bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of legume research and extension in New Zealand (1990–2022)
Authors: Moot Derrick J. 
Published: November 2022

Legumes have underpinned transformational change on New Zealand sheep and beef farms over the last 30 years. This was through an emphasis on ewe nutrition based on lucerne or red clover dominant pastures, and increased use of subterranean and white clovers on uncultivatable hill country. Pre- and post-weaning lamb growth rates have increased, and enabled earlier slaughter of heavier lambs. The farm systems results include greater numbers of hoggets mated, higher lambing percentages and greater ewe efficiency (kg lamb weaned/kg ewe mated). Extension packages to support legume use have compared growth rates of resident and legume-based pastures, economic analyses of successful farms and management packages for the most appropriate legume in different environments. Over the same period, the dairy industry rapidly expanded in cow numbers and area onto flat irrigated land on the Canterbury Plains. The nitrogen deficiency of perennial ryegrass was overcome by a linear increase in nitrogen fertiliser use. Environmental concerns from this intensification has led to a legislated nitrogen cap of 190 kg/ha.year. This, coupled with a recent trebling in urea price, has returned attention to increasing the white clover content of these pastures. Nitrogen applications can be minimised by using diverse pastures sown with a legume, herb and <8 kg/ha of perennial ryegrass. Work on other legumes, including annuals and those with condensed tannins, has to date failed to increase their use in most pastoral settings, with the exception of the perennial lupin which is adapted to high-aluminium soils in the South Island High Country.
Potential relevance of a motor skill “proficiency barrier” on health‐related fitness in youth
Authors: Abrams T. Cade , Terlizzi Bryan M. , De Meester An , Sacko Ryan S. , Irwin J. Megan , Luz Carlos , Rodrigues Luís Paulo , Cordovil Rita , Lopes Vítor P. , Schneider Kirsten , Stodden David F. 
Published: November 2022

ABSTRACTThis study investigated the potential impact of a motor skill proficiency barrier on measures of cardiorespiratory (CRF) and musculoskeletal (MSF) fitness in youth. A sample of 241 youth (114 girls) aged 10 ‐ 18 years, completed the Motor Competence Assessment battery with composite scores indexed according to age‐ and gender‐adjusted percentile scores. Motor competence (MC) levels were categorized as low (≤ 25%tile – proficiency barrier), moderate (≥ 26%tile to < 75%tile), and high (≥ 75%tile). CRF levels (Health Risk, Needs Improvement, and Healthy) were assessed using the Fitnessgram® 20 m PACER test. Low (≤ 20%tile), moderate (≥ 21%tile to ≤ 80%tile), and high (≥ 80%tile) MSF levels were assessed using grip strength normative data. Two 3 × 3 chi‐square tests were conducted to determine the probability of MC level predicting CRF and MSF levels. Results demonstrated statistically significant models for performance on both the PACER (χ2[4, N = 241] = 22.65, p < .001) and grip strength (χ2[4, N = 241] = 23.95, p < .001). Strong evidence of a proficiency barrier impacting CRF was noted, as no low skilled youth met the “Healthy” fitness zone standards for PACER performance. Evidence supporting a barrier with grip strength was not as strong, as 20.8% of youth exhibiting low MC displayed high grip strength. However, all individuals with high levels of MC demonstrated at least moderate grip strength. Results emphasize the importance of developing MC during childhood as it may provide a protective effect against unhealthy CRF and MSF across youth.
Fabrication of vertically aligned CNT- vanadium oxide hybrid architecture with enhanced compressibility and supercapacitor performance
Authors: Arya Nitika , Verma Divya , Balakrishnan Viswanath 
Published: November 2022

Abstract
The demand for energy storage devices in wearable electronics effectuates a requisition for compressible and flexible supercapacitors with high performance and mechanical reliability. We report the fabrication of vanadium oxide hybrid with VACNT and its electrochemical supercapacitor performance along with the compression response. Compressive modulus of 730 ± 40 kPa is obtained for bare VACNT forest whereas its hybrid with vanadium oxide shows a compressive modulus of 240 ± 60 kPa. Controlled CVD process enabled the formation of porous CNT architecture coated with vanadium oxide particles due to the simultaneous reduction of V2O5 and partial oxidation of CNT forest. Vanadium oxide decorated on vertically aligned carbon nanotubes acts as the active material for supercapacitor applications. A 17 folds increase in areal capacitance and 36 folds increase in volumetric capacitance are observed on depositing vanadium oxide particles on the VACNT forest. High coulombic efficiency of 97.8% is attained even after 10 000 charge-discharge cycles indicating the high stability of the hybrid.
Characterisation of the auxiliary heating power delivered by the 40 keV neutral beam injectors on the COMPASS tokamak
Authors: Bogar K , Varju J , Havlicek J , Stockel J , Podolnik A , Hron M , Panek R 
Published: November 2022

Abstract
Two identical neutral beam injectors (NBIs) have been installed on the COMPASS tokamak. Each of them is capable of producing a deuterium (or hydrogen, helium) neutral beam with nominal power of up to 400 kW at 40 keV. Since the COMPASS tokamak is a compact machine, the design of the neutral beams was carefully optimized to fit the neutral beam through the narrow ports of the tokamak. However, once the neutral beams are operated out of the scope of their optimal parameters, additional power losses occur due to neutral beam scraping. This article investigates the amount of power loss due to neutral beam scraping. The losses are calculated using the neutral beam models and measured neutral beam parameters. The calculated results are compared with the measured power delivered into the plasma. Two different neutral beam models are employed. One describes the neutral beam as a sum of small beamlets, which are Gaussian-like. The second one describes the neutral beam as a single Gaussian beam. The amount of the power lost to scraping is determined by both models and compared. Neutral beam parameters, the input parameters for both models, are derived from the Doppler-shifted spectra emitted by fast neutral atoms. It is shown that when operating NBIs at nominal parameters, the scraping losses are negligible (

<

5% ). If the NBIs are operated too far from the nominal parameters, the scraping losses can reach up to ∼60% of the NBI output power. As the highest fractional losses occur with low power NBI, the beam duct is capable of withstanding the corresponding power loads. The expected auxiliary heating power

P

A
U
X

, the power entering the tokamak chamber carried by fast neutrals, is benchmarked against the additional plasma input power observed in the measured plasma parameters

P

N
B
I

. The additional plasma input power

P

N
B
I

is derived from the plasma power balance. The power balance terms are independent of the neutral beam model used for the auxiliary heating power calculation

P

A
U
X

. The results of the power balance evaluation reveal a difference between two NBIs installed on COMPASS. One of the injectors systematically delivers 17% less power than the other into the plasma given the same beam parameters. It is concluded that the additional losses occur before the beam enters the tokamak chamber.
Overview of the 36th International Conference, 36th Eg-MRS 202
Authors: Aly Arafa H. 
Published: November 2022

The overview describes the main directions and results of the 36th Eg-MRS International Conference, 36th Eg-MRS-2022 held in Cairo, Egypt, 24-25 September 2022. It gives the details about the participants and the proceedings.
The Volume contains Proceedings of the 36th Eg-MRS International Conference, Eg-MRS-2022:
Modernization, Innovations and Progress” which was held in Cairo, Egypt in September 24-25, 2022.. The Conference held online using Zoom due to COVID-19.
The purpose of the Conference is to share the results and prospects of the achievements in using advanced scientific, innovative and information technologies in materials sciences and its applications.
In fact, this is the third year of publishing a special issue of Eg-MRS international conferences under the umbrella of IOP material sciences and engineering. The first one was in November 2019; Hurghada, Egypt [1]. The second and third was in August 2020 & July 2022 which was online due to COVID-19 [2,3 ]
All conference organizers/editors are required to declare details about their peer review. Therefore, please provide the following information:
• Type of peer review: Single-blind / Double-blind / Triple-blind / Open / Other (please describe) Double-blind

• Conference submission management system: Online: https://cutt.us/mo8G5

• Number of submissions received: 50

• Number of submissions sent for review: 30

• Number of submissions accepted: 11

• Acceptance Rate (Number of Submissions Accepted / Number of Submissions Received × 100): 22%

• Average number of reviews per paper: 3

• Total number of reviewers involved: 20

• Any additional info on review process: No

• Contact person for queries: Prof Arafa H.Aly; arafaaly@aucegypt.edu

Please submit this form along with the rest of your files on the submission date written in your publishing agreement.
The information you provide will be published as part of your proceedings.
Prognostic Importance of Atrial Fibrillation and Anticoagulation in Alcoholic Versus Dilated Cardiomyopathy
Authors: Manivannan Alan , Schou Morten , Monahan Kevin M , Helm Robert , Ko Darae , Fosbøl Emil , Køber Lars , Gustafsson Finn , Gislason Gunnar H , Torp-Pedersen Christian , Andersson Charlotte 
Published: November 2022

Abstract

Aims
Limited data exist to describe the prognostic impact of atrial fibrillation (AF) and oral anticoagulation on patients with alcoholic cardiomyopathy (ACM) compared with dilated cardiomyopathy (DCM) and were investigated in this study.

Methods
Using Danish nationwide registries, a cohort analysis was conducted to assess the prognostic differences for patients with a first diagnosis of ACM versus DCM with and without AF 1994–2018 (followed until end 2019). Our study also assessed differences in mortality following initiation of anticoagulation in both populations.

Results
Totally, 1237 patients with ACM (33% with AF) and 17,211 individuals with DCM (33% with AF) were included. Those with ACM were more often men (89 versus 71%) and younger than patients with DCM (mean age 56 versus 64 years). Cumulative 5-year mortality was greater among patients with ACM, compared with DCM, regardless of AF (ACM with AF 49% [95% CI: 44–54%], ACM without AF 48% [45–53%], DCM with AF 41% [39–42%], DCM without AF 30% [29–31%], P &lt; 0.0001). The prognosis associated with AF was statistically significantly different in people with ACM and DCM (adjusted hazards ratio 0.85 [95% CI: 0.74–0.98] versus 1.04 [1.00–1.09] in ACM and DCM, P &lt; 0.0001). The mortality associated with oral anticoagulation was similar in ACM and DCM (hazards ratio 0.81 [0.61–1.07] versus 0.87 [0.80–0.94], P = 0.49).

Conclusions
Patients with ACM had a worse prognosis when compared with patients with DCM, but this did not appear to be driven by AF. Patients with ACM were observed to have similar associated risk benefits of oral anticoagulation as DCM.
A toolkit for covalent docking with GOLD: from automated ligand preparation with KNIME to bound protein–ligand complexes
Authors: David Laurianne , Mdahoma Anissa , Singh Natesh , Buchoux Sébastien , Pihan Emilie , Diaz Constantino , Rabal Obdulia 
Published: November 2022

Abstract

Motivation
Current covalent docking tools have limitations that make them difficult to use for performing large-scale structure-based covalent virtual screening (VS). They require time-consuming tasks for the preparation of proteins and compounds (standardization, filtering according to the type of warheads), as well as for setting up covalent reactions. We have developed a toolkit to help accelerate drug discovery projects in the phases of hit identification by VS of ultra-large covalent libraries and hit expansion by exploration of the binding of known covalent compounds. With this application note, we offer the community a toolkit for performing automated covalent docking in a fast and efficient way.

Results
The toolkit comprises a KNIME workflow for ligand preparation and a Python program to perform the covalent docking of ligands with the GOLD docking engine running in a parallelized fashion.

Availability and implementation
The KNIME workflow entitled ‘Evotec_Covalent_Processing_forGOLD.knwf’ for the preparation of the ligands is available in the KNIME Hub https://hub.knime.com/emilie_pihan/spaces.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
Authors: Fang Zhuoqing , Liu Xinyuan , Peltz Gary 
Published: November 2022

Abstract

Motivation
Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes. However, the currently available tools used to perform GSEA have a limited ability to analyze large datasets, which is particularly problematic for the analysis of single-cell data. To overcome this limitation, we developed a GSEA package in Python (GSEApy), which could efficiently analyze large single-cell datasets.

Results
We present a package (GSEApy) that performs GSEA in either the command line or Python environment. GSEApy uses a Rust implementation to enable it to calculate the same enrichment statistic as GSEA for a collection of pathways. The Rust implementation of GSEApy is 3-fold faster than the Numpy version of GSEApy (v0.10.8) and uses &gt;4-fold less memory. GSEApy also provides an interface between Python and Enrichr web services, as well as for BioMart. The Enrichr application programming interface enables GSEApy to perform over-representation analysis for an input gene list. Furthermore, GSEApy consists of several tools, each designed to facilitate a particular type of enrichment analysis.

Availability and implementation
The new GSEApy with Rust extension is deposited in PyPI: https://pypi.org/project/gseapy/. The GSEApy source code is freely available at https://github.com/zqfang/GSEApy. Also, the documentation website is available at https://gseapy.rtfd.io/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease
Authors: Didelot Xavier , Helekal David , Kendall Michelle , Ribeca Paolo 
Published: November 2022

AbstractMotivationThe ability to distinguish imported cases from locally acquired cases has important consequences for the selection of public health control strategies. Genomic data can be useful for this, for example, using a phylogeographic analysis in which genomic data from multiple locations are compared to determine likely migration events between locations. However, these methods typically require good samples of genomes from all locations, which is rarely available.ResultsHere, we propose an alternative approach that only uses genomic data from a location of interest. By comparing each new case with previous cases from the same location, we are able to detect imported cases, as they have a different genealogical distribution than that of locally acquired cases. We show that, when variations in the size of the local population are accounted for, our method has good sensitivity and excellent specificity for the detection of imports. We applied our method to data simulated under the structured coalescent model and demonstrate relatively good performance even when the local population has the same size as the external population. Finally, we applied our method to several recent genomic datasets from both bacterial and viral pathogens, and show that it can, in a matter of seconds or minutes, deliver important insights on the number of imports to a geographically limited sample of a pathogen population.Availability and implementationThe R package DetectImports is freely available from https://github.com/xavierdidelot/DetectImports.Supplementary informationSupplementary data are available at Bioinformatics online.
Metabolic patterns in brain 18F-fluorodeoxyglucose PET relate to aetiology in paediatric dystonia
Authors: Tsagkaris Stavros , Yau Eric K C , McClelland Verity , Papandreou Apostolos , Siddiqui Ata , Lumsden Daniel E , Kaminska Margaret , Guedj Eric , Hammers Alexander , Lin Jean-Pierre 
Published: November 2022

Abstract
There is a lack of imaging markers revealing the functional characteristics of different brain regions in paediatric dystonia. In this observational study, we assessed the utility of [18F]2-fluoro-2-deoxy-D-glucose (FDG)-PET in understanding dystonia pathophysiology by revealing specific resting awake brain glucose metabolism patterns in different childhood dystonia subgroups. PET scans from 267 children with dystonia being evaluated for possible deep brain stimulation surgery between September 2007 and February 2018 at Evelina London Children’s Hospital (ELCH), UK, were examined. Scans without gross anatomical abnormality (e.g. large cysts, significant ventriculomegaly; n = 240) were analysed with Statistical Parametric Mapping (SPM12). Glucose metabolism patterns were examined in the 144/240 (60%) cases with the 10 commonest childhood-onset dystonias, focusing on nine anatomical regions. A group of 39 adult controls was used for comparisons. The genetic dystonias were associated with the following genes: TOR1A, THAP1, SGCE, KMT2B, HPRT1 (Lesch Nyhan disease), PANK2 and GCDH (Glutaric Aciduria type 1). The acquired cerebral palsy (CP) cases were divided into those related to prematurity (CP-Preterm), neonatal jaundice/kernicterus (CP-Kernicterus) and hypoxic-ischaemic encephalopathy (CP-Term). Each dystonia subgroup had distinct patterns of altered FDG-PET uptake. Focal glucose hypometabolism of the pallidi, putamina or both, was the commonest finding, except in PANK2, where basal ganglia metabolism appeared normal. HPRT1 uniquely showed glucose hypometabolism across all nine cerebral regions. Temporal lobe glucose hypometabolism was found in KMT2B, HPRT1 and CP-Kernicterus. Frontal lobe hypometabolism was found in SGCE, HPRT1 and PANK2. Thalamic and brainstem hypometabolism were seen only in HPRT1, CP-Preterm and CP-term dystonia cases. The combination of frontal and parietal lobe hypermetabolism was uniquely found in CP-term cases. PANK2 cases showed a distinct combination of parietal hypermetabolism with cerebellar hypometabolism but intact putaminal-pallidal glucose metabolism. HPRT1, PANK2, CP-kernicterus and CP-preterm cases had cerebellar and insula glucose hypometabolism as well as parietal glucose hypermetabolism. The study findings offer insights into the pathophysiology of dystonia and support the network theory for dystonia pathogenesis. ‘Signature’ patterns for each dystonia subgroup could be a useful biomarker to guide differential diagnosis and inform personalized management strategies.
Ependyma: a new target for autoantibodies in neuromyelitis optica?
Authors: Bigotte Maxime , Gimenez Marie , Gavoille Antoine , Deligiannopoulou Adamantia , El Hajj Aseel , Croze Severine , Goumaidi Abdelghafar , Malleret Gael , Salin Paul , Giraudon Pascale , Ruiz Anne , Marignier Romain 
Published: November 2022

Abstract
Neuromyelitis optica (NMO) is an autoimmune demyelinating disease of the central nervous system characterized by the presence of autoantibodies (called NMO-IgG) targeting aquaporin-4. Aquaporin-4 is expressed at the perivascular foot processes of astrocytes, in the glia limitans, but also at the ependyma. Most studies have focused on studying the pathogenicity of NMO-IgG on astrocytes, and NMO is now considered an astrocytopathy. However, periependymal lesions are observed in NMO suggesting that ependymal cells could also be targeted by NMO-IgG. Ependymal cells regulate CSF-parenchyma molecular exchanges and CSF flow, and are a niche for sub-ventricular neural stem cells. Our aim was to examine the effect of antibodies from NMO patients on ependymal cells. We exposed two models, i.e. primary cultures of rat ependymal cells and explant cultures of rat lateral ventricular wall whole mounts, to purified IgG of NMO patients (NMO-IgG) for 24 hours. We then evaluated the treatment effect using immunolabelling, functional assays, ependymal flow analysis and bulk RNA sequencing. For each experiment, the effects were compared with those of purified IgG from a healthy donors and non-treated cells. We found that: (i) NMO-IgG induced aquaporin-4 agglomeration at the surface of ependymal cells and induced cell enlargement in comparison to controls. In parallel, it induced an increase in gap junction connexin-43 plaque size; (ii) NMO-IgG altered the orientation of ciliary basal bodies and functionally impaired cilia motility; (iii) NMO-IgG activated the proliferation of sub-ventricular neural stem cells; (iv) treatment with NMO-IgG up-regulated the expression of pro-inflammatory cytokines and chemokines in the transcriptomic analysis. Our study showed that NMO-IgG can trigger an early and specific reactive phenotype in ependymal cells, with functional alterations of intercellular communication and cilia, activation of sub-ventricular stem cell proliferation and the secretion of pro-inflammatory cytokines. These findings suggest a key role for ependymal cells in the early phase of NMO lesion formation.
Trajectories of De Ritis ratio with risk of hepatocellular carcinoma and liver-related mortality following direct-acting antivirals for HCV: a retrospective longitudinal study up to 10 years
Authors: Jia Linna , Yue Ming , Wang Yidi , Ye Xiangyu , Zou Yanzheng , Zhang Amei , Feng Yue , Xia Xueshan , Yang Sheng , Yu Rongbin , Huang Peng 
Published: November 2022

AbstractThe De Ritis ratio has good diagnostic accuracy in patients with chronic viral liver disease. However, its prognostic utility has remained controversial. This study was to identify different trajectories of De Ritis ratio in those hepatitis C patients cured and analyze the relationship between trajectory groups and risk of hepatocellular carcinoma (HCC) with liver-related mortality by the retrospective cohort study. This retrospective longitudinal cohort included 1241 patients with hepatitis C who underwent antiviral therapy since follow-up in 2012. De Ritis ratio trajectories were identified by the latent class growth mixed model. Patients were grouped into subgroups by De Ritis ratio according to longitudinal trajectories. The endpoints were HCC and liver-related mortality. Three distinct trajectory groups were characterized for serum De Ritis ratio: low-stable, middle-stable and high-rising. Fifty-one HCC and 11 liver-related mortality were recorded and tracked. Compared to the low-stable group, the adjusted hazard ratios (HRs) and 95% confidence interval (CI) associated with HCC and liver-related mortality were 2.02 (1.12 to 3.63), 9.36 (3.61 to 24.29), for the middle-stable, and high-rising group, respectively. Notably, the high-rising trajectory group still had prognostic significance after adjusting for preoperative levels. Likewise, for the high-rising trajectory group of sustained virological response, the HRs (95% CI) were 2.85 (1.03 to 10.75) for HCC and liver-related mortality, and in patients with cirrhosis, the HRs (95% CI) were 3.44 (1.64 to 7.19) and 4.35 (1.27 to 14.84) in the middle-stable trajectory group and the high-rising trajectory group, respectively. The dynamic measurements of De Ritis ratio are recommended to monitor the prognosis of Hepatitis C patients.