bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimally invasive endoscopic hematoma evacuation vs best medical management for spontaneous basal-ganglia intracerebral hemorrhage
Authors: Goyal Nitin , Tsivgoulis Georgios , Malhotra Konark , Katsanos Aristeidis H , Pandhi Abhi , Alsherbini Khalid A , Chang Jason J , Hoit Daniel , Alexandrov Andrei V , Elijovich Lucas , Fiorella David , Nickele Christopher , Arthur Adam S 
Published: January 2019

BackgroundWe conducted a case-control study to assess the relative safety and efficacy of minimally invasive endoscopic surgery (MIS) for clot evacuation in patients with basal-ganglia intracerebral hemorrhage (ICH).MethodsWe evaluated consecutive patients with acute basal-ganglia ICH at a single center over a 42-month period. Patients received either best medical management according to established guidelines (controls) or MIS (cases). The following outcomes were compared before and after propensity-score matching (PSM): in-hospital mortality; discharge National Institutes of Health Stroke Scale score; discharge disposition; and modified Rankin Scale scores at discharge and at 3 months.ResultsAmong 224 ICH patients, 19 (8.5%) underwent MIS (mean age, 50.9±10.9; 26.3% female, median ICH volume, 40 (IQR, 25–51)). The interventional cohort was younger with higher ICH volume and stroke severity compared with the medically managed cohort. After PSM, 18 MIS patients were matched to 54 medically managed individuals. The two cohorts did not differ in any of the baseline characteristics. The median ICH volume at 24 hours was lower in the intervention group (40 cm3(IQR, 25–50) vs 15 cm3(IQR, 5–20); P<0.001). The two cohorts did not differ in any of the pre-specified outcomes measures except for in-hospital mortality, which was lower in the interventional cohort (28% vs 56%; P=0.041).ConclusionsMinimally invasive endoscopic hematoma evacuation was associated with lower rates of in-hospital mortality in patients with spontaneous basal-ganglia ICH. These findings support a randomized controlled trial of MIS versus medical management for ICH.
Biomarkers and clinical outcomes in COPD: a systematic review and meta-analysis
Authors: Fermont Jilles M , Masconi Katya L , Jensen Magnus T , Ferrari Renata , Di Lorenzo Valéria A P , Marott Jacob M , Schuetz Philipp , Watz Henrik , Waschki Benjamin , Müllerova Hana , Polkey Michael I , Wilkinson Ian B , Wood Angela M 
Published: January 2019

BackgroundConventional measures to evaluate COPD may fail to capture systemic problems, particularly musculoskeletal weakness and cardiovascular disease. Identifying these manifestations and assessing their association with clinical outcomes (ie, mortality, exacerbation and COPD hospital admission) is of increasing clinical importance.ObjectiveTo assess associations between 6 min walk distance (6MWD), heart rate, fibrinogen, C reactive protein (CRP), white cell count (WCC), interleukins 6 and 8 (IL-6 and IL-8), tumour necrosis factor-alpha, quadriceps maximum voluntary contraction, sniff nasal inspiratory pressure, short physical performance battery, pulse wave velocity, carotid intima-media thickness and augmentation index and clinical outcomes in patients with stable COPD.MethodsWe systematically searched electronic databases (August 2018) and identified 61 studies, which were synthesised, including meta-analyses to estimate pooled HRs, following Meta-analysis of Observational Studies in Epidemiology (MOOSE) and Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines.ResultsShorter 6MWD and elevated heart rate, fibrinogen, CRP and WCC were associated with higher risk of mortality. Pooled HRs were 0.80 (95% CI 0.73 to 0.89) per 50 m longer 6MWD, 1.10 (95% CI 1.02 to 1.18) per 10 bpm higher heart rate, 3.13 (95% CI 2.14 to 4.57) per twofold increase in fibrinogen, 1.17 (95% CI 1.06 to 1.28) per twofold increase in CRP and 2.07 (95% CI 1.29 to 3.31) per twofold increase in WCC. Shorter 6MWD and elevated fibrinogen and CRP were associated with exacerbation, and shorter 6MWD, higher heart rate, CRP and IL-6 were associated with hospitalisation. Few studies examined associations with musculoskeletal measures.ConclusionFindings suggest 6MWD, heart rate, CRP, fibrinogen and WCC are associated with clinical outcomes in patients with stable COPD. Use of musculoskeletal measures to assess outcomes in patients with COPD requires further investigation.Trial registration numberCRD42016052075.
Structural, electronic and magnetic properties of stoichiometric cobalt oxide clusters (CoO)nq (n=3−10,q=0,+1): A modified basin-hopping Monte Carlo algorithm with spin-polarized DFT
Authors: Daud Mohammad Noh 
Published: January 2019

The structural, electronic and magnetic properties of the neutral and cationic cobalt oxide clusters (CoO)[Formula: see text] ([Formula: see text], [Formula: see text]) have been studied using a modified basin-hopping Monte Carlo (BHMC) algorithm refined by spin-polarized DFT. A systematic search of global minimum structures predicts new global minima of (CoO)[Formula: see text] and reproduced other minima that are in excellent agreement with previous works. For most low-spin and high-spin states, the structural transition from planar-like to compact structure occurs at (CoO)[Formula: see text], which is in contrast with the general notion that the structural changes at (CoO)[Formula: see text]. Supported by the results of the binding energy, second-order total energy difference, chemical hardness, chemical potential and HOMO-LUMO gap confirms the stability of (CoO)4. Results of the spin magnetic moments for the global minima show that (CoO)4 and (CoO)8 spin configurations exhibit a fully antiferromagnetic (AFM) ordering, while (CoO)9 spin displays the highest ferromagnetic (FM) ordering. Interestingly, elongation of Co–Co bond in (CoO)4 causes O being polarized by the neighboring Co atoms that accordingly follows the Goodenough-Kanamori-Anderson rule of FM super-exchange coupling for the Co-O-Co structural rearrangement to 90∘ ([Formula: see text] structure) in order to accommodate the spin magnetic ordering changes. This rearrangement is a result of the valence band being shifted away from the Fermi level to lower energy causing high population of the spin-up density of state and leading to the asymmetrical polarization of the whole (CoO)4 structure. As far as the dissociation energy surfaces are concerned, the first ever such surfaces are constructed corresponding to [Formula: see text], which identify a complete dissociation pathway linking the cationic and neutral clusters and finally confirm (CoO)[Formula: see text] as the most stable cluster compared to the rest.
Modeling the dynamics of black holes through balanced equations of motion
Authors: Gallo Emanuel , Moreschi Osvaldo M. 
Published: January 2019

We present a general approach for the formulation of equations of motion for astrophysical compact objects in general relativistic theories. The objects are modeled as relativistic particles, which are assumed to be moving in a geometric background which in turn is asymptotically flat. The background can be affected by the compact object; so that our approach can be applied to binary systems; by concentrating on the main contributions coming from back reaction effects due to gravitational radiation. Our premises are different from the traditional post-Newtonian and self-force approaches since we make strong use of the asymptotic properties of the self geometry of the particle; as is described below. In particular, we use a center of mass setting, and relativistic individual dynamical times for each object. We expect our model to complement the other approaches in different regimes.
Along-strike variations in thin-skinned thrusting style controlled by pre-existing basement structure in the easternmost Jura Mountains (Northern Switzerland)
Authors: Malz Alexander , Madritsch Herfried , Jordan Peter , Meier Beat , Kley Jonas 
Published: January 2019

Abstract
A detailed analysis of the Late Miocene Mandach Thrust, a key tectonic structure of the easternmost Jura Mountains (northern Alpine foreland), is presented providing insights into the modes of along-strike structural cover–basement interactions in a classical foreland setting. Our study builds on the construction, restoration and forward modelling of eight closely spaced cross-sections constrained by depth-migrated 2D seismics and geological maps. The results indicate predominantly thin-skinned thrust tectonics without significant inversion of underlying basement structures. However, inherited pre-thrusting normal faults exerted a strong control on the observed thrusting style, changing along-strike from a comparatively simple geometry to a complex, partly overthrust, partly reactivated normal fault. The observed variations relate to changes in the relief of the mechanical basement and the characteristics of pre-thrusting normal faults. The thrust's complexity is further increased by the local activation of secondary detachment horizons and possibly along-strike sedimentary facies changes within the thrust-faulted sedimentary sequence. The variations in thrusting style go along with subtle changes in shortening that may point towards as yet undetected transfer structures. As such, our structural analysis of the Mandach Thrust provides an improved understanding of the fault's kinematics and serves to highlight existing exploration uncertainties.
Blaze-Tasks
Authors: Pirkelbauer Peter , Wilson Amalee , Peterson Christina , Dechev Damian 
Published: January 2019

Compared to threads, tasks are a more fine-grained alternative. The task parallel programming model offers benefits in terms of better performance portability and better load-balancing for problems that exhibit nonuniform workloads. A common scenario of task parallel programming is that a task is recursively decomposed into smaller sub-tasks. Depending on the problem domain, the number of created sub-tasks may be nonuniform, thereby creating potential for significant load imbalances in the system. Dynamic load-balancing mechanisms will distribute the tasks across available threads. The final result of a computation may be modeled as a reduction over the results of all sub-tasks.
This article describes a simple, yet effective prototype framework, Blaze-Tasks, for task scheduling and task reductions on shared memory architectures. The framework has been designed with lock-free techniques and generic programming principles in mind. Blaze-Tasks is implemented entirely in C++17 and is thus portable. To load-balance the computation, Blaze-Tasks uses task stealing. To manage contention on a task pool, the number of lock-free attempts to steal a task depends on the distance between thief and pool owner and the estimated number of tasks in a victim’s pool. This article evaluates the Blaze framework on Intel and IBM dual-socket systems using nine benchmarks and compares its performance with other task parallel frameworks. While Cilk outperforms Blaze on Intel on most benchmarks, the evaluation shows that Blaze is competitive with OpenMP and other library-based implementations. On IBM, the experiments show that Blaze outperforms other approaches on most benchmarks.
Frizzled-7 Is Required for Wnt Signaling in Gastric Tumors with and Without Apc Mutations
Authors: Flanagan Dustin J. , Barker Nick , Costanzo Natasha S. Di , Mason Elizabeth A. , Gurney Austin , Meniel Valerie S. , Koushyar Sarah , Austin Chloe R. , Ernst Matthias , Pearson Helen B. , Boussioutas Alex , Clevers Hans , Phesse Toby J. , Vincan Elizabeth 
Published: January 2019

Abstract

A subset of patients with gastric cancer have mutations in genes that participate in or regulate Wnt signaling at the level of ligand (Wnt) receptor (Fzd) binding. Moreover, increased Fzd expression is associated with poor clinical outcome. Despite these findings, there are no in vivo studies investigating the potential of targeting Wnt receptors for treating gastric cancer, and the specific Wnt receptor transmitting oncogenic Wnt signaling in gastric cancer is unknown. Here, we use inhibitors of Wnt/Fzd (OMP-18R5/vantictumab) and conditional gene deletion to test the therapeutic potential of targeting Wnt signaling in preclinical models of intestinal-type gastric cancer and ex vivo organoid cultures. Pharmacologic targeting of Fzd inhibited the growth of gastric adenomas in vivo. We identified Fzd7 to be the predominant Wnt receptor responsible for transmitting Wnt signaling in human gastric cancer cells and mouse models of gastric cancer, whereby Fzd7-deficient cells were retained in gastric adenomas but were unable to respond to Wnt signals and consequently failed to proliferate. Genetic deletion of Fzd7 or treatment with vantictumab was sufficient to inhibit the growth of gastric adenomas with or without mutations to Apc. Vantictumab is currently in phase Ib clinical trials for advanced pancreatic, lung, and breast cancer. Our data extend the scope of patients that may benefit from this therapeutic approach as we demonstrate that this drug will be effective in treating patients with gastric cancer regardless of APC mutation status.

Significance:
The Wnt receptor Fzd7 plays an essential role in gastric tumorigenesis irrespective of Apc mutation status, therefore targeting Wnt/Fzd7 may be of therapeutic benefit to patients with gastric cancer.
Urinary Biomarkers of Carcinogenic Exposure among Cigarette, Waterpipe, and Smokeless Tobacco Users and Never Users of Tobacco in the Golestan Cohort Study
Authors: Etemadi Arash , Poustchi Hossein , Chang Cindy M. , Blount Benjamin C. , Calafat Antonia M. , Wang Lanqing , De Jesus Victor R. , Pourshams Akram , Shakeri Ramin , Shiels Meredith S. , Inoue-Choi Maki , Ambrose Bridget K. , Christensen Carol H. , Wang Baoguang , Murphy Gwen , Ye Xiaoyun , Bhandari Deepak , Feng Jun , Xia Baoyun , Sosnoff Connie S. , Kamangar Farin , Brennan Paul , Boffetta Paolo , Dawsey Sanford M. , Abnet Christian C. , Malekzadeh Reza , Freedman Neal D. 
Published: January 2019

Abstract

Background:
How carcinogen exposure varies across users of different, particularly noncigarette, tobacco products remains poorly understood.

Methods:
We randomly selected 165 participants of the Golestan Cohort Study from northeastern Iran: 60 never users of any tobacco, 35 exclusive cigarette, 40 exclusive (78% daily) waterpipe, and 30 exclusive smokeless tobacco (nass) users. We measured concentrations of 39 biomarkers of exposure in 4 chemical classes in baseline urine samples: tobacco alkaloids, tobacco-specific nitrosamines (TSNA), polycyclic aromatic hydrocarbons (PAH), and volatile organic compounds (VOC). We also quantified the same biomarkers in a second urine sample, obtained 5 years later, among continuing cigarette smokers and never tobacco users.

Results:
Nass users had the highest concentrations of tobacco alkaloids. All tobacco users had elevated TSNA concentrations, which correlated with nicotine dose. In both cigarette and waterpipe smokers, PAH and VOC biomarkers were higher than never tobacco users and nass users, and highly correlated with nicotine dose. PAH biomarkers of phenanthrene and pyrene and two VOC metabolites (phenylmercapturic acid and phenylglyoxylic acid) were higher in waterpipe smokers than in all other groups. PAH biomarkers among Golestan never tobacco users were comparable to those in U.S. cigarette smokers. All biomarkers had moderate to good correlations over 5 years, particularly in continuing cigarette smokers.

Conclusions:
We observed two patterns of exposure biomarkers that differentiated the use of the combustible products (cigarettes and waterpipe) from the smokeless product. Environmental exposure from nontobacco sources appeared to contribute to the presence of high levels of PAH metabolites in the Golestan Cohort.

Impact:
Most of these biomarkers would be useful for exposure assessment in a longitudinal study.
Efficacy and Safety of the Biosimilar ABP 215 Compared with Bevacizumab in Patients with Advanced Nonsquamous Non–small Cell Lung Cancer (MAPLE): A Randomized, Double-blind, Phase III Study
Authors: Thatcher Nicholas , Goldschmidt Jerome H. , Thomas Michael , Schenker Michael , Pan Zhiying , Paz-Ares Rodriguez Luis , Breder Valery , Ostoros Gyula , Hanes Vladimir 
Published: January 2019

Abstract

Purpose:
This phase III study compared clinical efficacy and safety of the biosimilar ABP 215 with bevacizumab reference product (RP) in patients with advanced nonsquamous non–small cell lung cancer (NSCLC).

Patients and Methods:
Patients were randomized 1:1 to ABP 215 or bevacizumab 15 mg/kg every three weeks for 6 cycles. All patients received carboplatin and paclitaxel every three weeks for ≥4 and ≤6 cycles. The primary efficacy endpoint was risk ratio of objective response rate (ORR); clinical equivalence was confirmed if the 2-sided 90% confidence interval (CI) of the risk ratio was within the margin of 0.67 to 1.5. Secondary endpoints included risk difference of ORR, duration of response (DOR), progression-free survival (PFS), and overall survival (OS); pharmacokinetics, adverse events (AEs), and incidence of antidrug antibodies (ADAs) were monitored.

Results:
A total of 820 patients were screened; 642 were randomized to ABP 215 (n = 328) and bevacizumab (n = 314). Overall, 128 (39.0%) and 131 (41.7%) patients in the ABP 215 and bevacizumab groups, respectively, had objective responses [ORR risk ratio: 0.93 (90% CI, 0.80–1.09)]. In the ABP 215 and bevacizumab group, 308 (95.1%) and 289 (93.5%) patients, respectively, had at least 1 AE; 13 (4.0%) and 11 (3.6%) experienced a fatal AE. Anti-VEGF toxicity was low and comparable between treatment groups. At week 19, median trough serum drug concentration was 132 μg/mL (ABP 215 group) and 129 μg/mL (bevacizumab group). No patient tested positive for neutralizing antibodies.

Conclusions:
ABP 215 is similar to bevacizumab RP with respect to clinical efficacy, safety, immunogenicity, and pharmacokinetics. The totality of evidence supports clinical equivalence of ABP 215 and bevacizumab.
Genomic Landscape of Pancreatic Adenocarcinoma in Younger versus Older Patients: Does Age Matter?
Authors: Ben-Aharon Irit , Elkabets Moshe , Pelossof Raphael , Yu Kenneth H. , Iacubuzio-Donahue Christine A. , Leach Steven D. , Lowery Maeve A. , Goodman Karyn A. , O'Reilly Eileen M. 
Published: January 2019

Abstract

Purpose:
State-of-the-art genomic analyses of pancreatic adenocarcinoma (PDAC) have yielded insight into signaling pathways underlying carcinogenesis. PDAC is characterized by substantial genomic heterogeneity. We aimed to determine whether early-onset PDAC (EOPC; ≤55 years) displays a distinctive molecular landscape from average-age onset PDAC (AOPC; ≥70 years).

Experimental Design:
Three distinct datasets for PDAC were analyzed. In the first, patients undergoing treatment at Memorial Sloan Kettering (MSK) were consented for MSK-IMPACT next-generation sequencing. The second cohort analyzed was The Cancer Genome Atlas (TCGA) dataset for differences in somatic mutations, gene expression, and protein expression. The third dataset was an Australian cohort of PDAC. Clinical data were correlated with genomic analyses.

Results:
A total of 293 samples were analyzed, yielding 90 patients aged ≤55 years and 203 patients aged ≥70 years. Among the genes known to be associated with carcinogenesis, SMAD4 displayed higher mutation rates in younger patients. Comprehensive transcriptomic analysis of cellular pathways indicated that the TGFβ pathway has increased activation, and the expression levels of phospho-GSK3 were higher in EOPC. Survival outcomes revealed no differences between age groups.

Conclusions:
These exploratory analyses suggest that there may be somatic gene alterations within the population of patients with early-onset PDAC that involve unique cellular pathways compared with average-onset PDAC. Former studies imply these cellular pathways may play a role in smoking-related PDAC carcinogenesis. Larger genomic datasets are warranted for future evaluation to extend these observations.
Immune Exclusion-Wnt/CTNNB1 Class Predicts Resistance to Immunotherapies in HCC
Authors: Pinyol Roser , Sia Daniela , Llovet Josep M. 
Published: January 2019

Abstract
Next-generation sequencing has provided information on actionable targets and biomarkers of response in oncology. In hepatocellular carcinoma (HCC), Wnt/CTNNB1 mutations characterize the immune-excluded class (cold tumors) and might represent the biomarkers predicting resistance to immune checkpoint inhibitors. Large-scale validation of these data is needed to customize immunotherapy in advanced HCC.
See related article by Harding et al., p. 2116
Uncovering the hidden microbiota in hospital and built environments: New approaches and solutions
Authors: Christoff Ana P , Sereia Aline FR , Hernandes Camila , de Oliveira Luiz FV 
Published: January 2019

Microorganisms are widely distributed all over the Earth, inhabiting very diverse natural ecosystems, from the human body to inanimate indoor environments. Until recently, the methods most commonly used to study microbes have been culture-dependent approaches relying on the phenotypic evaluation of isolates that can grow in laboratory conditions. Given the advances in molecular biology and high-throughput DNA sequencing methodologies, scientists could expand their microbiome knowledge to microorganisms that do not grow well in the laboratory or have been considered too difficult and laborious to be cultivated. Culture-independent methods such as direct DNA sequencing can be performed for many samples at once, revealing the entire microbial profile of the samples and making possible the rapid characterization of the whole environmental microbiome. Investigating the microbiome profile of indoor environments such as hospitals, houses, offices and other buildings is of major concern because it could include a number of opportunistic, pathogenic or nosocomial microbes. Additionally, these environments could serve as reservoirs of virulence or antimicrobial resistance, which could be spread by humans or other vectors. High-throughput DNA sequencing has enabled large-scale microbiome screening for multiple indoor areas in a single analysis. Using this approach, we can easily track microorganisms in the environment and monitor microbiome composition related to hygiene processes or environment quality. Gaining such information and resolution regarding indoor microbiome analysis can lend very important assistance for epidemiological surveillance. Impact statement Research concerning the microbiome of indoor environments like hospitals, houses or buildings could have several implications for human health. Today, there is an ongoing shift in the paradigm of microbial analysis, from single isolated bacterial samples to entire microbiome profiles using high-throughput DNA sequencing methods. The use of sequencing methods in several studies has revealed an unprecedented microbial diversity in indoor environments, leading to a larger comprehension of the entire microbiome context. Here, we present a review of these microbiome studies using high-throughput DNA sequencing, including some new approaches and ideas that can be broadly applied in microbial tracking and epidemiological surveillance of indoor environments.