bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Dose Optimisation of Golimumab in Nonresponders to Induction Treatment for Ulcerative Colitis Is Effective and Supported by Pharmacokinetic Data
Authors: Philip George , Cornillie Freddy , Adedokun J Omoniyi , Melsheimer Richard , Rutgeerts Paul , Colombel Jean-Frédéric , Marano Colleen 
Published: March 2019

AbstractBackground and AimsIn nonresponders to golimumab induction for ulcerative colitis, we assessed clinical response rates and golimumab serum concentrations when the 100-mg dose was used early in the course of maintenance.MethodsThis post-hoc analysis of golimumab maintenance dosing [in the PURSUIT-M study] examined clinical outcomes and golimumab concentrations in early [Week 6] responders and nonresponders to induction, including subgroups based on body weight.ResultsIn nonresponders to golimumab induction [assessed at Week 6], the 100-mg maintenance dose [starting at Week 6] resulted in a meaningful proportion [28.1%] of patients achieving a partial Mayo response at Week 14. After 1 year of maintenance, clinical outcome [response, remission, mucosal healing, corticosteroid-free state] rates in these “late” [Week 14] responders were similar to those in early [Week 6] responders. Golimumab concentrations in early nonresponders were approximately half those of early responders, suggesting that early nonresponders had more rapid golimumab clearance. Examined by body weight, the early nonresponders weighing <80 kg and receiving 100 mg had golimumab concentrations similar to the early responders [weighing <80 kg or ≥80 kg and receiving 50 mg or 100 mg, respectively].ConclusionsEarly use of the 100-mg maintenance dose leads to positive clinical outcomes in a meaningful proportion of patients who did not respond to golimumab at Week 6. Early nonresponders <80 kg who received the 100-mg maintenance dose achieved adequate golimumab concentrations and a clinically meaningful proportion of these patients had a late clinical response.PURSUIT-M protocol number C0524T18; ClinicalTrials.gov, NCT00488631; EudraCT, 2006-003399-37.
Do individual surgeon volumes affect outcomes in thoracic surgery?†
Authors: Harrison Sebron , Sun Tiany , Kamel Mohamed K , Cleary Corbin , Stiles Brendon M , Altorki Nasser K , Sedrakyan Art 
Published: March 2019

Abstract

OBJECTIVES:
Minimum volume standards for thoracic surgical procedures have been advocated to improve outcomes. However, such standards are controversial within the thoracic surgery literature, and the methodology to determine cut points between high- and low-volume hospitals has been criticized. Furthermore, while multiple studies have examined hospital volume and its relationship with outcomes, there have been very few attempts to study this issue from the perspective of the individual thoracic surgeon. The aim of this study was to determine if surgeon volume is associated with differences in outcomes using a large state-wide database.

METHODS:
The study utilized the New York State Department of Health Statewide Planning and Research Cooperative (SPARCS) data for analysis. Patients who underwent major lung resections including sublobar resection, lobectomy and pneumonectomy from 1995 to 2014 were included and were categorized into 3 subgroups based on the extent of resection. Patient characteristics included age, gender, race, insurance and comorbidities. Surgeon information was obtained by using a unique identifier. Average annual surgical volumes of sublobar resection, lobectomy and pneumonectomy were calculated separately and grouped into 3 categories based on the tertiles. Demographic data and comorbidities were compared between the various volume groups to analyse the resulting complications. Primary outcomes were in-hospital mortality and 30-day readmission.

RESULTS:
There were a total of 99 576 major lung resections performed between 1995 and 2014 in the SPARCS database. Among these, the majority were wedge or segmental resections (n = 54 953, 55.2%) followed by lobectomy (n = 40 421, 40.6%) and pneumonectomy (n = 4202, 4.2%). In-hospital mortality was significantly greater for low-volume surgeons compared to high-volume surgeons for all resection groups. Additionally, low-volume surgeons had higher 30-day readmission rates for patients undergoing lobectomy and pneumonectomy. However, low-volume surgeons as a group were more likely to operate on black patients and patients with Medicaid, and black race was an independent predictor of mortality across all resection groups. The vast majority of surgeons performing lobectomy (89.5%) were in the low-volume group.

CONCLUSIONS:
Low-volume surgeons had higher rates of in-hospital mortality compared to their high-volume counterparts. However, the vast majority of surgeons performing lobectomy (89.5%) were in the low-volume group, and low-volume surgeons operated on higher percentages of black patients. These findings suggest that minimal volume standards would significantly impact the current delivery of thoracic surgery in the US.
Common workflow language (CWL)-based software pipeline for de novo genome assembly from long- and short-read data
Authors: Korhonen Pasi K , Hall Ross S , Young Neil D , Gasser Robin B 
Published: March 2019

ABSTRACT

Background
Here, we created an automated pipeline for the de novoassembly of genomes from Pacific Biosciences long-read and Illumina short-read data using common workflow language (CWL). To evaluate the performance of this pipeline, we assembled the nuclear genomes of the eukaryotes Caenorhabditis elegans (~100 Mb), Drosophila melanogaster (~138 Mb), and Plasmodium falciparum (~23 Mb) directly from publicly accessible nucleotide sequence datasets and assessed the quality of the assemblies against curated reference genomes.

Findings
We showed a dependency of the accuracy of assembly on sequencing technology and GC content and repeatedly achieved assemblies that meet the high standards set by the National Human Genome Research Institute, being applicable to gene prediction and subsequent genomic analyses.

Conclusions
This CWL pipeline overcomes current challenges of achieving repeatability and reproducibility of assembly results and offers a platform for the re-use of the workflow and the integration of diverse datasets. This workflow is publicly available via GitHub (https://github.com/vetscience/Assemblosis) and is currently applicable to the assembly of haploid and diploid genomes of eukaryotes.
Absenteeism in the Public and the Private Sector: Does the Public Sector Attract High Absence Employees?
Authors: Mastekaasa Arne 
Published: March 2019

AbstractEvidence from many countries shows that public sector employees have considerably higher rates of absenteeism than have private sector employees. Based on regression analyses of a large probability sample of the Norwegian population, this article shows that most of the sector difference in long-term absence can be accounted for by taking into consideration the sociodemographic characteristics of the workforce and the occupational composition in the two sectors. A clear sector difference in short-term absenteeism cannot be accounted for in this way. A direct effect of the working or employment conditions in the two sectors is also not a likely explanation, since workers who switch between the sectors are not more absent when they are in the public than when they are in the private sector. Thus, the high level of short-term absenteeism in the public sector seems to be due to a selection of absence-prone individuals to the sector. Since motivational factors are likely to be relatively more important for short-term than for long-term, these findings indicate that lower work attendance motivation in public sector employees may be the main driver. These patterns are consistent with an economic explanation in which people with low attendance motivation select to the public sector, since the work attendance incentives are weaker there. The degree to which the results are compatible with the theory public service motivation is also discussed.
Testing general relativity using binary extreme-mass-ratio inspirals
Authors: Han Wen-Biao , Chen Xian 
Published: March 2019

Abstract
It is known that massive black holes (MBHs) of $10^{5-7}\, \mathrm{ M}_\odot$ could capture small compact objects to form extreme-mass-ratio inspirals (EMRIs). Such systems emit gravitational waves (GWs) in the band of the Laser Interferometer Space Antenna (LISA) and are ideal probes of the space–time geometry of MBHs. Recently, we have shown that MBHs could also capture stellar-mass binary black holes (about $10\, \mathrm{ M}_\odot$) to form binary-EMRIs (b-EMRIs) and, interestingly, a large fraction of the binaries coalesce due to the tidal perturbation by the MBHs. Here we further show that the coalescence could be detected by LISA as glitches in EMRI signals. We propose an experiment to use the multiband (102 and 10−3 Hz) glitch signals to test gravity theories. Our simulations suggest that the experiment could measure the mass and linear momentum lost via GW radiation, as well as constrain the mass of gravitons, to a precision that is one order of magnitude better than the current limit.
The distance, supernova rate, and supernova progenitors of NGC 6946
Authors: Eldridge J J , Xiao Lin 
Published: March 2019

ABSTRACT
The distance to the fireworks galaxy NGC 6946 is highly uncertain. Recent distance estimates using the tip of the red giant branch of 7.7 to 7.8 Mpc are larger than the distance commonly assumed for studying supernovae in this galaxy of 5.9 Mpc. Here we use the high supernova rate of the galaxy to derive the star formation rate and predict the galaxy’s FUV flux. We also account for dust extinction by different methods to derive a distance of 7.9 ± 4.0 Mpc for NGC 6946. We then use the new distance to re-evaluate the understanding of the supernova progenitors 2002hh, 2004et, 2017eaw, the possible electron capture event 2008S, and the possible black hole forming event N6946-BH1. For the latter two exotic events the new distance improves the consistency between the observed progenitors and the stellar models that give rise to these events. From our findings we strongly recommend that all future studies of NGC 6946 must use the greater distance to the galaxy of 7.72 ± 0.32 Mpc of Anand, Rizzi & Tully (2018).
The Emerging Role of Biomarkers in Adaptive Modulation of Clinical Brain Stimulation
Authors: Hoang Kimberly B , Turner Dennis A 
Published: March 2019

Abstract
Therapeutic brain stimulation has proven efficacious for treatment of nervous system diseases, exerting widespread influence via disease-specific neural networks. Activation or suppression of neural networks could theoretically be assessed by either clinical symptom modification (ie, tremor, rigidity, seizures) or development of specific biomarkers linked to treatment of symptomatic disease states. For example, biomarkers indicative of disease state could aid improved intraoperative localization of electrode position, optimize device efficacy or efficiency through dynamic control, and eventually serve to guide automatic adjustment of stimulation settings. Biomarkers to control either extracranial or intracranial stimulation span from continuous physiological brain activity, intermittent pathological activity, and triggered local phenomena or potentials, to wearable devices, blood flow, biochemical or cardiac signals, temperature perturbations, optical or magnetic resonance imaging changes, or optogenetic signals. The goal of this review is to update new approaches to implement control of stimulation through relevant biomarkers. Critical questions include whether adaptive systems adjusted through biomarkers can optimize efficiency and eventually efficacy, serve as inputs for stimulation adjustment, and consequently broaden our fundamental understanding of abnormal neural networks in pathologic states. Neurosurgeons are at the forefront of translating and developing biomarkers embedded within improved brain stimulation systems. Thus, criteria for developing and validating biomarkers for clinical use are important for the adaptation of device approaches into clinical practice.
The Effectiveness of Percutaneous Balloon Compression, Thermocoagulation, and Glycerol Rhizolysis for Trigeminal Neuralgia in Multiple Sclerosis
Authors: Noorani Imran , Lodge Amanda , Vajramani Girish , Sparrow Owen 
Published: March 2019

Abstract

BACKGROUND
Balloon compression (BC), thermocoagulation (TC), and glycerol rhizolysis (GR) are percutaneous surgical options for trigeminal neuralgia (TN). Whether the outcomes of these procedures in multiple sclerosis -related TN (MS-TN) are as effective as in idiopathic TN (ITN) is unknown.

OBJECTIVE
To retrospectively compare pain relief, complications, and durability achieved by these 3 types of procedures in MS-TN and ITN.

METHODS
Two hundred and four patients with typical TN were treated percutaneously: 33 had MS-TN (64 procedures) and 171 had ITN (329 procedures). All were performed by 1 of 2 neurosurgeons; interviews enabled long-term data to be gathered by an independent observer.

RESULTS
MS-TN patients (53.1%) had Barrow Neurological Institute pain scores of I or II after a percutaneous procedure, compared with 59.3% in the ITN cohort; there was no difference in initial relief between the 2 groups overall (P = .52). There was a trend toward fewer complications in MS-TN compared with ITN (23.4% vs 33.7%, respectively; P = .058). Kaplan–Meier analysis demonstrated no difference in durability of relief in MS-TN (median 23.0 mo) compared with ITN overall (median 24.0 mo; P = .75). Subgroup analysis demonstrated longer relief from BC and TC compared with GR in MS-TN (P = .013). Multivariate analysis confirmed that although the presence of MS does not predict durability of outcome, postoperative numbness (P = .0046) and undergoing a repeat procedure (P = .037) were significant predictors.

CONCLUSION
BC and TC are safe and effective in MS-TN. Postoperative numbness is the strongest prognostic factor in MS-TN.
The Politics of Peace
Authors: Goedde Petra 
Published: March 2019

Abstract
This study explores the emerging politics of peace, both as an ideal and as a pragmatic aspect of international relations during the early Cold War. By tracing the myriad ways in which a broad spectrum of people involved in and affected by the Cold War used, altered, and fought over this seemingly universal concept, it deconstructs the assumed binary between realist and idealist foreign policy approaches generally accepted among contemporary policymakers. It argues that a politics of peace emerged in the 1950s and 1960s as a result of a gradual convergence between idealism and realism. A transnational politics of peace succeeded only when idealist objectives met the needs of realist political ambition. It maps three dynamic arenas that together shaped the global discourse on peace: Cold War states, peace advocacy groups, and anticolonial liberationists. The thematic focus on peace moves transnationally where transnational discourses on peace emerged. It reveals the transnational networks that challenged and eventually undermined the Cold War order. It deterritorializes the Cold War by revealing the multiple divides that emerged within each Cold War camp, as peace activists challenged their own governments over the right path toward global peace, and also challenged each other over the best strategy. The Politics of Peace assumes a global perspective once peace advocates confronted the violence of national liberation movements in the Third World. It thus demonstrates that the Cold War was both more ubiquitous and less territorial than previously assumed.
Orbital mass in ANCA-associated vasculitides: data on clinical, biological, radiological and histological presentation, therapeutic management, and outcome from 59 patients
Authors: Durel Cécile-Audrey , Hot Arnaud , Trefond Ludovic , Aumaitre Olivier , Pugnet Gregory , Samson Maxime , Abad Sébastien , Belot Alexandre , Blanchard-Delaunay Claire , Cohen Pascal , Cohen-Aubard Fleur , Cottin Vincent , Crestani Bruno , Moreuil Claire De , Durupt Stéphane , Garzaro Margaux , Girszyn Nicolas , Godeau Bertrand , Hachulla Eric , Jamilloux Yvan , Jego Patrick , Killian Martin , Lazaro Estibaliz , Le Gallou Thomas , Liozon Eric , Martin Thierry , Papo Thomas , Perlat Antoinette , Pillet Pascal , Guillevin Loïc , Terrier Benjamin 
Published: March 2019

Abstract

Objective
Orbital mass is a rare and sight-threatening manifestation of ANCA-associated vasculitides, which remains a therapeutic challenge. We aimed to describe the presentation, therapeutic management and outcome of ANCA-associated vasculitides-related orbital mass.

Methods
We conducted a French nationwide retrospective study of patients with orbital mass in the setting of ANCA-associated vasculitides according to ACR criteria and/or Chapel Hill Consensus Conference definitions.

Results
Fifty-nine patients [33 women, median age 46 (range 7–90) years] were included. Fifty-six (95%) patients had granulomatosis with polyangiitis, two eosinophilic granulomatosis with polyangiitis and one microscopic polyangiitis. Orbital mass was unilateral in 47 (80%) cases, and seemed to develop from ENT involvement in most cases. Orbital mass biopsy was available in 32 (54%) patients, showing lymphoplasmacytic infiltration in 65%, fibrosis in 55%, granulomas in 48% and vasculitis in 36%. All patients but one received glucocorticoids as first-line therapy associated with immunosuppressive agents in 82%, mainly cyclophosphamide. Response to therapy was noted in 52% of patients treated with cyclophosphamide compared with 91% of those treated with rituximab. Twenty-seven (46%) patients required a second-line therapy because of relapse (59%) or refractory course (41%). Sequelae included visual impairment in 28%, with definitive blindness in 17%. Refractory course was associated with PR3-ANCA positivity, visual loss and contiguous pachymeningitis.

Conclusion
Orbital mass is associated with refractory course and high frequency of sequelae, especially blindness. Refractory course is associated with PR3-ANCA positivity, visual loss and contiguous pachymeningitis.
Toward perfect reads: short reads correction via mapping on compacted de Bruijn graphs
Authors: Limasset Antoine , Flot Jean-François , Peterlongo Pierre 
Published: March 2019

AbstractMotivationsShort-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information.ResultsWe propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis ofk-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads thank-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond.Availability and ImplementationThe implementation is open source and available athttp://github.com/Malfoy/BCOOLunder the Affero GPL license and as a Bioconda package.ContactAntoine Limassetantoine.limasset@gmail.com& Jean-François Flotjflot@ulb.ac.be& Pierre Peterlongopierre.peterlongo@inria.fr
Spatial distribution and spread potential of sixteen Leptospira serovars in a subtropical region of Brazil
Authors: Jara Manuel , Escobar Luis E. , Rodriges Rogério O. , Frias Alba , Sanhueza Juan , Machado Gustavo 
Published: March 2019

SummaryLeptospirosis is a bacterial disease that represents a major problem in animal and public health due to its high prevalence and widespread distribution. This zoonotic disease is most prevalent in tropical environments where conditions favor pathogen survival. The ecological preferences of Leptospira serovars are poorly understood, limiting our knowledge of where and when outbreaks can occur, which may result in misinformed prevention and control plans. While the disease can occur consistently in time and space in tropical regions, research on the ecology of Leptospirosis remains limited in subtropical regions. This research gap regarding Leptospira ecology brings public and veterinary health problems, impacting local economies. To fill this gap of knowledge, we propose to assess geographic and ecological features among Leptospira serovars in a subtropical area of Brazil where Leptospirosis is endemic to (i) highlight environmental conditions that facilitate or limit Leptospira spread and survival and (ii) reconstruct its geographical distribution. An ecological niche modeling framework was used to characterize and compare Leptospira serovars in both geographical and environmental space. Our results show that, despite the geographic overlap exhibited by the different serovars assessed, we found ecological divergence among their occupied ecological niches. Ecological divergences were expressed as ranges of potential distributions and environmental conditions found suitably by serovar, being Sejroe the most asymmetric. Most important predictors for the potential distribution of most serovars were soil pH (31.7%) and landscape temperature (24.2%). Identification of environmental preferences will allow epidemiologists to better infer the presence of a serovar based on the environmental characteristics of regions rather than inferences based solely on historical epidemiological records. Including geographic and ecological ranges of serovars also may help to forecast transmission potential of Leptospira in public health and the food animal practice.
The Genomic Ecosystem of Transposable Elements in Maize
Authors: Stitzer Michelle C. , Anderson Sarah N. , Springer Nathan M. , Ross-Ibarra Jeffrey 
Published: March 2019

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017