but rather a skill that depends on the acquisition of relevant professional knowledge and experience.
Effects of maternal confidence and competence on maternal parenting stress in newborn care
Authors: Liu Chien‐Chi , Chen Yueh‐Chih , Yeh Yen‐Po , Hsieh Yeu‐Sheng 
Published: July 2011

liu c.‐c., chen y.‐c., yeh y.‐p. & hsieh y.‐s.
(2011) Effects of maternal confidence and competence on maternal parenting stress in newborn care. Journal of Advanced Nursing 68(4), 908–918.AbstractAim.  This paper is a report of a correlational study of the relations of maternal confidence and maternal competence to maternal parenting stress during newborn care.Background.  Maternal role development is a cognitive and social process influenced by cultural and family contexts and mother and child characteristics. Most knowledge about maternal role development comes from western society. However, perceptions of the maternal role in contemporary Taiwanese society may be affected by contextual and environmental factors.Methods.  A prospective correlational design was used to recruit 372 postpartum Taiwanese women and their infants from well‐child clinics at 16 health centres in central Taiwan. Inclusion criteria for mothers were gestational age >37 weeks, ≥18 years old, and healthy, with infants <4 months old. Data were collected between August 2007 and January 2008 using a self‐report questionnaire on mothers’ and infants’ demographic variables, maternal confidence, maternal competence and self‐perceived maternal parenting stress.Results.  After controlling for maternal parity and infant temperament, high maternal confidence and competence were associated with low maternal parenting stress. Maternal confidence influenced maternal parenting stress both directly and indirectly via maternal competence.Conclusion.  To assist postpartum women in infant care programmes achieve positive outcomes, nurses should evaluate and bolster mothers’ belief in their own abilities. Likewise, nurses should not only consider mothers’ infant care skills, but also mothers’ parity and infant temperament. Finally, it is crucial for nurses and researchers to recognize that infant care programmes should be tailored to mothers’ specific maternal characteristics.
Cestode genomics – progress and prospects for advancing basic and applied aspects of flatworm biology
Authors: OLSON P. D. , ZAROWIECKI M. , KISS F. , BREHM K. 
Published: July 2011

SummaryCharacterization of the first tapeworm genome, Echinococcus multilocularis, is now nearly complete, and genome assemblies of E. granulosus, Taenia solium and Hymenolepis microstoma are in advanced draft versions. These initiatives herald the beginning of a genomic era in cestodology and underpin a diverse set of research agendas targeting both basic and applied aspects of tapeworm biology. We discuss the progress in the genomics of these species, provide insights into the presence and composition of immunologically relevant gene families, including the antigen B‐ and EG95/45W families, and discuss chemogenomic approaches toward the development of novel chemotherapeutics against cestode diseases. In addition, we discuss the evolution of tapeworm parasites and introduce the research programmes linked to genome initiatives that are aimed at understanding signalling systems involved in basic host–parasite interactions and morphogenesis.
Leishmania infantum LeIF and its recombinant polypeptides modulate interleukin IL‐12p70, IL‐10 and tumour necrosis factor‐α production by human monocytes
Authors: BARHOUMI M. , GARNAOUI A. , KAABI B. , TANNER N. K. , GUIZANI I. 
Published: July 2011

SummaryLeishmania eukaryotic initiation factor (LeIF) antigen, a Leishmania protein, was shown to induce IL‐12, IL‐10 and tumour necrosis factor‐α (TNF‐α) production by human monocytes‐derived macrophages and dendritic cells from healthy individuals. This cytokine‐inducing activity was previously found to be located in the amino‐terminal region of LeIF protein. This study aimed at characterizing the cytokine‐inducing activity of Leishmania infantum LeIF [Leishmania (L.) infantum (LieIF)] and at defining the fragments necessary for inducing cytokine secretion. Eleven rationally designed recombinant polypeptides, corresponding to the entire LeIF protein or parts of it, were expressed and used to stimulate monocytes from healthy individuals. Leishmania (L.) infantum was able to induce IL‐12p70, IL‐10 and TNF‐α secretion in human monocytes. In addition, both amino‐ (1–226) and carboxyl‐terminal (196–403) parts of the protein were shown to induce significant levels of the three cytokines analysed. However, IL‐12p70‐inducing activity was not significant when monocytes were stimulated with the fragments 129–226 and 129–261, inferring that IL‐12p70‐inducing activity was primarily located within amino acids 1–129 and 261–403. Although the full‐length LieIF protein was a more potent inducer than the tested fragments, a significant cytokine‐inducing activity was maintained in smaller amino acid regions. This work suggests that cytokine‐inducing activity of LieIF or its parts could be exploited in vaccination or immunotherapy protocols.