bluuebunny/crossref_metadata_2025_split huggingface dataset:
Women and power: a theoretical approach using the example of copreneurial businesses
Authors: Hirigoyen Gérard , Villeger Amélie 
Published: January 2017

AbstractDespite the gradual recognition of strategic issues related to the integration of women into the economy, female entrepreneurship continues to receive little attention. Family business research attributes this situation to a lack of recognition given to the (decisive) role of women in these organizations. However, there is one type of family governance that formally acknowledges the man/woman combination: the copreneurial company. Copreneurs are couples who run a business together. This theoretical article highlights the role of women in the copreneurial context by distinguishing between formal and informal power- the latter being primarily held by women, but which is no less influential. The distribution of power reduces opposition costs between partners and the social costs of non-compliance, and improves the clarity of the entrepreneurial structure. Moreover, it increases satisfaction and a feeling of equality between the partners. These results can be generalized and shed light on the role of women in other entrepreneurial and social contexts. This article is published as part as part of a collection on the role of women in management and business.
Service induced fcc→hcp martensitic transformation in a Co-based superalloy
Authors: Vacchieri E. , Costa A. , Roncallo G. , Cacciamani G. 
Published: January 2017

Co-based superalloy, ECY768, applied on gas turbine vanes, shows the presence of cracks after service. EBSD studies revealed hcp transformation in the base material near cracked regions. This phase arises from a martensitic transformation of fcc matrix and bestows high fragility. The phase transformation is related to temperature and loading distribution that characterises components in service. However, at the service temperatures, the hcp transformation is not expected for ECY768. An in-house thermodynamic database was developed using the Calphad approach and thermodynamic calculations were applied to the complicated alloy composition for phase stability range evaluation. Moreover, a testing campaign was planned to artificially create this martensitic transformation and to comprehend the influence of plastic strain on fcc-hcp transformation. The transformation mechanisms were understood and some methods were developed for hcp-phase removal through refurbishment heat treatment. This paper is part of a thematic issue on the 9th International Charles Parsons Turbine and Generator Conference. All papers have been revised and extended before publication in Materials Science and Technology.
Improvement of pitting corrosion resistance of stainless steel by electric current pulse
Authors: Jia D. B. , Dai W. B. , Tang G. P. , Xu C. Z. , Tian X. Z. , Yu J. K. 
Published: January 2017

The electric current pulse (ECP) was applied on the liquidus of 304 stainless steel during solidification and the pitting corrosion of the water-quenched specimens was explored in the present work. The results revealed that the utilisation of ECP can inhibit manganese sulphide from segregating around oxide inclusions during solidification and consequently, the pitting corrosion resistance of ECPed steel was significantly improved. Hence, the application of ECP during solidification might be an efficient way to improve the pitting corrosion resistance of the 304 stainless steel. This paper is part of a themed issue on Materials in External Fields.
Changes in biosynthesis of exopolysaccharide in Lactococcus lactis subspecies cremoris treated by moderate pulsed electric field treatment
Authors: Ohba Tetsuro , Uemura Kunihiko , Nabetani Hiroshi 
Published: January 2017

Abstract
Metabolome analysis and physicochemical analyses were executed with cell extracts of a Lactococcus lactis subspecies cremoris strain treated by moderate pulsed electric field (PEF) to elucidate the mechanism of enhanced production of exopolysaccharide (EPS) by the treatment. Metabolome analysis by capillary electrophoresis time of flight mass spectrometry annotated 224 metabolites from the cytoplasmic extract of the strain, which, however, showed no significant changes in metabolites related to the EPS production. Electron microscopic observation and chemical analysis of undecaprenoids as carrier of EPS biosynthetic intermediates suggested that PEF treatment dissociated immature EPSs from the intermediates due to the focal electro-condensation of hydrogen ions at the cell surface. Thus, liberated undecaprenyl phosphates were recycled efficiently, which resulted in mass increase of EPS with smaller molecular weight. The study suggested the feasibility of moderate PEF treatment as a food processing technique and revealed the mechanism of enhanced production of EPS by the treatment.
Development and application of an algorithm to compute weighted multiple glycan alignments
Authors: Hosoda Masae , Akune Yukie , Aoki-Kinoshita Kiyoko F 
Published: January 2017

AbstractMotivationA glycan consists of monosaccharides linked by glycosidic bonds, has branches and forms complex molecular structures. Databases have been developed to store large amounts of glycan-binding experiments, including glycan arrays with glycan-binding proteins. However, there are few bioinformatics techniques to analyze large amounts of data for glycans because there are few tools that can handle the complexity of glycan structures. Thus, we have developed the MCAW (Multiple Carbohydrate Alignment with Weights) tool that can align multiple glycan structures, to aid in the understanding of their function as binding recognition molecules.ResultsWe have described in detail the first algorithm to perform multiple glycan alignments by modeling glycans as trees. To test our tool, we prepared several data sets, and as a result, we found that the glycan motif could be successfully aligned without any prior knowledge applied to the tool, and the known recognition binding sites of glycans could be aligned at a high rate amongst all our datasets tested. We thus claim that our tool is able to find meaningful glycan recognition and binding patterns using data obtained by glycan-binding experiments. The development and availability of an effective multiple glycan alignment tool opens possibilities for many other glycoinformatics analysis, making this work a big step towards furthering glycomics analysis.Availability and Implementationhttp://www.rings.t.soka.ac.jpSupplementary informationSupplementary data are available at Bioinformatics online.
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
Authors: Heirendt Laurent , Thiele Ines , Fleming Ronan M T 
Published: January 2017

Abstract

Motivation
Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations.

Results
DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.

Availability and Implementation
The code is freely available on github.com/opencobra/COBRA.jl. The documentation can be found at opencobra.github.io/COBRA.jl.

Supplementary information
Supplementary data are available at Bioinformatics online.
Protein multiple sequence alignment benchmarking through secondary structure prediction
Authors: Le Quan , Sievers Fabian , Higgins Desmond G 
Published: January 2017

Abstract

Motivation
Multiple sequence alignment (MSA) is commonly used to analyze sets of homologous protein or DNA sequences. This has lead to the development of many methods and packages for MSA over the past 30 years. Being able to compare different methods has been problematic and has relied on gold standard benchmark datasets of ‘true’ alignments or on MSA simulations. A number of protein benchmark datasets have been produced which rely on a combination of manual alignment and/or automated superposition of protein structures. These are either restricted to very small MSAs with few sequences or require manual alignment which can be subjective. In both cases, it remains very difficult to properly test MSAs of more than a few dozen sequences. PREFAB and HomFam both rely on using a small subset of sequences of known structure and do not fairly test the quality of a full MSA.

Results
In this paper we describe QuanTest, a fully automated and highly scalable test system for protein MSAs which is based on using secondary structure prediction accuracy (SSPA) to measure alignment quality. This is based on the assumption that better MSAs will give more accurate secondary structure predictions when we include sequences of known structure. SSPA measures the quality of an entire alignment however, not just the accuracy on a handful of selected sequences. It can be scaled to alignments of any size but here we demonstrate its use on alignments of either 200 or 1000 sequences. This allows the testing of slow accurate programs as well as faster, less accurate ones. We show that the scores from QuanTest are highly correlated with existing benchmark scores. We also validate the method by comparing a wide range of MSA alignment options and by including different levels of mis-alignment into MSA, and examining the effects on the scores.

Availability and Implementation
QuanTest is available from http://www.bioinf.ucd.ie/download/QuanTest.tgz

Supplementary information
Supplementary data are available at Bioinformatics online.
FASTdoop: a versatile and efficient library for the input of FASTA and FASTQ files for MapReduce Hadoop bioinformatics applications
Authors: Ferraro Petrillo Umberto , Roscigno Gianluca , Cattaneo Giuseppe , Giancarlo Raffaele 
Published: January 2017

Abstract

Summary
MapReduce Hadoop bioinformatics applications require the availability of special-purpose routines to manage the input of sequence files. Unfortunately, the Hadoop framework does not provide any built-in support for the most popular sequence file formats like FASTA or BAM. Moreover, the development of these routines is not easy, both because of the diversity of these formats and the need for managing efficiently sequence datasets that may count up to billions of characters. We present FASTdoop, a generic Hadoop library for the management of FASTA and FASTQ files. We show that, with respect to analogous input management routines that have appeared in the Literature, it offers versatility and efficiency. That is, it can handle collections of reads, with or without quality scores, as well as long genomic sequences while the existing routines concentrate mainly on NGS sequence data. Moreover, in the domain where a comparison is possible, the routines proposed here are faster than the available ones. In conclusion, FASTdoop is a much needed addition to Hadoop-BAM.

Availability and Implementation
The software and the datasets are available at http://www.di.unisa.it/FASTdoop/.

Supplementary information
Supplementary data are available at Bioinformatics online.
VCF-kit: assorted utilities for the variant call format
Authors: Cook Daniel E , Andersen Erik C 
Published: January 2017

Abstract

Summary
The variant call format (VCF) is a popular standard for storing genetic variation data. As a result, a large collection of tools has been developed that perform diverse analyses using VCF files. However, some tasks common to statistical and population geneticists have not been created yet. To streamline these types of analyses, we created novel tools that analyze or annotate VCF files and organized these tools into a command-line based utility named VCF-kit. VCF-kit adds essential utilities to process and analyze VCF files, including primer generation for variant validation, dendrogram production, genotype imputation from sequence data in linkage studies, and additional tools.

Availability and Implementation
https://github.com/AndersenLab/VCF-kit
Eye problems in a woman with Churg-Strauss syndrome
Authors: Pierce Benjamin D. , Donald Carrlene B. , Mendez Anthony P. 
Published: January 2017

ABSTRACT
Churg-Strauss syndrome is a rare, systemic vasculitis of unknown cause. Ocular involvement is a rare but established complication and can lead to vision damage or blindness if not treated promptly. Treatment of ocular manifestations corresponds with systemic treatment of the disease and consists primarily of corticosteroids.
Multidimensional Prognostic Modelling in People With Chronic Axial Low Back Pain
Authors: Rabey Martin , Smith Anne , Beales Darren , Slater Helen , O’Sullivan Peter 
Published: January 2017

Objectives:
To derive prognostic models for people with chronic low back pain (CLBP) (n=294) based upon an extensive array of potentially prognostic multidimensional factors.

Materials and Methods:
This study entered multidimensional data (demographics, pain characteristics, pain responses to movement, behaviors associated with pain, pain sensitivity, psychological, social, health, lifestyle) at baseline, and interventions undertaken, into prognostic models for pain intensity, disability, global rating of change and bothersomeness at 1-year.

Results:
The prognostic model for higher pain intensity (explaining 23.2% of the variance) included higher baseline pain intensity and punishing spousal interactions, and lower years in education, while participating in exercise was prognostic of lower pain intensity. The model for higher disability (33.6% of the variance) included higher baseline disability, longer forward bending time, psychological principal component scores representing negative pain-related cognitions and punishing spousal interactions; while exercising was prognostic of lower disability. The odds of reporting global rating of change much/very much improved were increased by participating in exercise, having leg pain as well as CLBP and having greater chronic pain acceptance. The receiver operating characteristic area under the curve was 0.72 indicating acceptable discrimination. The odds of reporting very/extremely bothersome CLBP were increased by having higher baseline pain intensity, longer forward bending time and receiving injection(s); while higher age, more years in education and having leg pain decreased the odds (receiver operating characteristic area under the curve, 0.80; acceptable discrimination).

Discussion:
The variance explained by prognostic models was similar to previous reports, despite an extensive array of multidimensional baseline variables. This highlights the inherent multidimensional complexity of CLBP.
Does Transection of the C2 Nerve Roots During C1 Lateral Mass Screw Placement for Atlantoaxial Fixation Result in a Superior Outcome?
Authors: Badhiwala Jetan H. , Nassiri Farshad , Witiw Christopher D. , Mansouri Alireza , Almenawer Saleh A. , Fehlings Michael G. 
Published: January 2017

Study Design.
Systematic review and meta-analysis.

Objective.
To evaluate the clinical and functional outcomes of transection of the C2 roots during C1 lateral mass screw placement for atlantoaxial fixation.

Summary of Background Data.
Transection of the C2 nerve roots has been recommended during atlantoaxial fixation to facilitate C1 lateral mass screw placement and possibly reduce postoperative occipital neuralgia, although this practice remains controversial.

Methods.
We searched MEDLINE, EMBASE, Web of Science, and the Cochrane Library for studies evaluating the outcomes of C1-2 fixation involving sacrifice of the C2 roots. We calculated transformed proportions with 95% confidence intervals (CI) for the outcomes of occipital neuralgia, numbness, bony fusion, and procedural morbidity. For studies comparing C2 transection with nerve sparing surgery, we performed meta-analyses for the outcomes of occipital neuralgia, occipital numbness, blood loss, and operative time.

Results.
Eight observational studies (N = 393) met eligibility criteria. The rate of postoperative occipital neuralgia among included studies was 0% to 25%; occipital numbness, 6.7% to100%; bony fusion, 96.7% to 100%; and procedural morbidity, 0% to 14.3%. Among comparative studies, C2 transection was associated with a higher rate of occipital numbness [odds ratio (OR) 178.6 (95% CI 26.6 to 1198.4)], lower blood loss [mean difference (MD) −195.3 mL (95% CI −317.7 to −72.8 mL)] and shorter operative times [MD −57.5 mins (95% CI −76.9 to −38.2 mins)] than when the C2 roots were spared. We found no difference in rates of occipital neuralgia [OR 1.44 (95% CI 0.45 to 4.68)].

Conclusion.
Transection of the C2 nerve roots appears to be a viable, safe option when undertaking placement of C1 lateral mass screws. The procedure is associated with reduced operative duration and blood loss, increased rate of occipital numbness, and no change in the rate of occipital neuralgia. However, given the relatively low quality of evidence, prospective, controlled studies to evaluate this strategy are recommended.

Level of Evidence: N /A
Erythema Nodosum Leprosum–Like Lesions Are a Histopathologic Pattern in Whipple's Disease and a Sign of the Immune Reconstitution Inflammatory Syndrome: A Case Series and Review of the Literature
Authors: Liersch Julia , Carlotti Agnès , Theunis Anne , Leonard Alexandra , Barrett Mary , Carlson John Andrew , Schaller Jörg 
Published: January 2017

Abstract:
Inflammatory and subcutaneous nodules can arise in treated and untreated cases of Whipple disease (WD). The inflammatory immune reconstitution syndrome describes paradoxical clinical inflammatory worsening of a preexisting condition because of a return of immune function. Clinicopathologic examination of 4 patients with WD who presented with erythema nodosum leprosum (ENL)–like lesions and the findings of a systematic review of this phenomenon revealed that ENL-like lesions occurred in predominantly middle-aged male patients who suffered from WD, mostly on the legs. Patients showed a nonvasculitic, mostly septal panniculits with neutrophils, macrophages, and lymphocytes. Numerous bacteria-laden periodic acid–Schiff + macrophages and free bacilli were detected in the dermis, as well as subcutaneous septae and adipose lobules. These lesions occurred in both untreated and treated patients as part of inflammatory immune reconstitution syndrome. In conclusion, ENL-like lesions represent a characteristic histopathologic pattern associated with WD, which can occur in different contexts whenever there is a change in the immunological status of the patient. This change can be triggered by antimicrobial treatment, immunomodulatory and immunosuppressant therapy, or occur spontaneously, rarely.
Safety and Effectiveness of Juvéderm Ultra Plus Injectable Gel in Correcting Severe Nasolabial Folds in Chinese Subjects
Authors: Li Dong , Xie Yun , Li Qin , Sun Jiaming , Jiang Ping , Jia Yi , Murphy Diane K. , Li Qingfeng 
Published: January 2017

Background:
Hyaluronic acid dermal fillers are effective in correcting severe nasolabial folds (NLFs) in non-Asian populations. We assessed safety and effectiveness of Juvéderm Ultra Plus in a Chinese population.

Methods:
This double-blind study randomized Chinese subjects with severe NLFs to Juvéderm Ultra Plus (24 mg/mL) in 1 NLF and Restylane injectable gel (20 mg/mL) in the other NLF. NLFs were evaluated using the validated 5-point photonumeric Allergan NLF Severity Scale (0 is “no wrinkle” and 4 is “very deep wrinkle”). Investigator-assessed responder rates (primary outcome at 6 months), NLF mean improvements, and subject-assessed responder rates and preference were assessed.

Results:
Of 124 subjects randomized, 122 completed the 6-month visit. NLFs treated with Juvéderm Ultra Plus required less volume than those treated with Restylane (median [range]: 0.80 [0.3–2.0] vs 1.00 [0.3–1.9]; P<0.001). Investigator-assessed responder rates were 90.4% for Juvéderm Ultra Plus and 89.6% for Restylane, establishing noninferiority of Juvéderm Ultra Plus. Mean (SD) improvements in NLF Severity Scale scores from baseline at 6 months were 1.5 (0.75) for Juvéderm Ultra Plus and 1.6 (0.73) for Restylane. Subject-assessed responder rates were similar to investigator-assessed rates (87.3%, Juvéderm Ultra Plus; 83.9%, Restylane). Of subjects reporting a preference, 62.1% preferred Juvéderm Ultra Plus. The most common treatment site responses were swelling and tenderness; most were mild or moderate in severity and resolved without intervention. Juvéderm Ultra Plus had fewer severe treatment site responses than Restylane.

Conclusion:
In this study in Chinese subjects, Juvéderm Ultra Plus was safe and effective for correcting severe NLFs.
Prostaglandin E1 Increases Microcirculation in Random Pattern Flaps on Rats Measured with Laser Doppler Perfusion Imaging
Authors: Tønseth Kim Alexander , Sneistrup Christian , Berg Thomas Moe 
Published: January 2017

Background:
Reconstructive procedures with pedicled and free flaps are associated with a risk of ischemia. Prostaglandin E1 (PGE1) is a hormone-like substance with known antiischemic and tissue-protective effects. The aim of this study was to evaluate the effect of PGE1 on the microcirculation in random pattern skin flaps on rats.

Methods:
Twenty-four rats were divided into 2 groups: an intervention group given PGE1 for 6 hours and a control group given saline. The flap (2 × 10 cm) was created on the back of the rats, and the microcirculation was monitored with laser Doppler perfusion imaging in 5 different zones (1, proximal; 5, distal) before surgery and after 60, 180, and 360 minutes postoperatively.

Results:
Before surgery, there was no difference in the perfusion in any zones between the intervention group and the control group. The mean perfusion values in zone 1 in the intervention group were significantly higher than those in the control group at 60, 180, and 360 minutes postoperatively (P = 0.02, P = 0.05, and P = 0.04, respectively). At 360 minutes, we also found significantly higher levels of perfusion in the intervention group in zones 4 and 5 (P = 0.05 and P = 0.03, respectively) compared with the controls. Comparing the perfusion at 360 to 60 minutes in the intervention group, we found a significant increase in microcirculation in all zones, which were not seen in the control group.

Conclusion:
PGE1 increased perfusion in the dermal random pattern flaps on rats.
CENTRAL MACULAR THICKNESS IN 6.5-YEAR-OLD CHILDREN BORN EXTREMELY PRETERM IS STRONGLY ASSOCIATED WITH GESTATIONAL AGE EVEN WHEN ADJUSTED FOR RISK FACTORS
Authors: Molnar Anna E. C. , Rosén Rebecka M. , Nilsson Maria , Larsson Eva K. B. , Holmström Gerd E. , Hellgren Kerstin M. 
Published: January 2017

Purpose:
To assess the macular thickness in 6.5-year-old children born extremely preterm (EPT) in comparison with children born at term and to investigate risk factors associated with the macular thickness in the preterm group.

Methods:
A population-based study of 6.5-year-old children born before the gestational age of 27 weeks and age-matched control subjects. Macular assessments with optical coherence tomography were performed, and the results were compared with neonatal risk factors and sex.

Results:
Adequate optical coherence tomography measurements were obtained from 134 children born EPT (mean gestational age of 25 weeks [range 23–26]) and 145 control subjects. The mean (range) of central macula thickness was significantly increased (P < 0.001) in the EPT group (right eyes: 282 μm [238–356], left eyes: 283 μm [229–351]), compared with the control group (right eyes: 249 μm [208–293], left eyes: 248 μm [207–290]). A multiple linear mixed model analysis of the EPT group revealed gestational age, retinopathy of prematurity, and male gender as important risk factors for an increased macular thickness. The macular thickness decreased by 3.9 μm per gestational week, when adjusted for retinopathy of prematurity and sex.

Conclusion:
Extremely preterm birth constitutes a substantial risk factor for a thick central macula, even when adjusted for retinopathy of prematurity and male gender.