bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic and clinical characterization of stromal infiltration markers in prostate cancer
Authors: Mahal Brandon A. , Alshalalfa Mohammed , Zhao Shuang G. , Beltran Himisha , Chen William S. , Chipidza Fallon , Davicioni Elai , Karnes R. Jeffrey , Ku Sheng‐Yu , Lotan Tamara L. , Muralidhar Vinayak , Rebbeck Timothy R. , Schaeffer Edward M. , Spratt Daniel E. , Feng Felix Y. , Nguyen Paul L. 
Published: January 2020

BackgroundThe progression of prostate cancer is a complex, multistep process that involves molecular alterations in cells of the tumor and the microenvironment, with associated interactions between the stroma and epithelium. Genomic expression analyses of stromal infiltration markers were performed to determine the significance thereof in prostate cancer.MethodsGenome‐wide expression profiles of formalin‐fixed, paraffin‐embedded radical prostatectomy samples were evaluated from a prospective registry cohort (n = 5239) and 3 retrospective institutional cohorts (n = 1135). Two independent stromal gene expression signatures implied stromal infiltration. Cox proportional hazards regression defined the association between stromal infiltration expression and metastasis‐free survival (MFS).ResultsStromal expression scores were correlated with stromal signature genes and with other key stromal markers (CAV1, VIM, and TAGLN), basal activity, and CD3 and CD4 immune biomarkers (r > 0.5 for all). The top decile of stromal expression was associated with high genomic risk scores (Decipher ≥ 0.6) , high Cancer of the Prostate Risk Assessment–Postsurgical scores, Gleason 9 to 10 disease, and a higher risk for metastasis (hazard ratio, 2.35; 95% CI, 1.37‐4.02; P = .001). A higher stromal infiltration score was also associated with decreased expression of DNA repair genes and higher radiation sensitivity genomic scores. Postoperative radiation therapy (RT) was associated with an MFS benefit for patients with high stromal scores, but not for patients with low stromal scores (Pinteraction = .02).ConclusionsExpression of stromal infiltration markers is correlated with prostate cancer aggressiveness/progression and may be predictive of a response to RT. Stromal infiltration markers should be studied and considered for incorporation into clinical prognostication and decision making.
Machine learning approaches to study glioblastoma: A review of the last decade of applications
Authors: Valdebenito Jessica , Medina Felipe 
Published: January 2020

AbstractBackgroundGlioblastoma (GB, formally glioblastoma multiforme) is a malignant type of brain cancer that currently has no cure and is characterized by being highly heterogeneous with high rates of re‐incidence and therapy resistance. Thus, it is urgent to characterize the mechanisms of GB pathogenesis to help researchers identify novel therapeutic targets to cure this devastating disease. Recently, a promising approach to identifying novel therapeutic targets is the integration of tumor omics data with clinical information using machine learning (ML) techniques.Recent findingsML has become a valuable addition to the researcher's toolbox, thanks to its flexibility, multidimensional approach, and a growing community of users. The goal of this review is to introduce basic concepts and applications of ML for studying GB to clinicians and practitioners who are new to data science. ML applications include exploring large data sets, finding new relevant patterns, predicting outcomes, or merely understanding associations of the complex molecular networks presented within the tumor. Here, we review ML applications published between 2008 and 2018 and discuss ML strategies intending to identify new potential therapeutic targets to improve the management and treatment of GB.ConclusionsML applications to study GB vary in purpose and complexity, with positive results. In GB studies, ML is often used to analyze high‐dimensional datasets with prediction or classification as a primary goal. Despite the strengths of ML techniques, they are not fail‐safe and methodological issues can occur in GB studies that use them. This is why researchers need to be aware of these issues when planning and appraising studies that apply ML to the study of GB.
The optimal number of sensors for a digital imaging system from the perspective of metamer mismatching
Authors: Zhang Xiandou , Wang Mengmeng , Wei Minchen , Wang Yong , Liu Shuo 
Published: January 2020

AbstractMetamer mismatching occurs in both the human visual system and digital imaging systems. Increasing the number of sensors in digital imaging systems is an efficient method to reduce the degree of metamer mismatching. This study investigates the number of sensors that are needed for the digital imaging systems to have a similar ability to the human sensor system in distinguishing colors from the perspective of metamer mismatching. Optimal spectral reflectance was generated, and a dataset with more than 47 million previously collected practical spectral reflectance functions was used to derive the metameric color pairs. Different sets of Gaussian‐shaped functions were designed to model the spectral sensitivity functions of the digital imaging systems. Both the metamer mismatching volumes and color differences were used to characterize the degree of metamer mismatching for pairs of samples, which were metameric to the imaging systems but appeared different to the human sensor system. The results show that the practical metamer mismatching volumes are substantially smaller than the theoretical ones. The results also show that both the metamer mismatching volumes and color differences are significantly reduced by increasing the number of sensors from three to five for the digital imaging system but are only slightly reduced by further increasing the number of sensors from five to seven. This indicates that five sensors is an efficient and optimal solution for an imaging system with Gaussian‐shaped sensors to have a similar ability in distinguishing colors compared to the human sensor system.
How does domestic violence influence the likelihood of settlement in mediation? New data answers old questions
Authors: Raines Susan S. , Indovina Vittorio 
Published: January 2020

AbstractThis study seeks empirical evidence to answer critical questions surrounding domestic violence (DV) and mediation: Are survivors of DV being coerced into reaching unfair and unsafe agreements? Do all DV behaviors have the same impact on settlement? Does stalking predict impasse less than a history of physical violence? Do survivors feel safe in mediation compared to adjudication or attorney‐negotiated settlement? This study answers these critical questions in order to understand which cases are likely to benefit from mediation. This research empowers screeners, mediators, court employees and attorneys to better discern which cases are most likely to benefit from mediation.
Sacubitril‐Valsartan in a routine community population: attention to volume status critical to achieving target dose
Authors: Pharithi Rebabonye B. , Ferre‐Vallverdu Maria , Maisel Alan S. , O'Connell Eoin , Walshe Myra , Sweeney Claire , Barton James , McDonald Kathrine , O'Hare Daniel , Watson Chris , Gallagher Joe , Ledwidge Mark , McDonald Kenneth 
Published: January 2020

AbstractAimsIn the PARADIGM‐heart failure trial, sacubitril‐valsartan demonstrated a reduction in heart failure admissions and reduced all‐cause mortality in patients with heart failure with reduced ejection fraction. Although real world data have shown similar benefits regarding efficacy and safety, there has been difficulty in achieving the target dose (TD). The factors preventing the achievement of TD remains unclear.This study assesses the tolerability, ability to achieve, and factors linked to attaining TD in a routine clinical population.Methods and resultsThis is a retrospective single‐centre review of patients switched from angiotensin‐converting enzyme inhibitors/angiotensin receptor blockers to sacubitril‐valsartan between May 2016 and August 2018. Baseline and follow‐up clinical characteristics and biomarker profiles were collected. Univariate and multivariate analyses were used to analyse predictors of achieving TD. Clinical response to sacubitril‐valsartan was defined as a reduction in N terminal pro BNP of ≥30%, or an increase in left ventricular ejection fraction of ≥5% compared with baseline values.To date, a total of 322 patients (75% male patients) have been switched to sacubitril‐valsartan. Those still in the titration phase were excluded (n = 25). Sacubitril‐valsartan was not tolerated in 40 patients (12.4%). Those intolerant were older (73.4 years [68.3, 80.6] vs. 69.1 years [61.2, 76]; P = 0.003) and had worse renal function with estimated glomerular filtration rate (53.5 mL/min/1.72 m2 [36.8, 60.2] vs 60 mL/min/1.72 m2 [47, 77]; P ≤ 0.001). Of the remaining 257 patients, TD (97/103 mg BD) was achieved in 194 patients (75.5%), while 37 patients (11.4%) were maintained on 49/51 mg BD and 26 patients (8.1%) remained on 24/26 mg BD. Symptomatic hypotension (74.6%) was the main impediment to attaining TD, followed by renal deterioration (12.7%), and to a lesser extent hyperkalaemia and gastrointestinal symptoms (4.8% each). Diuretic dose decrease was achieved in 37.2% of patients, and this was the strongest independent predictor of achieving TD (odds ratio = 2.1; 95% confidence interval [1.16, 3.8]; P = 0.014). Responder status by N terminal pro BNP criterion was observed in 99 of 214 patients (46.3%) while 70 of 142 (49.3%) attained the left ventricular ejection fraction response status. Achieving this response was independently linked to achieving TD.ConclusionsSacubitril‐valsartan was well tolerated. Achievement of TD was possible in the majority of the cohort and was linked to response metrics. Reduction in diuretic was required in a large percentage of the population and was the strongest predictor of attaining TD. Therefore, careful clinical attention to volume status assessment is essential to maximising the benefits of sacubitril‐valsartan.
Human body odor increases familiarity for faces during encoding‐retrieval task
Authors: Cecchetto Cinzia , Fischmeister Florian Ph. S. , Gorkiewicz Sarah , Schuehly Wolfgang , Bagga Deepika , Parma Valentina , Schöpf Veronika 
Published: January 2020

AbstractOdors can increase memory performance when presented as context during both encoding and retrieval phases. Since information from different sensory modalities is integrated into a unified conceptual knowledge, we hypothesize that the social information from body odors and faces would be integrated during encoding. The integration of such social information would enhance retrieval more so than when the encoding occurs in the context of common odors. To examine this hypothesis and to further explore the underlying neural correlates of this behavior, we have conducted a functional magnetic resonance imaging study in which participants performed an encoding‐retrieval memory task for faces during the presentation of common odor, body odor or clean air. At the behavioral level, results show that participants were less biased and faster in recognizing faces when presented in concomitance with the body odor compared to the common odor. At the neural level, the encoding of faces in the body odor condition, compared to common odor and clean air conditions, showed greater activation in areas related to associative memory (dorsolateral prefrontal cortex), odor perception and multisensory integration (orbitofrontal cortex). These results suggest that face and body odor information were integrated and as a result, participants were faster in recognizing previously presented material.
Prevalence of NUT carcinoma in head and neck: Analysis of 362 cases with literature review
Authors: Lee Taebum , Cho Junhun , Baek Chung‐Hwan , Son Young‐Ik , Jeong Han‐Sin , Chung Man Ki , Hong Sang Duk , Ahn Yong Chan , Oh Dong Ryul , Noh Jae Myoung , Park Keunchil , Ahn Myung‐Ju , Kim Hyung‐Jin , Kim Yi Kyung , Ko Young Hyeh 
Published: January 2020

AbstractBackgroundNuclear protein in testis (NUT) carcinoma is a poorly differentiated carcinoma defined by the presence of NUT gene rearrangement. In the head and neck, the true prevalence of NUT carcinoma is unknown.MethodsWe retrospectively investigated NUT expression with clinicopathologic features in 362 patients of poorly differentiated or undifferentiated carcinomas in the head and neck, and reviewed the literature reports.ResultsFour (4/362, 1.1%) cases showed strong nuclear expression for NUT‐specific monoclonal antibody, and all these tumors were in the sinonasal tract (4/40, 10%). The clinical outcome and histology were diverse unlike previously described. Although previous studies reported different frequency results according to study subjects, frequencies in sinonasal tract are relatively constant (10/80, 12.5%).ConclusionsThis is the largest study on the prevalence of NUT carcinoma in head and neck areas. It is important to include in the differential diagnosis of poorly differentiated carcinoma, particularly in the sinonasal tract.
Heterogeneous investment horizons, risk regimes, and realized jumps
Authors: Erdemlioglu Deniz , Gradojevic Nikola 
Published: January 2020

AbstractThis paper introduces a new empirical framework to identify the regimes of jump‐type tail risk over multiple trading horizons. Our approach combines the hidden Markov regime‐switching model with realized jumps, which allows us to examine the tail risk exposure of investors at different investment scales. Applying our method to data on bonds, stocks, and currencies, we find evidence that market risk linked to jumps exhibits time‐varying regime shifts and horizon‐dependence. We show that high‐frequency trading does not contribute to market instability, as measured by jump risk. The European bond market appears to be more vulnerable to downside (left‐tail) jump risk, relative to the U.S. Treasury bond market. Market jump fear embedded in the VIX exhibits vertical clustering where both risk regimes at low frequencies remain unchanged at higher frequencies. These results suggest that the premium for jump risk not only depends on stress periods, but also on the frequency at which investors trade financial assets.
Spring to summer nitrogen level in a brackish lake is higher in abundant snowmelt years: Correlation and causation
Authors: Shizuka Kazunori , Maie Nagamitsu , Nagasaki Masayasu , Kakino Wataru , Tanji Hajime 
Published: January 2020

AbstractEutrophication is an issue of concern in many brackish lakes with an agricultural watershed. The amount of snowfall in snowy areas is anticipated to decline because of global climate change. The aim of this study was to assess the impact of changes in the inflow of snowmelt on the nutrient concentrations of a downstream brackish lake. In Lake Ogawara, a brackish lake in a snow‐covered agricultural area of Japan, we examined the relationships between inflowing river discharge (D/C) during spring and total nitrogen (TN) and total phosphorus (TP) concentrations in the mixolimnion of the lake ([TNmix] and [TPmix], respectively) using 29 yr of monitoring data. In addition, we assessed the causal relationship between the D/C and the lake nutrient concentrations. There was large year‐to‐year variation in D/C during April (D/CApr), which accounted for 7–31% of the mixolimnion volume. Significant positive correlations were observed between D/CApr and [TNmix] from the ensuing April to September. On an annual basis, 49% of the interannual variation of the mean [TNmix] during the ensuing April to September was explained by the interannual variation of D/CApr. Therefore, D/CApr could be useful as a simple index to [TNmix] in the ensuing spring to summer. It is notable that the relationships between D/CApr and [TNmix] from April to September was indicated to be acausal by statistical causal inference. Common climate conditions that increase D/CApr (i.e., a cold winter with a high level of precipitation) were found to drive other biogeochemical processes that increased [TNmix] during the ensuing spring to summer.
Simplifying the clinical classification of polymerase gamma (POLG) disease based on age of onset; studies using a cohort of 155 cases
Authors: Hikmat Omar , Naess Karin , Engvall Martin , Klingenberg Claus , Rasmussen Magnhild , Tallaksen Chantal ME , Brodtkorb Eylert , Ostergaard Elsebet , de Coo I. F. M , Pias‐Peleteiro Leticia , Isohanni Pirjo , Uusimaa Johanna , Darin Niklas , Rahman Shamima , Bindoff Laurence A. 
Published: January 2020

SummaryBackgroundVariants in POLG are one of the most common causes of inherited mitochondrial disease. Phenotypic classification of POLG disease has evolved haphazardly making it complicated and difficult to implement in everyday clinical practise. The aim of our study was to simplify the classification and facilitate better clinical recognition.MethodsA multinational, retrospective study using data from 155 patients with POLG variants recruited from seven European countries.ResultsWe describe the spectrum of clinical features associated with POLG variants in the largest known cohort of patients. While clinical features clearly form a continuum, stratifying patients simply according to age of onset—onset prior to age 12 years; onset between 12 and 40 years and onset after the age of 40 years, permitted us to identify clear phenotypic and prognostic differences. Prior to 12 years of age, liver involvement (87%), seizures (84%), and feeding difficulties (84%) were the major features. For those with onset between 12 and 40 years, ataxia (90%), peripheral neuropathy (84%), and seizures (71%) predominated, while for those with onset over 40 years, ptosis (95%), progressive external ophthalmoplegia (89%), and ataxia (58%) were the major clinical features. The earlier the onset the worse the prognosis. Patients with epilepsy and those with compound heterozygous variants carried significantly worse prognosis.ConclusionBased on our data, we propose a simplified POLG disease classification, which can be used to guide diagnostic investigations and predict disease course.
The Influence of Water Depth on Energy Availability for Ducks
Authors: Behney Adam C. 
Published: January 2020

ABSTRACTHabitat management and planning strategies for nonbreeding ducks are focused on providing enough energy to support a desired number of individuals. Therefore, regional estimates of energy availability for nonbreeding ducks are required to determine if sufficient habitat exists for them. I used core sampling to estimate food and energy density in 6 types of water bodies (i.e., actively and passively managed emergent wetlands, playas, small and large reservoirs, and sloughs) in northeastern Colorado, USA, during 3 sampling occasions throughout 2 nonbreeding seasons, 2015–2016 and 2016–2017. Also, I used precise depth measurements to estimate the percentage of each site that was shallow enough to facilitate feeding by dabbling ducks as a way to correct overall energy density to reflect availability to ducks. Emergent wetlands contained the greatest food and energy density, followed by playas and sloughs, and reservoirs contained little food or energy. Fall depletion of food was greatest in actively managed emergent wetlands and spring depletion was greatest in sloughs and passively managed emergent wetlands. Mean percentage of passively managed emergent wetlands, actively managed emergent wetlands, small reservoirs, large reservoirs, and sloughs shallower than 50 cm was 37%, 77%, 10%, 4%, and 83%, respectively. Incorporating these estimates into the energetic carrying capacity model developed by the Playa Lakes Joint Venture for eastern Colorado resulted in a 54% decrease in overall duck energy day estimates, which is below what is needed to support population goals. This research identifies the need for additional wetland restoration in eastern Colorado to meet energy requirements of nonbreeding ducks and provides information to conservation planners to make more informed decisions about the extent and location of wetland restoration activities. © 2020 The Authors. The Journal of Wildlife Management published by Wiley Periodicals, Inc. on behalf of The Wildlife Society.
Genetic Characteristics of Restored Elk Populations in Kentucky
Authors: Youngmann Jordan L. , Deyoung Randy W. , Demarais Stephen , Strickland Bronson K. , Jenkins Gabe 
Published: January 2020

ABSTRACTTranslocations are a common management practice to restore or augment populations. Understanding the genetic consequences of translocation efforts is important for the long‐term health of restored populations. The restoration of elk (Cervus canadensis) to Kentucky, USA, included source stocks from 6 western states, which were released at 8 sites in southeastern Kentucky during 1997–2002. We assessed genetic diversity in restored herds and compared genetic similarity to source stocks based on 15 microsatellite DNA loci. Genetic variation in the restored populations was comparable to source stocks (allelic richness = 3.52 and 3.50;expected heterozygosity = 0.665 and 0.661 for restored and source, respectively). Genetic differentiation among all source and restored populations ranged from 0.000 to 0.065 for pairwise FSTand 0.034 to 0.161 for pairwise Nei's DA. Pairwise genetic differentiation and Bayesian clustering revealed that stocks from Utah and North Dakota, USA, contributed most to restored populations. Other western stocks appeared less successful and were not detected with our data, though our sampling was not exhaustive. We also inferred natural movements of elk among release sites by the presence of multiple genetic stocks. The success of the elk restoration effort in Kentucky may be due, in part, to the large number of elk (n = 1,548), repeated releases, and use of diverse source stocks. Future restoration efforts for elk in the eastern United States should consider the use of multiple stock sources and a large number of individuals. In addition, preservation of genetic samples of founder stock will enable detailed monitoring in the future. © 2020 The Authors. TheJournal of Wildlife Managementpublished by Wiley Periodicals, Inc. on behalf of The Wildlife Society.
Mixotrophic uptake of organic compounds by coccolithophores
Authors: Godrijan Jelena , Drapeau David , Balch William M. 
Published: January 2020

AbstractOsmotrophy is one of the main modes of mixotrophic acquisition of carbon by phytoplankton, but historically it has been under‐investigated and its physiological and ecological relevance remains poorly understood. Here, we investigate osmotrophy in coccolithophores. Coccolithophores are one of the major contributors to the ocean biomass inhabiting both euphotic and subeuphotic depths in the marine environment. Coccolithophores demonstrate the potential to utilize a wide array of organic compounds in darkness. In experiments with BioLog Ecoplates, we screened a wide array of organic compounds as potential carbon sources, and observed that the major types of organic compounds taken up by coccolithophores were primarily carbohydrates along with a few amino acids and polymers. Furthermore, in subsequent radiotracer experiments, the uptake rates of14C‐labeled dissolved organic carbon compounds in the dark were low relative to the maximal rates of photosynthetic carbon fixation in the light. The time course of uptake for some compounds suggests constitutive capacity for their transport, while for others the transport appears to be activated. Nonetheless, the collective slow uptake rate of a large array of organic compounds found in seawater, might be the only way that osmotrophy could fuel significant coccolithophore growth in the deep euphotic and subeuphotic zones in the sea.