bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quasilinear turbulent particle and heat transport modelling with a neural-network-based approach founded on gyrokinetic calculations and experimental data
Authors: Narita E. , Honda M. , Nakata M. , Yoshida M. , Hayashi N. 
Published: September 2021

Abstract
A novel quasilinear turbulent transport model DeKANIS has been constructed founded on the gyrokinetic analysis of JT-60U plasmas. DeKANIS predicts particle and heat fluxes fast with a neural network (NN) based approach and distinguishes diffusive and non-diffusive transport processes. The original model only considered particle transport, but its capability has been extended to cover multi-channel turbulent transport. To solve a set of particle and heat transport equations stably in integrated codes with DeKANIS, the NN model embedded in DeKANIS has been modified. DeKANIS originally determined turbulent saturation levels semi-empirically based on JT-60U experimental data, but now it can also estimate them using a theory-based saturation rule. The new saturation model is still partly connected to experimental data, but it offers the potential for applying DeKANIS independently of the device.
A study on the enhancement of the tribological properties of nitrile-butadiene rubber reinforced by nano-ZnO particles from an atomic view
Authors: He Enqiu , Wang Shijie , Tang Liming , Chen Jichi 
Published: September 2021

Abstract
In this study, three-layer molecular models of frictional pair containing nitrile-butadiene rubber matrix reinforced by nano-ZnO particle as the core and Fe layers as the counterparts are first developed. Molecular dynamics simulations are then conducted to explore the enhanced effects of nano-ZnO particle on tribological behaviors of NBR matrix. The simulation results show that the frictional coefficient of NBR matrix can be efficiently reduced of approximately 30% by incorporation of nano-ZnO particle. In order to reveal the atomic inherent mechanisms on the enhanced effects, the radius of gyration, concentration profiles, velocities distributions and temperature profiles of NBR chains are calculated and discussed in detail. Through quantitative validations of experimental works, it can be finally concluded that by incorporation of nano-ZnO particle, due to the strong vdW adsorption forces, NBR chains can be efficiently restricted around the surface of nano-ZnO particle, leading to the whole NBR matrix to perform better ability to avoid adhesive wear phenomenon, better deformation resistance, lower friction coefficients and wear loss, et al In addition, it is also proved that the proposed molecular modeling and dynamics simulation methods can be an efficient way to provide inherent mechanisms for studying tribological properties of nano-ZnO/NBR matrix in addition to experimental works.
The water droplet erosion resistance of Ni-based composite coating through laser cladding
Authors: Gong Yuling , Cui Chen , Wu Meiping , Miao Xiaojin 
Published: September 2021

Abstract
Water droplet erosion (WDE) usually occurs in TC4 turbine blades under actual working conditions, which seriously endangers the safe and stable operation of the turbine. To solve the problem of WDE in TC4 turbine blades under high-speed solid-liquid impact, CeO2/Ni60A composite coatings with different laser powers were successfully developed on the surface of TC4 by using laser cladding technology. The working environment of the turbine blade under high- speed solid-liquid impact was simulated by water jet technique, and the effect of laser power on the coating resistance to water droplet erosion was analyzed. It can be seen from the results that the coating was composed of α-Ti, Ti2Ni, TiB2 and TiC, and laser power had a significant influence on the growth of grain structure. At 6000 W laser power, the average microhardness of the coating reached 1105 HV0.3, i.e., 3.25 times of TC4 substrate. However, too high laser power made the hard phases of TiC and TiB2 brittle. In the water droplet erosion experiment, the high power resulted in the cracks in the coating. At the laser power of 5000 W, the grain refinement effect was the best. The width and depth of water erosion were 0.908 mm and 0.148 mm, respectively, which were lower than TC4 substrate by 27.5% and 41.5% times. The preparation of CeO2/Ni60A coatings on the surface of TC4 alloy was effective to solve the problem of WDE in TC4 turbine blades and prolong the service life of TC4 blades. Moreover, the finer the grain structure in the coating, the better the WDE resistance.
Aggregation and thermally induced photo-physics and structural ordering of thiophene-quinoxaline copolymer
Authors: Tegegne Newayemedhin A 
Published: September 2021

Abstract
Aggregation and thermally induced photo-physics of a low band gap thiophene-quinoxaline copolymer (TQ1) was investigated. The S0 ⟶ S1 transition of TQ1 in solution is found to be due to an intra-molecular charge transfer state while the excited state in aggregated TQ1 chains was due to intra and inter-chain excitons. On the other hand, the emission of TQ-1 recorded at 85 °C for more than 300 h confirmed that thermal stress hampers the inter-chain interaction as confirmed by the disappearance of the vibronic shoulder ascribed to it in the PL. In addition, it was observed that the PL intensity has drastically decreased while its absorption showed smaller change due to annealing for less than 40 h which confirmed either the introduction of new non-radiative channels or coiling of the copolymer due to thermal stress. The evolution XRD traces of TQ1 with thermal stress confirmed that it takes higher energy to break the long-range order than the molecular bonds in the copolymer.
DIMPL: a bioinformatics pipeline for the discovery of structured noncoding RNA motifs in bacteria
Authors: Brewer Kenneth I , Gaffield Glenn J , Puri Malavika , Breaker Ronald R 
Published: September 2021

Abstract

Summary
Recent efforts to identify novel bacterial structured noncoding RNA (ncRNA) motifs through searching long, GC-rich intergenic regions (IGRs) have revealed several new classes, including the recently validated HMP-PP riboswitch. The DIMPL (Discovery of Intergenic Motifs PipeLine) discovery pipeline described herein enables rapid extraction and selection of bacterial IGRs that are enriched for structured ncRNAs. Moreover, DIMPL automates the subsequent computational steps necessary for their functional identification.

Availability and implementation
The DIMPL pipeline is freely available as a Docker image with an accompanying set of Jupyter notebooks. Full instructions for download and use are available at https://github.com/breakerlab/dimpl.

Supplementary information
Supplementary data are available at Bioinformatics online.
SWIMmeR: an R-based software to unveiling crucial nodes in complex biological networks
Authors: Paci Paola , Fiscon Giulia 
Published: September 2021

Abstract

Summary
We present SWIMmeR, an open-source version of its predecessor SWIM (SWitchMiner) that is a network-based tool for mining key (switch) genes that are associated with intriguing patterns of molecular co-abundance and may play a crucial role in phenotypic transitions in various biological settings. SWIM was originally written in MATLAB®, a proprietary programming language that requires the purchase of a license to install, manipulate, operate and run the software. Over the last years, SWIM has sparked a widespread interest within the scientific community thanks to the promising results obtained through its application in a broad range of phenotype-specific scenarios, spanning from complex diseases to grapevine berry maturation. This success has created the call for it to be distributed in a freely accessible, open-source, runtime environment, such as R, aimed at a general audience of non-expert users that cannot afford the leading proprietary solution. SWIMmeR is provided as a comprehensive collection of R functions and it also includes several additional features that make it less intensive in terms of computer time and more efficient in terms of usability and further implementation and extension.

Availability and implementation
The SWIMmeR source code is freely available at https://github.com/sportingCode/SWIMmeR.git, along with a practical user guide, including a usage example of its application on breast cancer dataset.

Supplementary information
Supplementary data are available at Bioinformatics online.
Increased expression of SLC25A1/CIC causes an autistic-like phenotype with altered neuron morphology
Authors: Rigby Michael J , Orefice Nicola Salvatore , Lawton Alexis J , Ma Min , Shapiro Samantha L , Yi Sue Y , Dieterich Inca A , Frelka Alyssa , Miles Hannah N , Pearce Robert A , Yu John Paul J , Li Lingjun , Denu John M , Puglielli Luigi 
Published: September 2021

Abstract
N ε-lysine acetylation within the lumen of the endoplasmic reticulum is a recently characterized protein quality control system that positively selects properly folded glycoproteins in the early secretory pathway. Overexpression of the endoplasmic reticulum acetyl-CoA transporter AT-1 in mouse forebrain neurons results in increased dendritic branching, spine formation and an autistic-like phenotype that is attributed to altered glycoprotein flux through the secretory pathway. AT-1 overexpressing neurons maintain the cytosolic pool of acetyl-CoA by upregulation of SLC25A1, the mitochondrial citrate/malate antiporter and ATP citrate lyase, which converts cytosolic citrate into acetyl-CoA. All three genes have been associated with autism spectrum disorder, suggesting that aberrant cytosolic-to-endoplasmic reticulum flux of acetyl-CoA can be a mechanistic driver for the development of autism spectrum disorder.
We therefore generated a SLC25A1 neuron transgenic mouse with overexpression specifically in the forebrain neurons.
The mice displayed autistic-like behaviours with a jumping stereotypy. They exhibited increased steady-state levels of citrate and acetyl-CoA, disrupted white matter integrity with activated microglia and altered synaptic plasticity and morphology. Finally, quantitative proteomic and acetyl-proteomic analyses revealed differential adaptations in the hippocampus and cortex.
Overall, our study reinforces the connection between aberrant cytosolic-to-endoplasmic reticulum acetyl-CoA flux and the development of an autistic-like phenotype.
Cognitive ocular motor deficits and white matter damage chronically after sports-related concussion
Authors: Symons Georgia F , Clough Meaghan , Mutimer Steven , Major Brendan P , O’Brien William T , Costello Daniel , McDonald Stuart J , Chen Zhibin , White Owen , Mychasiuk Richelle , Law Meng , Wright David K , O’Brien Terence J , Fielding Joanne , Kolbe Scott C , Shultz Sandy R 
Published: September 2021

AbstractA history of concussion has been linked to long-term cognitive deficits; however, the neural underpinnings of these abnormalities are poorly understood. This study recruited 26 asymptomatic male Australian footballers with a remote history of concussion (i.e. at least six months since last concussion), and 23 non-collision sport athlete controls with no history of concussion. Participants completed three ocular motor tasks (prosaccade, antisaccade and a cognitively complex switch task) to assess processing speed, inhibitory control and cognitive flexibility, respectively. Diffusion tensor imaging data were acquired using a 3 T MRI scanner, and analysed using tract-based spatial statistics, to investigate white matter abnormalities and how they relate to ocular motor performance. Australian footballers had significantly slower adjusted antisaccade latencies compared to controls (P = 0.035). A significant switch cost (i.e. switch trial error &gt; repeat trial error) was also found on the switch task, with Australian footballers performing increased magnitude of errors on prosaccade switch trials relative to prosaccade repeat trials (P = 0.023). Diffusion tensor imaging analysis found decreased fractional anisotropy, a marker of white matter damage, in major white matter tracts (i.e. corpus callosum, corticospinal tract) in Australian footballers relative to controls. Notably, a larger prosaccade switch cost was significantly related to reduced fractional anisotropy in anterior white matter regions found to connect to the prefrontal cortex (i.e. a key cortical ocular motor centre involved in executive functioning and task switching). Taken together, Australian footballers with a history of concussion have ocular motor deficits indicative of poorer cognitive processing speed and cognitive flexibility, which are related to reduce white matter integrity in regions projecting to important cognitive ocular motor structures. These findings provide novel insights into the neural mechanisms that may underly chronic cognitive impairments in individuals with a history of concussion.
Defining cardiovascular toxicities of cancer therapies: an International Cardio-Oncology Society (IC-OS) consensus statement
Authors: Herrmann Joerg , Lenihan Daniel , Armenian Saro , Barac Ana , Blaes Anne , Cardinale Daniela , Carver Joseph , Dent Susan , Ky Bonnie , Lyon Alexander R , López-Fernández Teresa , Fradley Michael G , Ganatra Sarju , Curigliano Giuseppe , Mitchell Joshua D , Minotti Giorgio , Lang Ninian N , Liu Jennifer E , Neilan Tomas G , Nohria Anju , O'Quinn Rupal , Pusic Iskra , Porter Charles , Reynolds Kerry L , Ruddy Kathryn J , Thavendiranathan Paaladinesh , Valent Peter 
Published: September 2021

Abstract
The discipline of Cardio-Oncology has seen tremendous growth over the past decade. It is devoted to the cardiovascular (CV) care of the cancer patient, especially to the mitigation and management of CV complications or toxicities of cancer therapies, which can have profound implications on prognosis. To that effect, many studies have assessed CV toxicities in patients undergoing various types of cancer therapies; however, direct comparisons have proven difficult due to lack of uniformity in CV toxicity endpoints. Similarly, in clinical practice, there can be substantial differences in the understanding of what constitutes CV toxicity, which can lead to significant variation in patient management and outcomes. This document addresses these issues and provides consensus definitions for the most commonly reported CV toxicities, including cardiomyopathy/heart failure and myocarditis, vascular toxicity, and hypertension, as well as arrhythmias and QTc prolongation. The current document reflects a harmonizing review of the current landscape in CV toxicities and the definitions used to define these. This consensus effort aims to provide a structure for definitions of CV toxicity in the clinic and for future research. It will be important to link the definitions outlined herein to outcomes in clinical practice and CV endpoints in clinical trials. It should facilitate communication across various disciplines to improve clinical outcomes for cancer patients with CV diseases.
Quantifying the impact of regional variations in COVID-19 infections and hospitalizations across Ireland
Authors: Roe M , Wall P , Mallon P , Sundaram D , Kumawat J , Horgan M 
Published: September 2021

Abstract

Background
As most COVID-19 transmission occurs locally, targeted measures where the likelihood of infection and hospitalization is highest may be a prudent risk management strategy. To date, in the Republic of Ireland, a regional comparison of COVID-19 cases and hospitalizations has not been completed. Here, we investigate (i) the variation in rates of confirmed infection and hospital admissions within geographical units of the Republic of Ireland and (ii) frequency of deviations in risk of infection or risk of hospitalization.

Methods
We analyzed routinely collected, publicly available data available from the National Health Protection and Surveillance Centre and Health Service Executive from nine geographical units, known as Community Health Organization areas. The observational period included 206 14-day periods (1 September 2020–15 April 2021).

Results
A total of 206 844 laboratory-confirmed cases and 7721 hospitalizations were reported. The national incidence of confirmed infections was 4508 [95% confidence interval (CI) 4489–4528] per 100 000 people. The risk of hospital admission among confirmed cases was 3.7% (95% CI 3.5–3.9). Across geographical units, the likelihood that rolling 14-day risk of infection or hospitalization exceeded national levels was 9–86% and 0–88%, respectively. In the most affected regions, we estimate this resulted in an excess of 15 180 infections and 1920 hospitalizations.

Conclusions
Responses to future COVID-19 outbreaks should consider the risk and harm of infection posed to people living in specific regions. Given the recent surges of COVID-19 cases in Europe, every effort should be made to strengthen local surveillance and to tailor community-centred measures to control transmission.
Epidemiology and Clinical Impact of Respiratory Coinfections at Diagnosis of Pneumocystis jirovecii Pneumonia
Authors: Lécuyer Romain , Issa Nahema , Tessoulin Benoit , Lavergne Rose-Anne , Morio Florent , Gabriel Frederic , Canet Emmanuel , Bressollette-Bodin Céline , Guillouzouic Aurélie , Boutoille David , Raffi François , Lecomte Raphael , Le Turnier Paul , Deschanvres Colin , Camou Fabrice , Gaborit Benjamin Jean ,   PRONOCYSTIS Study Group, Raffi Francois , Boutoille David , Biron Charlotte , Lefebvre Maeva , Jean Gaborit Benjamin , Le Turnier Paul , Deschanvres Colin , Lecomte Raphael , Chauveau Marie , Lécuyer Romain , Asquier-Khati Antoine , Le Pape Patrice , Morio Florent , Lavergne Rose-Anne , Jeddi Fakhri , Corvec Stéphane , Bemer Pascale , Caillon Jocelyne , Guillouzouic Aurélie , Leroy Anne-Gaëlle , Lakhal Karim , Cinotti Raphaël , Roquilly Antoine , Asehnoune Karim , Reignier Jean , Canet Emmanuel , Zambon Olivier , Seguin Amélie , Miailhe Arnaud-Félix , Xavier Blanc François , Bretonniere Cédric , Morin Paul , Camou Fabrice , Issa Nahéma , Guisset Olivier , Mourissoux Gaelle , Delhaes Laurence , Accoceberry Isabelle , Gabriel Frederic 
Published: September 2021

Abstract

Background
The role of respiratory coinfections at diagnosis of Pneumocystis jirovecii pneumonia (PcP) on clinical impact has been underestimated.

Methods
A retrospective observational study was conducted January 2011 to April 2019 to evaluate respiratory coinfections at diagnosis of PcP patients in 2 tertiary care hospitals. Coinfection was defined by identification of pathogens from P. jirovecii-positive samples.

Results
Of 7882 respiratory samples tested for P. jirovecii during the 8-year study, 328 patients with diagnosis of PcP were included. Mean age was 56.7 (SD 14.9) years, 193 (58.8%) were male, 74 (22.6%) had positive HIV serology, 125 (38.1%) had viral coinfection, 76 (23.2%) bacterial coinfection, and 90-day mortality was 25.3%. In the overall population, 90-day mortality was independently associated with solid tumor underlying disease (odds ratio [OR], 11.8; 95% confidence interval [CI], 1.90–78.0; P = .008), sepsis-related organ failure assessment score (SOFA) at admission (OR, 1.62; 95% CI, 1.34–2.05; P&lt; .001), and cytomegalovirus (CMV) respiratory coinfection (OR, 3.44; 95% CI, 1.24–2.90; P = .02). Among HIV-negative patients, respiratory CMV coinfection was associated with worse prognosis, especially when treated with adjunctive corticosteroid therapy.

Conclusions
Respiratory CMV coinfection at PcP diagnosis was independently associated with increased 90-day mortality, specifically in HIV-negative patients.
Trace mineral source impacts rumen trace mineral metabolism and fiber digestion in steers fed a medium-quality grass hay diet
Authors: Guimaraes Octavio , Jalali Sam , Wagner John J , Spears Jerry W , Engle Terry Eugene 
Published: September 2021

Abstract
Twelve Angus steers (BW 452.8 ± 6.1 kg) fitted with ruminal cannulae were used to determine the impact of trace mineral (TM) source on digestibility, ruminal volatile fatty acid (VFA) composition, ruminal soluble concentrations of Cu, Zn, and Mn, and relative binding strength of trace minerals located in the rumen insoluble digesta fraction. Steers were fed a medium-quality grass hay diet (DM basis: 10.8% CP, 63.1% neutral detergent fiber [NDF], 6.9 mg Cu/kg, 65.5 mg Mn/kg, and 39.4 mg Zn/kg) supplemented with protein for 21 d. Treatments consisted of either sulfate (STM) or hydroxy (HTM) sources (n = 6 steers/treatment) to provide 20, 40, and 60 mg supplemental Cu, Mn, and Zn/kg DM, respectively. Following a 21-d adaptation period, total fecal output was collected for 5 d. Dry matter (P &lt; 0.07) and CP (P &lt; 0.06) digestibility tended to be reduced, and NDF (P &lt; 0.04) and acid detergent fiber (ADF) (P &lt; 0.05) digestibility were reduced in STM- vs. HTM-supplemented steers. On day 6, ruminal fluid was collected at 0, 2, and 4 h post-feeding and analyzed for VFA. There were no treatment x time interactions for VFA. Steers receiving HTM had less (P &lt; 0.02) molar proportions of butyric acid and greater (P &lt; 0.05) total VFA concentrations than STM-supplemented steers. Steers were then fed the same diet without supplemental Cu, Zn, or Mn for 14 d. On day 15 steers received a pulse dose of 20 mg Cu, 40 mg Mn, and 60 mg Zn/kg DM from either STM or HTM (n = 6 steers/treatment). Ruminal samples were obtained at 2-h intervals starting at −4 and ending at 24 h relative to dosing. There was a treatment x time interaction (P &lt; 0.03) for ruminal soluble Cu, Mn, and Zn concentrations. Ruminal soluble mineral concentrations were greater (P &lt; 0.05) for Cu at 4, 6, 8, 10, 12, and 14 h; for Mn at 4 and 6 h; and for Zn at 4, 6, and 8 h post-dosing in STM compared with HTM-supplemented steers. Copper concentrations were greater (P &lt; 0.05) at 12 and 24 h and Zn concentrations in ruminal solid digesta were greater at 24 h in HTM-supplemented steers. Upon dialysis against Tris-EDTA, the percent Zn released from digesta was greater (P &lt; 0.05) at 12 h (P &lt; 0.03) and 24 h (P &lt; 0.05), and the percent Cu released was greater (P &lt; 0.02) at 24 h post-dosing in HTM steers when compared with STM-supplemented steers. Results indicate that Cu and Zn from HTM have low solubility in the rumen and appear to be less tightly bound to ruminal solid digesta than Cu and Zn from STM. The lower ruminal soluble concentrations of Cu and Zn in steers given HTM were associated with greater fiber digestibility.
Granger Causality Testing in High-Dimensional VARs: A Post-Double-Selection Procedure
Authors: Hecq Alain , Margaritella Luca , Smeekes Stephan 
Published: September 2021

AbstractWe develop an LM test for Granger causality in high-dimensional (HD) vector autoregressive (VAR) models based on penalized least squares estimations. To obtain a test retaining the appropriate size after the variable selection done by the lasso, we propose a post-double-selection procedure to partial out effects of nuisance variables and establish its uniform asymptotic validity. We conduct an extensive set of Monte-Carlo simulations that show our tests perform well under different data generating processes, even without sparsity. We apply our testing procedure to find networks of volatility spillovers and we find evidence that causal relationships become clearer in HD compared to standard low-dimensional VARs.