bluuebunny/crossref_metadata_2025_split huggingface dataset:
Secondhand Smoke is Associated with Hearing Threshold Shifts in Obese Adults
Authors: Lin Yuan-Yung , Wu Li-Wei , Kao Tung-Wei , Wu Chen-Jung , Yang Hui-Fang , Peng Tao-Chun , Lin Yu-Jen , Chen Wei-Liang 
Published: September 2016

AbstractHearing loss resulted from multiple intrinsic and extrinsic factors. Secondhand smoke (SHS) and obesity had been reported to be related to hearing loss. This study explored the possible associations of SHS and obesity with the hearing threshold. The relations between SHS and the hearing threshold in subjects from three different body mass index classes were analyzed. Our study included data from 1,961 subjects aged 20–69 years that were obtained from the National Health and Nutrition Examination Survey for the years 1999–2004. After adjusting for potential confounding factors, the subjects with the higher tertiles of serum cotinine levels tended to have higher hearing thresholds than those with the lowest tertile of serum cotinine levels (for both trends, p < 0.05). Notably, the obese subjects with the higher tertiles of serum cotinine levels had significantly higher hearing thresholds for high frequencies and low frequencies than those with the lowest tertile of serum cotinine levels (for both trends, p < 0.05). Our study showed a significant positive association between SHS exposure and hearing thresholds in the adult population, especially in obese individuals. Based on our findings, avoiding exposure to SHS, especially in obese adults, may decrease the risk of hearing loss.
Impact of clinical context on acute kidney injury biomarker performances: differences between neutrophil gelatinase-associated lipocalin and L-type fatty acid-binding protein
Authors: Asada Toshifumi , Isshiki Rei , Hayase Naoki , Sumida Maki , Inokuchi Ryota , Noiri Eisei , Nangaku Masaomi , Yahagi Naoki , Doi Kent 
Published: September 2016

AbstractApplication of acute kidney injury (AKI) biomarkers with consideration of nonrenal conditions and systemic severity has not been sufficiently determined. Herein, urinary neutrophil gelatinase-associated lipocalin (NGAL), L-type fatty acid-binding protein (L-FABP) and nonrenal disorders, including inflammation, hypoperfusion and liver dysfunction, were evaluated in 249 critically ill patients treated at our intensive care unit. Distinct characteristics of NGAL and L-FABP were revealed using principal component analysis: NGAL showed linear correlations with inflammatory markers (white blood cell count and C-reactive protein), whereas L-FABP showed linear correlations with hypoperfusion and hepatic injury markers (lactate, liver transaminases and bilirubin). We thus developed a new algorithm by combining urinary NGAL and L-FABP with stratification by the Acute Physiology and Chronic Health Evaluation score, presence of sepsis and blood lactate levels to improve their AKI predictive performance, which showed a significantly better area under the receiver operating characteristic curve [AUC-ROC 0.940; 95% confidential interval (CI) 0.793–0.985] than that under NGAL alone (AUC-ROC 0.858, 95% CI 0.741–0.927, P = 0.03) or L-FABP alone (AUC-ROC 0.837, 95% CI 0.697–0.920, P = 0.007) and indicated that nonrenal conditions and systemic severity should be considered for improved AKI prediction by NGAL and L-FABP as biomarkers.
Flux linkage estimation based loss of excitation relay for synchronous generator
Authors: Abedini Moein , Sanaye‐Pasand Majid , Davarpanah Mahdi 
Published: September 2016

Loss of excitation (LOE) event threatens both the generator and power system stability. Numerous approaches have been proposed for LOE detection, most of which use the impedance trajectory. Such methods may maloperate under system disturbances, especially power swings. This study presents a new approach for LOE detection by estimating the field flux linkage participation (FFLP) in the stator flux linkage. Intrinsically, this newly defined index mainly depends on the generator excitation system and thus highly reduces when an LOE takes place. The FFLP parameter can easily be calculated using stator voltage and current signals. All kinds of LOE events cannot be studied using most available simulation software. To cover all of them, utilising state variables, a generator model connected to a power system is implemented. Performed simulation studies demonstrate that the proposed strategy not only considerably decreases the LOE relay operation time, but also improves the LOE relay security against system disturbances. In addition, the proposed approach is experimentally evaluated on a 10 kVA synchronous generator.
BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals
Authors: Kim Minsuk , Sun Gwanggyu , Lee Dong-Yup , Kim Byung-Gee 
Published: September 2016

Abstract

Motivation
Modulation of regulatory circuits governing the metabolic processes is a crucial step for developing microbial cell factories. Despite the prevalence of in silico strain design algorithms, most of them are not capable of predicting required modifications in regulatory networks. Although a few algorithms may predict relevant targets for transcriptional regulator (TR) manipulations, they have limited reliability and applicability due to their high dependency on the availability of integrated metabolic/regulatory models.

Results
We present BeReTa (Beneficial Regulator Targeting), a new algorithm for prioritization of TR manipulation targets, which makes use of unintegrated network models. BeReTa identifies TR manipulation targets by evaluating regulatory strengths of interactions and beneficial effects of reactions, and subsequently assigning beneficial scores for the TRs. We demonstrate that BeReTa can predict both known and novel TR manipulation targets for enhanced production of various chemicals in Escherichia coli. Furthermore, through a case study of antibiotics production in Streptomyces coelicolor, we successfully demonstrate its wide applicability to even less-studied organisms. To the best of our knowledge, BeReTa is the first strain design algorithm exclusively designed for predicting TR manipulation targets.

Availability and Implementation
MATLAB code is available at https://github.com/kms1041/BeReTa (github).

Supplementary information
Supplementary data are available at Bioinformatics online.
DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics
Authors: Wieczorek Samuel , Combes Florence , Lazar Cosmin , Giai Gianetto Quentin , Gatto Laurent , Dorffer Alexia , Hesse Anne-Marie , Couté Yohann , Ferro Myriam , Bruley Christophe , Burger Thomas 
Published: September 2016

Abstract

Summary
DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser.

Availability and implementation
DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages.
stringMLST: a fast k-mer based tool for multilocus sequence typing
Authors: Gupta Anuj , Jordan I King , Rishishwar Lavanya 
Published: September 2016

Abstract
Rapid and accurate identification of the sequence type (ST) of bacterial pathogens is critical for epidemiological surveillance and outbreak control. Cheaper and faster next-generation sequencing (NGS) technologies have taken preference over the traditional method of amplicon sequencing for multilocus sequence typing (MLST). But data generated by NGS platforms necessitate quality control, genome assembly and sequence similarity searching before an isolate’s ST can be determined. These are computationally intensive and time consuming steps, which are not ideally suited for real-time molecular epidemiology. Here, we present stringMLST, an assembly- and alignment-free, lightweight, platform-independent program capable of rapidly typing bacterial isolates directly from raw sequence reads. The program implements a simple hash table data structure to find exact matches between short sequence strings (k-mers) and an MLST allele library. We show that stringMLST is more accurate, and order of magnitude faster, than its contemporary genome-based ST detection tools.

Availability and Implementation
The source code and documentations are available at http://jordan.biology.gatech.edu/page/software/stringMLST.

Supplementary information
Supplementary data are available at Bioinformatics online.
ReliableGenome: annotation of genomic regions with high/low variant calling concordance
Authors: Popitsch Niko ,   WGS500 Consortium, Schuh Anna , Taylor Jenny C 
Published: September 2016

Abstract

Motivation
The increasing adoption of clinical whole-genome resequencing (WGS) demands for highly accurate and reproducible variant calling (VC) methods. The observed discordance between state-of-the-art VC pipelines, however, indicates that the current practice still suffers from non-negligible numbers of false positive and negative SNV and INDEL calls that were shown to be enriched among discordant calls but also in genomic regions with low sequence complexity.

Results
Here, we describe our method ReliableGenome (RG) for partitioning genomes into high and low concordance regions with respect to a set of surveyed VC pipelines. Our method combines call sets derived by multiple pipelines from arbitrary numbers of datasets and interpolates expected concordance for genomic regions without data. By applying RG to 219 deep human WGS datasets, we demonstrate that VC concordance depends predominantly on genomic context rather than the actual sequencing data which manifests in high recurrence of regions that can/cannot be reliably genotyped by a single method. This enables the application of pre-computed regions to other data created with comparable sequencing technology and software. RG outperforms comparable efforts in predicting VC concordance and false positive calls in low-concordance regions which underlines its usefulness for variant filtering, annotation and prioritization. RG allows focusing resource-intensive algorithms (e.g. consensus calling methods) on the smaller, discordant share of the genome (20–30%) which might result in increased overall accuracy at reasonable costs. Our method and analysis of discordant calls may further be useful for development, benchmarking and optimization of VC algorithms and for the relative comparison of call sets between different studies/pipelines.

Availability and Implementation
RG was implemented in Java, source code and binaries are freely available for non-commercial use at https://github.com/popitsch/wtchg-rg/.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Connection Between Thwarted Belongingness, Alcohol Consumption, Suicidal, and Homicidal Ideation in a Criminal Justice Sample
Authors: Waesche Matthew C. , Clark Charles Brendan , Cropsey Karen L. 
Published: September 2016

Background:
To determine if thwarted belongingness in combination with frequent alcohol use increased suicidal and homicidal ideation when known predictors were controlled for (eg, depressive disorders, anxiety disorders, drug use, race, sex, age, and employment status).

Method:
This study utilized an archival database. Participants were 574 individuals at an outpatient substance abuse treatment facility who were under community corrections supervision. The average age was 34.5 (SD = 10.9) years; there were 371 (64.6%) men and 287 (50.0%) Black participants. Data were originally gathered from face-to-face interviews with the participants by their case manager or an intake specialist when they entered treatment. Self-reported suicidal and homicidal ideation was used as a dependent variable in unadjusted and adjusted binary logistic regressions to determine the influence of thwarted belongingness and frequent alcohol use.

Results:
Thwarted belongingness alone (ie, without frequent alcohol use) was associated with risk for suicidal ideation, and was approaching significance for homicidal ideation. The combination of thwarted belongingness and frequent alcohol use was associated with the greatest risk for suicidal and homicidal ideation. Cocaine use and employment status were also identified as significant predictors for suicidal and homicidal ideation in the fully adjusted models.

Conclusions:
Thwarted belongingness in combination with frequent alcohol use seems to have a large and meaningful relationship with both suicidal and homicidal ideation. Additional research is needed to better understand the relationship between alcohol, thwarted belongingness, and outcomes such as suicide and homicide.
Do Transcortical Screws in a Locking Plate Construct Improve the Stiffness in the Fixation of Vancouver B1 Periprosthetic Femur Fractures? A Biomechanical Analysis of 2 Different Plating Constructs
Authors: Lochab Jasjit , Carrothers Andrew , Wong Edwin , McLachlin Stewart , Aldebeyan Wassim , Jenkinson Richard , Whyne Cari , Nousiainen Markku T. 
Published: September 2016

Objectives:
This biomechanical study compared Vancouver B1 periprosthetic femur fractures fixed with either a locking plate and anterior allograft strut construct or an equivalent locking plate with locking attachment plates construct in paired cadaveric specimens.

Methods:
After 9 pairs of cadaveric femora were implanted with a cemented primary total hip arthroplasty, an oblique osteotomy was created distal to the cement mantle. Femora underwent fixation with either: (1) a locking plate with anterior strut allograft (locking compression plating (LCP)-Allograft) or (2) a locking plate with 2 locking attachment plates (LAPs) (LCP-LAP). Construct stiffness was compared in nondestructive mechanical testing for 2 modes of compression (20 degrees abduction and 20 degrees flexion), 2 four-point bending directions (anterior–posterior and medial–lateral), and torsion. A final load to failure test evaluated the axial compression required to achieve fracture gap closure or construct yield. Fixation was compared through paired t tests (α = 0.05).

Results:
The LCP-Allograft construct demonstrated higher stiffness values in compressive abduction (207 ± 57 vs.151 ± 40 N/mm), torsion (1666 ± 445 vs. 1125 ± 160 N mm/degree) and medial–lateral four-point bending (413 ± 135 vs. 167 ± 68 N/mm) compared with the LCP-LAP construct (P < 0.05). No differences were identified between the 2 constructs in compressive flexion, anterior–posterior bending, or the load to failure test (P > 0.05).

Conclusion:
Use of the anterior allograft strut created a stiffer construct compared with the LCP-LAP for the treatment of a Vancouver B1 periprosthetic femur fracture only in loading modes with increased medial–lateral bending. Although these static load results are indicative of the early postoperative environment, further fatigue testing is required to better understand the importance of the reduced medial–lateral stiffness over a longer period.
Identifying biomarkers to select patients with early breast cancer suitable for extended adjuvant endocrine therapy
Authors: Abramovitz Mark , Krie Amy , Dey Nandini , De Pradip , Williams Casey , Leyland-Jones Brian 
Published: September 2016

Purpose of review
In this review, we summarize recent and current biomarkers and assays that are being considered in the selection of suitable patients with estrogen receptor-positive early breast cancer for extended (years 5–10) adjuvant endocrine therapy (AET).

Recent findings
Women with estrogen receptor-positive early-stage breast cancer (65% of cases) continue to have late risk for distant recurrence extending beyond 5 years from surgery. Recent large trials have consistently demonstrated improvement for prolonging endocrine therapy. However, endocrine therapy can cause women bothersome side effects and can negatively impact quality of life. Determining which patients remain at risk for disease recurrence and predicting which of these patients would derive the most benefit from the addition of extended AET are key issues faced by patients and oncologists today. A number of predictive molecular assays have been developed and are being considered as tools to be used in guiding the implementation of adjuvant systemic therapy.

Summary
The future holds much promise and as more information and understanding is acquired, treatment regimens will increasingly incorporate clinically validated biomarker assays in the decision-making process that will be of great benefit to these patients. Proving clinical utility, though, will ultimately decide their implementation.
Treatment of brain metastasis: current status and future directions
Authors: Rudà Roberta , Franchino Federica , Soffietti Riccardo 
Published: September 2016

Purpose of review
The purpose of this review is to highlight the most recent advances in the management of brain metastases.

Recent findings
Role of local therapies (surgery and stereotactic radiosurgery), new approaches to minimize cognitive sequelae following whole-brain radiotherapy and advances in targeted therapies have been reviewed.

Summary
The implications for clinical trials and daily practice of the increasing use of stereotactic radiosurgery in multiple brain metastases and upfront targeted agents in asymptomatic brain metastases are discussed.
Utility of flow cytometry studies in the management of patients with multiple myeloma
Authors: Paiva Bruno , Merino Juana , San Miguel Jesús F. 
Published: September 2016

Purpose of reviewAlthough the input of multiparameter flow cytometry (MFC) into the clinical management of multiple myeloma patients has faced some reluctance, continuously growing evidence supports the utility of MFC in this disease.Recent findingsMFC immunophenotyping of bone marrow and peripheral blood plasma cells affords cost-effective assessment of clonality, and provides prognostic information on the risk of progression in smoldering multiple myeloma, and the identification of active multiple myeloma patients with dismal outcome (e.g., high numbers of circulating tumor cells) or long-term survival despite suboptimal responses through the characterization of monoclonal gammopathy of undetermined significance-like phenotypes. Extensive data indicate that minimal residual disease (MRD) monitoring can be used as biomarker to evaluate treatment efficacy and act as surrogate for survival. The time has come to address within clinical trials the exact role of baseline risk factors and MRD monitoring for tailored therapy in multiple myeloma, which implies systematic usage of highly sensitive cost-effective, readily available, and standardized MRD techniques such as MFC.SummaryNext-generation MFC should be considered mandatory in the routine evaluation of multiple myeloma patients both at diagnosis and after therapy, and represents an attractive technique to integrate with high-throughput DNA and RNA-seq methods to help in understanding the mechanisms behind dissemination and chemoresistance of multiple myeloma.
Shift toward Mechanical Isolation of Adipose-derived Stromal Vascular Fraction: Review of Upcoming Techniques
Authors: Condé-Green Alexandra , Kotamarti Vasanth S. , Sherman Lauren S. , Keith Jonathan D. , Lee Edward S. , Granick Mark S. , Rameshwar Pranela 
Published: September 2016

Background:
Standard isolation of adipose stromal vascular fraction (SVF) requires the use of collagenase and is considered more than “minimally manipulated” by current good manufacturing practice requirements. Alternatively, nonenzymatic isolation methods have surfaced using physical forces to separate cells from the adipose matrix. The purpose of this study was to review the literature on the use of mechanical isolation protocols and compare the results. The implication for use as a standard procedure in practice is discussed.

Methods:
A systematic review of the literature was performed on mechanical isolation of SVF with a search of six terms on PubMed and Medline databases. One thousand sixty-six articles were subject to evaluation by predetermined inclusion and exclusion criteria.

Results:
Two level 2 evidence articles and 7 in vitro studies were selected. SVF was isolated using automated closed systems or by subjecting the lipoaspirate to centrifugation only or by shaking or vortexing followed by centrifugation. Six articles reported isolation in laboratory settings and three inside the operating room. Stromal vascular cells expressed CD34, and CD44, CD73, CD90, and CD105, and differentiated along adipogenic and osteogenic lineages. When compared with enzymatic methods, mechanical isolation required less time but yielded fewer cells. Both case–control studies reported improved volume retention with cell-supplemented fat grafts for breast reconstruction.

Conclusions:
Mechanical isolation methods are alternatives to circumvent safety issues posed by enzymatic protocols. However, randomized comparative studies with long-term clinical outcomes using mechanically isolated stromal vascular cells are needed to identify their ideal clinical applications.
Change in Accommodation and Ocular Aberrations in Keratoconus Patients Fitted With Scleral Lenses
Authors: Yildiz Elvin , Toklu Meltem Tunca , Vural Ece Turan , Yenerel Nursal Melda , Bardak Handan , Kumral Esra Turkseven , Bardak Yavuz 
Published: September 2016

Purpose:
To evaluate the accommodative response to different accommodative stimulus and to determine the changes in ocular higher-order aberrations with accommodation in keratoconus patients fitted with mini scleral lenses.

Material and Methods:
The study included 15 keratoconus patients wearing mini scleral lenses (Misa Scleral Lens—Microlens, Arnhem, the Netherlands) and 15 keratoconus patients wearing rigid gas permeable lenses. Hartmannn Shack aberrometer (IRX-3; Imagine Eyes, Orsay, France) was used for the evaluation of accommodation. Accommodative responses to the accommodative stimulus ranging from 0.5 to 5.0 diopters (D) with intervals of 0.5 D were recorded. Spherical, coma, trefoil aberration, and root mean square (RMS) of total higher-order aberrations (HOAs, third to sixth orders) at baseline, at 2.5 D stimulus, and at 5 D stimulus were also recorded.

Results:
Although accommodative response to accommodative stimulus of 0.5 to 2.5 D (with 0.5 D intervals) was similar in both groups, accommodative response to accommodative stimulus of 3.0 to 5.0 D was significantly lower in keratoconus group wearing mini scleral lenses. The coma, spherical, trefoil aberrations, and the RMS of total HOAs at baseline, at 2.5 D stimulus, and at 5 D stimulus were not significantly different between the groups. However, changes in the coma and trefoil aberrations and RMS of total HOA with 2.5 D and 5.0 D stimulus were significant only in the RGP group.

Conclusions:
Accommodative response to increasing accommodative stimulus was found to be impaired in keratoconus patients wearing mini scleral lenses.