bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variance in Anterior Cruciate Ligament Reconstruction Graft Selection based on Patient Demographics and Location within the Multicenter Orthopaedic Outcomes Network Cohort
Authors: Kraeutler Matthew , Vidal Armando , McCarty Eric , Bravman Jonathan , Wolcott Michelle , Houck Darby ,   MOON Knee Group
Published: July 2017

AbstractThe purpose of this study is to determine whether any regional or age-related patterns exist in graft choice for patients undergoing primary anterior cruciate ligament reconstruction (ACLR) within a large multicenter consortium. A retrospective cohort study was performed using data collected from the Multicenter Orthopaedic Outcomes Network (MOON) on patients having undergone primary ACLR. Patients were stratified by age group (younger than 20, 20–29, 30–39, 40–49, and 50+ years) and four demographic regions (Midwest, Southeast, Northeast, and West). A total of 2,149 patients (1,288 males, 861 females) were included. At least 70% of the patients were treated by a single surgeon in three of the four demographic regions. There were no clinically significant differences in body mass index (BMI), and no statistically significant differences in Marx activity rating scale (p > 0.05) between regions within any particular age group. There were significant differences in the proportion of autografts versus allografts used for primary ACLR between regions in every age group (p < 0.01). There were also significant differences in autograft (p < 0.001) and allograft (p < 0.001) harvest location based on demographic region. The Southeast and Northeast were more likely to use bone-patellar-tendon-bone autograft while the West and Midwest were likely to use hamstring autograft. Within our consortium, regional patterns exist both in autograft versus allograft use in patients undergoing primary ACLR, as well as harvest location of autografts and allografts. Given the similarities in average patient BMI and activity level between regions, as well as the single surgeon influence in three of the four regions, the regional patterns in graft use are likely due to surgeon preference.
Revisiting the kit-split in Coloured South African English
Authors: Toefy Tracey 
Published: July 2017

Abstract
This paper seeks to provide a detailed sociophonetic analysis of kit vowel variation in Coloured South African English (CSAfE). 40 Coloured speakers (20 male; 20 female) from middle-class and working-class backgrounds were analysed using methods of automatic vowel measurement. 2,253 tokens of kit were isolated into phonological environments which condition the split: before and after velar consonants /k, g/, before /ŋ/, before palato-alveolar consonants /ʧ, ʃ, ʤ, ʒ/, after /h/, and word initially. Working-class CSAfE speakers displayed a wider split in the set: they used a higher and fronter variant in all conditioning environments, approximating [ɪ], while tokens in the unconditioned environments were produced in the region of [ə]. Middle-class speakers displayed a definite split, conditioned by the same environments, but with a smaller distance between the two values. The binary split maintains its vitality in this variety of South African English.
Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models
Authors: Chan Siu H J , Cai Jingyi , Wang Lin , Simons-Senftle Margaret N , Maranas Costas D 
Published: July 2017

Abstract

Motivation
In a genome-scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol−1. This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R).

Results
We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model. We identified significant departures after examining 64 published models. The biomass weights of 34 models differed by 5–50%, while 8 models have discrepancies &gt;50%. In total 20 models were manually curated. By maximizing the original versus corrected biomass reactions, flux balance analysis revealed &gt;10% differences in growth yields for 12 of the curated models. Biomass MW discrepancies are accentuated in microbial community simulations as they can cause significant and systematic errors in the community composition. Microbes with underestimated biomass MWs are overpredicted in the community whereas microbes with overestimated biomass weights are underpredicted. The observed departures in community composition are disproportionately larger than the discrepancies in the biomass weight estimate. We propose the presented procedure as a standard practice for metabolic reconstructions.

Availability and implementation
The MALTAB and Python scripts are available in the Supplementary Material.

Supplementary information
Supplementary data are available at Bioinformatics online.
SVmine improves structural variation detection by integrative mining of predictions from multiple algorithms
Authors: Xia Yuchao , Liu Yun , Deng Minghua , Xi Ruibin 
Published: July 2017

Abstract

Motivation
Structural variation (SV) is an important class of genomic variations in human genomes. A number of SV detection algorithms based on high-throughput sequencing data have been developed, but they have various and often limited level of sensitivity, specificity and breakpoint resolution. Furthermore, since overlaps between predictions of algorithms are low, SV detection based on multiple algorithms, an often-used strategy in real applications, has little effect in improving the performance of SV detection.

Results
We develop a computational tool called SVmine for further mining of SV predictions from multiple tools to improve the performance of SV detection. SVmine refines SV predictions by performing local realignment and assess quality of SV predictions based on likelihoods of the realignments. The local realignment is performed against a set of sequences constructed from the reference sequence near the candidate SV by incorporating nearby single nucleotide variations, insertions and deletions. A sandwich alignment algorithm is further used to improve the accuracy of breakpoint positions. We evaluate SVmine on a set of simulated data and real data and find that SVmine has superior sensitivity, specificity and breakpoint estimation accuracy. We also find that SVmine can significantly improve overlaps of SV predictions from other algorithms.

Availability and implementation
SVmine is available at https://github.com/xyc0813/SVmine.

Supplementary information
Supplementary data are available at Bioinformatics online.
Whistleblowing and the Law of Defamation: Does the Law Strike a Fair Balance Between the Rights of Whistleblowers, the Media, and Alleged Wrongdoers?
Authors: Lewis David 
Published: July 2017

Abstract
The Public Interest Disclosure Act only gives rights to workers and makes no mention of any connection with existing defamation provisions. However, whistleblowers and the media may have cause to fear the use alleged wrongdoers could make of the Defamation Act 2013. Having considered the human rights context, this article examines in detail whether or not current legislation strikes a reasonable balance between the rights of whistleblowers, alleged wrongdoers and the media. The author concludes that it is in society’s interest that the balance should be tilted in favour of those who make and disseminate honest allegations even if they turn out to be unfounded. Since the media play an important role in pressing for investigations of concerns that are raised and publicising the fact that wrongdoing has occurred, they too should be protected unless malice can be established.
Subcutaneously Placed Breast Implants after a Skin-Sparing Mastectomy: Do We Always Need ADM?
Authors: Singla Apresh , Singla Animesh , Lai Eric , Caminer David 
Published: July 2017

Background:
Immediate breast reconstruction is an acceptable treatment option after mastectomy for prophylaxis of early breast cancer. Different options exist for implant placement, incision technique, patient suitability, and institutional experience. This article is a case series exploring the feasibility and outcomes of patients undergoing immediate breast reconstruction using skin-sparing mastectomy without mesh or acellular dermal matrix (ADM) and with a vertical inframammary incision.

Methods:
A single-institution retrospective analysis was performed for all patients who underwent immediate single-stage reconstruction with subcutaneous silicon implants without ADM between 2009 and 2014 inclusive. Patient, operative and treatment variables were extracted. All patients with viable mastectomy skin flaps intraoperatively and at least 5 mm of subcutaneous tissue were eligible except for patients who were deemed too slim by the senior surgeon preoperatively and thus at risk of implant visibility or skin rippling.

Results:
There were 26 patients (bilateral n = 12 and unilateral n = 14) eligible for analysis, with a median long-term follow-up of 51.5 months. The majority of complications were classified as minor affecting 46.2% of the cohort (n = 12). There were 20 episodes of complications overall. The most frequent episodes were contour defects (x = 5), minor seroma (x = 4), and malrotation and minor infection (x = 3). There was 1 episode of capsular contracture.

Conclusion:
Skin-sparing mastectomy with immediate subcutaneous silicon implant reconstruction with a vertical incision and without the need for mesh or ADM is an acceptable and safe treatment option. Accurate patient selection and skin flap viability is the key to achieving optimal outcomes with this approach.
BARTONELLA HENSELAE NEURORETINITIS ASSOCIATED WITH CENTRAL RETINAL VEIN OCCLUSION, CHOROIDAL ISCHEMIA, AND ISCHEMIC OPTIC NEUROPATHY
Authors: Ghadiali Quraish , Ghadiali Larissa K. , Yannuzzi Lawrence A. 
Published: July 2017

Purpose:
We describe a healthy 37-year-old man with Bartonella henselae (B. henselae) neuroretinitis with concurrent central retinal vein occlusion and ischemic optic neuropathy resulting in optic atrophy and choroidal ischemia.

Methods:
Case report.

Results:
A 37-year-old man presented with unilateral decreased vision and a fundus examination consistent with neuroretinitis. Further imaging review supported a concurrent diagnosis of central retinal vein occlusion. Although initially negative, repeat serological testing for B. henselae infection was positive. Multimodal imaging displayed severe outer retinal disruption, ischemic optic neuropathy, and choroidal ischemia. The patient demonstrated near complete resolution of fundus findings and restoration of outer retinal architecture. Residual findings included optic disk pallor and ischemic choroidopathy.

Discussion:

B. henselae neuroretinitis may be associated with concurrent retinal vascular occlusive disease and ischemic optic neuropathy. Central retinal vein occlusion and choroidal ischemia leading to optic nerve atrophy are additional sequelae further expanding the clinical spectrum of this entity.
A Case of Verrucous Psoriasis
Authors: Sergeyenko Artem , Clay Tiffany , Guo Aibing Mary 
Published: July 2017

ABSTRACT
Psoriasis is a common, complex immune-mediated disease that may present with several clinical variants. Some of these variants include plaque-type psoriasis vulgaris and pustular, erythrodermic, and guttate psoriasis. We are presenting a case of the verrucous variant, a rare atypical presentation of psoriasis.
Can Preoperative CT Scans Be Used to Predict Facial Nerve Stimulation Following CI?
Authors: Hatch Jonathan L. , Rizk Habib G. , Moore Michael W. , Camposeo Elizabeth E. , Nguyen Shaun A. , Lambert Paul R. , Meyer Ted A. , McRackan Theodore R. 
Published: July 2017

Objectives:
1) To determine the ability of preoperative computed tomography (CT) to predict facial nerve stimulation (FNS) after cochlear implantation (CI). 2) To recognize the limitations of CT in predicting FNS.

Study Design:
Patient control study.

Setting:
Tertiary care academic medical center.

Subjects:
Adult patients with CI from 2003 to 2015.

Methods:
Patients with severe FNS (n = 4) were compared with randomly selected CI patients (n = 28). Three blinded reviewers evaluated preoperative temporal bone CT scans to measure the distance from the labyrinthine segment of the facial nerve to the basal turn of the cochlea and attempted to predict whether or not the subject had FNS after CI.

Results:
In total, 32 CT scans were evaluated representing 49 ears that underwent CI.
The distances (mm) measured from the labyrinthine segment of the facial nerve to the basal turn of the cochlea in both the axial (0.3 ± 0.3 versus 0.6 ± 0.3) and coronal (0.4 ± 0.2 versus 0.6 ± 0.2) orientation were significantly different between the two groups (p = 0.0001 and p = 0.0034) respectively. The intraclass correlation coefficient demonstrated good (K
> 0.7) reviewer correlation in both the reviewers’ measurements and predictions. The sensitivity, specificity, positive predictive value, and negative predictive value for preoperative CT scans to predict FNS were 38.5, 85.1, 19.2, and 93.8% respectively. The reviewers were 23% accurate in predicting FNS.

Conclusion:
Based on a blinded retrospective patient-control study, CT scan measurements show a significantly reduced distance between the labyrinthine facial nerve and the basal turn of the cochlea in patients with FNS. However, it is difficult to predict who will have FNS based on these measurements.
Activities in a social networking-based discussion group by endoscopic retrograde cholangiopancreatography doctors
Authors: Kang Xiaoyu , Zhao Lina , Liu Na , Wang Xiangping , Zhang Rongchun , Liu Zhiguo , Liang Shuhui , Yao Shaowei , Tao Qin , Jia Hui , Pan Yanglin , Guo Xuegang 
Published: July 2017

Background
Online social networking is increasingly being used among medical practitioners. However, few studies have evaluated its use in therapeutic endoscopy. Here, we aimed to analyze the shared topics and activities of a group of endoscopic retrograde cholangiopancreatography (ERCP) doctors in a social networking-based endoscopic retrograde cholangiopancreatography discussion group (EDG).

Materials and methods
Six ERCP trainers working in Xijing Hospital and 48 graduated endoscopists who had finished ERCP training in the same hospital were invited to join in EDG. All group members were informed not to divulge any private information of patients when using EDG. The activities of group members on EDG were retrospectively extracted. The individual data of the graduated endoscopists were collected by a questionnaire.

Results
From June 2014 to May 2015, 6924 messages were posted on EDG, half of which were ERCP related. In total, 214 ERCP-related topics were shared, which could be categorized into three types: sharing experience/cases (52.3%), asking questions (38.3%), and sharing literatures/advances (9.3%). Among the 48 graduated endoscopists, 21 had a low case volume of less than 50 per year and 27 had a high volume case volume of 50 or more. High-volume graduated endoscopists posted more ERCP-related messages (P=0.008) and shared more discussion topics (P=0.003) compared with low-volume graduated endoscopists. A survey showed that EDG was useful for graduated endoscopists in ERCP performance and management of post-ERCP complications, etc.

Conclusion
A wide range of ERCP-related topics were shared on the social networking-based EDG. The ERCP-related behaviors on EDG were more active in graduated endoscopists with an ERCP case volume of more than 50 per year.
The Use of Multistate Models to Examine Associations of Stress and Adherence With Transitions Among HIV Care States Observed in a Clinical HIV Cohort
Authors: Blitz Sandra , Antoniou Tony , Burchell Ann , Walmsley Sharon , Light Lucia , Gardner Sandra , Rourke Sean , Cooper Curtis , Kendall Claire , Loutfy Mona , Rachlis Anita , Wobeser Wendy , Benoit Anita , Raboud Janet ,   on behalf of the OHTN Cohort Study Team
Published: July 2017

Background:
The “cascade of care” is a framework for quantifying the trajectory of people with HIV along the continuum of HIV care. We extended this framework to recognize that individuals may transition back and forth between states of care and to identify factors associated with movement among states of care over time, with particular focus on stress, depression, and adherence.

Methods:
The Ontario HIV Treatment Network Cohort Study is a multisite HIV clinical cohort. We analyzed data from participants who had initiated antiretroviral therapy, achieved virologic suppression, completed ≥1 study questionnaire including psychosocial data, and had ≥1 viral load (VL) result within 2 years of a questionnaire. Follow-up time from the first suppressed VL was divided into 6-month intervals and classified into 1 of 3 states for HIV care retention: (1)
suppressed VL
(VL <50 copies/mL), (2)
unsuppressed VL
(VL >50 copies/mL), and (3)
unobserved
. Multistate models were used to determine the association of transitioning between states and time-updated demographic and clinical characteristics.

Results:
In total, 1842 participants were included. After multivariable adjustment, poor adherence [hazard ratio (HR) 1.88, 95% confidence interval (CI): 1.19 to 2.98) and stress (HR = 1.38; 95% CI: 1.04 to 1.83) were associated with transitions from suppressed to unsuppressed VL. Similarly, low adherence (HR = 1.52; 95% CI: 1.14 to 2.04) and stress (HR = 1.25; 95%: 1.03, 1.51) were associated with transitions from suppressed to unobserved states.

Conclusions:
Higher levels of stress and low adherence are associated with transitions to less favorable states of care. Interventions to manage stress and facilitate adherence may improve engagement in HIV care.
Magnetic Resonance Imaging in Psoriatic Arthritis
Authors: Maldonado-Ficco Hernán , Sheane Barry J. , Thavaneswaran Arane , Chandran Vinod , Gladman Dafna D. 
Published: July 2017

Objective
The aims of this study were to describe the indications for, and features of, axial/peripheral joint magnetic resonance imaging (MRI) in psoriatic arthritis (PsA) and to examine the influence of MRI findings on clinical practice.

Methods
All axial and peripheral (hand and/or foot) MRI scans on patients attending the Toronto PsA clinic l between 2003 and 2014 were included. Scan details were garnered from the radiologist’s official report. A chart review was performed to determine if MRI findings contributed to a change of treatment.

Results
One hundred sixty-eight scans were performed on 125 patients (135 axial and 33 peripheral). The mean age was 50.5 (SD, 11.5) years, with 51.2% being female. Mean duration of PsA was 11.2 (SD, 10.9) years. Of the axial scans, the majority were performed on the whole spine (excluding the sacrum) (27.4%) or the sacroiliac joints and spine together (45.2%). The predominant indications were for suspected inflammatory (51.1%) or degenerative (24.4%) disease. Magnetic resonance imaging revealed inflammatory and/or structural change in 34.1% versus 54.8% with degenerative changes. In MRI axial inflammation (n = 25), the majority (48%) had sacroiliac joint involvement, whereas 28% had inflammation at 2 or more sites.
Of the periphery, 60.6% of scans were on hands and 21.2% were on feet alone. The main indications were for suspected subclinical synovitis (78.8%). Inflammatory arthritis was the MRI diagnosis in 72.7%. Magnetic resonance imaging findings influenced treatment change (n = 32) in 56.3%, but were insufficient to effect treatment change without clinical findings (100%).

Conclusions
Magnetic resonance imaging is useful in evaluating patients with active PsA, particularly when suspecting inflammation and radiographic findings are unhelpful. In some cases, it can be used as an adjunct to clinical examination in determining treatment change.
DIscrete Dynamical Model of Mechanisms Determining the Relations of Biodiversity and Stability at Different Levels of Organization of Living Matter
Authors: Bespalov Yu. G , Nosov K. V. , Kabalyants P. S. 
Published: July 2017

AbstractThe paper aims at building the model of relations of biodiversity and stability at different levels of organization of living matter with the use of discrete dynamical models. The relations revealed in the study are illustrated by case studies of zooplankton community of the eutrophicated lake and the colorimetric parameters of the microalgae community of phytobenthos and phytoperiphyton. The results offer: (1) new approaches to estimating the risk of mass development of toxic cyanobacteria in eutrophicated reservoirs, and (2) new indicators for unmasking animals with protective coloring on the background of plant communities by image processing of digital photos.
Personalized intrinsic network topography mapping and functional connectivity deficits in Autism Spectrum Disorder
Authors: Dickie Erin W. , Ameis Stephanie H. , Viviano Joseph D. , Smith Dawn E. , Calarco Navona , Shahab Saba , Voineskos Aristotle N. 
Published: July 2017

AbstractBackgroundRecent advances demonstrate individually specific variation in brain architecture in healthy individuals using fMRI data. To our knowledge, the effects of individually specific variation in complex brain disorders have not been previously reported.MethodsWe developed a novel approach (Personalized Intrinsic Network topography, PINT) for localizing individually specific resting state networks using conventional resting state fMRI scans. Using cross-sectional data from participants with ASD (n=393) and TD controls (n=496) across 15 sites we tested: 1) effect of diagnosis and age on the variability of intrinsic network locations and 2) whether prior findings of functional connectivity differences in ASD as compared to TD remain after PINT application.ResultsWe found greater variability in the spatial locations of resting state networks within individuals with ASD as compared to TD. In TD participants, variability decreased from childhood into adulthood, and increased again in late-life, following a ‘U-shaped’ pattern, which was not present in those with ASD. Comparison of intrinsic connectivity between groups revealed that the application of PINT decreased the number of hypo-connected regions in ASD.ConclusionsOur results provide a new framework for measuring altered brain functioning in neurodevelopmental disorders that may have implications for tracking developmental course, phenotypic heterogeneity, and ultimately treatment response. We underscore the importance of accounting for individual variation in the study of complex brain disorders.