bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated annotation of keywords for proteins related to
mycoplasmataceae using machine learning techniques
Authors: Bazzan Ana L.C. , Engel Paulo M. , Schroeder Luciana F. , da Silva Sérgio C. 
Published: May 2011

Abstract
Motivation: With the increase in submission of sequences to public databases, the curators of these are not able to cope with the amount of information. The motivation of this work is to generate a system for automated annotation of data we are particularly interested in, namely proteins related to the Mycoplasmataceae family. Following previous works on automatic annotation using symbolic machine learning techniques, the present work proposes a method of automatic annotation of keywords (a part of the SWISS–PROT annotation procedure), and the validation, by an expert, of the annotation rules generated. The aim of this procedure is twofold: to complete the annotation of keywords of those proteins which is far from adequate, and to produce a prototype of the validation environment, which is aimed at an expert who does not have a deep knowledge of the structure of the current databases containing the necessary information s/he needs.
Results: As for the first objective, a rate of correct keywords annotation of 60% is reported in the literature. Our preliminary results show that with a slightly different method, applied this method to data related to Mycoplasmataceae only, we are able to increase that rate of correct annotation.
Contact: bazzan@inf.ufrgs.br
*Corresponding author; supported by CNPq
Multiple sequence alignment with arbitrary gap costs:
Computing an optimal solution using polyhedral combinatorics
Authors: Althaus Ernst , Caprara Alberto , Lenhof Hans-Peter , Reinert Knut 
Published: May 2011

Abstract
Multiple sequence alignment is one of the dominant problems in computational molecular biology. Numerous scoring functions and methods have been proposed, most of which result in NP-hard problems. In this paper we propose for the first time a general formulation for multiple alignment with arbitrary gap-costs based on an integer linear program (ILP). In addition we describe a branch-and-cut algorithm to effectively solve the ILP to optimality. We evaluate the performances of our approach in terms of running time and quality of the alignments using the BAliBase database of reference alignments. The results show that our implementation ranks amongst the best programs developed so far.
Contact: althaus@icsi.berkeley.edu
An efficient and accurate distance based algorithm to
reconstruct tandem duplication trees
Authors: Elemento Olivier , Gascuel Olivier 
Published: May 2011

Abstract
The problem of reconstructing the duplication tree of a set of tandemly repeated sequences which are supposed to have arisen through unequal recombination, was first introduced by Fitch (1977, Genetics, 86, 93–104), and has recently received a lot of attention. In this paper, we describe DTSCORE, a fast distance based algorithm to reconstruct tandem duplication trees, which is statistically consistent. As a cousin of the ADDTREE algorithm (Sattath and Tversky, 1977, Psychometrika, 42, 319–345), the raw DTSCORE has a time complexity in O(n5), where n is the number of observed repeated sequences. Through a series of algorithmic refinements, we improve its complexity to O(n4) in the worst case, but stress that the refined DTSCORE algorithm should perform faster with real data. We assess the topological accuracy of DTSCORE using simulated data sets, and compare it to existing reconstruction methods. The results clearly show that DTSCORE is more accurate than all the other methods we studied. Finally, we report the results of DTSCORE on a real dataset.
Supplementary information: http://www.lirmm.fr/w3ifa/MAAS/
Contact: gascuel@lirmm.fr
Grid computing for improving conformational sampling in NMR structure
calculation
Authors: Mareuil Fabien , Blanchet Christophe , Malliavin Thérèse E. , Nilges Michael 
Published: May 2011

Abstract
Motivation: Methods for automatic nuclear magnetic resonance (NMR) structure determination need to face a high level of ambiguity encountered in NMR spectra recorded by solid-state NMR and by solution NMR of partially unfolded proteins, leading to time-consuming calculations. The software package Ambiguous Restraints for Iterative Assignment (ARIA) allows for straightforward parallelization of the calculation, as the conformers can be generated in parallel on many nodes.
Results: Due to its architecture, the adaptation of ARIA to grid computing can be easily achieved by using the middleware glite and JDL (Job Description Language) scripts. This adaptation makes it possible to address highly ambiguous datasets, because of the much larger conformational sampling that can be generated by use of the grid computational power.
Availability: The version 2.3.1 of ARIA implemented on the grid is freely available from the ARIA web site: aria.pasteur.fr/downloads.
Contact: nilges@pasteur.fr; tere@pasteur.fr
PLIO: an ontology for formal description of protein–ligand interactions
Authors: Ivchenko Olga , Younesi Erfan , Shahid Mohammad , Wolf Antje , Müller Bernd , Hofmann-Apitius Martin 
Published: May 2011

Abstract
Motivation: Biomedical ontologies have proved to be valuable tools for data analysis and data interoperability. Protein–ligand interactions are key players in drug discovery and development; however, existing public ontologies that describe the knowledge space of biomolecular interactions do not cover all aspects relevant to pharmaceutical modelling and simulation.
Results: The protein–ligand interaction ontology (PLIO) was developed around three main concepts, namely target, ligand and interaction, and was enriched by adding synonyms, useful annotations and references. The quality of the ontology was assessed based on structural, functional and usability features. Validation of the lexicalized ontology by means of natural language processing (NLP)-based methods showed a satisfactory performance (F-score = 81%). Through integration into our information retrieval environment we can demonstrate that PLIO supports lexical search in PubMed abstracts. The usefulness of PLIO is demonstrated by two use-case scenarios and it is shown that PLIO is able to capture both confirmatory and new knowledge from simulation and empirical studies.
Availability: The PLIO ontology is made freely available to the public at http://www.scai.fraunhofer.de/bioinformatics/downloads.html.
Contact: martin.hofmann-apitius@scai.fraunhofer.de
Supplementary Information: Supplementary data are available at Bioinformatics online.
Clonality: an R package for testing clonal relatedness of two tumors from the same patient based on their genomic
profiles
Authors: Ostrovnaya Irina , Seshan Venkatraman E. , Olshen Adam B. , Begg Colin B. 
Published: May 2011

Abstract
Summary: If a cancer patient develops multiple tumors, it is sometimes impossible to determine whether these tumors are independent or clonal based solely on pathological characteristics. Investigators have studied how to improve this diagnostic challenge by comparing the presence of loss of heterozygosity (LOH) at selected genetic locations of tumor samples, or by comparing genomewide copy number array profiles. We have previously developed statistical methodology to compare such genomic profiles for an evidence of clonality. We assembled the software for these tests in a new R package called ‘Clonality’. For LOH profiles, the package contains significance tests. The analysis of copy number profiles includes a likelihood ratio statistic and reference distribution, as well as an option to produce various plots that summarize the results.
Availability: Bioconductor (http://bioconductor.org/packages/release/bioc/html/Clonality.html) and http://www.mskcc.org/mskcc/html/13287.cfm.
Contact: ostrovni@mskcc.org
A Description of Intraoperative Ventilator Management in Patients with Acute Lung Injury and the Use of Lung Protective Ventilation Strategies
Authors: Blum James M. , Maile Michael , Park Pauline K. , Morris Michelle , Jewell Elizabeth , Dechert Ronald , Rosenberg Andrew L. 
Published: May 2011

Background
The incidence of acute lung injury (ALI) in hypoxic patients undergoing surgery is currently unknown. Previous studies have identified lung protective ventilation strategies that are beneficial in the treatment of ALI. The authors sought to determine the incidence and examine the use of lung protective ventilation strategies in patients receiving anesthetics with a known history of ALI.

Methods
The ventilation parameters that were used in all patients were reviewed, with an average preoperative PaO₂/Fio₂ [corrected] ratio of ≤ 300 between January 1, 2005 and July 1, 2009. This dataset was then merged with a dataset of patients screened for ALI. The median tidal volume, positive end-expiratory pressure, peak inspiratory pressures, fraction inhaled oxygen, oxygen saturation, and tidal volumes were compared between groups.

Results
A total of 1,286 patients met criteria for inclusion; 242 had a diagnosis of ALI preoperatively. Comparison of patients with ALI versus those without ALI found statistically yet clinically insignificant differences between the ventilation strategies between the groups in peak inspiratory pressures and positive end-expiratory pressure but no other category. The tidal volumes in cc/kg predicted body weight were approximately 8.7 in both groups. Peak inspiratory pressures were found to be 27.87 cm H₂O on average in the non-ALI group and 29.2 in the ALI group.

Conclusion
Similar ventilation strategies are used between patients with ALI and those without ALI. These findings suggest that anesthesiologists are not using lung protective ventilation strategies when ventilating patients with low PaO₂/Fio₂ [corrected] ratios and ALI, and instead are treating hypoxia and ALI with higher concentrations of oxygen and peak pressures.
Recent status scores for version 6 of the Addiction Severity Index (ASI‐6)
Authors: Cacciola John S. , Alterman Arthur I. , Habing Brian , McLellan A. Thomas 
Published: May 2011

ABSTRACTAims  To describe the derivation of recent status scores (RSSs) for version 6 of the Addiction Severity Index (ASI‐6).Design  118 ASI‐6 recent status items were subjected to nonparametric item response theory (NIRT) analyses followed by confirmatory factor analysis (CFA). Generalizability and concurrent validity of the derived scores were determined.Setting and participants  A total of 607 recent admissions to variety of substance abuse treatment programs constituted the derivation sample; a subset (n = 252) comprised the validity sample.Measurements  The ASI‐6 interview and a validity battery of primarily self‐report questionnaires that included at least one measure corresponding to each of the seven ASI domains were administered.Findings  Nine summary scales describing recent status that achieved or approached both high scalability and reliability were derived; one scale for each of six areas (medical, employment/finances, alcohol, drug, legal, psychiatric) and three scales for the family/social area. Intercorrelations among the RSSs also supported the multi‐dimensionality of the ASI‐6. Concurrent validity analyses yielded strong evidence supporting the validity of six of the RSSs (medical, alcohol, drug, employment, family/social problems, psychiatric). Evidence was weaker for the legal, family/social support and child problems RSSs. Generalizability analyses of the scales to males versus females and whites versus blacks supported the comparability of the findings, with slight exceptions.Conclusions  The psychometric analyses to derive Addiction Severity Index version 6 recent status scores support the multi‐dimensionality of the Addiction Severity Index version 6 (i.e. the relative independence of different life functioning areas), consistent with research on earlier editions of the instrument. In general, the Addiction Severity Index version 6 scales demonstrate acceptable scalability, reliability and concurrent validity. While questions remain about the generalizability of some scales to population subgroups, the overall findings coupled with updated and more extensive content in the Addiction Severity Index version 6 support its use in clinical practice and research.
A Phylogeny‐Based Comparison of Tarantula Spider Anti‐Predator Behavior Reveals Correlation of Morphology and Behavior
Authors: Blatchford Richard , Walker Sean , Marshall Samuel 
Published: May 2011

AbstractWe studied anti‐predator strategies in nine species of tarantulas from Asia, Africa, and the Americas. Tarantulas in the New World possess urticating hairs which induce inflammation when in contact with vertebrate mucus membranes and skin. In contrast, tarantulas from the Old World lack this defense but are observed to exhibit a much greater willingness to escalate to an active defense when provoked. We had three goals: (1) describe the behaviors exhibited by each taxon in response to two levels of provocation, (2) look for the presence of alternative classes of anti‐predator strategy as predicted by the Old World–New World dichotomy in aggressive defense, and (3) examine the evolution of these behaviors in the context of the phylogeny of the group. We compared the response of nine different mygalomorph spider genera to two levels of aversive stimuli: puffs of air and prodding. We found that the overall structure of the defensive behavior was similar between the different taxa, consisting of fleeing, rearing, striking, and biting. Some genera did exhibit unique behaviors such as stridulating (Hysterocrates) or rocking (Haplopelma and Selenocosmia). We found that the genera from the New World exhibited low levels of escalation in their defense behaviors, while those from the Old World readily escalated to striking and biting. Our findings are consistent with the hypothesis that the possession of urticating hairs is associated with very low levels of active defense behaviors such as striking and biting. The phylogenetic analysis indicates that both the notable levels of aggression displayed by the African taxa tested and the relative passivity of the New World tarantulas each represents a synapomorphy.
The long‐term survival of Phytophthora cinnamomi in mature Banksia grandis killed by the pathogen
Authors: Collins S. , McComb J. A. , Howard K. , Shearer B. L. , Colquhoun I. J. , Hardy G. E. St. J. 
Published: May 2011

SummaryThe ability of Phytophthora cinnamomi to survive long dry periods is the key to its persistence in the south‐west of Western Australia. It has been proposed that dead Banksia grandis are a significant long‐term reservoir for P. cinnamomi inoculum. To test this, 36 healthy B. grandis trees were inoculated in April 1999, and the presence of viable propagules in planta was determined between 2 and 34 months after tree death. By 10 months after inoculation, 75% of the trees had died, with the remaining seven trees dying by 22 months. The pathogen was more commonly recovered from bark than from wood, except from those trees that died at 22 months, and more commonly from above‐ground trunks than below‐ground trunks and roots until 8 months after plant death. In trees that died 12 months after inoculation, P. cinnamomi was recovered from 60% of trunk and root core samples at 3 months, declining to 33% at 10 months, 5.5% at 12 months and 0.1% at 34 months after tree death. In trees that died at 22 months, P. cinnamomi was recovered from 87% of trunk and root samples 2 months after tree death, decreasing to 0.5% by 33 months. This study suggests that the pathogen does not have a saprotrophic phase within dead B. grandis tissue, and B. grandis is unlikely to be a long‐term reservoir for P. cinnamomi. However, the manipulation of the density of B. grandis and the use of fire to facilitate the breakdown of dead Banksia trunks in the Eucalyptus marginata (jarrah) forest may reduce the spread and impact of P. cinnamomi.
Effect of β‐glucosidase on the meat quality and digestibility in broilers
Authors: Qian L. C. , Sun J. Y. , Fu S. J. 
Published: May 2011

SummaryThis study investigated the effects of supplementary β‐glucosidase on the carcass composition, meat quality, weight of digestive organ and apparent digestibility in male broilers. Two hundred and forty male, 1‐day avine broiler chicks were randomly allocated into four treatment groups and fed with corn–soya bean meal supplemented with 0 (control), 0.6, 1.2 and 1.8 U/g of β‐glucosidase respectively. The results showed that there were no significant differences (p > 0.05) among groups in carcass composition (percentages of eviscerated yield, half‐eviscerated yield, muscle yield of breast and leg). However, adding 0.6 U/g β‐glucosidase to the diet not only altered the meat quality by decreasing the drip loss ratio (p < 0.05) and relative lightness (L*) value (p < 0.01), increasing relative redness (a*) value (p < 0.01), but also significantly decreased the pancreas to body weight ratio (p < 0.05), however, with little effect on liver, proventriculus and gizzard to body weight ratio (p > 0.05). The length and width of duodenum villus were not affected by the addition of β‐glucosidase, but the coefficients of total tract apparent digestibility of protein and fat increased by 9.02% (p < 0.05) and 7.40% (p < 0.01) respectively; the parameters of ash were not affected by β‐glucosidase addition (p < 0.05). This study provided valuable information for evaluation of the effect of supplementary β‐glucosidase on the meat quality and digestibility of broilers.
Mortality 6 years after inpatient treatment of female Japanese patients with eating disorders associated with alcoholism
Authors: Suzuki Kenji , Takeda Aya , Yoshino Aihide 
Published: May 2011

Aims:  This study was conducted to clarify the mortality of patients with eating disorders associated with alcoholism. We focused on the mortality rate 6 years after inpatient treatment of patients with eating disorders associated with alcoholism compared with eating disorder patients without alcoholism and alcoholic patients without eating disorders.Methods:  The subjects were 164 female Japanese patients 30 years of age or younger with eating disorders or alcoholism who were inpatients at some time during the period from 1990 to 1998 at the Japanese National Hospital Organization, Kurihama Alcoholism Center. A semi‐structured interview concerning alcohol problems, eating problems, psychiatric disorders and other clinical characteristics was conducted at the time of the first admission. A survey concerning survival was conducted in October 2001, and 100% of the patients were followed up.Results:  The mortality of the 47 eating disorder patients with alcoholism, 86 eating disorder patients without alcoholism, and 31 alcoholics without eating disorders was 27.7%, 3.5%, and 19.4%, respectively, at 6 years after inpatient treatment, showing significant differences. On the Kaplan–Meier survival curves, the mortality of the eating disorder patients with alcoholism was significantly higher than that of the patients without alcoholism, but not significantly higher than that of young female alcoholics without eating disorders. The 13 eating disorder patients with alcoholism who had died were five anorexia nervosa and seven bulimia nervosa patients.Conclusion:  The results of the study suggest that comorbid alcoholism is a major factor in the death of anorexia nervosa and bulimia nervosa patients.
Targeted mutation of the calbindin D28k gene selectively alters nonvisual photosensitivity
Authors: Butler Matthew P. , LeSauter Joseph , Sichel Amarynth N. , Silver Rae 
Published: May 2011

AbstractLight intensity is an important determinant of diverse physiological and behavioral responses within the non‐image‐forming visual system. Thresholds differ among various photic responses, namely control of circadian rhythms, vigilance state, activity level and pupil constriction, but the mechanisms that regulate photosensitivity are not known. Calbindin D28k (CalB) is a calcium‐binding protein associated with light processing in the mammalian circadian clock. Loss‐of‐function studies indicate that CalB‐deficient mice (CalB−/−) have deficits in their ability to entrain to light–dark cycles. To explore the role of CalB in modulating photosensitivity, thresholds for three behaviors mediated by the non‐image‐forming visual system (entrainment, masking and pupillary light reflex; PLR) were compared in CalB−/− and wildtype mice, and the localization of CalB protein in these circuits was examined in adult and juvenile mice. The results reveal a divergence in how CalB affects thresholds to photic cues among these responses. Entrainment and masking were 40‐ to 60‐fold less sensitive in CalB−/− than in wildtype mice. On the other hand, the PLR in CalB−/− mice was 80‐ to 200‐fold more sensitive. Though CalB is expressed in the retina and in brain circuits regulating entrainment we found no CalB expression in any component of the PLR pathway, namely the olivary pretectal nucleus, Edinger–Westphal nucleus and ciliary ganglion. The behavioral and anatomical data together suggest that, in normal animals, the retinal response to light is blunted in the presence of CalB, but responsiveness of the higher order processes that transduce afferent retinal input is enhanced.
GOD, VALUE, AND NATURALISM
Authors: Ellis Fiona 
Published: May 2011

AbstractI consider whether there are philosophical developments which can deepen our understanding of God. I focus upon the relation between experience and physical things and the nature of value. I reject the narrow limits of experience presupposed by the verificationist, and the related monopoly of science on reality. I recommend a conception of reality which is rich enough to accommodate physical things and also the intertwining of value in the natural world. I detect structural similarities between these two problems and the problem of God, and consider how they might be related at the level of content.
Relaxin promotes growth and maturation of mouse neonatal cardiomyocytes in vitro: clues for cardiac regeneration
Authors: Nistri Silvia , Pini Alessandro , Sassoli Chiara , Squecco Roberta , Francini Fabio , Formigli Lucia , Bani Daniele 
Published: May 2011

AbstractThe demonstration that the adult heart contains myocardial progenitor cells which can be recruited in an attempt to replace the injured myocardium has sparkled interest towards novel molecules capable of improving the differentiation of these cells. In this context, the peptide hormone relaxin (RLX), recently validated as a cardiovascular hormone, is a promising candidate. This study was designed to test the hypothesis that RLX may promote the growth and maturation of mouse neonatal immature cardiomyocytes in primary culture. The cultures were studied at 2, 12, 24 and 48 hrs after the addition of human recombinant H2 RLX (100 ng/ml), the main circulating form of the hormone, or plain medium by combining molecular biology, morphology and electrophysiology. RLX modulated cell proliferation, promoting it at 2 and 12 hrs and inhibiting it at 24 hrs; RLX also induced the expression of both cardiac‐specific transcription factors (GATA‐4 and Nkx2‐5) and cardiac‐specific structural genes (connexin 43, troponin T and HCN4 ion channel) at both the mRNA and protein level. Consistently, RLX induced the appearance of ultrastructural and electrophysiological signs of functionally competent, mature cardiomyocytes. In conclusion, this study provides novel circumstantial evidence that RLX specifically acts on immature cardiomyocytes by promoting their proliferation and maturation. This notion suggests that RLX, for which the heart is both a source and target organ, may be an endogenous regulator of cardiac morphogenesis during pre‐natal life and could participate in heart regeneration and repair, both as endogenous myocardium‐derived factor and exogenous cardiotropic drug, during adult life.