bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incorporating prior information into differential network analysis using non-paranormal graphical models
Authors: Zhang Xiao-Fei , Ou-Yang Le , Yan Hong 
Published: April 2017

Abstract

Motivation
Understanding how gene regulatory networks change under different cellular states is important for revealing insights into network dynamics. Gaussian graphical models, which assume that the data follow a joint normal distribution, have been used recently to infer differential networks. However, the distributions of the omics data are non-normal in general. Furthermore, although much biological knowledge (or prior information) has been accumulated, most existing methods ignore the valuable prior information. Therefore, new statistical methods are needed to relax the normality assumption and make full use of prior information.

Results
We propose a new differential network analysis method to address the above challenges. Instead of using Gaussian graphical models, we employ a non-paranormal graphical model that can relax the normality assumption. We develop a principled model to take into account the following prior information: (i) a differential edge less likely exists between two genes that do not participate together in the same pathway; (ii) changes in the networks are driven by certain regulator genes that are perturbed across different cellular states and (iii) the differential networks estimated from multi-view gene expression data likely share common structures. Simulation studies demonstrate that our method outperforms other graphical model-based algorithms. We apply our method to identify the differential networks between platinum-sensitive and platinum-resistant ovarian tumors, and the differential networks between the proneural and mesenchymal subtypes of glioblastoma. Hub nodes in the estimated differential networks rediscover known cancer-related regulator genes and contain interesting predictions.

Availability and Implementation
The source code is at https://github.com/Zhangxf-ccnu/pDNA

Supplementary information
Supplementary data are available at Bioinformatics online.
Practical steps toward integrating economic, social and institutional elements in fisheries policy and management
Authors: Stephenson Robert L. , Benson Ashleen J. , Brooks Kate , Charles Anthony , Degnbol Poul , Dichmont Catherine M. , Kraan Marloes , Pascoe Sean , Paul Stacey D. , Rindorf Anna , Wiber Melanie 
Published: April 2017

AbstractWhile international agreements and legislation call for incorporation of four pillars of sustainability, the social (including cultural), economic and institutional aspects (the ‘human dimension’) have been relatively neglected to date. Three key impediments have been identified: a relative lack of explicit social, economic and institutional objectives; a general lack of process (frameworks, governance) for routine integration of all four pillars of sustainability; and a bias towards biological considerations. Practical integration requires a ‘systems’ approach with explicit consideration of strategic and operational aspects of management; multidisciplinary or transdisciplinary evaluations; practical objectives for the four pillars of sustainability; appropriate participation; and a governance system that is able to integrate these diverse considerations in management. We challenge all involved in fisheries to immediately take five practical steps toward integrating ecological, economic, social and institutional aspects: (1) Adopt the perspective of the fishery as a ‘system’ with interacting natural, human and management elements; (2) Be aware of both strategic and operational aspects of fisheries assessment and management; (3) Articulate overarching objectives that incorporate all four pillars of sustainability; (4) Encourage appropriate (and diverse) disciplinary participation in all aspects of research, evaluation and management; and (5) Encourage development of (or emulate) participatory governance.
The influence of complex structure on the spatial dynamics of Atlantic cod (Gadus morhua) in the Gulf of Maine
Authors: Guan Lisha , Chen Yong , Staples Kevin W , Cao Jie , Li Bai 
Published: April 2017

AbstractAtlantic cod (Gadus morhua) in the Gulf of Maine (GOM) is an iconic marine fishery stock that has experienced a substantial distributional shift since the mid-1990s. A geostatistical delta-generalized linear mixed model was utilized to hindcast yearly season-specific distributions of GOM cod. These distributions were calculated using the spring and fall bottom trawl survey data for the stock, along with cell-based bathymetry and bottom temperature data for the study area for the years 1982–2013. The centre of stock distribution (the centre of gravity), spatial extent in latitude and longitude, area occupied and median habitat temperature were estimated annually to quantify changes in the spatial dynamics of GOM cod. Time series of these distributional metrics were then used to evaluate the influences of climate change and density-dependent habitat selection on GOM cod’s distribution. Results showed that the rapid southwestward shift in the stock distribution after the late 1990s could not simply be attributed to decreasing stock abundance or warming bottom temperatures. The observed shift in cod distribution requires further investigation on whether it is possibly a result of other factors, like fluctuating productivity among subpopulations.
Estimating escapement of fish and invertebrates in a Danish anchor seine
Authors: Noack Thomas , Madsen Niels , Mieske Bernd , Frandsen Rikke P , Wieland Kai , Krag Ludvig A 
Published: April 2017

Abstract
The codend is generally presumed to be the place where the main selectivity of fish occurs in towed fishing gears, but other parts of the net have been found to contribute to the selectivity process of several invertebrate species. This means that conventional selectivity or survival studies may ignore the selectivity of net parts other than the codend for certain species. By attaching 12 small meshed collecting bags to different parts of a Danish anchor seine net and conducting normal commercial fishing activities, this study showed that there is a substantial escapement of fish and (especially) invertebrates from the forward parts of the seine net. For seven species of demersal fish, most fish escaped through the lower panel close to the codend. All invertebrate species were found in higher numbers in the collecting bags than in the codend where many organisms escaped in the lower panel of the wings or the belly. Mean levels of visible damage ranged from 1.00 to 3.25 for collected invertebrates and were similar for all gear parts. Common starfish (Asterias rubens), however, showed highest damage in the extension part of the net.
Does Intrawound Vancomycin Application During Spine Surgery Create Vancomycin-Resistant Organism?
Authors: Chotai Silky , Wright Patty W. , Hale Andrew T. , Jones Whitney A. , McGirt Matthew J. , Patt Joshua C. , Devin Clinton J. 
Published: April 2017

Abstract

BACKGROUND: Surgical site infection (SSI) following spine surgery is a morbid and expensive complication. The use of intrawound vancomycin is emerging as a solution to reduce SSI. The development of vancomycin-resistant pathogens is an understandable concern.

OBJECTIVE: To determine the occurrence of vancomycin-resistant SSI in patients with and without use of intrawound vancomycin.

METHODS: Patients undergoing elective spine surgery were dichotomized based on whether intrawound vancomycin was applied. Outcome was occurrence of SSI requiring return to the operating room within postoperative 90 days. The intrawound culture and vancomycin minimal inhibitory concentrations (MIC) were reviewed. Analyses were conducted to compare the pathogen profile and MIC for vancomycin in patients who received vancomycin and those who did not.

RESULTS: Of the total 2802 patients, 43% (n = 1215) had intrawound vancomycin application during the index surgery. The use of vancomycin was associated with significantly lower deep SSI rates (1.6% [n = 20] vs 2.5% [n = 40], P = .02). The occurrence of Staphylococcus aureus SSI was significantly lower in the patients who had application of intrawound vancomycin (32% vs 65%, P = .003). None of the patients who had application of intrawound vancomycin powder, and subsequently developed an S aureus SSI, demonstrated pathogens with resistance to vancomycin. All patients had MIC < 2 μg/mL, the vancomycin susceptibility threshold. The occurrence of gram-negative SSI (28% vs 7%) and culture negative fluid collection (16% vs 5%) was higher in the vancomycin cohort.

CONCLUSIONS: The use of intrawound vancomycin during the index spine surgery was protective against SSI following spine surgery. The application of intrawound vancomycin during index surgery does not appear to create vancomycin-resistant organisms in the event of an SSI.
Frontal Keyhole Craniotomy for Resection of Low- and High-Grade Gliomas
Authors: Burks Joshua D , Conner Andrew K , Bonney Phillip A , Glenn Chad A , Smitherman Adam D , Ghafil Cameron A , Briggs Robert G , Baker Cordell M , Kirch Nicholas I , Sughrue Michael E 
Published: April 2017

Abstract

BACKGROUND
Minimally invasive techniques are increasingly being used to access intra-axial brain lesions.

OBJECTIVE
To describe a method of resecting frontal gliomas through a keyhole craniotomy and share the results with these techniques.

METHODS
We performed a retrospective review of data obtained on all patients undergoing resection of frontal gliomas by the senior author between 2012 and 2015. We describe our technique for resecting dominant and nondominant gliomas utilizing both awake and asleep keyhole craniotomy techniques.

RESULTS
After excluding 1 patient who received a biopsy only, 48 patients were included in the study. Twenty-nine patients (60%) had not received prior surgery. Twenty-six patients (54%) were diagnosed with WHO grade II/III tumors, and 22 patients (46%) were diagnosed with glioblastoma. Twenty-five cases (52%) were performed awake. At least 90% of the tumor was resected in 35 cases (73%). Three of 43 patients with clinical follow-up experienced permanent deficits.

CONCLUSION
We provide our experience in using keyhole craniotomies for resecting frontal gliomas. Our data demonstrate the feasibility of using minimally invasive techniques to safely and aggressively treat these tumors.
Endoscopic Endonasal Approach to the Ventral Jugular Foramen: Anatomical Basis, Technical Considerations, and Clinical Series
Authors: Vaz-Guimaraes Francisco , Nakassa Ana Carolina I. , Gardner Paul A. , Wang Eric W. , Snyderman Carl H. , Fernandez-Miranda Juan C. 
Published: April 2017

Abstract

BACKGROUND: Surgical exposure of the jugular foramen (JF) is challenging given its complex regional anatomy and proximity to critical neurovascular structures.

OBJECTIVE: To describe the anatomical basis, surgical technique, and outcomes of a group of patients who underwent the endoscopic endonasal approach to the JF.

METHODS: Five silicon-injected anatomical specimens were prepared for dissection. Additionally, a chart review was conducted through our patient database, searching for endonasal exposure of the JF. Demographic data, clinical presentation, pathological findings, extent of resection in the JF, and occurrence of complications were analyzed.

RESULTS: The endonasal exposure of the JF requires 3 sequential steps: a transpterygoid, a “far-medial,” and an “extreme-medial” approach. Mobilization or transection of the cartilaginous portion of the eustachian tube (ET) is necessary. In the clinical series, cranial neuropathies were the presenting symptoms in 16 patients (89%). Eighteen tumors (10 chondrosarcomas, 7 chordomas, 1 adenocarcinoma) extended secondarily into the JF. Total tumor resection was achieved in 10 patients (56%), near total (≥90%) in 6 (33%), and subtotal (<90%) in 2 (11%). ET dysfunction (75% of cases), transient palatal numbness (17%), cerebrospinal fluid leakage (17%), and lower cranial nerve palsy (17%) were the most common postoperative complications. There were no carotid artery or jugular vein injuries.

CONCLUSION: The endoscopic endonasal approach to the JF requires mobilization or transection of the cartilaginous portion of the ET. This maneuver provides a safe infrapetrosal surgical route to the JF. It may be considered a valid option, in well-selected cases, for resection of malignant and recurrent cranial base tumors.
Surgery After Primary Radiation Treatment for Sporadic Vestibular Schwannomas: Case Series
Authors: Breshears Jonathan D. , Osorio Joseph A. , Cheung Steven W. , Barani Igor J. , Theodosopoulos Philip V. 
Published: April 2017

Abstract

BACKGROUND: As radiation has become an increasingly popular primary treatment option for sporadic vestibular schwannomas, there is a minority of tumors that do not respond favorably to radiation. Data on repeat radiosurgery are emerging, and salvage surgery has been associated with increased technical difficulty and poor facial nerve outcomes.

OBJECTIVE: To review the current literature and report our results with surgical resection of sporadic vestibular schwannomas that have failed primary radiation treatment.

METHODS: This is a retrospective, single-surgeon case series of patients with sporadic vestibular schwannomas who failed primary radiation treatment and underwent subsequent surgical resection. We analyze demographics, clinical information, and intraoperative findings, focusing on facial nerve functional outcomes and extent of resection.

RESULTS: Between 2006 and 2015, 10 patients with sporadic vestibular schwannomas whose only prior treatment was radiation underwent microsurgical resection. Eight of 10 patients had a postoperative House-Brackmann score of 1 at a median follow-up of 14 months, while 2 patients had House-Brackmann score of 4. Gross total resection was achieved in 7 of 10 cases. Near total resection was achieved in 2 cases, and only subtotal resection was achieved in 1 case.

CONCLUSION: Salvage surgery is a safe and effective option after failure of primary radiation and may offer benefits over repeat radiosurgery.
Resection of Temporal Neocortex During Multiple Hippocampal Transections for Mesial Temporal Lobe Epilepsy Does not Affect Seizure or Memory Outcome
Authors: Girgis Fady , Greil Madeline E , Fastenau Philip S , Sweet Jennifer , Lüders Hans , Miller Jonathan P 
Published: April 2017

Abstract

BACKGROUND
Multiple hippocampal transection (MHT) is a surgical treatment for mesial temporal lobe epilepsy associated with improved postoperative neuropsychological outcomes compared with lobectomy.

OBJECTIVE
To determine whether resection of the amygdala and anterior temporal neocortex during MHT affects postoperative seizure/memory outcome.

METHODS
Seventeen patients with normal magnetic resonance imaging and stereo-electroencephalogram-proven drug-resistant dominant mesial temporal lobe epilepsy were treated with MHT. Nine patients underwent MHT alone (MHT–) and 8 patients underwent MHT plus removal of the amygdala and anterior 4.5 cm of temporal neocortex lateral to the fusiform gyrus (MHT+). Verbal and visual-spatial memory were assessed in all patients preoperatively and in 14 patients postoperatively using the Wechsler Memory Scale. Postoperative seizure control was assessed at 12 months for all patients.

RESULTS
Overall, 11 of 17 patients (64.7%) were Engel class 1 at 1 year (6/9 MHT–, 5/8 MHT+, P = .38), and 10 of 14 patients (71.4%) had no significant postoperative decline in either verbal or visual memory (6/8 MHT–, 4/6 MHT+, P = .42). Verbal memory declined in 2 of 8 MHT– and 1 of 6 MHT+ patients, and visual memory declined in 1 of 8 MHT– and 2 of 6 MHT+ patients. Two patients had improved visual memory postoperatively, both in the MHT+ group.

CONCLUSION
MHT on the dominant side is associated with high rates of seizure freedom and favorable memory preservation outcomes regardless of the extent of neocortical resection. Preservation of the temporal neocortex and amygdala during MHT does not appear to decrease the risk of postoperative memory decline, nor does it alter seizure outcome.
Intracranial Bypass of Posterior Inferior Cerebellar Artery Aneurysms: Indications, Technical Aspects, and Clinical Outcomes
Authors: Bonda David J. , Labib Mohamad , Katz Jeffrey M. , Ortiz Rafael A. , Chalif David , Setton Avi , Langer David J. , Dehdashti Amir R. 
Published: April 2017

Abstract

BACKGROUND: For some posterior inferior cerebellar artery (PICA) aneurysms, there is no constructive endovascular or direct surgical clipping option. Intracranial bypass is an alternative to a deconstructive technique.

OBJECTIVE: To evaluate the clinical features, surgical techniques, and outcome of PICA aneurysms treated with bypass and obliteration of the diseased segment.

METHODS: Retrospective review of PICA aneurysms treated via intracranial bypass was performed. Outcome measurements included postoperative stroke, cranial nerve deficits, gastrostomy/tracheostomy requirement, bypass patency, modified Rankin scale (mRS) at discharge, and mRS at 6 mo.

RESULTS: Seven patients with PICA aneurysms treated with intracranial bypass were identified. Five had fusiform aneurysms (4 ruptured, 1 unruptured), 1 had a giant partially thrombosed saccular aneurysm (unruptured), and 1 had a dissecting traumatic aneurysm (ruptured). Two aneurysms were at the anteromedullary segment, 4 at the lateral medullary segment, and 1 at the tonsillomedullary segment. Three patients underwent PICA-to-PICA side to side anastomoses, 2 PICA-to-PICA reanastomosis, 1 vertebral artery-to-PICA bypass, and 1 occipital artery-PICA bypass. Six out of 7 aneurysms were obliterated surgically and 1 with additional endovascular occlusion after the bypass. All bypasses were patent intraoperatively; 2 were later demonstrated occluded without radiological signs or symptoms of stroke. No patients had new cranial nerve deficit postoperatively. With the exception of 1 death due to pulmonary emboli 3 mo postoperatively, all others remain at a mRS ≤ 2.

CONCLUSION: Constructive bypass and aneurysm obliteration remains a viable alternative for treatment of PICA aneurysms not amenable to direct surgical clipping or to a vessel-preserving endovascular option.
Political parties and non-standard employment: an analysis of France, Germany, Italy and Spain
Authors: Picot Georg , Menéndez Irene 
Published: April 2017

Abstract
Recent research has shown that new labour market divides resulting from the rise of non-standard employment (NSE) are reflected in the political preferences of the workers affected. Yet, our knowledge of the stance of political parties on the issue is extremely limited, even descriptively. Do they address NSE in the context of election campaigns—if so, which parties do? How do they frame non-standard work and what policies do they propose? The article tackles these questions by analysing party programmes in four large Continental and Southern Europe states where NSE is widespread and poorly integrated into the systems of social protection. We find that attention to and criticism of non-standard work follows a left–right distribution, but we also find differences within the left: left-libertarian parties address the issue more specifically, while more traditional left-wing parties often link it to other labour concerns.
Gene-Tree Reconciliation with MUL-Trees to Resolve Polyploidy Events
Authors: Thomas Gregg W C , Ather S Hussain , Hahn Matthew W 
Published: April 2017

AbstractPolyploidy can have a huge impact on the evolution of species, and it is a common occurrence, especially in plants. The two types of polyploids—autopolyploids and allopolyploids—differ in the level of divergence between the genes that are brought together in the new polyploid lineage. Because allopolyploids are formed via hybridization, the homoeologous copies of genes within them are at least as divergent as orthologs in the parental species that came together to form them. This means that common methods for estimating the parental lineages of allopolyploidy events are not accurate, and can lead to incorrect inferences about the number of gene duplications and losses. Here, we have adapted an algorithm for topology-based gene-tree reconciliation to work with multi-labeled trees (MUL-trees). By definition, MUL-trees have some tips with identical labels, which makes them a natural representation of the genomes of polyploids. Using this new reconciliation algorithm we can: accurately place allopolyploidy events on a phylogeny, identify the parental lineages that hybridized to form allopolyploids, distinguish between allo-, auto-, and (in most cases) no polyploidy, and correctly count the number of duplications and losses in a set of gene trees. We validate our method using gene trees simulated with and without polyploidy, and revisit the history of polyploidy in data from the clades including both baker’s yeast and bread wheat. Our re-analysis of the yeast data confirms the allopolyploid origin and parental lineages previously identified for this group. The method presented here should find wide use in the growing number of genomes from species with a history of polyploidy. [Polyploidy; reconciliation; whole-genome duplication.]
Hepatitis C infection
Authors: Pozza Renee , Hill Catherine , Hefner Anna Marie , Vawter Beth , Hassanein Tarek 
Published: April 2017

Abstract:
Hepatitis C virus (HCV) is a major cause of chronic liver disease worldwide. Due to the asymptomatic nature of the infection, many acute cases of HCV infection are left undiagnosed, so screening individuals at risk is an important public health priority. New medications offer sustained virologic response rates of over 95%, fewer adverse reactions, and shorter durations of therapy. This article reviews the new treatment guidelines for the evaluation and management of patients with HCV infection.
Associations Between Physician Empathy, Physician Characteristics, and Standardized Measures of Patient Experience
Authors: Chaitoff Alexander , Sun Bob , Windover Amy , Bokar Daniel , Featherall Joseph , Rothberg Michael B. , Misra-Hebert Anita D. 
Published: April 2017

Purpose
To identify correlates of physician empathy and determine whether physician empathy is related to standardized measures of patient experience.

Method
Demographic, professional, and empathy data were collected during 2013–2015 from Cleveland Clinic Health System physicians prior to participation in mandatory communication skills training. Empathy was assessed using the Jefferson Scale of Empathy. Data were also collected for seven measures (six provider communication items and overall provider rating) from the visit-specific and 12-month Consumer Assessment of Healthcare Providers and Systems Clinician and Group (CG-CAHPS) surveys. Associations between empathy and provider characteristics were assessed by linear regression, ANOVA, or a nonparametric equivalent. Significant predictors were included in a multivariable linear regression model. Correlations between empathy and CG-CAHPS scores were assessed using Spearman rank correlation coefficients.

Results
In bivariable analysis (n = 847 physicians), female sex (P < .001), specialty (P < .01), outpatient practice setting (P < .05), and DO degree (P < .05) were associated with higher empathy scores. In multivariable analysis, female sex (P < .001) and four specialties (obstetrics–gynecology, pediatrics, psychiatry, and thoracic surgery; all P < .05) were significantly associated with higher empathy scores. Of the seven CG-CAHPS measures, scores on five for the 583 physicians with visit-specific data and on three for the 277 physicians with 12-month data were positively correlated with empathy.

Conclusions
Specialty and sex were independently associated with physician empathy. Empathy was correlated with higher scores on multiple CG-CAHPS items, suggesting improving physician empathy might play a role in improving patient experience.