bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental study of density gradient-driven micro-instabilities and the confinement degradation during H-mode in EAST
Authors: CHEN Fei , LI Yadong , WANG Xiaojie , WU Guojiang , LI Pan , GENG Jingsen , WANG Yuhao , SUN Pengjun , LI Erzhong , ZHOU Tianfu , ZHAO Hailin , ZANG Qing , WANG Shouxin , LIU Haiqing , JIN Yifei , LYU Bo , BAE Cheonho , LI Jiangang 
Published: March 2023

Abstract
A broadband (BB) mode is observed by collective Thomson scattering diagnostics in repeatable shots of EAST and analyzed for the first time. This BB mode usually grows during L–H transitions, featuring a BB quasi-coherent mode with increasing frequency. During H-mode operations, it is characterized by steady-state BB in the high-frequency range (f ∼ 200–2000 kHz), at the electron scale (k

θ

ρ
s = 1‒2), mainly driven by the density gradient, and is sensitive to the value of η
e in the region of interest (ρ = 0.4‒0.8), where

η

e

=

R
/

L

T

e

/

R
/

L

n

e

is the ratio of the normalized electron temperature gradient and density gradient, and the region ρ = 0.4‒0.8 usually has a relatively low collisionality (v
eff < 5). The frequency of BB is found to be dependent on the electron temperature and density gradient, which is a typical feature of electron-driven turbulence. A negative correlation between the energy confinement and the intensity of the BB turbulence during H-mode has been found, which indicates a strong electron thermal transport induced by the BB turbulence. The BB significantly decreases the electron temperature and causes flatter electron temperature profiles in the region of interest (ρ = 0.4‒0.8), thus making η
e decrease and the BB destabilize further. These characteristics of BB are related to the theoretical density gradient-driven trapped electron mode. It should be noted that this mode is not observed by other diagnostics in EAST, and shows very different features to the coherent modes in the edge.
Evaluation of graphical models for multi-group metabolomics data
Authors: Zhao Hang , Dai Pin-yuan , Yu Xiao-jin , He Jie-yu , Zhao Chao , Yin Li-hong 
Published: March 2023

AbstractGaussian graphical model is a strong tool for identifying interactions from metabolomics data based on conditional correlation. However, data may be collected from different stages or subgroups of subjects with heterogeneity or hierarchical structure. There are different integrating strategies of graphical models for multi-group data proposed by data scientists. It is challenging to select the methods for metabolism data analysis.This study aimed to evaluate the performance of several different integrating graphical models for multi-group data and provide support for the choice of strategy for similar characteristic data.We compared the performance of seven methods in estimating graph structures through simulation study. We also applied all the methods in breast cancer metabolomics data grouped by stages to illustrate the real data application.The method of Shaddox et al. achieved the highest average area under the receiver operating characteristic curve and area under the precision-recall curve across most scenarios, and it was the only approach with all indicators ranked at the top. Nevertheless, it also cost the most time in all settings. Stochastic search structure learning tends to result in estimates that focus on the precision of identified edges, while BEAM, hierarchical Bayesian approach and birth–death Markov chain Monte Carlo may identify more potential edges. In the real metabolomics data analysis from three stages of breast cancer patients, results were in line with that in simulation study.
iEssLnc: quantitative estimation of lncRNA gene essentialities with meta-path-guided random walks on the lncRNA-protein interaction network
Authors: Zhang Ying-Ying , Liang De-Min , Du Pu-Feng 
Published: March 2023

Abstract
Gene essentiality is defined as the extent to which a gene is required for the survival and reproductive success of a living system. It can vary between genetic backgrounds and environments. Essential protein coding genes have been well studied. However, the essentiality of non-coding regions is rarely reported. Most regions of human genome do not encode proteins. Determining essentialities of non-coding genes is demanded. We developed iEssLnc models, which can assign essentiality scores to lncRNA genes. As far as we know, this is the first direct quantitative estimation to the essentiality of lncRNA genes. By taking the advantage of graph neural network with meta-path-guided random walks on the lncRNA-protein interaction network, iEssLnc models can perform genome-wide screenings for essential lncRNA genes in a quantitative manner. We carried out validations and whole genome screening in the context of human cancer cell-lines and mouse genome. In comparisons to other methods, which are transferred from protein-coding genes, iEssLnc achieved better performances. Enrichment analysis indicated that iEssLnc essentiality scores clustered essential lncRNA genes with high ranks. With the screening results of iEssLnc models, we estimated the number of essential lncRNA genes in human and mouse. We performed functional analysis to find that essential lncRNA genes interact with microRNAs and cytoskeletal proteins significantly, which may be of interest in experimental life sciences. All datasets and codes of iEssLnc models have been deposited in GitHub (https://github.com/yyZhang14/iEssLnc).
Inter-domain distance prediction based on deep learning for domain assembly
Authors: Ge Fengqi , Peng Chunxiang , Cui Xinyue , Xia Yuhao , Zhang Guijun 
Published: March 2023

Abstract
AlphaFold2 achieved a breakthrough in protein structure prediction through the end-to-end deep learning method, which can predict nearly all single-domain proteins at experimental resolution. However, the prediction accuracy of full-chain proteins is generally lower than that of single-domain proteins because of the incorrect interactions between domains. In this work, we develop an inter-domain distance prediction method, named DeepIDDP. In DeepIDDP, we design a neural network with attention mechanisms, where two new inter-domain features are used to enhance the ability to capture the interactions between domains. Furthermore, we propose a data enhancement strategy termed DPMSA, which is employed to deal with the absence of co-evolutionary information on targets. We integrate DeepIDDP into our previously developed domain assembly method SADA, termed SADA-DeepIDDP. Tested on a given multi-domain benchmark dataset, the accuracy of SADA-DeepIDDP inter-domain distance prediction is 11.3% and 21.6% higher than trRosettaX and trRosetta, respectively. The accuracy of the domain assembly model is 2.5% higher than that of SADA. Meanwhile, we reassemble 68 human multi-domain protein models with TM-score ≤ 0.80 from the AlphaFold protein structure database, where the average TM-score is improved by 11.8% after the reassembly by our method. The online server is at http://zhanglab-bioinf.com/DeepIDDP/.
Multivariable prediction model for both 90-day mortality and long-term survival for individual patients with perihilar cholangiocarcinoma: does the predicted survival justify the surgical risk?
Authors: van Keulen Anne-Marleen , Buettner Stefan , Erdmann Joris I , Pratschke Johann , Ratti Francesca , Jarnagin William R , Schnitzbauer Andreas A , Lang Hauke , Ruzzenente Andrea , Nadalin Silvio , Cescon Matteo , Topal Baki , Olthof Pim B , Groot Koerkamp Bas 
Published: March 2023

AbstractBackgroundThe risk of death after surgery for perihilar cholangiocarcinoma is high; nearly one in every five patients dies within 90 days after surgery. When the oncological benefit is limited, a high-risk resection may not be justified. This retrospective cohort study aimed to create two preoperative prognostic models to predict 90-day mortality and overall survival (OS) after major liver resection for perihilar cholangiocarcinoma.MethodsSeparate models were built with factors known before surgery using multivariable regression analysis for 90-day mortality and OS. Patients were categorized in three groups: favourable profile for surgical resection (90-day mortality rate below 10 per cent and predicted OS more than 3 years), unfavourable profile (90-day mortality rate above 25 per cent and/or predicted OS below 1.5 years), and an intermediate group.ResultsA total of 1673 patients were included. Independent risk factors for both 90-day mortality and OS included ASA grade III–IV, large tumour diameter, and right-sided hepatectomy. Additional risk factors for 90-day mortality were advanced age and preoperative cholangitis; those for long-term OS were high BMI, preoperative jaundice, Bismuth IV, and hepatic artery involvement. In total, 294 patients (17.6 per cent) had a favourable risk profile for surgery (90-day mortality rate 5.8 per cent and median OS 42 months), 271 patients (16.2 per cent) an unfavourable risk profile (90-day mortality rate 26.8 per cent and median OS 16 months), and 1108 patients (66.2 per cent) an intermediate risk profile (90-day mortality rate 12.5 per cent and median OS 27 months).ConclusionPreoperative risk models for 90-day mortality and OS can help identify patients with resectable perihilar cholangiocarcinoma who are unlikely to benefit from surgical resection. Tailored shared decision-making is particularly essential for the large intermediate group.
Physical activity as an exogenous risk factor for amyotrophic lateral sclerosis: a review of the evidence
Authors: Chapman Laura , Cooper-Knock Johnathan , Shaw Pamela J 
Published: March 2023

AbstractAmyotrophic lateral sclerosis (ALS) is a rapidly progressive and fatal neurodegenerative disorder. The only established epidemiological risk factors for ALS are male sex and increasing age. The role of physical activity has been debated as an environmental risk factor. Over the last decade multiple studies have attempted to delineate the architecture of ALS. These have not yet established definite risk factors, often due to low-powered studies, lack of focus on at-risk genotypes and sub-optimal methodology.We have conducted a review of all the studies published between 2009 and December 2021. The free text search terms were [(motor neuron disease) OR (MND) OR (Amyotrophic Lateral Sclerosis) OR (ALS)] AND [(Exercise) or (Physical Activity) or (PA) or (sport)]. We identified common themes, for example soccer, head injury and the physiological mechanisms that differ in ALS patients. We have analysed the relevant, available studies (n = 93), highlighting the underlying reasons for any reported discrepancies.Overall, we have found that the more highly powered studies using validated exposure methodologies, linked strenuous, anaerobic physical activity as a risk factor for ALS. Future large-scale studies focusing on specific at-risk genotypes and physical activity should be conducted to confirm this finding. This will strengthen the evidence already surrounding strenuous physical activity as an environmental risk factor for ALS and allow advice to be given to at-risk family members. Increasing our understanding of the genetic–environmental interactions in the pathophysiology of ALS will allow for the possibility of developing preventative therapeutic approaches.
Establishing Pragmatic Analytical Performance Specifications for Blood Beta-Hydroxybutyrate Testing
Authors: Kilpatrick Eric S , Butler Alexandra E , Atkin Stephen L , Sacks David B 
Published: March 2023

Abstract

Background
Currently, no authoritative guidelines exist recommending the analytical performance specification (APS) of blood beta-hydroxybutyrate (BOHB) testing in order to meet the clinical needs of patients. This study has applied existing diabetic ketoacidosis (DKA) BOHB diagnostic thresholds and the recommended rates of fall in BOHB concentrations during DKA treatment to establish pragmatic APSs for BOHB testing.

Methods
Required analytical performance was based on 2 clinical requirements: (a) to reliably distinguish between non-adjacent DKA BOHB diagnostic categories of &lt;0.6, 0.6 to 1.5, 1.6 to 2.9, and ≥3 mmol/L, and (b) to be assured that a measured 0.5 mmol/L reduction in BOHB indicates the true concentration is at least falling (meaning &gt;0 mmol/L decline).

Results
An analytical coefficient of variation (CV) of &lt;21.5% could reliably distinguish all non-adjacent diagnostic categories with &gt;99% certainty, assuming zero bias. In contrast, within-day CVs of 4.9%, 7.0%, and 9.1% at 3 mmol/L BOHB were required to assure truly falling ketone concentrations with 99% (optimal), 95% (desirable), and 90% (minimal) probability, respectively. These CVs are larger at lower BOHB concentrations and smaller at higher concentrations.

Conclusions
Reliable tracking of changes in BOHB during DKA treatment largely drives the requirement for analytical performance. These data can be used to guide minimal, desirable, and optimal performance targets for BOHB meters and laboratory assays.
Role of Machine Learning on Key Extraction for Data Privacy Preservation of Health Care Sectors in IoT Environment
Authors: Kathavate Pravin Narayan 
Published: March 2023

Abstract
Privacy and security in the medical field are major aspects to consider in the current era. This is due to the huge necessity for data among providers, payers and patients, respectively. Recently, more researchers are making their contributions in this field under different aspects. But, there need more enhancements concerning security. In this circumstance, this paper intends to propose a new IoT-dependent health care privacy preservation model with the impact of the machine learning algorithm. Here, the information or data from IoT devices is subjected to the proposed sanitization process via generating the optimal key. In this work, the utility of the machine learning model is the greatest gateway to generating optimal keys as it is already trained with the neural network. Moreover, identifying the optimal key is the greatest crisis, which is done by a new Improved Dragonfly Algorithm algorithm. Thereby, the sanitization process works, and finally, the sanitized data are uploaded to IoT. The data restoration is the inverse process of sanitization, which gives the original data. Finally, the performance of the proposed work is validated over state-of-the-art models in terms of sanitization and restoration analysis.
Accuracy of Transperineal Ultrasonography for Assessing Rectal Lesions in Paediatric Ulcerative Colitis: A Prospective Study
Authors: Jimbo Keisuke , Hosoi Kenji , Suzuki Mitsuyoshi , Kyodo Reiko , Maruyama Kimiko , Arai Nobuyasu , Sato Masamichi , Miyata Eri , Hoshino Eri , Kudo Takahiro , Shimizu Toshiaki 
Published: March 2023

Abstract

Background and Aims
Transabdominal ultrasonography [TAUS] appears comparable to colonoscopy for evaluating ulcerative colitis [UC] activity, but it has low accuracy in rectal evaluation. In this study, the accuracy of transperineal ultrasonography [TPUS] for evaluating rectal activity was compared to that of colonoscopy in paediatric UC cases.

Methods
Faecal calprotectin [FCP] values and TPUS and colonoscopic findings were compared prospectively in paediatric UC cases. Rectal wall thickening [RWT] and rectal wall flow [RWF] on power Doppler evaluated by TPUS were compared with the colonoscopy findings and were also measured on TAUS and assessed for the concordance rate of each finding.

Results
Thirty Mayo endoscopic sub-score [MES] 0–1 UC cases and 57 MES 2–3 UC cases were enrolled. FCP, RWT and RWF showed significant differences between the two groups [p &lt; 0.05]. RWT and RWF were independent predictors of UC endoscopic activity, showing sensitivity of 95.8% and specificity of 100% with RWT ≥ 4.5 mm and positive RWF. The concordance rates between TPUS and TAUS findings in MES 2–3 were moderate to fair, whereas those in MES 0–1 were fair to poor. The concordance rates between ultrasonic examiners were good for both TAUS and TPUS.

Conclusions
TPUS may evaluate rectal activity of UC with accuracy comparable to endoscopy. If accurate ultrasonic screening for the total colon can be performed by TPUS and TAUS, repeated evaluation of short-term treatment response may be possible.
Inflammatory process of the COVID-19 fulminant myocarditis in the multimodality imaging: a case report
Authors: Hara Satoshi , Miwa Naoyuki , Hachiya Hitoshi , Sasano Tetsuo 
Published: March 2023

AbstractBackgroundCardiac manifest of COVID-19 infection was widely reported. The pathophysiology is thought the combination of direct damage caused by viruses and myocardial inflammation caused by immune responses. We tracked the inflammatory process of fulminant myocarditis associated with COVID-19 infection using multi-modality imaging.Case SummaryA 49-year-old male with COVID-19 went into cardiac arrest from severe left ventricular dysfunction and cardiac tamponade. He was treated with steroids, remdesivir, and tocilizumab but failed to maintain circulation. He recovered with pericardiocentesis and veno-arterial extracorporeal membrane oxygenation in addition to the immune suppression treatment. In this case, a series of chest computed tomography (CT) was performed on Days 4, 7, and 18 and cardiac magnetic resonance (MR) on Days 21, 53, and 145.DiscussionAnalysis of the inflammatory findings on CT in this case showed that intense inflammation around the pericardial space was observed at an early stage of the disease. Although inflammatory findings in the pericardial space and chemical markers had improved according to non-magnetic resonance imaging (MRI) tests, the MRI revealed a notable long inflammatory period more than 50 days.
Sex-based differences in risk of ischaemic stroke or systemic embolism after BNT162b2 or CoronaVac COVID-19 vaccination in patients with atrial fibrillation: a self-controlled case series and nested case-control study
Authors: Ye Xuxiao , Huang Caige , Yan Vincent Ka Chun , Kang Wei , Fan Min , Tsang Gigi Kwan Chi , Ho Clarissa Mung Yee , Lip Gregory Y H , Yiu Kai-Hang , Tse Hung-Fat , Ma Tiantian , Qin Xiwen , Chui Celine Sze Ling , Lai Francisco Tsz Tsun , Wong Carlos King Ho , Wan Eric Yuk Fai , Li Xue , Lee Cheuk Kwong , Hung Ivan Fan Ngai , Wong Ian Chi Kei , Chan Esther Wai Yin 
Published: March 2023

Abstract

Aims
Patients with atrial fibrillation (AF) have a higher risk of ischaemic stroke or systemic embolism, with a greater risk for female patients. This study aims to evaluate the risk of ischaemic stroke or systemic embolism and bleeding following COVID-19 vaccination in patients with AF and the sex differences.

Methods and results
Self-controlled case series (SCCS) analysis was conducted to evaluate the risk of ischaemic stroke or systemic embolism and bleeding following BNT162b2 or CoronaVac in patients with AF, using the territory-wide electronic medical records from the Hospital Authority and vaccination records from the Department of Health in Hong Kong. Patients with a primary diagnosis of ischaemic stroke, systemic embolism, or bleeding in the inpatient setting between 23 February 2021 and 31 March 2022 were included. A nested case-control analysis was also conducted with each case randomly matched with 10 controls according to sex, age, Charlson comorbidity index, and date of hospital admission. Conditional Poisson regression was used in the SCCS analysis, and conditional logistic regression was used in the nested case-control analysis to assess the risks, and all analyses were stratified by sex and type of vaccines. Among 51 158 patients with AF, we identified an increased risk of ischaemic stroke or systemic embolism after the first dose of BNT162b2 in SCCS analysis during 0–13 days [incidence rate ratio 6.60, 95% confidence interval (CI) 1.51–28.77] and 14–27 days (6.53, 95% CI 1.31–32.51), and nested case-control analysis during 0–13 days (adjusted odds ratio 6.21, 95% CI 1.14–33.91) and 14–27 days (5.52, 95% CI 1.12–27.26) only in female patients. The increased risk in female patients following the first dose of CoronaVac was only detected during 0–13 days (3.88, 95% CI 1.67–9.03) in the nested case-control analysis. No increased risk of ischaemic stroke or systemic embolism was identified in male patients, and no increased risk of bleeding was detected in all patients with AF for both vaccines. An increased risk of ischaemic stroke or systemic embolism after COVID-19 was also observed in both females (17.42, 95% CI 5.08–59.73) and males (6.63, 95% CI 2.02–21.79).

Conclusions
The risk of ischaemic stroke or systemic embolism after COVID-19 vaccination was only increased in female patients with AF. However, as the risk after COVID-19 was even higher, proactive uptake of COVID-19 vaccines is recommended to prevent the potential severe outcomes after infection.
Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans
Authors: Morton Elizabeth A , Hall Ashley N , Cuperus Josh T , Queitsch Christine 
Published: March 2023

Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
Mid-latitude and equatorial core surface flow variations derived from observatory and satellite magnetic data
Authors: Ropp G , Lesur V 
Published: March 2023

SUMMARY
A series of models of the Earth magnetic field and core surface flow have been simultaneously and sequentially co-estimated from year 1999 to 2022. The models were derived from magnetic satellite and ground observatory data using a linear Kalman filter approach and prior statistics based on numerical dynamo simulations. The core field and secular variation model components present the same characteristics as the most recent core field models with slightly higher resolution in time. A principal component analysis of the core surface flow series of models shows that the largest flow variations are observed at high latitudes and under the western part of the Pacific Ocean. Filtering out the flow variation periods longer than ∼11.5 yr leads to a filtered azimuthal flow that presents ∼7 yr periodicities with patterns propagating westward by ∼60° longitude per year. These patterns are present mainly at mid- and equatorial latitudes. They are compatible with a perturbation of the main flow made of small columnar flows with rotation axis intersecting the core–mantle boundary between 10° and 15° latitudes, and flow speed of less than 5 km yr–1. Present at all longitudes, these columnar flows are particularly strong under the Pacific Ocean after 2013. They can also be clearly identified under the Atlantic Ocean from 2005 to 2015.