bluuebunny/crossref_metadata_2025_split huggingface dataset:
Apricot Kernel Oil Ameliorates Cyclophosphamide‐Associated Immunosuppression in Rats
Authors: Tian Honglei , Yan Haiyan , Tan Siwei , Zhan Ping , Mao Xiaoying , Wang Peng , Wang Zhouping 
Published: June 2016

AbstractThe effects of dietary apricot kernel oil (AKO), which contains high levels of oleic and linoleic acids and lower levels of α‐tocopherol, were evaluated in a rat model of cyclophosphamide‐induced immunosuppression. Rats had intraperitoneal injection with cyclophosphamide to induce immunosuppression and were then infused with AKO or normal saline (NS) for 4 weeks. Enzyme‐linked immunosorbent assays were used to detect antimicrobial factors in lymphocytes and anti‐inflammatory factors in hepatocytes. Hematoxylin & eosin staining was conducted prior to histopathological analysis of the spleen, liver, and thymus. Significant differences were observed between the immune functions of the healthy control group, the normal saline group, and the AKO group. Compared to the normal saline‐treated group, lymphocytes isolated from rats administered AKO showed significant improvement in immunoglobulin (Ig)A, IgM, IgG, interleukin (IL)‐2, IL‐12, and tumor necrosis factor‐α (TNF‐α) levels (p < 0.01). Liver tissue levels of malondialdehyde and activities of superoxide dismutase and glutathione peroxidase indicated reduced oxidative stress in rats treated with AKO (p < 0.01). Dietary AKO positively affected rat growth and inhibited cyclophosphamide‐associated organ degeneration. These results suggested that AKO may enhance the immune system in vivo. These effects may reflect the activities of intermediate oleic and linoleic acid metabolites, which play a vital role in the immune system, and the α‐tocopherol in AKO may further enhance this phenomenon. Thus, the use of AKO as a nutritional supplement can be proposed to ameliorate chemotherapy‐associated immunosuppression.
Optimization of Enzymatic Process Condition for Protein Enrichment, Sugar Recovery and Digestibility Improvement of Soy Flour
Authors: Loman Abdullah A. , Ju Lu‐Kwang 
Published: June 2016

AbstractSoy protein is a valuable nutritional supplement for food and animal feed. While protein constitutes ~50 % of defatted soy flour (SF), it coexists with complex carbohydrates (30–35 %) which may have anti‐nutritional effects. An enzymatic process can remove the carbohydrate and produce protein‐enriched soy products. The hydrolysate with monomerized carbohydrates is valuable fermentation feedstock. In this study, Aspergillus niger and Trichoderma reesei enzymes were compared for use in the process. Effects of pH (3.2–6.4), temperature (40–60 °C), enzyme‐to‐SF ratio (0–2 ml/g) and SF loading (150–350 g/l) were evaluated for the enzymatic conversion of SF carbohydrate to reducing sugar (YRS) and total soluble carbohydrate (YTC) in the hydrolysate. Effects of these single factors and interactions between factors were investigated. Optimal pH and temperature were similar for both enzymes: pH 4.8 and 50–51 °C for YTC, and pH 5.1–5.2 and 48–51 °C for YRS. The two enzymes also gave similar protein contents in resultant soy protein concentrates, i.e., 74–75 % with 2 ml/g enzyme broth and 150 g/l SF, which were higher than the 64–68 % protein in commercial concentrates. A. niger enzyme was significantly more effective in carbohydrate conversion, achieving YRS = 75 % and YTC = 78 % with 2 ml/g enzyme and 150 g/l SF, higher than the YRS (30 %) and YTC (64 %) obtained with T. reesei enzyme. Monomerization was essentially complete in hydrolysate produced with A. niger enzyme.
Untangling tau imaging
Authors: Villemagne Victor L. , Okamura Nobuyuki , Rowe Christopher C. 
Published: June 2016

AbstractIn vivo imaging of tau deposits is providing a better understanding of the temporal and spatial tau deposition in the brain, allowing a more comprehensive insight into the causes, diagnoses, and potentially treatment of tauopathies such as Alzheimer's disease, progressive supranuclear palsy, corticobasal syndrome, chronic traumatic encephalopathy, and some variants of frontotemporal lobar degeneration. The assessment of tau deposition in the brain over time will allow a deeper understanding of the relationship between tau and other variables such as cognition, genotype, and neurodegeneration, as well as assessing the role tau plays in ageing. Preliminary human studies suggest that tau imaging could also be used as a diagnostic, prognostic, and theranostic biomarker, as well as a surrogate marker for target engagement, patient recruitment, and efficacy monitoring for disease‐specific therapeutic trials.
Results of collagen sling placement following the partial removal of a synthetic midurethral sling
Authors: Hogewoning Cornelis R.C. , Elzevier Henk W. , Pelger Rob C.M. , Hogewoning Cornelis J.A. 
Published: June 2016

AbstractObjectiveTo assess results of placement of the Pelvilace collagen sling following partial removal of a primary synthetic sling because of late complications.MethodsA retrospective study was undertaken of patients with late complications after midurethral sling surgery who underwent placement of a Pelvilace sling at a center in the Netherlands between January 2006 and January 2011. A postoperative questionnaire was used to evaluate the continence status and continence‐related quality of life. Patients scoring 0 in the Urogenital Distress Inventory stress symptoms section were considered cured. The subjective improvement or deterioration in symptoms was scored using the Patient Global Impression of Improvement (PGI‐I).ResultsThe questionnaire was completed and returned by 32 (84%) of 38 patients after a mean follow‐up of 54.3 months. Nine (28%) patients were deemed cured. Among 29 patients who had not undergone a third surgery, the PGI‐I showed a postoperative improvement in 14 (48%). The other 15 patients rated their postoperative situation as little improved, unchanged, or deteriorated. Further subanalysis showed clear differences in postoperative results between the different types of late complications (erosion and/or displacement).ConclusionThe concomitant placement of a collagen sling following partial removal of a primary polypropylene sling shows reasonable results for specific complications.
Falls and Fear of Falling After Stroke: A Case‐Control Study
Authors: Goh Hui‐Ting , Nadarajah Mohanasuntharaam , Hamzah Norhamizan Binti , Varadan Parimalaganthi , Tan Maw Pin 
Published: June 2016

AbstractBackgroundFalls are common after stroke, with potentially serious consequences. Few investigations have included age‐matched control participants to directly compare fall characteristics between older adults with and without stroke. Further, fear of falling, a significant psychological consequence of falls, has only been examined to a limited degree as a risk factor for future falls in a stroke population.ObjectiveTo compare the fall history between older adults with and without a previous stroke and to identify the determinants of falls and fear of falling in older stroke survivors.DesignCase‐control observational study.SettingPrimary teaching hospital.ParticipantsSeventy‐five patients with stroke (mean age ± standard deviation, 66 ± 7 years) and 50 age‐matched control participants with no previous stroke were tested.MethodsFall history, fear of falling, and physical, cognitive, and psychological function were assessed. A χ2 test was performed to compare characteristics between groups, and logistic regression was performed to determine the risk factors for falls and fear of falling.Main Outcome MeasuresFall events in the past 12 months, Fall Efficacy Scale–International, Berg Balance Scale, Functional Ambulation Category, Fatigue Severity Scale, Montreal Cognitive Assessment, and Patient Healthy Questionnaire–9 were measured for all participants. Fugl‐Meyer Motor Assessment was used to quantify severity of stroke motor impairments.ResultsTwenty‐three patients and 13 control participants reported at least one fall in the past 12 months (P = .58). Nine participants with stroke had recurrent falls (≥2 falls) compared with none of the control participants (P < .01). Participants with stroke reported greater concern for falling than did nonstroke control participants (P < .01). Female gender was associated with falls in the nonstroke group, whereas falls in the stroke group were not significantly associated with any measured outcomes. Fear of falling in the stroke group was associated with functional ambulation level and balance. Functional ambulation level alone explained 22% of variance in fear of falling in the stroke group.ConclusionsCompared with persons without a stroke, patients with stroke were significantly more likely to experience recurrent falls and fear of falling. Falls in patients with stroke were not explained by any of the outcome measures used, whereas fear of falling was predicted by functional ambulation level. This study has identified potentially modifiable risk factors with which to devise future prevention strategies for falls in patients with stroke.Level of EvidenceIII
Diversity and divergence of the glioma-infiltrating T-cell receptor repertoire
Authors: Sims Jennifer S. , Grinshpun Boris , Feng Yaping , Ung Timothy H. , Neira Justin A. , Samanamud Jorge L. , Canoll Peter , Shen Yufeng , Sims Peter A. , Bruce Jeffrey N. 
Published: June 2016

SignificanceHigh-throughput sequencing of T-cell receptor (TCR) repertoires provides a high-dimensional biomarker for monitoring the immune system. We applied this approach, measuring the extent to which the TCR repertoires of T-cell populations infiltrating malignant brain tumors diverge from their peripheral blood. Our analytical strategy separates the statistical properties of the repertoire derived from VJ cassette combination usage from the VJ-independent contribution that reflects the antigen-binding component of the receptor. We discovered a TCR signature strongly inversely correlated with the VJ-independent divergence between the peripheral and tissue-infiltrating repertoires of these patients. Importantly, this signature is detectable in peripheral blood and could serve as a means of noninvasively monitoring immune response in patients.
MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data
Authors: Ulyantsev Vladimir I. , Kazakov Sergey V. , Dubinkina Veronika B. , Tyakht Alexander V. , Alexeev Dmitry G. 
Published: June 2016

Abstract
Motivation: High-throughput metagenomic sequencing has revolutionized our view on the structure and metabolic potential of microbial communities. However, analysis of metagenomic composition is often complicated by the high complexity of the community and the lack of related reference genomic sequences. As a start point for comparative metagenomic analysis, the researchers require efficient means for assessing pairwise similarity of the metagenomes (beta-diversity). A number of approaches were used to address this task, however, most of them have inherent disadvantages that limit their scope of applicability. For instance, the reference-based methods poorly perform on metagenomes from previously unstudied niches, while composition-based methods appear to be too abstract for straightforward interpretation and do not allow to identify the differentially abundant features.
Results: We developed MetaFast, an approach that allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. For multiple metagenomes, the resulting representation is used to obtain a pairwise similarity matrix. The dimensional structure of the metagenomic components preserved in our algorithm reflects the inherent subspecies-level diversity of microbiota. The method is computationally efficient and especially promising for an analysis of metagenomes from novel environmental niches.
Availability and Implementation: Source code and binaries are freely available for download at https://github.com/ctlab/metafast. The code is written in Java and is platform independent (tested on Linux and Windows x86_64).
Contact: ulyantsev@rain.ifmo.ru
Supplementary information: Supplementary data are available at Bioinformatics online.
DBSI server: DNA binding site identifier
Authors: Sukumar Shravan , Zhu Xiaolei , Ericksen Spencer S. , Mitchell Julie C. 
Published: June 2016

Abstract
Summary: Protein–nucleic acid interactions are among the most important intermolecular interactions in the regulation of cellular events. Identifying residues involved in these interactions from protein structure alone is an important challenge. Here we introduce the webserver interface to DNA Binding Site Identifier (DBSI), a powerful structure-based SVM model for the prediction and visualization of DNA binding sites on protein structures. DBSI has been shown to be a top-performing model to predict DNA binding sites on the surface of a protein or peptide and shows promise in predicting RNA binding sites.
Availability and Implementation: Server is available at http://dbsi.mitchell-lab.org
Contact: jcmitchell@wisc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling
Authors: Bhattacharya Debswapna , Cao Renzhi , Cheng Jianlin 
Published: June 2016

Abstract
Motivation: Recent experimental studies have suggested that proteins fold via stepwise assembly of structural units named ‘foldons’ through the process of sequential stabilization. Alongside, latest developments on computational side based on probabilistic modeling have shown promising direction to perform de novo protein conformational sampling from continuous space. However, existing computational approaches for de novo protein structure prediction often randomly sample protein conformational space as opposed to experimentally suggested stepwise sampling.
Results: Here, we develop a novel generative, probabilistic model that simultaneously captures local structural preferences of backbone and side chain conformational space of polypeptide chains in a united-residue representation and performs experimentally motivated conditional conformational sampling via stepwise synthesis and assembly of foldon units that minimizes a composite physics and knowledge-based energy function for de novo protein structure prediction. The proposed method, UniCon3D, has been found to (i) sample lower energy conformations with higher accuracy than traditional random sampling in a small benchmark of 6 proteins; (ii) perform comparably with the top five automated methods on 30 difficult target domains from the 11th Critical Assessment of Protein Structure Prediction (CASP) experiment and on 15 difficult target domains from the 10th CASP experiment; and (iii) outperform two state-of-the-art approaches and a baseline counterpart of UniCon3D that performs traditional random sampling for protein modeling aided by predicted residue-residue contacts on 45 targets from the 10th edition of CASP.
Availability and Implementation: Source code, executable versions, manuals and example data of UniCon3D for Linux and OSX are freely available to non-commercial users at http://sysbio.rnet.missouri.edu/UniCon3D/.
Contact: chengji@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Designing robust watermark barcodes for multiplex long-read sequencing
Authors: Ezpeleta Joaquín , Krsticevic Flavia J , Bulacio Pilar , Tapia Elizabeth 
Published: June 2016

Abstract

Motivation
To attain acceptable sample misassignment rates, current approaches to multiplex single-molecule real-time sequencing require upstream quality improvement, which is obtained from multiple passes over the sequenced insert and significantly reduces the effective read length. In order to fully exploit the raw read length on multiplex applications, robust barcodes capable of dealing with the full single-pass error rates are needed.

Results
We present a method for designing sequencing barcodes that can withstand a large number of insertion, deletion and substitution errors and are suitable for use in multiplex single-molecule real-time sequencing. The manuscript focuses on the design of barcodes for full-length single-pass reads, impaired by challenging error rates in the order of 11%. The proposed barcodes can multiplex hundreds or thousands of samples while achieving sample misassignment probabilities as low as 10−7 under the above conditions, and are designed to be compatible with chemical constraints imposed by the sequencing process.

Availability and Implementation
Software tools for constructing watermark barcode sets and demultiplexing barcoded reads, together with example sets of barcodes and synthetic barcoded reads, are freely available at www.cifasis-conicet.gov.ar/ezpeleta/NS-watermark.
Validated Assessment Scales for Décolleté Wrinkling and Pigmentation
Authors: Landau Marina , Geister Thorin L. , Leibou Lior , Blessmann-Gurk Birgit , Görtelmeyer Roman , Frand Jacob , Grice Jenny , Pooth Rainer ,   on behalf of the Validation Assessment Scales Group
Published: June 2016

BACKGROUND
Décolleté aging includes skin dyspigmentation, laxity, and visible wrinkling. The development of globally accepted scales for the assessment of décolleté aging is essential for aesthetic research and patient evaluation.

OBJECTIVE
To develop a set of grading scales for the objective assessment of décolleté aging criteria and establish the reliability and validity of these scales.

MATERIALS AND METHODS
To describe age-related changes to the décolleté, 3 photonumeric grading scales were created and validated: décolleté wrinkles—at rest, décolleté wrinkles—dynamic, and décolleté pigmentation—at rest. Thirteen aesthetic experts rated photographs of the décolleté of 50 women at rest and at dynamic “hand-to-elbow” positions in 2 validation sessions. Responses were analyzed to assess interrater and intrarater reliability.

RESULTS
Interrater and intrarater reliability were both “almost perfect” (≥0.81, intraclass correlation coefficient and weighted kappa) for décolleté wrinkles—dynamic, summary score for décolleté, and estimated age. Reliability was “substantial” (0.61–0.80) for all other décolleté assessments. There was high correlation between all décolleté scales, estimated age, and estimated aesthetic treatment effort.

CONCLUSION
Consistent outcomes between raters and by individual raters at different time points confirm the reliability of the décolleté grading scales, indicating that they will be a valuable tool for use in clinical research and practice.
Effectiveness and Safety of Bivalirudin During Percutaneous Coronary Intervention in Acute Coronary Syndrome in the Real World: CARTAGOMAX Study
Authors: Cascón-Pérez José Domingo , Abellán-Huerta José , Giner-Caro José Antonio , Dau-Villareal Derek Farid , Mármol-Lozano Rosario , Jaulent-Huertas Leticia , Bonilla-Pacheco Yaiza Isabel , Ruiz-Abellón María del Carmen , Picó-Aracil Francisco , Castillo-Moreno Juan Antonio 
Published: June 2016

Abstract:
The CARTAGOMAX study assessed the safety and efficacy of bivalirudin during real-world cardiac intervention. This was a single-center prospective study. Patients with acute coronary syndrome undergoing percutaneous coronary intervention were anticoagulated with bivalirudin alone or unfractionated heparin plus a glycoprotein IIb/IIIa inhibitor. Propensity score matching was performed to control for baseline imbalances and yielded 1168 patients. There was lower incidence of the composite outcome of death from any cause or major bleeding at 30 days (P = 0.005), 6 months (P = 0.005), and 12 months (P = 0.001) of follow-up in the bivalirudin group, compared with the heparin plus glycoprotein inhibitor group. The administration of bivalirudin was associated with lower rate of all-cause mortality at 1 year of follow-up (P = 0.009). The incidence of major bleeding was lower in the bivalirudin group at 1, 6, and 12 months of follow-up (P = 0.002, P = 0.013 and P = 0.017, respectively). The incidence of stroke and reinfarction were similar between groups during follow-up. The rate of stent thrombosis were slightly higher in the bivalirudin group, without reaching statistical significance at 1 and 12 months of follow-up (P = 0.06, P = 0.04, P = 0.07 at 1, 6, and 12 months, respectively). The CARTAGOMAX study found that the use of bivalirudin during percutaneous coronary intervention was associated with lower incidence of the composite outcome of death from any cause or major bleeding during follow-up. The use of bivalirudin was associated with similar rates of stroke, reinfarction, and stent thrombosis compared with heparin plus glycoprotein inhibitor. Bivalirudin proved to be a safe and effective anticoagulant during percutaneous coronary intervention.
Clinical Management of the Breast-Feeding Mother–Infant Dyad in Recovery From Opioid Dependence
Authors: Busch Deborah W. 
Published: June 2016

Abstract
Human milk is one of the most health-promoting and cost-effective nutritional substances known to humankind. Breastmilk provides substantial and remarkable physiological and psychological health benefits. Within the last decade, there has been a resurgence of breast-feeding in the United States and worldwide and an increased awareness of the immense health benefits for mothers, infants, and societies that support it. Each mother–baby dyad is a unique pair, with distinct relationships, biases, barriers, and obstacles. This article aims to address clinical management for the opioid-recovering breast-feeding dyad and to translate current evidenced-based practice findings, recommendations, and resources to best support this unique population. The recovering breast-feeding mother and newborn with opioid dependence deserve special consideration and expert care to foster their recovery and breast-feeding efforts. It is our moral and ethical responsibility as healthcare professionals to enable, foster, and promote breast-feeding among all families, especially those who stand to benefit the greatest. Substance recovery cannot be treated in isolation, nor can breast-feeding efforts; an interdisciplinary professional team effort promises the greatest chances for recovery success. With appropriate evidence-based practice support, training, and intervention by knowledgeable professionals, many women can overcome the biases and obstacles associated with opioid recovery to successfully breast-feed their babies.