bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Six Sigma Approach to Analyze Time-to-Assembly Variance of Surgical Trays in a Sterile Services Department
Authors: Fogliatto Flavio S. , Anzanello Michel J. , Tortorella Guilherme L. , Schneider Daniela S. S. , Pereira Cintia G. R. , Schaan Beatriz D. 
Published: March 2017

Introduction:
We analyze the assembly of surgical trays in a hospital's sterile services department. The department assembles 520 different tray setups. However, tray assembly times are unknown, imposing a challenge to production planners. To respond to demand, workers from other departments are often called, leading to higher operational costs and more frequent quality problems due to workers' poor training and inconsistency.

Methods:
Conducting traditional time-motion studies is infeasible in such a high variety production setting. Thus, we used design of experiments to optimize the data acquisition. Assembly times of 36 trays were sampled using a 2-factor nested factorial design. Through regression analysis, we built a model to estimate completion times of trays not sampled in the experiment.

Results:
A prediction model with 90.8% accuracy was obtained from the experimental data. The model was validated with assembly times from several trays not included in the experiment. Predicted assembly times had an absolute error of 7.83% on average compared with observed assembly times.

Conclusions:
Design of experiments and regression analysis combined were able to optimize time data acquisition using a small sample of trays, resulting in a model that predicted assembly times within an acceptable margin of error.
Round and Oval Window Anatomic Variability: Its Implication for the Vibroplasty Technique
Authors: Mancheño Marta , Aristegui Miguel , Sañudo Jose Ramon 
Published: March 2017

Objective:The objective of this study is to evaluate the anatomical variability of round and oval window regions and its relationship with their closest structures, to determine its implication on the fitting and stabilization of the middle ear implant Vibrant Soundbridge.Methods:Variations of the anatomy of round and oval window regions were assessed in a total of 85 human dissected temporal bones. Afterward, we evaluated the adaptation and subsequent stabilization of the floating mass transducer (FMT) of the Vibrant Soundbridge in 67 cases in round window (RW) and in 22 cases in oval window (OW), and the influence that the variability of the different anatomical features examined had on this stabilization. We also assessed access and surgeon's view of the RW niche through the facial recess approach.Results:Stabilization of the FMT in the RW was achieved in 53 (79%) of the 67 cases; we found that the less favorable anatomical conditions for stabilization were: membrane smaller than 1.5 mm, presence of a high jugular bulb and a narrow or very narrow RW niche. Frequently, two or more of these conditions happened simultaneously. In seven cases (22%) access to the RW through facial recess approach did not allow positioning the FMT in place. OW stabilization succeeded in 18 (82%) of the 22 cases.Conclusion:Round and oval window vibroplasty are difficult surgical techniques. To place the FMT directly on the OW may be easier as we do not have to drill the niche. In both regions there are some anatomical conditions that hinder fitting the FMT and even make it impossible. Once fitted, the main problem is to achieve good stabilization of the device.
Comparison of Experts and Residents Performing a Complex Procedure in a Temporal Bone Surgery Simulator
Authors: Ioannou Ioanna , Zhou Yun , Wijewickrema Sudanthi , Piromchai Patorn , Copson Bridget , Kennedy Gregor , O’Leary Stephen 
Published: March 2017

Objective:
To investigate the use of automated metrics from a virtual reality (VR) temporal bone surgery simulator to determine how the performance of experts and trainees differs when performing a complex otological procedure (mastoidectomy with posterior tympanotomy and cochleostomy).

Study Design:
Cohort study.

Methods:
Using the University of Melbourne VR temporal bone surgery simulator, seven ENT consultants and seven ENT residents performed two trials of the surgical approach to cochlear implantation on a virtual temporal bone. Simulator recordings were used to calculate a range of automated metrics for each stage of the procedure, capturing efficiency, technique characteristics, drilled bone regions, and damage to vital anatomical structures.

Results:
Results confirm that experts drilled more efficiently than residents. Experts generally used larger burrs and applied higher forces, resulting in faster material removal. However, they exercised more caution when drilling close to anatomical structures. Residents opened the temporal bone more widely, but neglected important steps in obtaining a clear view toward the round window, such as thinning the external ear canal wall and skeletonizing the medial aspect of the facial nerve. Residents used higher magnification and reoriented the temporal bone more often than experts.

Conclusion:
VR simulation provides metrics that allow the objective analysis of surgical technique, and identification of differences between the performance of surgical residents and their senior colleagues. The performance of residents could be improved with more guidance regarding how much force they should apply, what burr size they should use, how they should orient the bone, and for cochlear implant surgery guidance regarding anatomical regions requiring particular attention, to visualize the round window.
Clinical efficacy and tolerability of direct-acting antivirals in elderly patients with chronic hepatitis C
Authors: Sherigar Jagannath M. , Gayam Vijay , Khan Arifa , Mukhtar Osama , Arefiev Yavgeniy , Khalid Mazin , Siddiqui Imran , Rangaraju Ayyappa M. , Budhathoki Nibash , Mansour Mohammed , Guss Debra , Mohanty Smruti R. 
Published: March 2017

Background
There is a lack of evidence-based data on aged patients with newer direct-acting antivirals (DAAs) and with shorter duration of treatment regimens involving DAAs with or without ribavirin (RBV) and pegylated interferon (Peg IFN).

Patients and methods
Medical records of 240 patients treated with DAAs with or without Peg IFN and RBV between January 2013 and July 2015 were retrospectively analyzed. Patients were divided into two groups: patients aged 65 years and older (N=84) and patients aged younger than 65 years (N=156). Pretreatment baseline patient characteristics, treatment efficacy, factors affecting sustained virologic response at 12 weeks after treatment, and adverse reactions were compared between the groups.

Results
No statistically significant difference was observed with end of treatment response (98.8 vs. 98%, P=0.667) and sustained virologic response at 12 weeks after treatment (93.1 vs. 94.1%, P=0.767) between patients aged 65 and older and those younger than 65 years of age. Fatigue was the most common adverse event recorded (32.5%), followed by anemia (19.6%), leukopenia (11.7%), thrombocytopenia (10%), skin rash (8.3%), and headache (7.9%). The RBV dose was reduced in eight (8%) patients and four patients discontinued the RBV treatment because of severe anemia. RBV dose reduction or discontinuation did not reach statistical significance (P=0.913). Increased fibrosis, cirrhosis, aspartate aminotransferase, alanine aminotransferase, hemoglobin, and platelet levels seem to affect the sustained virologic response in the elderly. Twelve (6.28%) patients failed to respond to treatment and the failure rate was not significant (P=0.767) between the groups.

Conclusion
DAAs with or without IFN and RBV in the standard recommended 12 or 24-week treatment regimens are effective, well tolerated, and may be safely extended to elderly patients infected with chronic hepatitis C.
Predictors of Impaired HDL Function in HIV-1 Infected Compared to Uninfected Individuals
Authors: Kelesidis Theodoros , Oda Michael N. , Borja Mark S. , Yee Yumin , Ng Kit F. , Huynh Diana , Elashoff David , Currier Judith S. 
Published: March 2017

Objective:High-density lipoprotein (HDL) function rather than absolute level may be a more accurate indicator for cardiovascular disease (CVD). Novel methods can measure HDL function using patient samples. The objective of this study is to identify factors that may contribute to HDL dysfunction in chronic treated HIV-1 infection.Design:Retrospective study of HDL function measured in 2 ways in HIV-1–infected men with low overall CVD risk and healthy men with no known CVD risk matched by race to the HIV-1–infected participants.Methods:We examined patient-level factors associated with 2 different measures of HDL dysfunction: reduced antioxidant function (oxidized HDL, HDLox) and reduced HDL-apoA-I exchange (HAE), a measure of HDL remodeling, in the HIV infected and control men. Multivariable-adjusted linear regression analyses were used adjusting for false discovery rate, age, race, body mass index (BMI), CD4 count, viremia, CVD risk, smoking, lipids, apoA-I, and albumin.Results:In multivariate analysis among HIV-1–infected men (n = 166) (median age 45 years, CD4 T-cell count 505 cells/mm3, 30.1% were viremic), higher BMI, lower apoA-I, and lower albumin were among the most notable correlates of higher HDLox and lower HAE (P< 0.05). In HIV-1 uninfected participants, lower albumin and higher BMI were associated with lower HAE and higher HDLox, respectively (P≤ 0.05). HDLox was inversely related to HAE in HIV-1–infected individuals (P< 0.001).Conclusions:Increased HDLox correlates with reduced HAE in chronic HIV-1 infection. Higher BMI, lower apoA-I, and albumin were identified as factors associated with HDL dysfunction in chronic HIV-1 infection using 2 independent methods.
Environmental perturbations lead to extensive directional shifts in RNA processing
Authors: Richards A. L. , Watza D. , Findley A. , Alazizi A. , Wen X. , Pai A. A. , Pique-Regi R. , Luca F. 
Published: March 2017

AbstractEnvironmental perturbations have large effects on both organismal and cellular traits, including gene expression, but the extent to which the environment affects RNA processing remains largely uncharacterized. Recent studies have identified a large number of genetic variants associated with variation in RNA processing that also have an important role in complex traits; yet we do not know in which contexts the different underlying isoforms are used. Here, we comprehensively characterized changes in RNA processing events across 89 environments in five human cell types and identified 15,300 event shifts (FDR = 15%) comprised of eight event types in over 4,000 genes. Many of these changes occur consistently in the same direction across conditions, indicative of global regulation by trans factors. Accordingly, we demonstrate that environmental modulation of splicing factor binding predicts shifts in intron retention, and that binding of transcription factors predicts shifts in AFE usage in response to specific treatments. We validated the mechanism hypothesized for AFE in two independent datasets. Using ATAC-seq, we found altered binding of 64 factors in response to selenium at sites of AFE shift, including ELF2 and other factors in the ETS family. We also performed AFE QTL mapping in 373 individuals and found an enrichment for SNPs predicted to disrupt binding of the ELF2 factor. Together, these results demonstrate that RNA processing is dramatically changed in response to environmental perturbations through specific mechanisms regulated by trans factors.Author SummaryChanges in a cell’s environment and genetic variation have been shown to impact gene expression. Here, we demonstrate that environmental perturbations also lead to extensive changes in alternative RNA processing across a large number of cellular environments that we investigated. These changes often occur in a non-random manner. For example, many treatments lead to increased intron retention and usage of the downstream first exon. We also show that the changes to first exon usage are likely dependent on changes in transcription factor binding. We provide support for this hypothesis by considering how first exon usage is affected by disruption of binding due to treatment with selenium. We further validate the role of a specific factor by considering the effect of genetic variation in its binding sites on first exon usage. These results help to shed light on the vast number of changes that occur in response to environmental stimuli and will likely aid in understanding the impact of compounds to which we are daily exposed.
Towards water-free biobanks: long-term dry-preservation at room temperature of desiccation-sensitive enzyme luciferase in air-dried insect cells
Authors: Kikuta Shingo , Watanabe Shunsuke J. , Sato Ryoichi , Gusev Oleg , Nesmelov Alexander , Sogame Yoichiro , Cornette Richard , Kikawada Takahiro 
Published: March 2017

AbstractDesiccation-tolerant cultured cells Pv11 derived from the anhydrobioticPolypedilum vanderplankiembryo endure complete desiccation because of their ametabolic state and resume their metabolism after rehydration. These features led us to develop a novel dry preservation technology for enzymes as it was still unclear whether Pv11 cells preserved an exogenous enzyme in the dry state. This study shows that Pv11 cells protect an exogenous desiccation-sensitive enzyme, luciferase, preserving the enzymatic activity even after dry storage for 372 days at room temperature. A process including pre-incubation with trehalose, dehydration, storage, and rehydration allowed Pv11 (Pvll-Luc) cells stably expressing luciferase to survive desiccation and still emit luminescence caused by luciferase after rehydration. Luminescence produced by luciferase in Pvll-Luc cells after rehydration did not significantly decrease in presence of a translation inhibitor, showing that the activity did not derive fromde novoenzyme synthesis following the resumption of cell metabolism. These findings indicate that the surviving Pv11 cells almost completely protect luciferase during desiccation. Lacking of the preincubation step resulted in the loss of luciferase activity after rehydration. We showed that preincubation with trehalose associated to induction of desiccation-tolerant related genes in Pv11 cells allowed effectivein vivopreservation of enzymes in the dry state.
Trichoderma reeseicomplete genome sequence, repeat-induced point mutation and partitioning of CAZyme gene clusters
Authors: Li Wan-Chen , Huang Chien-Hao , Chen Chia-Ling , Chuang Yu-Chien , Tung Shu-Yun , Wang Ting-Fang 
Published: March 2017

AbstractTrichoderma reesei(Ascomycota, Pezizomycotina) QM6a is a model fungus for a broad spectrum of physiological phenomena, including plant cell wall degradation, industrial production of enzymes, light responses, conidiation, sexual development, polyketide biosynthesis and plant-fungal interactions. The genomes of QM6a and its high-enzyme producing mutants have been sequenced by second-generation-sequencing methods and are publicly available from the Joint Genome Institute (JGI). While these genome sequences have offered useful information for genomic and transcriptomic studies, their limitations and especially their short read lengths make them poorly suited for some particular biological problems, including assembly, genome-wide determination of chromosome architecture and genetic modification or engineering. We integrated Pacific Biosciences and Illumina sequencing platforms for the highest-quality genome assembly yet achieved, revealing seven telomere-to-telomere chromosomes (34,922,528 bp; 10877 genes) with 1630 newly-predicted genes and >1.5 Mb of new sequences. Most new sequences are located on AT-rich blocks, including 7 centromeres, 14 subtelomeres and 2329 interspersed AT-rich blocks. The seven QM6a centromeres separately consist of 24 conserved repeats and 37 putative centromere-encoded genes. These findings open up a new perspective for future centromere and chromosome architecture studies. Next, we demonstrate that sexual crossing readily induced cytosine-to-thymine point mutations on both tandem and unlinked duplicated sequences. We also show by bioinformatic analysis thatTrichoderma reeseihas evolved a robust repeat-induced point mutation (RIP) system to accumulate AT-rich sequences, with longer AT-rich blocks having more RIP mutations. The widespread distribution of AT-rich blocks correlates genome-wide partitions with gene clusters, explaining why clustering of genes has been reported to not influence gene expression inTrichoderma reesei. Compartmentation of ancestral gene clusters by AT-rich blocks might promote flexibilities that are evolutionarily advantageous in this fungus’ soil habitats and other natural environments. Our analyses, together with the complete genome sequence, provide a better blueprint for biotechnological and industrial applications.
Detection of cooperatively bound transcription factor pairs using ChIP-seq peak intensities and expectation maximization
Authors: Datta Vishaka , Siddharthan Rahul , Krishna Sandeep 
Published: March 2017

AbstractTranscription factors (TFs) often work cooperatively, where the binding of one TF to DNA enhances the binding affinity of a second TF to a nearby location. Such cooperative binding is important for activating gene expression from promoters and enhancers in both prokaryotic and eukaryotic cells. Existing methods to detect cooperative binding of a TF pair rely on analyzing the sequence that is bound. We propose a method that uses, instead, only ChIP-seq peak intensities and an expectation maximization (CPI-EM) algorithm. We validate our method using ChIP-seq data from cells where one of a pair of TFs under consideration has been genetically knocked out. Our algorithm relies on our observation that cooperative TF-TF binding is correlated with weak binding of one of the TFs, which we demonstrate in a variety of cell types, includingE. coli, S. cerevisiaeandM. musculuscells. We show that this method performs significantly better than a predictor based only on the ChIP-seq peak distance of the TFs under consideration. This suggests that peak intensities contain information that can help detect the cooperative binding of a TF pair. CPI-EM also outperforms an existing sequence-based algorithm in detecting cooperative binding. The CPI-EM algorithm is available athttps://github.com/vishakad/cpi-em.
Contribution oftransregulatory eQTL to cryptic genetic variation inC. elegans
Authors: Snoek L. Basten , Sterken Mark G. , Bevers Roel P. J. , Volkers Rita J. M. , van’t Hof Arjen , Brenchley Rachel , Riksen Joost A. G. , Cossins Andrew , Kammenga Jan E. 
Published: March 2017

AbstractBackgroundCryptic genetic variation (CGV) is the hidden genetic variation that can be unlocked by perturbing normal conditions. CGV can drive the emergence of novel complex phenotypes through changes in gene expression. Although our theoretical understanding of CGV has thoroughly increased over the past decade, insight into polymorphic gene expression regulation underlying CGV is scarce. Here we investigated the transcriptional architecture of CGV in response to rapid temperature changes in the nematodeCaenorhabditis elegans. We analyzed regulatory variation in gene expression (and mapped eQTL) across the course of a heat stress and recovery response in a recombinant inbred population.ResultsWe measured gene expression over three temperature treatments: i) control, ii) heat stress, and iii) recovery from heat stress. Compared to control, exposure to heat stress affected the transcription of 3305 genes, whereas 942 were affected in recovering animals. These affected genes were mainly involved in metabolism and reproduction. The gene expression pattern in recovering animals resembled both the control and the heat-stress treatment. We mapped eQTL using the genetic variation of the recombinant inbred population and detected 2626 genes with an eQTL in the heat-stress treatment, 1797 in the control, and 1880 in the recovery. Thecis-eQTL were highly shared across treatments. A considerable fraction of thetrans-eQTL (40-57%) mapped to 19 treatment specifictrans-bands. In contrast tocis-eQTL,trans-eQTL were highly environment specific and thus cryptic. Approximately 67% of thetrans-eQTL were only induced in a single treatment, with heat-stress showing the most uniquetrans-eQTL.ConclusionsThese results illustrate the highly dynamic pattern of CGV across three different environmental conditions that can be evoked by a stress response over a relatively short time-span (2 hours) and that CGV is mainly determined by response relatedtransregulatory eQTL.
Assembling metagenomes, one community at a time
Authors: van der Walt Andries J. , Van Goethem Marc W. , Ramond Jean-Baptiste , Makhalanyane Thulani P. , Reva Oleg , Cowan Don A. 
Published: March 2017

AbstractBackgroundMetagenomics allows unprecedented access to uncultured environmental microorganisms. The analysis of metagenomic sequences facilitates gene prediction and annotation, and enables the assembly of draft genomes, including uncultured members of a community. However, while several platforms have been developed for this critical step, there is currently no clear framework for the assembly of metagenomic sequence data.ResultsTo assist with selection of an appropriate metagenome assembler we evaluated the capabilities of nine prominent assembly tools on nine publicly-available environmental metagenomes, as well as three simulated datasets. Overall, we found that SPAdes provided the largest contigs and highestN50values across 6 of the 9 environmental datasets, followed by MEGAHIT and metaSPAdes. MEGAHIT emerged as a computationally inexpensive alternative to SPAdes, assembling the most complex dataset using less than 500 GB of RAM and within 10 hours.ConclusionsWe found that assembler choice ultimately depends on the scientific question, the available resources and the bioinformatic competence of the researcher. We provide a concise workflow for the selection of the best assembly tool.
Network analysis of patient flow in two UK acute care hospitals identifies key sub-networks for A&E performance
Authors: Bean Daniel M. , Stringer Clive , Beeknoo Neeraj , Teo James , Dobson Richard J. B. 
Published: March 2017

AbstractThe topology of the patient flow network in a hospital is complex, comprising hundreds of overlapping patient journeys, and is a determinant of operational efficiency. To understand the network architecture of patient flow, we performed a data-driven network analysis of patient flow through two acute hospital sites of King’s College Hospital NHS Foundation Trust. Administration databases were queried for all intra-hospital patient transfers in an 18- month period and modelled as a dynamic weighted directed graph. A ‘core’ subnetwork containing only 13-17% of all edges channelled 83-90% of the patient flow, while an ‘ephemeral’ network constituted the remainder. Unsupervised cluster analysis and differential network analysis identified sub-networks where traffic is most associated with A&E performance the following day. Increased flow to clinical decision units was associated with the best A&E performance in both sites. The component analysis also detected a weekend effect on patient transfers which was not associated with performance. We have performed the first data-driven hypothesis-free analysis of patient flow which can enhance understanding of whole healthcare systems. Such analysis can drive transformation in healthcare as it has in industries such as manufacturing.
JfxNgs: A BAM/VCF viewer with javascript-based filtering/reformatting functionalities
Authors: Lindenbaum Pierre , Karakachoff Matilde , Redon Richard 
Published: March 2017

AbstractMotivationVisualizing BAM and VCF files is a common task for biologists, but they’re missing a way to filter and to explore the details of each short-read or variation.ResultsIn that context, we wrote an interactive java-based interface namedJfxNgsthat uses javascript snippets to filter and reformat BAM and VCF files.Availabilityhttps://github.com/lindenb/jvarkit/blob/master/docs/JfxNgs.mdContactpierre.lindenbaum@univ-nantes.fr.