bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Perioperative Pain and Recovery in Women Undergoing Vaginal Reconstruction Versus Robotic Sacrocolpopexy
Authors: Westermann Lauren B. , Crisp Catrina C. , Mazloomdoost Donna , Kleeman Steven D. , Pauls Rachel N. 
Published: January 2017

Background
In this study of patients undergoing vaginal hysterectomy with either robotic or vaginal prolapse repair, there was no difference in quality of life in the weeks following surgery; however, less narcotics were used, less pain was documented by nurses and Surgical Pain Scale (SPS), and better performance on voiding trials was noted in those undergoing robotic sacrocolpopexy.

Objectives
Minimally invasive surgery for pelvic organ prolapse is the preferred surgical route for optimal recovery. However, information regarding patient-centered outcomes among various techniques is lacking. We sought to describe pain and quality of life in patients undergoing vaginal hysterectomy with uterosacral ligament suspension (USLS) compared with robotic-assisted sacrocolpopexy (RSC).

Methods
This institutional review board–approved prospective cohort study enrolled consecutive patients undergoing vaginal hysterectomy with USLS or with RSC. The primary outcome was pain on postoperative day 1 using the SPS. Nursing verbal pain scores, narcotic usage, surgical data, and Short-Form Health Survey 12 at baseline and 2 and 6 weeks after surgery were collected. A sample size calculation revealed 37 subjects per group would be required.

Results
Seventy-eight women were enrolled (USLS, n = 39; RSC, n = 39). There were no significant differences in scores on the SPS between groups. Subjects undergoing RSC had lower nursing verbal pain scores (P = 0.04), less narcotic consumption (P = 0.02), and lower estimated blood loss (P = 0.01) and were less likely to fail voiding trials (P < 0.001); however, surgery duration was longer (P < 0.001). After controlling for age, regression analysis revealed SPS “worst pain” was lower in the robotic arm (P = 0.01), but not in other scales of the SPS. At 2 and 6 weeks postoperatively, Short-Form Health Survey 12 scores were not different between cohorts.

Conclusions
Both USLS and RSC are minimally invasive, with similar quality-of-life scores after surgery. However, the robotic approach may be associated with less pain, less narcotic use, and better performance in voiding trials. Surgeons should consider these findings when counseling patients regarding treatment options.
Readmission and Reoperation After Surgery for Pelvic Organ Prolapse
Authors: Hokenstad Erik D. , Glasgow Amy E. , Habermann Elizabeth B. , Occhino John A. 
Published: January 2017

Objectives
We aimed to determine the rates of readmission and reoperation for patients undergoing surgery for pelvic organ prolapse (POP).

Methods
The American College of Surgeons National Surgical Quality Improvement Program Participant User File was used to select all surgeries performed for POP from 2012 through 2014. The cohort was then reviewed for unplanned readmissions and unplanned reoperations within 30 days of POP surgery. Patient and procedural factors associated with readmission or reoperation were compared using χ2 analyses and Student t test. Multivariable logistic regression determined independent risk factors for both readmission and reoperation.

Results
A total of 23,419 patients underwent surgery for POP. Of these, there were 435 (1.9%) readmissions and 341 (1.5%) reoperations within 30 days. Median numbers of days from index procedure to readmission or reoperation were 9 and 8 days, respectively. Those who were readmitted had higher American Society of Anesthesia (ASA) scores, longer operative times, and longer lengths of stay than those who were not readmitted (all P < 0.001). Patients who underwent unplanned reoperation also had higher ASA scores, longer operative times, and longer lengths of stay than those who did not undergo reoperation (all P < 0.01). The most common reasons for readmission were surgical site infection (SSI) (19.3%) and non-SSI (15.9%). The most common reason for reoperation was urologic (27.6%) such as cystoscopy or stent placement.

Conclusions
Readmission and reoperation rates are relatively low for patients undergoing surgery for POP. Infection, both SSI and non-SSI, accounted for 35.2% of readmissions. Identification of ASA score of 3 or higher, longer total operating time, and increased length of stay is associated with unplanned readmission and reoperation.
Levator Ani Muscle Defects in Patients With Surgical Failure
Authors: Wyman Allison M. , Greene Kristie A. , Bassaly Renee , Hahn Lindsey , Patton Simon , Miladinovic Branko , Hoyte Lennox 
Published: January 2017

Introduction
The objective of the study was to use a well-described system of measuring levator ani (LA) muscle defects from magnetic resonance images to evaluate whether major defects are correlated to an increased risk of surgical failure.

Methods
A retrospective cohort study performed on patients who underwent laparoscopic uterosacral ligament suspension from 2010 to 2012. Surgical failure was defined as a composite score of anatomic bulge beyond the hymen with sensation of bulge or repeat treatment of prolapse via pessary or surgery by 1-year follow-up. Levator ani muscle defects were graded by a score of 0 (no defect), 1 (<50% muscle bulk missing), 2 (>50% muscle bulk missing), or 3 (complete loss of muscle). Total score is the sum from both graded sides, with 0 classified as having no defect, 1 to 3 classified as having minor defects, and 4 to 6 classified as having major defects. Dichotomous values of LA major defects were compared against dichotomous values of surgical outcomes via a contingency table. Fisher exact test was then performed to correlate major defects to surgical success/failure. P value of less than 0.05 was considered statistically significant.

Results
Sixty-six women met the inclusion criteria. Thirteen (19.6%) patients met the criteria for surgical failure at 1 year. Of the 13, 54% (7) had a major defect, and 46% (6) had a minor or no defect (odds ratio, 1.31; 95% confidence interval, 0.39–4.41; P = 0.762).

Conclusions
We did not find a statistical correlation to surgical failure after a laparoscopic uterosacral ligament suspension with LA muscle defects on preoperative magnetic resonance images within this specific patient population.
Euthecosomata (Mollusca, Gastropoda, Thecosomata). Taxonomic review
Authors: Rampal Jeannine 
Published: January 2017

ABSTRACTThe Euthecosomata Meisenheimer, 1905, holoplanktonic Mollusca with coiled or straight shell were respectively classified in Limacinoidea Gray, 1847 and Cavolinioidea Gray, 1850. In a biometrical analysis (Rampal 1973) a first change had occurd in this last superfamily: the conica shell generaCreseisRang, 1828,BoasiaDall, 1889,StyliolaGray, 1850 andHyalocylisFol, 1875 were gathered into the Creseidae Rampal, 1973. Therefore it was necessary to carry on this study using molecular data. Our recent cladistic and molecular analyses as well as palaeontologic data led to a systematic and phylogenetic revision of the Euthecosomata: the Limacinoidea and of the Creseidae are not monophyletic, the other straight shells Euthecosomata are monophyletic (Corseet al.2013).The Limacinoidea are invalidated; they are split into three families: Limacinidae Gray, 1847, Heliconoididae n. fam. and Thieleidae n. fam. The Creseidae Rampal, 1973 are validated but at least there are two generaCreseisRang, 1828 andBoasiaDall, 1889;StyliolaandHyalocylisare consideredincertae sedis.In the Cavoliniidae Gray, 1850 there are four subfamily: Cuvierininae Gray, 1850, Cliinae Jeffreys, 1869, Diacriinae n. subfam., Cavoliniinae Gray, 1850. The Creseidae Rampal, 1973 and the Cavoliniidae Gray, 1850 belong to the Cavolinioidea Gray, 1850. The species rank of most taxa is confirmed. New genera are proposed or reinstated:Telodiacrian. gen.,Hyalaeade Blainville, 1821,BoasiaDall, 1889. The fossilVaginellaDaudin, 1800 is included within the Cuvierininae Gray, 1847. The spiral fossilAltaspiratellaKorobkov, 1966 is no longer considered part of the Limacinidae Gray, 1847.Two phylogenetic hypotheses are analysed. According to molecular analyses in COI there is the double emergency of straight shell from two coiled shell lineages; in 28S there is monophyly; this last hypothesis we have kapt is the most parsimonious but requires some reserve and new investigations (Corseet al.2013).
Active diffusion and advection in theDrosophilaooplasm result from the interplay of the actin and microtubule cytoskeletons
Authors: Drechsler Maik , Giavazzi Fabio , Cerbino Roberto , Palacios Isabel M. 
Published: January 2017

ABSTRACTTransport in cells occurs via a delicate interplay of passive and active processes, including diffusion, directed transport and advection. Despite progresses in super-resolution microscopy, discriminating and quantifying these processes is a challenge, requiring tracking of rapidly moving, sub-diffraction objects in a crowded, noisy environment. Here we use Differential Dynamic Microscopy with different contrast mechanisms to provide a thorough characterization of the dynamics in theDrosophilaoocyte. We study the movement of vesicles and the elusive motion of a cytoplasmic F-actin mesh, a known regulator of cytoplasmic flows. We find that cytoplasmic motility constitutes a combination of directed motion and random diffusion. While advection is mainly attributed to microtubules, we find that active diffusion is driven by the actin cytoskeleton, although it is also enhanced by the flow. We also find that an important dynamic link exists between vesicles and cytoplasmic F-actin motion, as recently suggested in mouse oocytes.
Dual RNA sequencing (dRNA-Seq) of bacteria and their host cells
Authors: Marsh James W. , Hayward Regan , Shetty Amol , Mahurkar Anup , Humphrys Michael S. , Myers Garry S. A. 
Published: January 2017

AbstractBacterial pathogens subvert host cells by manipulating cellular pathways for survival and replication; in turn, host cells respond to the invading pathogen through cascading changes in gene expression. Deciphering these complex temporal and spatial dynamics to identify novel bacterial virulence factors or host response pathways is crucial for improved diagnostics and therapeutics. Dual RNA sequencing (dRNA-Seq) has recently been developed to simultaneously capture host and bacterial transcriptomes from an infected cell. This approach builds on the high sensitivity and resolution of RNA-Seq technology and is applicable to any bacteria that interact with eukaryotic cells, encompassing parasitic, commensal or mutualistic lifestyles. We pioneered dRNA-Seq to simultaneously capture prokaryotic and eukaryotic expression profiles of cells infected with bacteria, usingin vitro Chlamydia-infected epithelial cells as proof of principle. Here we provide a detailed laboratory and bioinformatics protocol for dRNA-seq that is readily adaptable to any host-bacteria system of interest.
Myosin II activity is not required forDrosophilatracheal branching morphogenesis
Authors: Ochoa-Espinosa Amanda , Harmansa Stefan , Caussinus Emmanuel , Affolter Markus 
Published: January 2017

AbstractTheDrosophilatracheal system consists of an interconnected network of monolayered epithelial tubes that ensures oxygen transport in the larval and adult body. During tracheal dorsal branch (DB) development, individual DBs elongate as a cluster of cells, led by tip cells at the front and trailing cells in the rear. Branch elongation is accompanied by extensive cell intercalation and cell lengthening of the trailing stalk cells. While cell intercalation is governed by Myosin II (MyoII)-dependent forces during tissue elongation in theDrosophilaembryo leading to germ-band extension, it remained unclear whether MyoII plays a similar active role during tracheal branch elongation and intercalation. Here, we use a nanobody-based approach to selectively knock-down MyoII in tracheal cells. Our data shows that despite the depletion of MyoII function, tip cells migration and stalk cell intercalation (SCI) proceeds at a normal rate. Therefore, our data confirms a model in which DB elongation and SCI in the trachea occurs as a consequence of tip cell migration, which produces the necessary forces for the branching process.Summary statementBranch elongation duringDrosophilatracheal development mechanistically resembles MyoII-independent collective cell migration; tensile forces resulting from tip cell migration are reduced by cell elongation and passive stalk cell intercalation.AbbreviationsDBDorsal branchDCDorsal closureE-CadE-CadherinGBEGerm-band extensionMRLCMyosin regulatory light chainMyoIIMyosin IISCIstalk cell intercalationSqhSpaghetti squashSxllSex lethalTCTip cellTrTracheomere
Building containerized workflows using the BioDepot-workflow-builder (Bwb)
Authors: Hung Ling-Hong , Hu Jiaming , Meiss Trevor , Ingersoll Alyssa , Lloyd Wes , Kristiyanto Daniel , Xiong Yuguang , Sobie Eric , Yeung Ka Yee 
Published: January 2017

AbstractWe present the BioDepot-workflow-builder (Bwb), a software tool that allows users to create and execute reproducible bioinformatics workflows using a drag-and-drop interface. Graphical widgets represent Docker containers executing a modular task. Widgets are then graphically linked to build bioinformatics workflows that can be reproducibly deployed across different local and cloud platforms. Each widget contains a form-based user interface to facilitate parameter entry and a console to display intermediate results. Bwb provides tools for rapid customization of widgets, containers and workflows. Saved workflows can be shared using Bwb’s native format or exported as shell scripts.
Software solutions for reproducible RNA-seq workflows
Authors: Meiss Trevor , Hung Ling-Hong , Xiong Yuguang , Sobie Eric , Yeung Ka Yee 
Published: January 2017

AbstractComputational workflows typically consist of many tools that are usually distributed as compiled binaries or source code. Each of these software tools typically depends on other installed software, and performance could potentially vary due to versions, updates, and operating systems. We show here that the analysis of mRNA-seq data can depend on the computing environment, and we demonstrate that software containers represent practical solutions that ensure the reproducibility of RNAseq data analyses.
MmpL3 is the flippase for mycolic acids in mycobacteria
Authors: Xu Zhujun , Meshcheryakov Vladimir A , Poce Giovanna , Chng Shu-Sin 
Published: January 2017

AbstractThe defining feature of the mycobacterial outer membrane (OM) is the presence of mycolic acids (MAs), which in part render the bilayer extremely hydrophobic and impermeable to external insults, including many antibiotics. While the biosynthetic pathway of MAs is well studied, the mechanism(s) by which these lipids are transported across the cell envelope is(are) much less known. MmpL3, an essential inner membrane (IM) protein, is implicated in MA transport, but its exact function has not been elucidated. It is believed to be the cellular target of several anti-mycobacterial compounds; however, evidence for direct inhibition of MmpL3 activity is also lacking. Here, we establish that MmpL3 is the MA flippase at the IM of mycobacteria, and is the molecular target of BM212, a 1,5-diarylpyrrole compound. We develop assays that selectively access mycolates on the surface ofMycobacterium smegmatisspheroplasts, allowing us to monitor flipping of MAs across the IM. Using these assays, we establish the mechanism-of-action of BM212 as a potent MmpL3 inhibitor, and employ it as a molecular probe to demonstrate the requirement for functional MmpL3 in the transport of MAs across the IM. Finally, we show that BM212 binds MmpL3 directly and inhibits its activity. Our work provides fundamental insights into OM biogenesis and MA transport in mycobacteria. Furthermore, our assays serve as an important platform for accelerating the validation of small molecules that target MmpL3, and their development as future anti-tuberculosis drugs.
Laminin α1 orchestrates VEGFA functions in the ecosystem of colorectal carcinoma
Authors: Mammadova-Bach E. , Rupp T. , Spenlé C. , Jivkov I. , Shankaranarayanan P. , Klein A. , Pisarsky L. , Méchine-Neuville A. , Cremel G. , Kedinger M. , De Wever O. , Ambartsumian N. , Robine S. , Pencreach E. , Guenot D. , Goetz J.G. , Simon-Assmann P. , Orend G. , Lefebvre O. 
Published: January 2017

SummaryTumor stroma remodeling is a key feature of malignant tumors and can promote cancer progression. Laminins are major constituents of basement membranes that physically separate the epithelium from the underlying stroma. By employing mouse models expressing high and low levels of the laminin α1 chain (LMα1), we highlighted its implication in a tumorstroma crosstalk, thus leading to increased colon tumor incidence, angiogenesis and tumor growth. The underlying mechanism involves attraction of carcinoma-associated fibroblasts by LMα1, VEGFA expression triggered by the complex integrin α2β1-CXCR4 and binding of VEGFA to LM-111, which in turn promotes angiogenesis, tumor cell survival and proliferation. A gene signature comprising LAMA1, ITGB1, ITGA2, CXCR4 and VEGFA has negative predictive value in colon cancer. Together, this information opens novel opportunities for diagnosis and anti-cancer targeting.
A High Quality Assembly of the Nile Tilapia (Oreochromis niloticus) Genome Reveals the Structure of Two Sex Determination Regions
Authors: Conte Matthew A , Gammerdinger William J , Bartie Kerry L , Penman David J , Kocher Thomas D 
Published: January 2017

AbstractWe report a high-quality assembly of the tilapia genome, a perciform fish important in aquaculture around the world. A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidatede novoassemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previousO. niloticusgenome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recentvasagene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both an ~9Mbp XY sex-determination region on LG1 inO. niloticus, and a ~50Mbp WZ sex-determination region on LG3 in the related speciesO. aureus.This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome.
Supporting decision-making in service supplier selection using a hybrid fuzzy extended AHP approach
Authors: Secundo Giustina , Magarielli Donato , Esposito Emilio , Passiante Giuseppina 
Published: January 2017

Purpose
Service supplier selection is a multi-criteria decision-making (MCDM) problem assuming a strategic role for the competitiveness of high-tech manufacturing companies. Nevertheless, especially for service quality evaluation, there is little empirical evidence of the practical usefulness of MCDM methodologies. Aiming to cover this gap between theoretical approaches and empirical applications, the purpose of this paper is to propose a fuzzy extended analytic hierarchy process (FEAHP) approach for service supplier evaluation.

Design/methodology/approach
A hybrid approach which combines some of the strengths of the analytic hierarchy process (AHP) and of the fuzzy set theory is presented, as organized into five steps. A case study is used to evaluate the applicability in a real company context.

Findings
The usability of the approach is demonstrated in an aerospace company for solving the supplier selection problem of a business software whose applications are still in infancy: a Test Data Management System (TDMS). The illustrative application contains both “general” criteria to be used for other service supplier selection contexts as well as service-specific criteria related to software selection.

Research limitations/implications
Even if the application regards the selection of a software supplier, the methodology can be generically extended to other services’ selection in complex manufacturing industries through the personalization of some criteria.

Practical implications
Implications can be derived both for business managers involved into the decision-making process and for suppliers identifying the most promising features of software quality.

Originality/value
The originality consists in the combination into a hybrid approach of the strong points of the AHP with the fuzzy set; the inclusion of multiple perspectives of decision criteria for service supplier selection, basically the “software product” and “supplier” ones; a real empirical application to test and demonstrate the efficacy and the practical utility of the proposed approach.
A methodology for the semantic and structural restructuring of BPMN models
Authors: Khlif Wiem , Ben-Abdallah Hanêne , Ben Ayed Nourchène Elleuch 
Published: January 2017

Purpose
Restructuring a business process (BP) model may enhance the BP performance and improve its understandability. So-far proposed restructuring methods use either refactoring which focuses on structural aspects, social network discovery which uses semantic information to guide the affiliation process during its analysis, or social network rediscovery which uses structural information to identify clusters of actors according to their relationships. The purpose of this paper is to propose a hybrid method that exploits both the semantic and structural aspects of a BP model.

Design/methodology/approach
The proposed method first generates a social network from the BP model. Second, it applies hierarchical clustering to determine the performers’ partitions; this step uses the social context which specifies features related to performers, and two new distances that account for semantic and structural information. Finally, it applies a set of behavioral and organizational restructuring rules adapted from the graph optimization domain; each rule uses the identified performers’ partitions and the business context to reduce particular quality metrics.

Findings
The efficiency of the proposed method is illustrated through well-established complexity metrics. The illustration is made through the development of a tool that fully supports the proposed method and proposes a strategy for the application of the restructuring rules.

Originality/value
The proposed method has the merit of combining the semantic and structural aspects of a Business Process Modeling Notation model to identify restructuring operations whose ordered application reduces the complexity of the initial model.