bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Systematic Study of Mixed Surfactant Solutions of a Cationic Ester‐Bonded Dimeric Surfactant with Cationic, Anionic and Nonionic Monomeric Surfactants in Aqueous Media
Authors: Fatma Nazish , Ansari Wajid Husain , Panda Manorama , Kabir‐ud‐Din  
Published: February 2013

AbstractA novel cationic biodegradable dimeric (gemini) surfactant, ethane‐1,2‐diyl bis(N,N‐dimethyl‐N‐hexadecylammoniumacetoxy) dichloride (16‐E2‐16), containing an ester‐linked spacer was synthesized. Its pure and mixed micellization properties with monomeric surfactants cetyl trimethyl ammonium chloride, cetyl pyridinium chloride, sodium dodecyl sulfate, sodium dodecyl benzene sulfonate, cetyl alcohol ethoxylate (20EO) and tert‐octylphenol ethoxylate (9.5EO) were investigated by surface tension measurements at 30 °C. The critical micelle concentration (CMC) of 16‐E2‐16 is well below that of cetyl trimethyl ammonium chloride containing the same number of carbon atoms in the hydrophobic tail per polar head. At different mole fractions of the gemini surfactant, the CMCs of the gemini‐conventional binary mixtures were determined and were found to be less than the ideal CMC values in all the cases indicating synergistic interactions. Aggregation number and Stern–Volmer constant, obtained by the fluorescence quenching technique, also support the synergistic behavior of the surfactant systems.
Longitudinal relations between personality traits and aspects of identity formation during adolescence
Authors: Hill Patrick L. , Allemand Mathias , Grob Sabine Zehnder , Peng Aristide , Morgenthaler Christoph , Käppler Christoph 
Published: February 2013

ABSTRACTThe current study focused on three aspects of identity development relevant to the adolescent years: being an authentic person, perceiving control over and consistency in one's environment, and having consistent expectations from close others. In a two‐wave study of adolescents (n= 750), we examined how these aspects change over the course of a year, as well as whether these aspects correspond to the Big Five personality traits. Results indicated three important findings. First, all three aspects evidenced the capacity for change over a year, and appeared more malleable than personality traits. Second, youth higher on all aspects reported a more adaptive personality profile. Third, changes on these aspects coincide with those on personality traits over the year. Findings are discussed with respect to future directions for studying the interplay of identity and personality development.
Use of Segmental Coordination Analysis of Nonparetic and Paretic Limbs During Obstacle Clearance in Community‐Dwelling Persons After Stroke
Authors: MacLellan Michael J. , Richards Carol L. , Fung Joyce , McFadyen Bradford J. 
Published: February 2013

ObjectiveTo use a segment coordination analysis to identify coordination differences between the paretic and nonparetic limbs for obstacle clearance in community‐dwelling persons after stroke.DesignWithin‐participant design.SettingGait analysis laboratory.ParticipantsSix community‐dwelling persons with a stroke (excluding cerebellar stroke).MethodsParticipants stepped over obstacles of 2 different heights (7.5% and 15% of leg length), leading alternately with their paretic and nonparetic limbs.Main Outcome MeasurementsKinematic data were collected, and segment elevation angles (absolute segment angular position with respect to vertical) were calculated for the thigh, shank, and foot segments. Established mathematical techniques related to the planar law of intersegmental coordination (principal component analysis to quantify covariance and temporal phase relationships among elevation angles) were then applied to compare and contrast the coordination of these segment elevation angle trajectories between paretic and nonparetic limbs.ResultsSegment covariance in elevation angles followed the planar law of intersegmental coordination during level walking (ie, 3 elevation angles that form a plane and the variance explained by 2 principal components) for both paretic and nonparetic limbs. During obstacle clearance, however, relationships between covariance plane characteristics and phase differences for elevation angles of adjacent segments differed in the nonparetic limb, likely related to a need for greater limb elevation for obstacle clearance during paretic limb support or an altered foot trajectory, which resulted from preobstacle foot placement.ConclusionsThe present coordination analysis suggests the preservation of basic control mechanisms in the paretic limb during obstacle clearance after stroke and also reveals its specific motor control compensations. However, a larger study with differing levels of stroke severity must be conducted to understand how the evaluation of intersegmental coordination during walking could guide treatment of specific locomotor control deficits in stroke rehabilitation.
A Comparison of Two Balance Measures to Predict Discharge Performance From Inpatient Stroke Rehabilitation
Authors: O'Dell Michael W. , Au Jessica , Schwabe Eric , Batistick Holly , Christos Paul J. 
Published: February 2013

ObjectiveTo compare the admission Berg Balance Scale (BBS) and Postural Assessment Scale for Stroke (PASS) in predicting outcomes at discharge from an inpatient rehabilitation unit (IRU). We hypothesized that discharge outcomes would be better predicted by (1) the PASS compared with the BBS, and (2) by the PASS changing position subscore compared with the PASS maintain posture subscore.DesignA retrospective study.SettingAn IRU in an academic medical center.ParticipantsFifty‐five subjects with stroke and mean (standard deviation [SD]) age of 71.5 ± 13.8 years, admission functional independence measures (FIM) of 57.2 ± 17.2 points, and IRU length of stay of 17.3 ± 9.7 days.Methodology/Main Outcome MeasurementsAdmission and discharge BBS and PASS scores, gait velocity (GV) at discharge, and selected FIM items at discharge were measured. GV was analyzed both as a continuous and categorical variable.ResultsThe Spearman rank correlation coefficient (r) was strong between admission BBS and PASS (r = 0.90, P < .0001). Correlations between admission BBS and PASS and discharge GV were 0.32 (P = .03) and 0.28 (P = .06), respectively. Analysis of variance was significant for both balance measures when grouped by the discharge gait speed category (P < .0001). Pairwise comparisons were significant between GV‐A and the other 2 categories but not between GV‐B and GV‐C. The magnitude of the observed correlation with discharge GV was greater for PASS maintain posture subscore (r = 0.35, P = .02) than for PASS changing position subscore (r = 0.23, P = .13). Both subscores were significantly associated with both toileting and transfers (r = 0.43‐0.56, all at least P ≤ .001).ConclusionsContrary to our hypotheses, the BBS and PASS performed equally well in our study sample and were best at predicting patients discharged in the slowest GV category. There were few differences between the PASS subscores. Further research should compare how well admission BBS and PASS predict gait velocity, falls, and other functional parameters in the community after IRU discharge.
Nonoperative Treatment for Femoroacetabular Impingement: A Systematic Review of the Literature
Authors: Wall Peter D.H. , Fernandez Miguel , Griffin Damian R. , Foster Nadine E. 
Published: February 2013

ObjectiveFemoroacetabular impingement (FAI) has been identified as a common cause of hip pain in young adults. However, it is not known whether an effective nonoperative treatment exists and whether there is any evidence to support such a treatment. The purpose of this review is to establish whether nonoperative treatments exist for FAI in the published literature and whether there is any evidence to support their use.TypeA systematic review.Literacy SurveyPubMed, Medline, EMBASE, CINAHL, AMED, and Cochrane Library databases were searched by using the following terms: femoroacetabular impingement, femoro‐acetabular impingement, and hip impingement. The search was limited to English only but with no time constraints.MethodologyThe review was undertaken at 2 academic institutions within the United Kingdom; any article that described or provided evidence that related to a nonoperative treatment for FAI was included. Fifty‐three articles met our criteria, of which, 48 were review and/or discussion based.SynthesisFive articles summarized primary experiments that described or evaluated nonoperative treatment, of which, 3 reported favorable outcomes. Many review and/or discussion articles (31 [65%]) indicated that a trial of conservative care was appropriate. Activity modification was most frequently recommended (39 [81%]), and nearly half promoted physical therapy as a treatment (23 [48%]).ConclusionThe review literature appears to promote initial nonoperative treatment for FAI. Although the available literature with experimental data is limited, there is a suggestion that physical therapy and activity modification confer some benefit to patients. Nonoperative treatment regimens, particularly physical therapy, need to be evaluated more extensively and rigorously, preferably against operative care, to determine the true clinical effectiveness.
Diverse property rights, institutions and decentralisation: Forest management by village forest councils in Uttarakhand
Authors: Singh Satyajit 
Published: February 2013

Abstract
This study of decentralised institutions for forest management brings out the varied dimensions of local institutions and politics as they interface with property rights and decentralisation. Unlike the economic literature on decentralisation that is dominated by normative and prescriptive arguments on how a shift towards decentralisation should take place, this paper makes a case for re-centering of the political in the decentralisation literature. This political study of decentralisation does not prescribe decentralisation rules, but weighs the different social, economic and ecological outcomes under varied local conditions. It takes note of the diversity of local institutions and politics in the interpretation of formal rules, power relations, legal rights, moral claims, social custom, and the establishment of informal institutional arrangements. This is done in the context of questioning the typologies of neat property regimes that are broadly categorised as — open-access, state, private and common property - in the economic literature. These widely accepted typologies are tested at the local level and it is found that ownership does not necessarily refer to control and use of resources. The paper highlights the heterogeneity of property regimes under which the village communities manage the forests, and points out that specific state-society relations in particular villages determine the entitlements of the villagers. Importantly, the nature of collective action on decentralisation and negotiation of institutional design has an impact on the consequences at the local level. As the local reality is based on varied local resources, institutions, political processes and social capital, uniform national or state policies have very different local outcomes. This paper asks if it is possible to evolve policies that incorporate diverse institutional arrangements with a combination of different kinds of property rights under decentralised local governance management.
Application of phase-plane method in generating minimum time solution for stable walking of biped robot with specified pattern of motion
Authors: Sadigh Mohammad Jafar , Mansouri Saeed 
Published: February 2013

SUMMARYWalking with a maximum speed is an interesting subject in the field of biped motion. Giving an answer to the question of “what is the maximum achievable speed of a certain biped walking with a physically acceptable pattern?” is the main objective of this work. In this paper, minimum time motion of biped was studied during one step that consists of single support phase (SSP) and double support phase (DSP). The minimum time problem is formulated with stability and non-slip conditions along with actuator limits expressed as some inequality constraints. In addition, certain kinematic constraints in terms of hip joint position are considered that ensure an acceptable walking pattern. A phase-plane technique is used to find the minimum time solution. A numerical simulation is given to shed some light on how the proposed method works. Validity and effectiveness of the method are verified by comparing the results with those of other researches.
The emission of compact jets powered by internal shocks
Authors: Malzac Julien 
Published: February 2013

AbstractThe emission of steady compact jets observed in the hard spectral state of X-ray binaries is likely to be powered by internal shocks caused by fluctuations of the outflow velocity. The dynamics of the internal shocks and the resulting spectral energy distribution (SED) of the jet is very sensitive to the shape of the Power Spectral Density (PSD) of the fluctuations of the jet Lorentz factor. I use Monte-Carlo simulations to investigate this dependence. It turns out that Lorentz factor fluctuations injected at the base of the jet with a flicker noise power spectrum (i.e. P(f) ∝ 1/f) naturally produce the canonical flat SED observed from radio to IR band in X-ray binary systems in the hard state. This model also predicts a strong, wavelength dependent, variability that resembles the observed one. In particular, strong sub-second variability is predicted in the infrared and optical bands.
Lense-Thirring QPO model testing by QPO phenomena in GX339-4 2010 outburst
Authors: Gao H. Q. , Qu J. L. , Zhang Z. , Zhou J. N. 
Published: February 2013

AbstractLense-Thirring QPO model is a promising model to explain QPO phenomena (Ingram et al. (2009)). In this model the QPO results from Lense-Thirring precession of a optical translucent inner hot flow in a truncated disc geometry. Now we check this model with different types QPO (see (Belloni et al. (2011)) for a recent review) of black hole transient (BHT) GX 339-4 2010 outburst and suggest type C QPOs are mainly coincident with this model prediction while type B QPOs are not.
Capacity, value neutrality and the ability to consider the future
Authors: Craigie Jillian 
Published: February 2013

AbstractCalls for the adoption of a universal capacity approach to replace dedicated mental health law are motivated by the idea that the measures designed to protect patient autonomy in legislation such as the Mental Capacity Act 2005 should apply to everyone, including people with a psychiatric diagnosis. In this article it is argued that a diachronic perspective on questions of mental capacity is necessary if capacity law is to play this broader role, but that employing this perspective in assessments of capacity undermines central patient autonomy preserving features of the legislation, which presents a moral dilemma.
Drug-SNPing: an integrated drug-based, protein interaction-based tagSNP-based pharmacogenomics platform for SNP genotyping
Authors: Yang Cheng-Hong , Cheng Yu-Huei , Chuang Li-Yeh , Chang Hsueh-Wei 
Published: February 2013

Abstract
Summary: Many drug or single nucleotide polymorphism (SNP)-related resources and tools have been developed, but connecting and integrating them is still a challenge. Here, we describe a user-friendly web-based software package, named Drug-SNPing, which provides a platform for the integration of drug information (DrugBank and PharmGKB), protein–protein interactions (STRING), tagSNP selection (HapMap) and genotyping information (dbSNP, REBASE and SNP500Cancer). DrugBank-based inputs include the following: (i) common name of the drug, (ii) synonym or drug brand name, (iii) gene name (HUGO) and (iv) keywords. PharmGKB-based inputs include the following: (i) gene name (HUGO), (ii) drug name and (iii) disease-related keywords. The output provides drug-related information, metabolizing enzymes and drug targets, as well as protein–protein interaction data. Importantly, tagSNPs of the selected genes are retrieved for genotyping analyses. All drug-based and protein–protein interaction-based SNP genotyping information are provided with PCR-RFLP (PCR-restriction enzyme length polymorphism) and TaqMan probes. Thus, users can enter any drug keywords/brand names to obtain immediate information that is highly relevant to genotyping for pharmacogenomics research.
Availability and implementation: Drug-SNPing and its user manual are freely available at http://bio.kuas.edu.tw/drug-snping/.
Contact: chuang@isu.edu.tw; yuhuei.cheng@gmail.com; changhw@kmu.edu.tw
Chemical rule-based filtering of MS/MS spectra
Authors: Reiz Beáta , Kertész-Farkas Attila , Pongor Sándor , Myers Michael P. 
Published: February 2013

Abstract
Motivation: Identification of proteins by mass spectrometry–based proteomics requires automated interpretation of peptide tandem mass spectrometry spectra. The effectiveness of peptide identification can be greatly improved by filtering out extraneous noise peaks before the subsequent database searching steps.
Results: Here we present a novel chemical rule-based filtering algorithm, termed CRF, which makes use of the predictable patterns (rules) of collision-induced peptide fragmentation. The algorithm selects peak pairs that obey the common fragmentation rules within plausible limits of mass tolerance as well as peak intensity and produces spectra that can be subsequently submitted to any search engine. CRF increases the positive predictive value and decreases the number of random matches and thus improves performance by 15–20% in terms of peptide annotation using search engines, such as X!Tandem. Importantly, the algorithm also achieves data compression rates of ∼75%.
Availability: The MATLAB source code and a web server are available at http://hydrax.icgeb.trieste.it/CRFilter/
Contact: myers@icgeb.org
Supplementary information: Supplementary data are available at Bioinformatics online.
A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies
Authors: Chen Min , Zang Miao , Wang Xinlei , Xiao Guanghua 
Published: February 2013

Abstract
Motivation: Much research effort has been devoted to the identification of enriched gene sets for microarray experiments. However, identified gene sets are often found to be inconsistent among independent studies. This is probably owing to the noisy data of microarray experiments coupled with small sample sizes of individual studies. Therefore, combining information from multiple studies is likely to improve the detection of truly enriched gene classes. As more and more data become available, it calls for statistical methods to integrate information from multiple studies, also known as meta-analysis, to improve the power of identifying enriched gene sets.
Results: We propose a Bayesian model that provides a coherent framework for joint modeling of both gene set information and gene expression data from multiple studies, to improve the detection of enriched gene sets by leveraging information from different sources available. One distinct feature of our method is that it directly models the gene expression data, instead of using summary statistics, when synthesizing studies. Besides, the proposed model is flexible and offers an appropriate treatment of between-study heterogeneities that frequently arise in the meta-analysis of microarray experiments. We show that under our Bayesian model, the full posterior conditionals all have known distributions, which greatly facilitates the MCMC computation. Simulation results show that the proposed method can improve the power of gene set enrichment meta-analysis, as opposed to existing methods developed by Shen and Tseng (2010, Bioinformatics, 26, 1316–1323), and it is not sensitive to mild or moderate deviations from the distributional assumption for gene expression data. We illustrate the proposed method through an application of combining eight lung cancer datasets for gene set enrichment analysis, which demonstrates the usefulness of the method.
Availability: http://qbrc.swmed.edu/software/
Contact: Min.Chen@UTSouthwestern.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Prediction of contact matrix for protein–protein interaction
Authors: González Alvaro J. , Liao Li , Wu Cathy H. 
Published: February 2013

Abstract
Motivation: Prediction of protein–protein interaction has become an important part of systems biology in reverse engineering the biological networks for better understanding the molecular biology of the cell. Although significant progress has been made in terms of prediction accuracy, most computational methods only predict whether two proteins interact but not their interacting residues—the information that can be very valuable for understanding the interaction mechanisms and designing modulation of the interaction. In this work, we developed a computational method to predict the interacting residue pairs—contact matrix for interacting protein domains, whose rows and columns correspond to the residues in the two interacting domains respectively and whose values (1 or 0) indicate whether the corresponding residues (do or do not) interact.
Results: Our method is based on supervised learning using support vector machines. For each domain involved in a given domain–domain interaction (DDI), an interaction profile hidden Markov model (ipHMM) is first built for the domain family, and then each residue position for a member domain sequence is represented as a 20-dimension vector of Fisher scores, characterizing how similar it is as compared with the family profile at that position. Each element of the contact matrix for a sequence pair is now represented by a feature vector from concatenating the vectors of the two corresponding residues, and the task is to predict the element value (1 or 0) from the feature vector. A support vector machine is trained for a given DDI, using either a consensus contact matrix or contact matrices for individual sequence pairs, and is tested by leave-one-out cross validation. The performance averaged over a set of 115 DDIs collected from the 3 DID database shows significant improvement (sensitivity up to 85%, and specificity up to 85%), as compared with a multiple sequence alignment-based method (sensitivity 57%, and specificity 78%) previously reported in the literature.
Contact: lliao@cis.udel.edu or wuc@cis.udel.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Protein signature-based estimation of metagenomic abundances including all domains of life and viruses
Authors: Klingenberg Heiner , Aßhauer Kathrin Petra , Lingner Thomas , Meinicke Peter 
Published: February 2013

AbstractMotivation: Metagenome analysis requires tools that can estimate the taxonomic abundances in anonymous sequence data over the whole range of biological entities. Because there is usually no prior knowledge about the data composition, not only all domains of life but also viruses have to be included in taxonomic profiling. Such a full-range approach, however, is difficult to realize owing to the limited coverage of available reference data. In particular, archaea and viruses are generally not well represented by current genome databases.Results: We introduce a novel approach to taxonomic profiling of metagenomes that is based on mixture model analysis of protein signatures. Our results on simulated and real data reveal the difficulties of the existing methods when measuring achaeal or viral abundances and show the overall good profiling performance of the protein-based mixture model. As an application example, we provide a large-scale analysis of data from the Human Microbiome Project. This demonstrates the utility of our method as a first instance profiling tool for a fast estimate of the community structure.Availability: http://gobics.de/TaxyPro.Contact: pmeinic@gwdg.deSupplementary information: Supplementary Material is available at Bioinformatics online.