bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of grading systems in stage I lung adenocarcinomas: a retrospective cohort study
Authors: Zombori Tamás , Furák József , Nyári Tibor , Cserni Gábor , Tiszlavicz László 
Published: July 2017

AimsThere is no internationally accepted grading system for lung adenocarcinoma despite the new WHO classification. The architectural grade, the Kadota grade and the Sica score were evaluated and compared with overall (OS) and disease-free survival (DFS).MethodsComprehensive histological subtyping was used in a series of resected stage I lung adenocarcinoma to identify subtypes of adenocarcinomas, the architectural grade, the Kadota grade, the Sica grade, the mitotic count, nuclear atypia, the presence of lymphovascular, vascular and airway propagation, necrosis, and micropapillary or solid growth pattern in any percentage. Statistical models fitted included Kaplan-Meier estimates and Cox proportional hazard regression models.Results261 stage I adenocarcinomas were included. The 5-year survivals of different subtypes were as follows: lepidic (n=40, OS: 92.5%; DFS 91.6%), acinar (n=54, OS: 81.8%; DFS: 68.6%), papillary (n=49, OS: 73.6%; DFS: 61.0%), solid (n=95, OS: 64.7%; DFS: 57.8%) and micropapillary (n=23, OS: 34.8%; DFS: 33.5%). Concerning the architectural grade, there were significant differences between OS and DFS of low and intermediate (pOS=0.005, pDFS<0.001), low and high (pOS<0.001, pDFS<0.001) and intermediate and high grades (pOS=0.002, pDFS<0.001). Low-grade and intermediate grade tumours did not differ in survival according to Kadota grade and Sica grade. In the multivariable model, architectural grade was found to be an independent prognostic marker. In another model, architectural pattern proved to be superior to architectural grade.ConclusionsOf the three grading systems compared, the architectural grade makes the best distinction between the outcome of low-grade, intermediate-grade and high-grade stage I adenocarcinomas.
Functional correlates of detailed body composition in healthy elderly subjects
Authors: Geisler Corinna , Schweitzer Lisa , Müller Manfred J. 
Published: July 2017

Methods of body composition analysis are now widely used to characterize health status, i.e., nutritional status, metabolic rates, and cardiometabolic risk factors. However, the functional correlates of individual body components have not been systematically analyzed. In this study, we have used a two-compartment model, which was assessed by air displacement plethysmography. Detailed body composition was measured by whole body magnetic resonance imaging in a healthy population of 40 Caucasians, aged 65–81 yr (20 men; body mass index range: 18.6–37.2 kg/m2). Physical, metabolic, as well as endocrine functions included pulmonary function, handgrip strength, gait speed, sit-to-stand test, physical activity, blood pressure, body temperature, resting energy expenditure (REE), liver and kidney functions (glomerular filtration rate), insulin sensitivity [homeostasis model assessment (HOMA)], plasma lipids, plasma leptin, testosterone, dehydroepiandrosterone, insulin-like growth factor I levels, thyroid status, vitamins, and inflammation. Individual body compartments were intercorrelated, e.g., skeletal muscle mass (SM) correlated with visceral adipose tissue ( r = 0.53) and kidneys ( r = 0.62). For the functional correlates, SM ( r = 0.58) and liver volume ( r = 0.63) were associated with REE, SM correlated with handgrip strength ( r = 0.57), and kidneys with glomerular filtration rate ( r = 0.57). While visceral adipose tissue correlated with HOMA ( r = 0.59), subcutaneous adipose tissue was related to plasma leptin levels ( r = 0.84). The subcutaneous adipose tissue-to-leptin relationship was moderated by inflammation increasing the explained variance of leptin levels by 4.0%. In linear regression analysis, detailed body composition explained variances in REE (75.0%), HOMA (41.0%), and leptin (78.0%) compared with a body mass index-based model (REE 16.0%, HOMA 31.0%, leptin 45.0%). In addition, detailed body composition explained 39.0% of the variance in kidney function. NEW & NOTEWORTHY BCA should be used to address specific body functions only. In clinical practice, there is need of a clear focus on the specific research question related to physical, metabolic, or endocrine functions.
Clinical Significance of Four Molecular Subtypes of Gastric Cancer Identified by The Cancer Genome Atlas Project
Authors: Sohn Bo Hwa , Hwang Jun-Eul , Jang Hee-Jin , Lee Hyun-Sung , Oh Sang Cheul , Shim Jae-Jun , Lee Keun-Wook , Kim Eui Hyun , Yim Sun Young , Lee Sang Ho , Cheong Jae-Ho , Jeong Woojin , Cho Jae Yong , Kim Joohee , Chae Jungsoo , Lee Jeeyun , Kang Won Ki , Kim Sung , Noh Sung Hoon , Ajani Jaffer A. , Lee Ju-Seog 
Published: July 2017

Abstract
Purpose: The Cancer Genome Atlas (TCGA) project recently uncovered four molecular subtypes of gastric cancer: Epstein–Barr virus (EBV), microsatellite instability (MSI), genomically stable (GS), and chromosomal instability (CIN). However, their clinical significances are currently unknown. We aimed to investigate the relationship between subtypes and prognosis of patients with gastric cancer.
Experimental Design: Gene expression data from a TCGA cohort (n = 262) were used to develop a subtype prediction model, and the association of each subtype with survival and benefit from adjuvant chemotherapy was tested in 2 other cohorts (n = 267 and 432). An integrated risk assessment model (TCGA risk score) was also developed.
Results: EBV subtype was associated with the best prognosis, and GS subtype was associated with the worst prognosis. Patients with MSI and CIN subtypes had poorer overall survival than those with EBV subtype but better overall survival than those with GS subtype (P = 0.004 and 0.03 in two cohorts, respectively). In multivariate Cox regression analyses, TCGA risk score was an independent prognostic factor [HR, 1.5; 95% confidence interval (CI), 1.2–1.9; P = 0.001]. Patients with the CIN subtype experienced the greatest benefit from adjuvant chemotherapy (HR, 0.39; 95% CI, 0.16–0.94; P = 0.03) and those with the GS subtype had the least benefit from adjuvant chemotherapy (HR, 0.83; 95% CI, 0.36–1.89; P = 0.65).
Conclusions: Our prediction model successfully stratified patients by survival and adjuvant chemotherapy outcomes. Further development of the prediction model is warranted. Clin Cancer Res; 23(15); 4441–9. ©2017 AACR.
Gene Copy Number Estimation from Targeted Next-Generation Sequencing of Prostate Cancer Biopsies: Analytic Validation and Clinical Qualification
Authors: Seed George , Yuan Wei , Mateo Joaquin , Carreira Suzanne , Bertan Claudia , Lambros Maryou , Boysen Gunther , Ferraldeschi Roberta , Miranda Susana , Figueiredo Ines , Riisnaes Ruth , Crespo Mateus , Rodrigues Daniel Nava , Talevich Eric , Robinson Dan R. , Kunju Lakshmi P. , Wu Yi-Mi , Lonigro Robert , Sandhu Shahneen , Chinnaiyan Arul M. , de Bono Johann S. 
Published: July 2017

Abstract
Purpose: Precise detection of copy number aberrations (CNA) from tumor biopsies is critically important to the treatment of metastatic prostate cancer. The use of targeted panel next-generation sequencing (NGS) is inexpensive, high throughput, and easily feasible, allowing single-nucleotide variant calls, but CNA estimation from this remains challenging.
Experimental Design: We evaluated CNVkit for CNA identification from amplicon-based targeted NGS in a cohort of 110 fresh castration-resistant prostate cancer biopsies and used capture-based whole-exome sequencing (WES), array comparative genomic hybridization (aCGH), and FISH to explore the viability of this approach.
Results: We showed that this method produced highly reproducible CNA results (r = 0.92), with the use of pooled germline DNA as a coverage reference supporting precise CNA estimation. CNA estimates from targeted NGS were comparable with WES (r = 0.86) and aCGH (r = 0.7); for key selected genes (BRCA2, MYC, PIK3CA, PTEN, and RB1), CNA estimation correlated well with WES (r = 0.91) and aCGH (r = 0.84) results. The frequency of CNAs in our population was comparable with that previously described (i.e., deep deletions: BRCA2 4.5%; RB1 8.2%; PTEN 15.5%; amplification: AR 45.5%; gain: MYC 31.8%). We also showed, utilizing FISH, that CNA estimation can be impacted by intratumor heterogeneity and demonstrated that tumor microdissection allows NGS to provide more precise CNA estimates.
Conclusions: Targeted NGS and CNVkit-based analyses provide a robust, precise, high-throughput, and cost-effective method for CNA estimation for the delivery of more precise patient care. Clin Cancer Res; 23(20); 6070–7. ©2017 AACR.
Neutrophil extracellular traps are increased in patients with acute ischemic stroke: prognostic significance
Authors: Vallés Juana , Santos María Teresa , Latorre Ana María , Tembl José , Salom Juan , Nieves Candela , Lago Aida , Moscardó Antonio 
Published: July 2017

SummaryNeutrophil extracellular traps (NETs) are networks of DNA, histones, and proteolytic enzymes produced by activated neutrophils through different mechanisms. NET formation is promoted by activated platelets and can in turn activate platelets, thus favoring thrombotic processes. NETs have been detected in venous and arterial thrombosis, but data in stroke are scarce. The aim of this study was to evaluate NETs in the plasma of patients with acute ischemic stroke and their potential association with baseline clinical characteristics, stroke severity, and one-year clinical outcomes. The study included 243 patients with acute ischemic stroke. Clinical and demographic data and scores of stroke severity (NIHSS and mRs) at onset and discharge were recorded. Markers of NETs (cell-free DNA, nucleosomes, and citrullinated histone 3 (citH3)), were determined in plasma. Patients were followed-up for 12 months after the ischemic event. NETs were significantly elevated in the plasma of patients with acute ischemic stroke when compared to healthy subjects. NETs were increased in patients who were over 65 years of age and in those with a history of atrial fibrillation (AF), cardioembolic stroke, high glucose levels, and severe stroke scores at admission and discharge. In multivariate analysis, elevated levels of citH3, the most specific marker of NETs, at onset were independently associated with AF and all-cause mortality at oneyear follow-up. NETs play a role in the pathophysiology of stroke and are associated with severity and mortality. In conclusion, citH3 may constitute a useful prognostic marker and therapeutic target in patients with acute stroke.
Impact of Stroke Center Certification on Mortality After Ischemic Stroke
Authors: Man Shumei , Schold Jesse D. , Uchino Ken 
Published: July 2017

Background and Purpose—
An increasing number of hospitals have been certified as primary stroke centers (PSCs). It remains unknown whether the action toward PSC certification has improved the outcome of stroke care. This study aimed to understand whether PSC certification reduced stroke mortality.

Methods—
We examined Medicare fee-for-service beneficiaries aged ≥65 years who were hospitalized between 2009 and 2013 for ischemic stroke. Hospitals were classified into 3 groups: new PSCs, the hospitals that received initial PSC certification between 2009 and 2013 (n=634); existing PSCs, the PSCs certified before 2009 (n=785); and non-SCs, the hospitals that have never been certified as PSCs (n=2640). Multivariate logistic regression and Cox proportional hazards model was used to compare the mortality among the 3 groups.

Results—

Existing PSCs were significantly larger than new PSCs as reflected by total number of beds and annual stroke admission (
P
<0.0001). Compared with existing PSCs, new PSCs had lower in-hospital (odds ratio, 0.862; 95% confidence interval [CI], 0.817–0.910) and 30-day mortality (hazard ratio [HR], 0.981; 95% CI, 0.968–0.993), after adjusting for patient demographics and comorbidities. Compared with non-SCs, new PSCs had lower adjusted in-hospital (odds ratio, 0.894; 95% CI, 0.848–0.943), 30-day (HR, 0.904; 95% CI, 0.892–0.917), and 1-year mortality (HR, 0.907; 95% CI, 0.898–0.915). Existing PSCs had lower adjusted 30-day (HR, 0.922; 95% CI, 0.911–0.933) and 1-year mortality (HR, 0.900; 95% CI, 0.892–0.907) than non-SCs.

Conclusions—
Obtaining stroke certification may reduce stroke mortality and overcome the disadvantage of being smaller hospitals. Further study of other outcome measures will be useful to improve stroke system of care.
Mechanical Thrombectomy Outcomes With and Without Intravenous Thrombolysis in Stroke Patients
Authors: Mistry Eva A. , Mistry Akshitkumar M. , Nakawah Mohammad Obadah , Chitale Rohan V. , James Robert F. , Volpi John J. , Fusco Matthew R. 
Published: July 2017

Background and Purpose—
Whether prior intravenous thrombolysis provides any additional benefits to the patients undergoing mechanical thrombectomy for large vessel, acute ischemic stroke remains unclear.

Methods—
We conducted a meta-analysis of 13 studies obtained through PubMed and EMBASE database searches to determine whether functional outcome (modified Rankin Scale) at 90 days, successful recanalization rate, and symptomatic intracerebral hemorrhage rate differed between patients who underwent mechanical thrombectomy with (MT+IVT) and without (MT−IVT) pre-treatment with intravenous thrombolysis.

Results—

MT+IVT patients compared with MT−IVT patients had better functional outcomes (modified Rankin Scale score, 0–2; summary odds ratio [OR], 1.27 [95% confidence interval (CI), 1.05–1.55];
P
=0.02; n=1769/1174), lower mortality (OR, 0.71 [95% CI, 0.55–0.91];
P
=0.006; n=1774/1202), and higher rate of successful recanalization (OR, 1.46 [95% CI, 1.09–1.96];
P
=0.01; n=1652/1216) without having increased odds of symptomatic intracerebral hemorrhage (OR, 1.11 [95% CI, 0.69–1.77];
P
=0.67; n=1471/1143). A greater number of MT+IVT patients required ≤2 passes with a neurothrombectomy device to achieve successful recanalization (OR, 2.06 [95% CI, 1.37–3.10];
P
=0.0005; n=316/231).

Conclusions—
Our results demonstrated that MT+IVT patients had better functional outcomes, lower mortality, higher rate of successful recanalization, requiring lower number of device passes, and equal odds of symptomatic intracerebral hemorrhage compared with MT−IVT patients. The results support the current guidelines of offering intravenous thrombolysis to eligible patients even if they are being considered for mechanical thrombectomy. Because the data are compiled from studies where the 2 groups differed based on eligibility for intravenous thrombolysis, randomized trials are necessary to accurately evaluate the added value of intravenous thrombolysis in patients treated with mechanical thrombectomy.
Surprisingly modern Latest Cretaceous– earliest Paleocene woods of India
Authors: Wheeler Elisabeth A. , Srivastava Rashmi , Manchester Steven R. , Baas Pieter , Wiemann Michael 
Published: July 2017

ABSTRACT

Background and approach
– The Deccan Intertrappean Beds of Central India contain a diverse assemblage of fossil plants, including petrified woods from 15 localities. These beds are dated at c. 67–64 Ma, i.e. latest Cretaceous–earliest Paleocene and span the K-Pg boundary, a significant time in angiosperm history. At this time, the Indian tectonic plate was halfway on its journey from Gondwana to its collision with Asia, and relatively close to the equator. We provide descriptions in IAWA Hardwood List codes for 47 species of Deccan fossil woods, based on our examination of thin sections of these woods, mostly holotypes that are housed at the Birbal Sahni Institute of Palaeobotany, Lucknow, India. An appendix lists all validly published Deccan wood species of which we are aware, including 52 that we were not able to examine.

Main results
– The Deccan fossil woods described herein include the oldest known occurrences of some orders, families or genera viz. Lamiales (Lamia-ceae), Achariaceae (Hydnocarpus-like wood), Anacardiaceae, Simaroubaceae (Ailanthus-like and Simarouba-like woods), subfamily Leeoideae (Vitaceae), subfamily Myrtoideae (Myrtaceae), subfamily Planchoideae (Lecythidaceae), tribe Castilleae (Moraceae), tribes Grewioideae and Sterculioideae (Malvaceae). These first fossil records are discussed with reference to other macrofossil and pollen records of the same or related clades. They complement recent work on the oldest known Olea and Connaraceae also documented by Deccan woods.For the Deccan woods we examined, we could confirm the earlier taxonomic assignment at least down to order or family level for 29 taxa. Ordinal level affinities are ambiguous for eight of the taxa. In two cases, we revised the taxonomic assignment to other families; for another eight, the original assignment was found to be incorrect, but we are unable to suggest alternative affinities.

Evolutionary implications
– Only 3% of all Deccan woods have scalariform perforations and the incidences of so-called specialized features in the Baileyan sense are high, so these woods have a remarkably “modern” aspect. This is anomalous in comparison with contemporaneous fossil woods from higher paleolatitudes, and seemingly they are more “derived” than the recent flora. In these respects, the Deccan woods constitute a unique assemblage. The low incidence of scalariform perforations suggests xeric conditions, while – in contrast – the low incidence of distinct growth ring boundaries suggests an aseasonal everwet climate. It is speculated that convergent xylem specialization, especially the selection for simple perforations, was enhanced by the climatic conditions found at low paleolatitudes with high temperatures as would characterize the Deccan Intertrappean Beds at the K-Pg boundary.
How Skillful are the Multiannual Forecasts of Atlantic Hurricane Activity?
Authors: Caron Louis-Philippe , Hermanson Leon , Dobbin Alison , Imbers Jara , Lledó Llorenç , Vecchi Gabriel A. 
Published: July 2017

Abstract
The recent emergence of near-term climate prediction, wherein climate models are initialized with the contemporaneous state of the Earth system and integrated up to 10 years into the future, has prompted the development of three different multiannual forecasting techniques of North Atlantic hurricane frequency. Descriptions of these three different approaches, as well as their respective skill, are available in the peer-reviewed literature, but because these various studies are sufficiently different in their details (e.g., period covered, metric used to compute the skill, measure of hurricane activity), it is nearly impossible to compare them. Using the latest decadal reforecasts currently available, we present a direct comparison of these three multiannual forecasting techniques with a combination of simple statistical models, with the hope of offering a perspective on the current state-of-the-art research in this field and the skill level currently reached by these forecasts. Using both deterministic and probabilistic approaches, we show that these forecast systems have a significant level of skill and can improve on simple alternatives, such as climatological and persistence forecasts.
Systematic Errors in South Asian Monsoon Simulation: Importance of Equatorial Indian Ocean Processes
Authors: Annamalai H. , Taguchi Bunmei , McCreary Julian P. , Nagura Motoki , Miyama Toru 
Published: July 2017

Abstract
Forecasting monsoon rainfall using dynamical climate models has met with little success, partly due to models’ inability to represent the monsoon climatological state accurately. In this article the nature and dynamical causes of their biases are investigated. The approach is to analyze errors in multimodel-mean climatological fields determined from CMIP5, and to carry out sensitivity experiments using a coupled model [the Coupled Model for the Earth Simulator (CFES)] that does represent the monsoon realistically. Precipitation errors in the CMIP5 models persist throughout the annual cycle, with positive (negative) errors occurring over the near-equatorial western Indian Ocean (South Asia). Model errors indicate that an easterly wind stress bias Δτ along the equator begins during April–May and peaks during November; the severity of the Δτ is that the Wyrtki jets, eastward-flowing equatorial currents during the intermonsoon seasons (April–May and October–November), are almost eliminated. An erroneous east–west SST gradient (warm west and cold east) develops in June. The structure of the model errors indicates that they arise from Bjerknes feedback in the equatorial Indian Ocean (EIO). Vertically integrated moisture and moist static energy budgets confirm that warm SST bias in the western EIO anchors moist processes that cause the positive precipitation bias there. In CFES sensitivity experiments in which Δτ or warm SST bias over the western EIO is artificially introduced, errors in the EIO are similar to those in the CMIP5 models; moreover, precipitation over South Asia is reduced. An overall implication of these results is that South Asian rainfall errors in CMIP5 models are linked to errors of coupled processes in the western EIO, and in coupled models correct representation of EIO coupled processes (Bjerknes feedback) is a necessary condition for realistic monsoon simulation.
Baroclinic Frontal Instabilities and Turbulent Mixing in the Surface Boundary Layer. Part II: Forced Simulations
Authors: Skyllingstad Eric D. , Duncombe Jenessa , Samelson Roger M. 
Published: July 2017

AbstractGeneration of ocean surface boundary layer turbulence and coherent roll structures is examined in the context of wind-driven and geostrophic shear associated with horizontal density gradients using a large-eddy simulation model. Numerical experiments over a range of surface wind forcing and horizontal density gradient strengths, combined with linear stability analysis, indicate that the dominant instability mechanism supporting coherent roll development in these simulations is a mixed instability combining shear instability of the ageostrophic, wind-driven flow with symmetric instability of the frontal geostrophic shear. Disruption of geostrophic balance by vertical mixing induces an inertially rotating ageostrophic current, not forced directly by the wind, that initially strengthens the stratification, damps the instabilities, and reduces vertical mixing, but instability and mixing return when the inertial buoyancy advection reverses. The resulting rolls and instabilities are not aligned with the frontal zone, with an oblique orientation controlled by the Ekman-like instability. Mean turbulence is enhanced when the winds are destabilizing relative to the frontal orientation, but mean Ekman buoyancy advection is found to be relatively unimportant in these simulations. Instead, the mean turbulent kinetic energy balance is dominated by mechanical shear production that is enhanced when the wind-driven shear augments the geostrophic shear, while the resulting vertical mixing nearly eliminates any effective surface buoyancy flux from near-surface, cold-to-warm, Ekman buoyancy advection.