bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irrigation Impact on Water and Energy Cycle During Dry Years Over the United States Using Convection‐Permitting WRF and a Dynamical Recycling Model
Authors: Yang Zhao , Qian Yun , Liu Ying , Berg Larry K. , Hu Huancui , Dominguez Francina , Yang Ben , Feng Zhe , Gustafson William I. , Huang Maoyi , Tang Qi 
Published: November 2019

AbstractAn irrigation scheme is implemented in the Weather Research and Forecasting (WRF) model to investigate irrigation impacts over the Continental U.S. (CONUS). Four major irrigated regions and two downwind regions were chosen to understand irrigation impacts over different climate regimes with a focus on irrigation‐induced changes on the water and energy cycles. The Dynamic Recycling Model (DRM) is employed to quantify precipitation induced by irrigation and the precipitation recycling ratios over each irrigated region. With the irrigation scheme, WRF improves the simulated precipitation, surface skin temperature, and energy fluxes compared to reference datasets. For the energy cycle, irrigation increases latent heat flux over the irrigated regions along with reduced sensible heat flux. The evaporative cooling effect induced by irrigation leads to a cooler surface and less outgoing longwave radiation at the surface. Irrigation also intensifies the hydrological cycle over the irrigated regions, reflected by the increased precipitation, evapotranspiration, recycling ratio, and moisture export. Downwind regions exhibit increased precipitation and evaporation, decreased moisture flux divergence, and less consistent variations in recycling ratio. The precipitation increases over the irrigated regions can be partly explained by the more unstable low‐level conditions, while reduced net moisture export is coincident with the precipitation increases over the downwind regions.
Motor cortex facilitation: a marker of attention deficit hyperactivity disorder co-occurrence in autism spectrum disorder
Authors: Pedapati Ernest V. , Mooney Lindsey N. , Wu Steve W. , Erickson Craig A. , Sweeney John A. , Shaffer Rebecca C. , Horn Paul S. , Wink Logan K. , Gilbert Donald L. 
Published: November 2019

AbstractThe neural correlates distinguishing youth with Autism Spectrum Disorder (ASD-) and ASD with co-occurring Attention Deficit Hyperactivity Disorder (ASD+) are poorly understood despite significant phenotypic and prognostic differences. Paired-pulse transcranial magnetic stimulation (TMS) measures, including intracortical facilitation (ICF), short interval cortical inhibition (SICI), and cortical silent period (CSP) were measured in an age matched cohort of youth with ASD- (n = 20), ASD + (n = 29), and controls (TDC) (n = 24). ASD− and ASD+ groups did not differ by IQ or social functioning; however, ASD+ had significantly higher inattention and hyperactivity ratings. ICF (higher ratio indicates greater facilitation) in ASD+ (Mean 1.0, SD 0.19) was less than ASD− (Mean 1.3, SD 0.36) or TDC (Mean 1.2, SD 0.24) (F2,68 = 6.5,p = 0.003; post-hoc tests, ASD+ vs either TDC or ASD−,p ≤ 0.05). No differences were found between groups for SICI or age corrected active/resting motor threshold (AMT/RMT). Across all ASD youth (ASD− and ASD+), ICF was inversely correlated with worse inattention (Conners-3 Inattention (r = −0.41;p < 0.01) and ADHDRS-IV Inattention percentile (r = −0.422,p < 0.01) scores. ICF remains intact in ASD− but is impaired in ASD+. Lack of ICF is associated with inattention and executive function across ASD. Taken with the present findings, ADHD may have a distinct electrophysiological “signature” in ASD youth. ICF may constitute an emerging biomarker to study the physiology of ADHD in ASD, which may align with disease prognosis or treatment response.
Overall and progression-free survival with cabazitaxel in metastatic castration-resistant prostate cancer in routine clinical practice: the FUJI cohort
Authors:   on behalf of the FUJI Investigators, Rouyer Magali , Oudard Stéphane , Joly Florence , Fizazi Karim , Tubach Florence , Jove Jérémy , Lacueille Clémentine , Lamarque Stéphanie , Guiard Estelle , Balestra Aurélie , Droz-Perroteau Cécile , Fourrier-Reglat Annie , Moore Nicholas 
Published: November 2019

Abstract

Background
Cabazitaxel is a treatment of metastatic castration-resistant prostate cancer (mCRPC) after docetaxel failure. The FUJI cohort aimed to confirm the real-life overall and progression-free survival (OS, PFS) and safety of cabazitaxel.

Methods
Multicentre, non-interventional cohort of French mCRPC patients initiating cabazitaxel between 2013 and 2015, followed 18 months.

Results
Four hundred one patients were recruited in 42 centres. At inclusion, median age was 70, main metastatic sites were bones (87%), lymph nodes (42%) and visceral (20%). 18% had cabazitaxel in 2nd-line treatment, 39% in 3rd-line and 43% in 4th-line or beyond. All had prior docetaxel, and 82% prior abiraterone, enzalutamide or both. Median duration of cabazitaxel treatment was 3.4 months. Median OS from cabazitaxel initiation was 11.9 months [95% CI: 10.1–12.9]. In multivariate analyses, grade ≥ 3 adverse events, visceral metastases, polymedication, and >5 bone metastases were associated with a shorter OS. Main grade ≥ 3 adverse events were haematological with 8% febrile neutropenia.

Conclusion
Real-life survival with cabazitaxel in FUJI was shorter than in TROPIC (pivotal trial, median OS 15.1 months) or PROSELICA (clinical trial 20 vs 25 mg/m2, median OS, respectively, 13.4 and 14.5 months). There was no effect of treatment-line on survival. No unexpected adverse concerns were identified.

Study registration
It was registered with the European Medicines Agency EUPASS registry, available at www.encepp.eu, as EUPAS10391. It has been approved as an ENCEPP SEAL study.
Survival after cancer in children, adolescents and young adults in the Nordic countries from 1980 to 2013
Authors: Rostgaard Klaus , Hjalgrim Henrik , Madanat-Harjuoja Laura , Johannesen Tom B. , Collin Sofia , Hjalgrim Lisa L. 
Published: November 2019

Abstract
Background
The present study aimed to assess whether the widespread concern of inferior cancer survival in adolescents and young adults (AYAs) compared with children and adults holds true in a Nordic setting with important differences in healthcare organisation compared with the United States (e.g. free access to healthcare) and the United Kingdom (e.g. young teenagers are treated in paediatric departments).

Methods
Five-year relative survival was calculated for 17 diagnostic groups in patients diagnosed in 2000–2013 in three diagnostic age categories: children (0–14 years), AYAs (15–24 years) and adults (25–34 years).

Results
For 13 out of 17 diagnostic groups examined, there was no difference in survival between AYAs and neighbouring age categories. For acute lymphoblastic leukaemias, astrocytomas, rhabdomyosarcomas and non-rhabdomyosarcoma soft tissue sarcomas we found survival in children to be superior to that in AYAs. For these four diagnostic groups, the rate of survival improvement over three calendar periods (1980–1989, 1990–1999 and 2000–2013) was not particularly low in AYAs compared with neighbouring age categories.

Conclusions
The present study suggests that in an affluent setting with free access to healthcare, meaningful differences in survival between AYA patients and either childhood or adult patients are a phenomenon of the past for most AYA cancer diagnostic groups.
Natural and non-natural antioxidative compounds: potential candidates for treatment of vascular calcification
Authors: Chao Chia-Ter , Yeh Hsiang-Yuan , Tsai You-Tien , Chuang Pei-Huan , Yuan Tzu-Hang , Huang Jenq-Wen , Chen Huei-Wen 
Published: November 2019

AbstractVascular calcification (VC) is highly prevalent in patients with advanced age, or those with chronic kidney disease and diabetes, accounting for substantial global cardiovascular burden. The pathophysiology of VC involves active mineral deposition by transdifferentiated vascular smooth muscle cells exhibiting osteoblast-like behavior, building upon cores with or without apoptotic bodies. Oxidative stress drives the progression of the cellular phenotypic switch and calcium deposition in the vascular wall. In this review, we discuss potential compounds that shield these cells from the detrimental influences of reactive oxygen species as promising treatment options for VC. A comprehensive summary of the current literature regarding antioxidants for VC is important, as no effective therapy is currently available for this disease. We systematically searched through the existing literature to identify original articles investigating traditional antioxidants and novel compounds with antioxidant properties with regard to their effectiveness against VC in experimental or clinical settings. We uncovered 36 compounds with antioxidant properties against VC pathology, involving mechanisms such as suppression of NADPH oxidase, BMP-2, and Wnt/β-catenin; anti-inflammation; and activation of Nrf2 pathways. Only two compounds have been tested clinically. These findings suggest that a considerable opportunity exists to harness these antioxidants for therapeutic use for VC. In order to achieve this goal, more translational studies are needed.
Multisite phosphorylation drives phenotypic variation in (p)ppGpp synthetase-dependent antibiotic tolerance
Authors: Libby Elizabeth A. , Reuveni Shlomi , Dworkin Jonathan 
Published: November 2019

AbstractIsogenic populations of cells exhibit phenotypic variability that has specific physiological consequences. Individual bacteria within a population can differ in antibiotic tolerance, but whether this variability can be regulated or is generally an unavoidable consequence of stochastic fluctuations is unclear. Here we report that a gene encoding a bacterial (p)ppGpp synthetase in Bacillus subtilis, sasA, exhibits high levels of extrinsic noise in expression. We find that sasA is regulated by multisite phosphorylation of the transcription factor WalR, mediated by a Ser/Thr kinase-phosphatase pair PrkC/PrpC, and a Histidine kinase WalK of a two-component system. This regulatory intersection is crucial for controlling the appearance of outliers; rare cells with unusually high levels of sasA expression, having increased antibiotic tolerance. We create a predictive model demonstrating that the probability of a given cell surviving antibiotic treatment increases with sasA expression. Therefore, multisite phosphorylation can be used to strongly regulate variability in antibiotic tolerance.
A meta-analysis of global fungal distribution reveals climate-driven patterns
Authors: Větrovský Tomáš , Kohout Petr , Kopecký Martin , Machac Antonin , Man Matěj , Bahnmann Barbara Doreen , Brabcová Vendula , Choi Jinlyung , Meszárošová Lenka , Human Zander Rainier , Lepinay Clémentine , Lladó Salvador , López-Mondéjar Rubén , Martinović Tijana , Mašínová Tereza , Morais Daniel , Navrátilová Diana , Odriozola Iñaki , Štursová Martina , Švec Karel , Tláskal Vojtěch , Urbanová Michaela , Wan Joe , Žifčáková Lucia , Howe Adina , Ladau Joshua , Peay Kabir Gabriel , Storch David , Wild Jan , Baldrian Petr 
Published: November 2019

AbstractThe evolutionary and environmental factors that shape fungal biogeography are incompletely understood. Here, we assemble a large dataset consisting of previously generated mycobiome data linked to specific geographical locations across the world. We use this dataset to describe the distribution of fungal taxa and to look for correlations with different environmental factors such as climate, soil and vegetation variables. Our meta-study identifies climate as an important driver of different aspects of fungal biogeography, including the global distribution of common fungi as well as the composition and diversity of fungal communities. In our analysis, fungal diversity is concentrated at high latitudes, in contrast with the opposite pattern previously shown for plants and other organisms. Mycorrhizal fungi appear to have narrower climatic tolerances than pathogenic fungi. We speculate that climate change could affect ecosystem functioning because of the narrow climatic tolerances of key fungal taxa.
Landscape determinants of density of blacklegged ticks, vectors of Lyme disease, at the northern edge of their distribution in Canada
Authors: Talbot Benoit , Slatculescu Andreea , Thickstun Charles R. , Koffi Jules K. , Leighton Patrick A. , McKay Roman , Kulkarni Manisha A. 
Published: November 2019

AbstractIn eastern North America, including Canada, Lyme disease is caused by Borrelia burgdorferi sensu stricto and transmitted to humans by the blacklegged tick, Ixodes scapularis. The last decade has seen a growing incidence of Lyme disease in Canada, following the northward range expansion of I. scapularis tick populations from endemic areas in eastern United States. This may be attributable to movement of the many hosts that they parasitize, including songbirds, deer and small mammals. In this study, we wanted to test the effect of spatial, temporal and ecological variables, on blacklegged tick density and infection rates, near the northern limit of their distribution in Ontario and Quebec, Canada. We found an effect of both proportion of forested areas and distance to roads, on density of I. scapularis ticks and prevalence of infection by B. burgdorferi. We also found an effect of both sampling year and ordinal sampling data on prevalence of infection by B. burgdorferi. In six adjacent sites showing evidence of reproducing I. scapularis populations, we found that forest composition and structure influenced density of I. scapularis ticks. Our results suggest that blacklegged tick density and infection rate in Canada may be influenced by a variety of factors.
Genome Wide Meta-Analysis identifies common genetic signatures shared by heart function and Alzheimer’s disease
Authors: Sáez M. E. , González-Pérez A. , Hernández-Olasagarre B. , Beà A. , Moreno-Grau S. , de Rojas I. , Monté-Rubio G. , Orellana A. , Valero S. , Comella J. X. , Sanchís D. , Ruiz A. 
Published: November 2019

AbstractEchocardiography has become an indispensable tool for the study of heart performance, improving the monitoring of individuals with cardiac diseases. Diverse genetic factors associated with echocardiographic measures have been previously reported. The impact of several apoptotic genes in heart development identified in experimental models prompted us to assess their potential association with human cardiac function. This study aimed at investigating the possible association of variants of apoptotic genes with echocardiographic traits and to identify new genetic markers associated with cardiac function. Genome wide data from different studies were obtained from public repositories. After quality control and imputation, a meta-analysis of individual association study results was performed. Our results confirmed the role of caspases and other apoptosis related genes with cardiac phenotypes. Moreover, enrichment analysis showed an over-representation of genes, including some apoptotic regulators, associated with Alzheimer’s disease. We further explored this unexpected observation which was confirmed by genetic correlation analyses. Our findings show the association of apoptotic gene variants with echocardiographic indicators of heart function and reveal a novel potential genetic link between echocardiographic measures in healthy populations and cognitive decline later on in life. These findings may have important implications for preventative strategies combating Alzheimer’s disease.
Quantification of intracellular N-terminal β-actin arginylation
Authors: Chen Li , Kashina Anna 
Published: November 2019

AbstractActin is a ubiquitous, essential, and highly abundant protein in all eukaryotic cells that performs key roles in contractility, adhesion, migration, and leading edge dynamics. The two non-muscle actins, β- and γ-, are ubiquitously present in every cell type and are nearly identical to each other at the amino acid level, but play distinct intracellular roles. The mechanisms regulating this distinction have been the focus of recent interest in the field. Work from our lab has previously shown that β-, but not γ-, actin undergoes N-terminal arginylation on Asp3. While functional evidence suggest that this arginylation may be important to actin’s function, progress in these studies so far has been hindered by difficulties in arginylated actin detection, precluding estimations of the abundance of arginylated actin in cells, and its occurrence in different tissues and cell types. The present study represents the first antibody-based quantification of the percentage of arginylated actin in migratory non-muscle cells under different physiological conditions, as well as in different cells and tissues. We find that while the steady-state level of arginylated actin is relatively low, it is consistently present in vivo, and is somewhat more prominent in migratory cells. Inhibition of N-terminal actin acetylation dramatically increases the intracellular actin arginylation level, suggesting that these two modifications may directly compete in vivo. These findings constitute an essential step in our understanding of actin regulation by arginylation, and in uncovering the dynamic interplay of actin’s N-terminal modifications in vivo.
Using a Single Daytime Performance Test to Identify Most Individuals at High-Risk for Performance Impairment during Extended Wake
Authors: St. Hilaire Melissa A. , Kristal Bruce S. , Rahman Shadab A. , Sullivan Jason P. , Quackenbush John , Duffy Jeanne F. , Barger Laura K. , Gooley Joshua J. , Czeisler Charles A. , Lockley Steven W. 
Published: November 2019

AbstractWe explored the predictive value of a neurobehavioral performance assessment under rested baseline conditions (evaluated at 8 hours awake following 8 hours of sleep) on neurobehavioral response to moderate sleep loss (evaluated at 20 hours awake two days later) in 151 healthy young participants (18–30 years). We defined each participant’s response-to-sleep-loss phenotype based on the number of attentional failures on a 10-min visual psychomotor vigilance task taken at 20 hours awake (resilient: less than 6 attentional failures, n = 26 participants; non-resilient: 6 or more attentional failures, n = 125 participants). We observed that 97% of rested participants with 2 or more attentional failures (n = 73 of 151) and 100% of rested participants with 3 or more attentional failures (n = 57 of 151) were non-resilient after moderate sleep loss. Our approach can accurately identify a significant proportion of individuals who are at high risk for neurobehavioral performance impairment from staying up late with a single neurobehavioral performance assessment conducted during rested conditions. Additional methods are needed to predict the future performance of individuals who are not identified as high risk during baseline.
Structures of GapR reveal a central channel which could accommodate B-DNA
Authors: Tarry Michael J. , Harmel Christoph , Taylor James A. , Marczynski Gregory T. , Schmeing T. Martin 
Published: November 2019

AbstractGapR is a nucleoid-associated protein required for the cell cycle of Caulobacter cresentus. We have determined new crystal structures of GapR to high resolution. As in a recently published structure, a GapR monomer folds into one long N-terminal α helix and two shorter α helices, and assembles into a tetrameric ring with a closed, positively charged, central channel. In contrast to the conclusions drawn from the published structures, we observe that the central channel of the tetramer presented here could freely accommodate B-DNA. Mutation of six conserved lysine residues lining the cavity and electrophoretic mobility gel shift experiments confirmed their role in DNA binding and the channel as the site of DNA binding. Although present in our crystals, DNA could not be observed in the electron density maps, suggesting that DNA binding is non-specific, which could be important for tetramer-ring translocation along the chromosome. In conjunction with previous GapR structures we propose a model for DNA binding and translocation that explains key published observations on GapR and its biological functions.
The β-oxidation pathway is downregulated during diapause termination in Calanus copepods
Authors: Skottene Elise , Tarrant Ann M. , Olsen Anders J. , Altin Dag , Østensen Mari-Ann , Hansen Bjørn Henrik , Choquet Marvin , Jenssen Bjørn M. , Olsen Rolf Erik 
Published: November 2019

AbstractCalanuscopepods are keystone species in marine ecosystems, mainly due to their high lipid content, which is a nutritious food source for e.g. juvenile fish. Accumulated lipids are catabolized to meet energy requirements during dormancy (diapause), which occurs during the last copepodite stage (C5). The current knowledge of lipid degradation pathways during diapause termination is limited. We characterized changes in lipid fullness and generated transcriptional profiles in C5s during termination of diapause and progression towards adulthood. Lipid fullness of C5s declined linearly during developmental progression, but more β-oxidation genes were upregulated in early C5s compared to late C5s and adults. We identified four possible master regulators of energy metabolism, which all were generally upregulated in early C5s, compared to late C5s and adults. We discovered that one of two enzymes in the carnitine shuttle is absent from the calanoid copepod lineage. Based on the geographical location of the sampling site, the field-samples were initially presumed to consist ofC. finmarchicus. However, the identification ofC. glacialisin some samples underlines the need for performing molecular analyses to reliably identifyCalanusspecies. Our findings contributes to a better understanding of molecular events occurring during diapause and diapause termination in calanoid copepods.
Integrating multi-platform genomic datasets for kidney renal clear cell carcinoma subtyping using stacked denoising autoencoders
Authors: Gu Tongjun , Zhao Xiwu 
Published: November 2019

AbstractClear cell renal cell carcinoma (ccRCC) is highly heterogeneous and is the most lethal cancer of all urologic cancers. We developed an unsupervised deep learning method, stacked denoising autoencoders (SdA), by integrating multi-platform genomic data for subtyping ccRCC with the goal of assisting diagnosis, personalized treatments and prognosis. We successfully found two subtypes of ccRCC using five genomics datasets for Kidney Renal Clear Cell Carcinoma (KIRC) from The Cancer Genome Atlas (TCGA). Correlation analysis between the last reconstructed input and the original input data showed that all the five types of genomic data positively contribute to the identification of the subtypes. The first subtype of patients had significantly lower survival probability, higher grade on neoplasm histology and higher stage on pathology than the other subtype of patients. Furthermore, we identified a set of genes, proteins and miRNAs that were differential expressed (DE) between the two subtypes. The function annotation of the DE genes from pathway analysis matches the clinical features. Importantly, we applied the model learned from KIRC as a pre-trained model to two independent datasets from TCGA, Lung Adenocarcinoma (LUAD) dataset and Low Grade Glioma (LGG), and the model stratified the LUAD and LGG patients into clinical associated subtypes. The successful application of our method to independent groups of patients supports that the SdA method and the model learned from KIRC are effective on subtyping cancer patients and most likely can be used on other similar tasks. We supplied the source code and the models to assist similar studies at https://github.com/tjgu/cancer_subtyping.