bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits
Authors: Lu Yihao , Oliva Meritxell , Pierce Brandon , Liu Jin , Chen Lin 
Published: October 2022

Abstract
The proliferation of association results from large-scale genetic and genomic studies provides opportunities and challenges to elucidate the disease/trait mechanisms and their operating cellular contexts. Motivated by a multi-tissue multi-omics analysis using genetics, methylome and transcriptome data from the Genotype-Tissue Expression (GTEx) project, we propose a method, X-ING (Cross-INtegrative Genomics), for cross-omics and cross-context integrative analysis of summary-level data. X-ING takes as input the statistic matrices from multiple omics studies, each with multivariate contexts. It models the latent binary association status of each statistic, and captures the omics-shared and context-shared major patterns in a hierarchical Bayesian model. Via the modeling of latent binary status, X-ING enables the cross-feature integration of effects from different effect distributions. The analysis of cis-genetic effects on methylome and transcriptome from GTEx characterizes the tissue- and omics-effect sharing patterns. The analysis of trans-genetic effects demonstrates enrichment of trans-associations in many disease/trait-relevant tissues. Many associations identified by X-ING are replicated using external data, with higher replication rates for multi-tissue or multi-omics effects.
A Systematic Survey of Technology Driven Diagnosis for ASD
Authors: Singh Uday , Shukla Shailendra , Gore Manoj Madhava 
Published: October 2022

Abstract
Autism Spectrum Disorder (ASD), according to The Diagnostic and Statistical Manual of Mental Disorders- Fifth Edition (DSM-5), is a neurodevelopmental disorder that includes deficits of social interaction and social communication with the presence of restricted/repetitive behaviors. Due to communication deficits, ASD children have difficulties in joint attention and social reciprocity. Genetic disorders and/or environmental aspects are the leading causes of ASD. In 2021, the Centers for Disease Control and Prevention reported that approximately 1 among 44children in the U.S. is diagnosed with ASD. As per World Health Organization, ASD affects 14 out of every 10,000 children in Asian countries, which is approximately 23 children per 10,000 children in India. The Reported work shows that the early detection and intervention of ASD improve the language and communication deficiency of ASD children. This paper provides a comprehensive survey on various approaches to monitoring and detecting ASD children. Some monitoring and detection approaches covered in the study are clinical-based detection, MachineLearning -based ASD detection, Internet of Things (IoT)-based ASDdetection, Affective state detection, and Self Injurious Behaviour (SIB)detection of autistic children. This review also lists the several unaddressed challenges of early ASD detection. The purpose of this article is to enhance the understanding, provide guidelines for the domain, and provide insight into developing more practical and close-to-market products.
Accurate intraoperative real-time blood flow assessment of the remnant stomach during robot-assisted distal pancreatectomy with celiac axis resection using indocyanine green fluorescence imaging and da Vinci Firefly technology
Authors: Saito Kenta , Mamoru Morimoto , Denda Yuki , Nonoyama Keisuke , Murase Hiromichi , Kato Tomokatsu , Hayashi Yuichi , Imafuji Hiroyuki , Ogawa Ryo , Takahashi Hiroki , Matsuo Yoichi , Takiguchi Shuji 
Published: October 2022

Abstract
Background: Ischemic gastropathy is one of the unique postoperative complications associated with distal pancreatectomy with celiac axis resection for locally advanced pancreatic cancer. Therefore, it is essential to evaluate blood flow to the stomach following a resection; however, no intraoperative procedures have been established to assess this issue. Herein we describe two cases in which intraoperative evaluation of real-time blood flow in the residual stomach was performed using indocyanine green fluorescence and da Vinci Firefly technology during a robot-assisted distal pancreatectomy with celiac axis resection.
Methods: Robot-assisted distal pancreatectomy with celiac axis resection was performed using a da Vinci Xi surgical system on two patients with locally advanced pancreatic cancer and suspected invasion of the celiac artery. ICG (0.5 mg/kg) was injected intravenously after resection to evaluate real-time blood flow of the stomach using a da Vinci Firefly system. Blood flow of the stomach was evaluated 60 seconds after the intravenous injection of ICG.
Results: Case 1 was confirmed that there was sufficient blood flow in the residual stomach. Therefore, reconstruction of the left gastric artery was not performed, and the surgery was completed with preservation of the entire stomach. Case 2 was performed a proximal gastrectomy at first because the tumor directly involved the gastric lesser curvature and the left gastric artery. Next, ICG was injected intravenously, and after confirming good blood flow in the residual stomach and stomach stump, an esophageal residual gastric anastomosis was performed. Good postoperative outcomes were achieved and there was no evidence of ischemic gastropathy and delayed gastric emptying in both two cases.
Conclusions: This method is very useful in determining whether or not to perform reconstruction of the left gastric artery and/or additional resection of the remnant stomach during a robot-assisted distal pancreatectomy with celiac axis resection.
Machine Learning Spectroscopy Based on Group Contribution and Molecule Contribution Methods
Authors: Fan Jinming , Qian Chao , Zhou Shaodong 
Published: October 2022

Abstract
A group contribution (GC) – molecule contribution (MC) – machine learning (ML) protocol for accurate prediction of absorption spectra is presented. Upon combination of ML with revised GC methods, both the maximum absorption wavelengths and the full spectra of various sorts of dyes are afforded accurately and efficiently – by using only a small data set for training. Further, by employing a MC method designed specifically for revGC and based on MC-interpretated mixing rule by, the spectra for mixtures are obtained with high accuracy. Considering that the revGC-MC-ML protocol combines chemical principles and data-driven tools, most likely, it will be proven efficient to solve molecular-property mattered problems in wider fields.
Tracing the timing and spatial extent of carbon transfer from Picea abies to ectomycorrhizal fungi under elevated CO2
Authors: Hobbie Erik A. , Keel Sonja G. , Klein Tamir , Rog Ido , Saurer Matthias , Siegwolf Rolf , Routhier Michael R. , Körner Christian 
Published: October 2022

Abstract
Background. The spatial extent and timing of carbon fluxes from mature trees to ectomycorrhizal fungi associated with different hosts is challenging to assess in natural forests but could provide insights into carbon dynamics of fungi differing in exploration capabilities.
Methods. We analyzed carbon movement into ectomycorrhizal sporocarps at the Swiss Forest Free-Air CO2 Enrichment (FACE) site in 2010 and 2011 during continuous labeling of five mature Picea abies (L.) H. Karst. with 13C-depleted CO2. Sporocarps were collected 0-6 m, 6-12 m, 12-18 m, and > 18 m from 13C-labeled trees. We then used stepwise regressions on patterns of 13C:12C ratios (δ13C) in ectomycorrhizal sporocarps as a function of distance (zone), solar radiation, fungal genus, and association type.
Results. 18%, 10%, 40%, and 32% of ectomycorrhizal sporocarps were associated with conifers, broad-leaved trees, both, or of unknown association, respectively. Conifer-associated sporocarps derived 58 ± 7%, 41 ± 10%, and 20 ± 7% of their carbon from labeled trees in the 0-6 m, 6-12 m and 12-18 m zones, respectively, whereas other sporocarps in the 0-6 m zone only derived 34 ± 4% of their carbon from labeled trees. Sporocarp δ13C correlated positively with solar radiation for the 16-19 days prior to sporocarp harvest.
Conclusions. These patterns indicated that (1) carbon spread further through conifer-associated mycorrhizal networks than through other fungal networks, and (2) carbon accumulation, storage, and transfer dynamics for sporocarp formation can take several weeks. Mature conifers supplied carbon to mycorrhizal fungi up to ~15 m from host trees.
The implementation of quality improvement facilitators in primary care settings in Quebec: a case study
Authors: Laberge Maude , Than Victoria , Tanguay France , Roch Geneviève 
Published: October 2022

Abstract
Background
Quality improvement (QI) facilitators were integrated into Quebec’s university affiliated primary care practices. After an evaluation demonstrated the QI facilitators’ key role in implementing a QI culture, the Ministry of Health and Social Services decided to test the intervention in non-academic primary care practices with a one-year pilot project in one regional health organization. This study aims to understand the role and implementation of QI facilitators in non-academic primary care practices, as well as to highlight levers and barriers to their contribution.
Methodology
A single embedded case study was used to understand the implementation of QI facilitators. Led as an organization participatory research, the conduct of this study involved knowledge users. The Conceptual Framework for Implementation Research was used for the development of the interview guide and data analysis. We used two sources of data: 1) with the support of knowledge users, we obtained relevant documents about the QI facilitators’ role, the governance and planned implementation strategies (n = 17); 2) we conducted 19 semi-structured interviews with QI facilitators (n = 6), managers (n = 7) and physicians (n = 6) that were involved in the implementation of the pilot. Directed content analysis, triangulated writing analytics memos from documentation, was used to understand the QI facilitators’ role enactment and contribution, as well as their integration in the COVID-19 context.
Results
All participants had a positive perception of the QI facilitators’ role on bringing a QI culture and on the implementation of primary care projects. Three explanatory factors could explain the barriers and levers to the implementation of QI facilitators. Being decentralized was considered as enabling a more personalized approach, in which QI facilitators could better respond to their respective territory’s needs. QI facilitators worked under a co-management structure that included the clinics’ medical directors and the territorial managers. This structure was seen as an enabler to the QI facilitators’ integration and to their contributions in coordinating projects meeting provincial guidelines in the COVID-19 context.
Conclusion
The implementation of QI facilitators was positive for non-academic primary care practices. This study suggests elements for public institutions and managers to consider in the implementation of such QI facilitators in primary care practices.
Long Noncoding RNA-Mediated Competing Endogenous RNA Networks in Atherosclerosis: Regulate VSMC proliferation, migration, and apoptosis
Authors: Liu Shali , Chen Ting , Tan Yao , Qin Jianning , Han Yang , Fan Wenjing , qu shunlin 
Published: October 2022

Abstract
Atherosclerosis (AS) is a chronic inflammatory disease promoted by damage to the morphology and function of vascular smooth muscle cells (VSMCs). AS is a leading cause of cardiovascular diseases such as coronary heart disease, cerebral infarction and peripheral vascular diseases, and has been reported to cause higher mortality and morbidity worldwide. Long non-coding RNAs (LncRNAs) and microRNAs (miRNAs) are two highly regarded non-coding RNAs with multiple biological functions in humans and animals. LncRNA are critical regulators in AS development, and miRNA are reported to exert their roles in the pathophysiology of AS. Recently, a large body of evidence shows that LncRNAs are involved in the proliferation, migration and apoptosis of VSMCs, and interact with miRNAs. Specifically, lncRNAs can function as competitive endogenous RNAs (ceRNAs), which can compete with miRNAs, thereby regulating the expression of their downstream target genes. However, the mechanism of lncRNA as ceRNA in atherosclerotic VSMCs is still unclear. This paper reviews the research progress of lncRNAs sponging miRNAs to affect AS via controlling VSMC proliferation, migration, and apoptosis.
Surface morphology and drilled hole accuracy of conductive ceramic composites Si 3 N 4 -TiN and MoSi 2 -SiC on EDMed surfaces
Authors: Selvarajan L. , Venkataramanan K 
Published: October 2022

Abstract
By using electro-discharge machining (EDM), conductive ceramic composites made of Silicon Nitride and Titanium Nitride (Si3N4-TiN) and intermetallic ceramic composite (MoSi2-SiC) were machined while performance metrics of crucial importance to the EDM process were measured. The two conductive ceramic composites are thoroughly examined using machining parameters including current, spark on time, spark off time, and dielectric pressure. For multiple responses of geometrical errors, such as circularity, cylindricity, and perpendicularity, as well as performance metrics like metal removal rate (MRR), electrode wear rate (EWR), wear ratio, and surface integrity on the machined surface of the workpiece and electrode. Taguchi’s based L9 Orthogonal array (OA) based onthe design of experiments(DOE) is used to carry out the experimental runs to identify the optimum parameters of Si3N4–TiN and MoSi2–SiC ceramic composite. By analyzing the performance of conductive ceramic composites, the optimized results achieved from these approaches are suggested to improve themetal removal rate and lower the tool wear ratio, surface roughness and geometrical tolerances. An elaborated investigation of material removal mechanism and the surface topographyas examined by the SEM instrument with EDAX report in the machined surface for both composites. By analysing the machined surface on the best hole with the best electrode and the worst hole with the worst electrode the surface textures from nine holes and electrodes for ceramic composites are studied. Thus, simultaneously analysed and established EDM process appears to be a promising method for producing excellent surfacesin anelectrically conductive Si3N4–TiN and MoSi2–SiC composite under slow process parameters condition of conductive ceramic composites.
Combined with network pharmacology to study the effect and mechanism of Sanhuang ointment on MRSA infection in the skin and soft tissue
Authors: Wang Tianming , Pan Haibang , Che Ying , Fu Qi , Chen Qian , Li Xiaoli , Cui Yan , Chen Quanxin , Wu Zhihang , Li Richen , Liu Mei , Yi Jianfeng , Wang Bo 
Published: October 2022

Abstract
Overview. Skin and soft tissue infection（SSTI）is a frequent clinical disease. Sanhuang ointment is a traditional Chinese medicine used to treat SSTI. However, the pharmacological effect and mechanism of Sanhuang ointment on SSTI remain unclear. In this study, we investigated the protective effect and mechanism of Sanhuang ointment on MRSA in the skin and soft tissue infections by network pharmacological analysis, followed by in vivo experimental validation.
Methods.Using network pharmacology, the active ingredients and disease targets of Sanhuang ointment were screened and intersected for GO and KEGG enrichment analysis. A rat model of skin and soft tissue infection was established and the pathological features were observed. Sanhuang ointment large, medium and small dose groups (1g, 0.5g, and 0.25g/animal, with the total amount of Vaseline, dispensed 1g/animal) and Mupirocin Ointment positive control group (0.5g/animal, with the total amount of Vaseline, dispensed 1g/animal) were used, respectively. The expression of key proteins of the IL-17/NF-κB signaling pathway and downstream inflammatory factors were analyzed by histomorphological observation, enzyme-linked immunosorbent assay, polymerase chain reaction, and Western blotting.
Results. Network pharmacology analysis confirmed that 119 active components and 275 target genes of Sanhuang ointment were identified and intersected with MRSA infection-related genes, and 34 target genes of Sanhuang ointment were found to be used for skin and soft tissue infection with MRSA. Sanhuang ointment (1g/mouse) could effectively ameliorate histopathological changes and significantly inhibit the expression of key proteins of the IL-17/NF-κB signaling pathway and downstream inflammatory factors (p < 0.05). Discussion and Conclusion This study suggests that Sanhuang ointment protects against MRSA infection and inhibits inflammation by inhibiting IL-17/NF-κB signaling pathway. This is important for the secondary development and new drug development of Sanhuang ointment.
Conclusion. Sanhuang ointment has a protective effect on MRSA infection and inhibits inflammation by inhibiting IL-17/NF-κB signaling pathway. This is important for the secondary development and new drug development of Sanhuang ointment.
Managing delayed or missed pregabalin doses in patients with focal epilepsy: A Monte Carlo simulation study
Authors: Xie Helin , Zheng You , Huang Weikun , Wang Chenyu , Song Shiwei , Dai Yihai , Huang Xian , Liu Maobai , Wu Xuemei 
Published: October 2022

Abstract
Purpose
Medication adherence is essential for effective seizure control. However, delayed or missed doses are inevitable in epilepsy pharmacotherapy. The current remedial measures recommended by the Food and Drug Administration (FDA) for missed or delayed pregabalin doses are generic and lack supporting clinical evidence. The present study used a Monte Carlo simulation to explore remedial strategies for delayed or missed pregabalin doses in patients with epilepsy.
Methods
A Monte Carlo simulation was performed using a published population pharmacokinetic (pop PK) model. The applicability of the FDA recommendations compared to five proposed remedial regimens (Strategies A–E) was assessed based on the total deviation time outside the on-therapy range.
Results
All proposed remedial strategies were associated with renal function and the duration of dosing delay. The total deviation times for Strategies C–E were shorter than those for Strategy A (skip the dose and take the next regular dose as scheduled) when pregabalin was taken near the next scheduled time. An alternative recommendation is to take 1.2-, 1.3-, or 1.5-fold the regular dose at the next scheduled time if a single dose is missed. In the case of two missed doses, it is advisable to administer 1.2-, 1.3-, or 1.7-fold the regular dose.
Conclusion
Model-based simulations provided quantitative evidence for the effectiveness and feasibility of remedial strategies for missed or delayed pregabalin doses. The proposed remedial strategies can help in supplementing or correcting FDA instructions and mitigating the risk of out-of-range treatment.
Dach1 attenuates airway inflammation in chronic obstructive pulmonary disease by activating Nrf2 signaling
Authors: Huang Qian , Gu Yiya , Wu Jixing , Zhan Yuan , Deng Zhesong , Chen Shanshan , Peng Maocuo , Yang Ruonan , Chen Jinkun , Xie Jungang 
Published: October 2022

Abstract

Background: Chronic obstructive pulmonary disease (COPD)is a small airway chronic inflammatory disease with impaired lung function primarily induced by cigarette smoke (CS). Reduced Dach1 expression has a vicious role in numerous disorders. but its role in COPD is rarely known. This study aims to elucidate the role and underlying mechanism of Dach1 in airway inflammation of COPD.
Methods:Dach1 expression in lung tissues of COPD patients has been calculated. Small airway epithelium-specific Dach1 knockdown mice and AAV-transfected Dach1 overexpressed mice were used to explore its role and potential for therapeutic targeting in experimental COPD induced by CS. Furtherly, we uncovered the promising mechanism of Dach1 in inflammation induced by cigarette smoke extract simulation (CSE) in vitro.
Results:The expression of Dach1 decreased in COPD patients compared to non-smokers and smoker without COPD, especially in small airway epithelium. Small airway epithelium-specific Dach1 knockdown aggravated mice airway inflammation and lung function decline caused by CS, while Dach1 overexpression protected mice from airway inflammation and lung function decline. In 16 HBE cells, Dach1 knockdown and overexpression promoted and inhibited the secretion of IL-6 and IL-8 after simulation of CSE, respectively. Nuclear factor erythroid 2-related factor 2 (Nrf2) was identified as novel downstream target of Dach1, which directly binds to its promoter. Induction of Dach1 alleviated inflammation by activating Nrf2 signaling.
Conclusions: Dach1 is decreased in COPD patients. Dach1 has protective effects against inflammation induced by CS by activating Nrf2 signaling pathway. Targeting Dach1 is a potential therapeutic strategy for COPD.
Heterogeneity on the steatosis related hepatic injuries of patients with metabolic associated fatty liver disease between Han Chinese and Caucasian
Authors: Lin Limin , Ye Junzhao , Dong Zhiyong , Feng Shiting , Liao Bing , Zhuang Xiaodong , Zhong Bihui 
Published: October 2022

Abstract
Background & Aims: Despite the increasing prevalence of metabolic-associated fatty liver disease (MAFLD) worldwide, the ethnic differences between Han Chinese and Caucasian inclinical features remainunknown.
Methods: This is a cross-sectional study comparing Han Chinese MAFLD patients from 2 University-affiliated Medical Centers of fatty liver in south China from January 2015 to January 2022 and Caucasian MAFLD patients from UK Biobank database. Liver fat content was defined using the magnetic resonance imaging proton density fat fraction (MRI-PDFF).
Results: Han Chinese MAFLD patients(n=588) had higher proportions of moderate and severe grades of steatosis than that of Caucasian MAFLD patients (n=829) (25.7% vs 16.4%, P<0.001). There was a linear positive correlation between serum alanine aminotransferase (ALT) levels and the average liver fat content（LFC）in Han Chinese MAFLD patients but not in Caucasian. Multivariate linear regression analysis demonstrated that such positive correlations between ALT levels and LFC remained (β' =0.192, P<0.001 in male patients; β'=0.229, P<0.001 in female patients), and patients with liver biopsies further confirmed that Han Chinese patients presenting more liver histological severity as LFC increased (median 14.97% vs. 23.14% vs. 25.99%, P=0.001).
Conclusions: Compared with Caucasians, Han Chinese MAFLD patients with higher LFC tended to suffer from higher risk of liver injury.