bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new framework for computational protein design through cost function network optimization
Authors: Traoré Seydou , Allouche David , André Isabelle , de Givry Simon , Katsirelos George , Schiex Thomas , Barbe Sophie 
Published: July 2013

Abstract
Motivation: The main challenge for structure-based computational protein design (CPD) remains the combinatorial nature of the search space. Even in its simplest fixed-backbone formulation, CPD encompasses a computationally difficult NP-hard problem that prevents the exact exploration of complex systems defining large sequence-conformation spaces.
Results: We present here a CPD framework, based on cost function network (CFN) solving, a recent exact combinatorial optimization technique, to efficiently handle highly complex combinatorial spaces encountered in various protein design problems. We show that the CFN-based approach is able to solve optimality a variety of complex designs that could often not be solved using a usual CPD-dedicated tool or state-of-the-art exact operations research tools. Beyond the identification of the optimal solution, the global minimum-energy conformation, the CFN-based method is also able to quickly enumerate large ensembles of suboptimal solutions of interest to rationally build experimental enzyme mutant libraries.
Availability: The combined pipeline used to generate energetic models (based on a patched version of the open source solver Osprey 2.0), the conversion to CFN models (based on Perl scripts) and CFN solving (based on the open source solver toulbar2) are all available at http://genoweb.toulouse.inra.fr/∼tschiex/CPD
Contacts: thomas.schiex@toulouse.inra.fr or sophie.barbe@insa-toulouse.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
A comparative analysis of algorithms for somatic SNV detection in cancer
Authors: Roberts Nicola D. , Kortschak R. Daniel , Parker Wendy T. , Schreiber Andreas W. , Branford Susan , Scott Hamish S. , Glonek Garique , Adelson David L. 
Published: July 2013

Abstract
Motivation: With the advent of relatively affordable high-throughput technologies, DNA sequencing of cancers is now common practice in cancer research projects and will be increasingly used in clinical practice to inform diagnosis and treatment. Somatic (cancer-only) single nucleotide variants (SNVs) are the simplest class of mutation, yet their identification in DNA sequencing data is confounded by germline polymorphisms, tumour heterogeneity and sequencing and analysis errors. Four recently published algorithms for the detection of somatic SNV sites in matched cancer–normal sequencing datasets are VarScan, SomaticSniper, JointSNVMix and Strelka. In this analysis, we apply these four SNV calling algorithms to cancer–normal Illumina exome sequencing of a chronic myeloid leukaemia (CML) patient. The candidate SNV sites returned by each algorithm are filtered to remove likely false positives, then characterized and compared to investigate the strengths and weaknesses of each SNV calling algorithm.
Results: Comparing the candidate SNV sets returned by VarScan, SomaticSniper, JointSNVMix2 and Strelka revealed substantial differences with respect to the number and character of sites returned; the somatic probability scores assigned to the same sites; their susceptibility to various sources of noise; and their sensitivities to low-allelic-fraction candidates.
Availability: Data accession number SRA081939, code at http://code.google.com/p/snv-caller-review/
Contact: david.adelson@adelaide.edu.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Naive binning improves phylogenomic analyses
Authors: Bayzid Md Shamsuzzoha , Warnow Tandy 
Published: July 2013

Abstract
Motivation: Species tree estimation in the presence of incomplete lineage sorting (ILS) is a major challenge for phylogenomic analysis. Although many methods have been developed for this problem, little is understood about the relative performance of these methods when estimated gene trees are poorly estimated, owing to inadequate phylogenetic signal.
Results: We explored the performance of some methods for estimating species trees from multiple markers on simulated datasets in which gene trees differed from the species tree owing to ILS. We included *BEAST, concatenated analysis and several ‘summary methods’: BUCKy, MP-EST, minimize deep coalescence, matrix representation with parsimony and the greedy consensus. We found that *BEAST and concatenation gave excellent results, often with substantially improved accuracy over the other methods. We observed that *BEAST’s accuracy is largely due to its ability to co-estimate the gene trees and species tree. However, *BEAST is computationally intensive, making it challenging to run on datasets with 100 or more genes or with more than 20 taxa. We propose a new approach to species tree estimation in which the genes are partitioned into sets, and the species tree is estimated from the resultant ‘supergenes’. We show that this technique improves the scalability of *BEAST without affecting its accuracy and improves the accuracy of the summary methods. Thus, naive binning can improve phylogenomic analysis in the presence of ILS.
Contact: tandy@cs.utexas.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Pulmonary Blood Flow Increases in Damaged Regions Directly after Acid Aspiration in Rats
Authors: Richter Torsten , Bergmann Ralf , Knels Lilla , Hofheinz Frank , Kasper Michael , Deile Martin , Pietzsch Jens , Ragaller Maximilian , Koch Thea 
Published: July 2013

Abstract

Background:
After gastric aspiration events, patients are at risk of pulmonary dysfunction and the development of severe acute lung injury and acute respiratory distress syndrome, which may contribute to the development of an inflammatory reaction. The authors’ aim in the current study was to investigate the role of the spatial distribution of pulmonary blood flow in the pathogenesis of pulmonary dysfunction during the early stages after acid aspiration.

Methods:
The authors analyzed the pulmonary distribution of radiolabeled microspheres in normal (n = 6) and injured (n = 12) anesthetized rat lungs using positron emission tomography, computed tomography, and histological examination.

Results:
Injured regions demonstrate increased pulmonary blood flow in association with reduced arterial pressure and the deterioration of arterial oxygenation. After acid aspiration, computed tomography scans revealed that lung density had increased in the injured regions and that these regions colocalized with areas of increased blood flow. The acid was instilled into the middle and basal regions of the lungs. The blood flow was significantly increased to these regions compared with the blood flow to uninjured lungs in the control animals (middle region: 1.23 [1.1; 1.4] (median [25%; 75%]) vs. 1.04 [1.0; 1.1] and basal region: 1.25 [1.2; 1.3] vs. 1.02 [1.0; 1.05], respectively). The increase in blood flow did not seem to be due to vascular leakage into these injured areas.

Conclusions:
The data suggest that 10 min after acid aspiration, damaged areas are characterized by increased pulmonary blood flow. The results may impact further treatment strategies, such as drug targeting.
Conserving tropical biodiversity via strategic spatiotemporal harvest planning
Authors: Ramage Benjamin S. , Marshalek Elaina C. , Kitzes Justin , Potts Matthew D. 
Published: July 2013

SummaryTropical timber production forests have the potential to harbour many species, but landscape‐level management strategies for minimizing extinctions are lacking.To develop relevant conservation guidelines, we investigated how harvest plans with different spatiotemporal patterns affected the persistence of sessile species with different traits and preharvest characteristics. We confronted this problem via an individual‐based simulation model.We explored several harvest plans with different levels of spatiotemporal aggregation, but equivalent total harvest area, and found that extinction probabilities for each plan varied with species traits and predisturbance characteristics. Most notably, plans with large contiguous harvest units yielded particularly high extinction probabilities for dispersal‐limited habitat specialists with clustered preharvest distributions. Differences between plans were small for some types of species, but highly aggregated plans yielded the highest extinction rates for all extinction‐prone groups.Synthesis and applications. Our simulations suggest that reducing the size of contiguous harvest units, even while total harvest area remains constant, may reduce extinction rates in tropical production forests (assuming that road‐related threats can be effectively managed). Our findings have important implications for tropical conservation efforts and also provide general insight into the compositional effects of disturbances with different spatiotemporal characteristics.
Adapting to conversation with semantic dementia: using enactment as a compensatory strategy in everyday social interaction
Authors: Kindell Jacqueline , Sage Karen , Keady John , Wilkinson Ray 
Published: July 2013

AbstractBackgroundStudies to date in semantic dementia have examined communication in clinical or experimental settings. There is a paucity of research describing the everyday interactional skills and difficulties seen in this condition.AimsTo examine the everyday conversation, at home, of an individual with semantic dementia.Methods & ProceduresA 71‐year‐old man with semantic dementia and his wife were given a video camera and asked to record natural conversation in the home situation with no researcher present. Recordings were also made in the home environment, with the individual with semantic dementia in conversation with a member of the research team. Conversation analysis was used to transcribe and analyse the data. Recurring features were noted to identify conversational patterns.Outcomes & ResultsAnalysis demonstrated a repeated practice by the speaker with semantic dementia of acting out a diversity of scenes (enactment). As such, the speaker regularly used direct reported speech along with paralinguistic features (such as pitch and loudness) and non‐vocal communication (such as body posture, pointing and facial expression) as an adaptive strategy to communicate with others in conversation.Conclusions & ImplicationsThis case shows that while severe difficulties may be present on neuropsychological assessment, relatively effective communicative strategies may be evident in conversation. A repeated practice of enactment in conversation allowed this individual to act out, or perform what he wanted to say, allowing him to generate a greater level of meaningful communication than his limited vocabulary alone could achieve through describing the events concerned. Such spontaneously acquired adaptive strategies require further attention in both research and clinical settings in semantic dementia and analysis of interaction in this condition, using conversation analysis, may be helpful.
Phonological therapy in jargon aphasia: effects on naming and neologisms
Authors: Bose Arpita 
Published: July 2013

AbstractBackgroundJargon aphasia is one of the most intractable forms of aphasia with limited recommendation on amelioration of associated naming difficulties and neologisms. The few naming therapy studies that exist in jargon aphasia have utilized either semantic or phonological approaches, but the results have been equivocal. Moreover, the effect of therapy on the characteristics of neologisms is less explored.AimsThis study investigates the effectiveness of a phonological naming therapy (i.e. phonological component analysis—PCA) on picture‐naming abilities and on quantitative and qualitative changes in neologisms for an individual with jargon aphasia (FF).Methods & ProceduresFF showed evidence of jargon aphasia with severe naming difficulties and produced a very high proportion of neologisms. A single‐subject multiple probe design across behaviours was employed to evaluate the effects of PCA therapy on the accuracy for three sets of words. In therapy, a phonological components analysis chart was used to identify five phonological components (i.e. rhymes, first sound, first sound associate, final sound and number of syllables) for each target word. Generalization effects—change in per cent accuracy and error pattern—were examined comparing pre‐ and post‐therapy responses on the Philadelphia Naming Test, and these responses were analysed to explore the characteristics of the neologisms. The quantitative change in neologisms was measured by change in the proportion of neologisms from pre‐ to post‐therapy and the qualitative change was indexed by the phonological overlap between target and neologism.Outcomes & ResultsAs a consequence of PCA therapy, FF showed a significant improvement in his ability to name the treated items. His performance in maintenance and follow‐up phases remained comparable with his performance during the therapy phases. Generalization to other naming tasks did not show a change in accuracy, but distinct differences in error pattern (an increase in proportion of real word responses and a decrease in proportion of neologisms) were observed. Notably, the decrease in neologisms occurred with a corresponding trend for increase in the phonological similarity between the neologisms and the targets.Conclusions & ImplicationsThis study demonstrated the effectiveness of a phonological therapy for improving naming abilities and reducing the amount of neologisms in an individual with severe jargon aphasia. The positive outcome of this research is encouraging, as it provides evidence for effective therapies for jargon aphasia and also emphasizes that use of the quality and quantity of errors may provide a sensitive outcome measure to determine therapy effectiveness, in particular for client groups who are difficult to treat.
Moisture sorption isotherms of dietetic Rabri at different storage temperatures
Authors: Ghayal Gajanan , Jha Alok , Sahu Jatindra K , Kumar Arvind , Gautam Anuj , Kumar Ravindra , Rasane Prasad 
Published: July 2013

Moisture sorption isotherms of dietetic Rabri were determined at 10, 25 and 37 °C over a water activity range of 0.113–0.868. Sorption isotherms at 37 °C were sigmoidal (type II) curves, while at 10 °C, they were of type V and Type I at 25 °C for both adsorption and desorption processes. Five sorption models were tested to fit the experimental data. Halsey's model for 10 °C, Caurie's model for 25 °C and Modified Mizrahi's model for 37 °C were found to be the best fit. There was a clear hysteresis effect at 10 °C, whereas the effect gradually decreased and diminished at 37 °C.
Implementation of the INTERGROWTH‐21st Project in Italy
Authors: Giuliani F , Bertino E , Oberto M , Di Nicola P , Gilli G , Knight HE , Cheikh Ismail L ,   for the International Fetal and Newborn Growth Consortium for the 21 Century (INTERGROWTH‐21)
Published: July 2013

Turin, Italy, was one of the two European sites for the INTERGROWTH‐21st Project. The sample for the Newborn Cross‐Sectional Study (NCSS) was drawn from two obstetric hospitals that together account for 79% of the city's approximately 12 000 births per year. Women were recruited for the Fetal Growth Longitudinal Study (FGLS) from ten antenatal clinics serving the city's largest obstetric hospital, Azienda Ospedaliera OIRM—S. Anna. Special activities to encourage participation and raise awareness of the project in this population included obtaining an endorsement from the coordinator of the city's antenatal care service, and disseminating information about the project to women through posters and leaflets in antenatal clinics. One of the major challenges at this site was the low recruitment rate in the early phase of FGLS because of the high prevalence of smoking and of women >35 years old in the population. The addition of six extra recruiting clinics served to increase the pool of potentially eligible women who could be screened and led to a marked improvement in the recruitment rate.
A British Investment Bank: Why and How?
Authors: Wigstrom Christian Westerlind 
Published: July 2013

AbstractThis article presents the case for a state‐owned British Investment Bank and discusses its institutional design and capitalisation on the basis of the experiences of the Nordic Investment Bank (BIB). Current supply‐side policies aimed at increasing investment in the infrastructure and small‐ and medium‐sized enterprise (SME) sectors are likely to fail because they neglect constraints and market failures on the demand side. In contrast, a commercially operated but mandate‐driven public investment bank can mitigate market failures on both sides by not only supplying capital on favourable terms to financially viable projects but also stimulating demand through policy‐signalling effects. A focus on offering additionality would be key to the BIB's success. In addition to the ‘economic case’ for the BIB, this article discusses the ‘political case’: how to make it interesting to a government bent on fiscal retrenchment.
Synchronous rise and fall of bark beetle and parasitoid populations in windthrow areas
Authors: Wermelinger B. , Obrist M. K. , Baur H. , Jakoby O. , Duelli P. 
Published: July 2013

Abstract
Windthrows in spruce forests provide a prime substrate for the population build‐up of bark beetles. Until now, no information has been available on the population development of associated parasitoids.
The development of bark beetle and parasitoid populations was monitored on cleared and uncleared windthrow areas for 4 years, corresponding to the second to fifth growing seasons after the storm.
The population level of both groups quickly increased synchronously from the second to the third season, and gradually declined thereafter until the fifth growing season. The parasitoids showed no time lag.
At the species level, the same pattern was found for the pest Ips typographus (L.) and its specific parasitoid Dinotiscus eupterus (Walk.).
During the 4 years under study, a succession of different bark beetle and parasitoid species was found.
Bark beetles and parasitoids were more abundant on uncleared windthrow areas than on cleared areas, whereas predatory beetles generally preferred the adjacent forest.
Once the deteriorated phloem quality precludes further bark beetle development, no more bark beetle‐relevant parasitoids are produced in windthrows.
Milk yield, gross composition and fatty acid profile of dual‐purpose Aosta Red Pied cows fed separate concentrate‐forage versus total mixed ration
Authors: Renna Manuela , Cornale Paolo , Lussiana Carola , Battaglini Luca Maria , Turille Germano , Mimosi Antonio 
Published: July 2013

AbstractThis study was designed to evaluate the effects of two feeding methods on milk yield, composition and fatty acid (FA) profile obtained from dual‐purpose cattle. Twenty‐four Aosta Red Pied cows beyond peak of lactation were assigned to two groups and fed hay and concentrates in the proportions 0.69 and 0.31 on a dry matter basis for 10 weeks. Concentrates were offered separately from forages 6 times a day (separate ration, SR) or as a total mixed ration (TMR). The feeding method did not significantly influence dry matter intake (16.8 vs. 16.9 kg/head/day for SR‐ and TMR‐fed cows, respectively), milk yield (17.4 vs. 17.5 kg/head/day), milk fat, protein and lactose contents (36.4 vs. 35.2, 33.5 vs. 32.8, and 47.3 vs. 47.4 g/kg) and yields (607.9 vs. 613.4, 567.4 vs. 572.7 and 805.5 vs. 829.7 g/head/day). The overall milk FA profile was very similar between groups. Milk concentrations of FA used as indirect markers of rumen function (C18:2 t10c12, odd‐ and branched‐chain FA) and the extent of ruminal biohydrogenation were comparable (P > 0.05) between SR‐ and TMR‐fed cows, suggesting that ruminal pH did not vary considerably as a consequence of the feeding strategy applied.
Inference for Optimal Dynamic Treatment Regimes Using an Adaptive m‐Out‐of‐n Bootstrap Scheme
Authors: Chakraborty Bibhas , Laber Eric B. , Zhao Yingqi 
Published: July 2013

AbstractSummaryA dynamic treatment regime consists of a set of decision rules that dictate how to individualize treatment to patients based on available treatment and covariate history. A common method for estimating an optimal dynamic treatment regime from data is Q‐learning which involves nonsmooth operations of the data. This nonsmoothness causes standard asymptotic approaches for inference like the bootstrap or Taylor series arguments to breakdown if applied without correction. Here, we consider the m‐out‐of‐n bootstrap for constructing confidence intervals for the parameters indexing the optimal dynamic regime. We propose an adaptive choice of m and show that it produces asymptotically correct confidence sets under fixed alternatives. Furthermore, the proposed method has the advantage of being conceptually and computationally much simple than competing methods possessing this same theoretical property. We provide an extensive simulation study to compare the proposed method with currently available inference procedures. The results suggest that the proposed method delivers nominal coverage while being less conservative than alternatives. The proposed methods are implemented in the qLearn R‐package and have been made available on the Comprehensive R‐Archive Network (http://cran.r‐project.org/). Analysis of the Sequenced Treatment Alternatives to Relieve Depression (STAR*D) study is used as an illustrative example.
FDR Control with Pseudo‐Gatekeeping Based on a Possibly Data Driven Order of the Hypotheses
Authors: Farcomeni A. , Finos L. 
Published: July 2013

AbstractSummaryWe propose a multiple testing procedure controlling the false discovery rate. The procedure is based on a possibly data driven ordering of the hypotheses, which are tested at the uncorrected level q until a suitable number is not rejected. When the order is data driven, larger effect sizes are considered first, therefore selecting more interesting hypotheses with larger probability. The proposed procedure is valid under independence for the test statistics. We also propose a modification which makes our procedure valid under arbitrary dependence. It is shown in simulation that we compare particularly well when the sample size is small. We conclude with an application to identification of molecular signatures of intracranial ependymoma. The methods are implemented in an R package (someMTP), freely available on CRAN.
BAS: Balanced Acceptance Sampling of Natural Resources
Authors: Robertson B. L. , Brown J. A. , McDonald T. , Jaksons P. 
Published: July 2013

SummaryTo design an efficient survey or monitoring program for a natural resource it is important to consider the spatial distribution of the resource. Generally, sample designs that are spatially balanced are more efficient than designs which are not. A spatially balanced design selects a sample that is evenly distributed over the extent of the resource. In this article we present a new spatially balanced design that can be used to select a sample from discrete and continuous populations in multi‐dimensional space. The design, which we call balanced acceptance sampling, utilizes the Halton sequence to assure spatial diversity of selected locations. Targeted inclusion probabilities are achieved by acceptance sampling. The BAS design is conceptually simpler than competing spatially balanced designs, executes faster, and achieves better spatial balance as measured by a number of quantities. The algorithm has been programed in an R package freely available for download.