bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of some aspects in supervised cell type identification for single-cell RNA-seq: classifier, feature selection, and reference construction
Authors: Ma Wenjing , Su Kenong , Wu Hao 
Published: September 2021

Abstract
Background
Cell type identification is one of the most important questions in single-cell RNA sequencing (scRNA-seq) data analysis. With the accumulation of public scRNA-seq data, supervised cell type identification methods have gained increasing popularity due to better accuracy, robustness, and computational performance. Despite all the advantages, the performance of the supervised methods relies heavily on several key factors: feature selection, prediction method, and, most importantly, choice of the reference dataset.

Results
In this work, we perform extensive real data analyses to systematically evaluate these strategies in supervised cell identification. We first benchmark nine classifiers along with six feature selection strategies and investigate the impact of reference data size and number of cell types in cell type prediction. Next, we focus on how discrepancies between reference and target datasets and how data preprocessing such as imputation and batch effect correction affect prediction performance. We also investigate the strategies of pooling and purifying reference data.

Conclusions
Based on our analysis results, we provide guidelines for using supervised cell typing methods. We suggest combining all individuals from available datasets to construct the reference dataset and use multi-layer perceptron (MLP) as the classifier, along with F-test as the feature selection method. All the code used for our analysis is available on GitHub (https://github.com/marvinquiet/RefConstruction_supervisedCelltyping).
Electroacupuncture for postoperative ileus after laparoscopic surgery on colorectal cancer: study protocol for a randomized controlled trial
Authors: Shao Jia-Kai , Liu Qian , Pei Wei , Wang Yu , Yang Na-Na , Qi Ling-Yu , Huang Jin , Yang Jing-Wen , Liu Cun-zhi 
Published: September 2021

AbstractBackgroundPostoperative ileus (POI) occurs in almost all patients after abdominal laparoscopic surgery, resulting in complications and increasing the length of hospitalization. Electroacupuncture has been used as an alternative therapy for gastrointestinal dysfunction, but its efficacy for POI is inconclusive. The study is designed to determine whether electroacupuncture can accelerate recovery from POI.Methods/designThis study is a three-arm, randomized controlled trial. A total of 105 patients will be randomized into a group receiving electroacupuncture at Tianshu (ST25), a group receiving electroacupuncture at Zusanli (ST36), or a control group in a 1:1:1 ratio. Patients in the electroacupuncture groups will receive electroacupuncture treatment for 4 days from the first day after surgery. The primary outcome consists of the time to first flatus and the time to first defecation. Secondary outcomes include the time to first tolerance of liquid and semiliquid food; the length of the hospital stay; postoperative pain, nausea, and vomiting; abdominal distension; the time to first get out of bed; and postoperative complications. The outcomes will be assessed by the patients themselves every day during hospitalization. Surgeons, nurses, assessors, and statisticians will be blinded to the group assignments. Patients in the two electroacupuncture groups, but not in the control group, will be blinded to the group assignments. The acupuncturists will not be blinded.DiscussionThe aim of this trial is to provide a nonpharmacological therapy for POI and may provide evidence of the effect of electroacupuncture at ST25 or ST36 on POI.Trial registrationChinese Clinical Trial RegistryChiCTR1900027466. Registered on 14 November 2019.
Standardised Outcomes in Nephrology – Chronic Kidney Disease (SONG-CKD): a protocol for establishing a core outcome set for adults with chronic kidney disease who do not require kidney replacement therapy
Authors: Evangelidis Nicole , Sautenet Benedicte , Madero Magdalena , Tong Allison , Ashuntantang Gloria , Sanabria Laura Cortes , de Boer Ian H. , Fung Samuel , Gallego Daniel , Levey Andrew S. , Levin Adeera , Lorca Eduardo , Okpechi Ikechi G. , Rossignol Patrick , Sola Laura , Usherwood Tim , Wheeler David C. , Cho Yeoungjee , Howell Martin , Guha Chandana , Scholes-Robertson Nicole , Widders Katherine , Gonzalez Andrea Matus , Teixeira-Pinto Armando , Viecelli Andrea K. , Bernier-Jean Amelie , Anumudu Samaya , Dunn Louese , Wilkie Martin , Craig Jonathan C. ,   on behalf of the SONG-CKD Investigators
Published: September 2021

Abstract
Background
Globally, over 1.2 million people die from chronic kidney disease (CKD) every year. Patients with CKD are up to 10 times more likely to die prematurely than progress to kidney failure requiring kidney replacement therapy. The burden of symptoms and impaired quality of life in CKD may be compounded by comorbidities and treatment side effects. However, patient-important outcomes remain inconsistently and infrequently reported in trials in patients with CKD, which can limit evidence-informed decision-making. The Standardised Outcomes in Nephrology – Chronic Kidney Disease (SONG-CKD) aims to establish a consensus-based core outcome set for trials in patients with CKD not yet requiring kidney replacement therapy to ensure outcomes of relevance to patients, caregivers and health professionals are consistently reported in trials.

Methods
SONG-CKD involves four phases: a systematic review to identify outcomes (domains and measures) that have been reported in randomised controlled trials involving adults with CKD who do not require kidney replacement therapy; stakeholder key informant interviews with health professionals involved in the care of adults with CKD to ascertain their views on establishing core outcomes in CKD; an international two-round online Delphi survey with patients, caregivers, clinicians, researchers, policy makers and industry representatives to obtain consensus on critically important outcome domains; and stakeholder consensus workshops to review and finalise the set of core outcome domains for trials in CKD.

Discussion
Establishing a core outcome set to be reported in trials in patients with CKD will enhance the relevance, transparency and impact of research to improve the lives of people with CKD.

Trial registration
Not applicable. This study is registered with the Core Outcome Measures in Effectiveness Trials (COMET) database: http://www.comet-initiative.org/Studies/Details/1653.
Evaluation of molecular assays to detect Leishmania donovani in Phlebotomus argentipes fed on post-kala-azar dermal leishmaniasis patients
Authors: Khan Md Anik Ashfaq , Faisal Khaledul , Chowdhury Rajashree , Nath Rupen , Ghosh Prakash , Ghosh Debashis , Hossain Faria , Abd El Wahed Ahmed , Mondal Dinesh 
Published: September 2021

Abstract
Background
Post-kala-azar dermal leishmaniasis (PKDL) caused by Leishmania donovani (LD) is a skin disorder that often appears after treatment of visceral leishmaniasis (VL) patients. PKDL patients are potential reservoirs of LD parasites, which can initiate a new epidemic of anthroponotic VL. Therefore, host infectiousness to its sand fly vector is a critical factor for transmission, and its accurate estimation can facilitate control strategies. At present, conventional microscopy serves as the reference method to detect parasites in its vector. However, low sensitivity of microscopy can be a limiting factor.

Methods
In this study, real-time quantitative PCR (LD-qPCR) and recombinase polymerase amplification (LD-RPA) assays were evaluated against microscopy for the detection of LD DNA extracted from live sand flies five days after controlled feeding on PKDL cases.

Results
The sensitivity of LD-qPCR and LD-RPA assays were found to be 96.43 and 100%, respectively, against microscopy for the selected fed sand flies (n = 28), and an absolute specificity of both molecular tools for apparently unfed sand flies (n = 30). While the proportion of infectious cases among 47 PKDL patients was estimated as 46.81% as defined by microscopic detection of LD in at least one fed sand fly per case, LD-RPA assay evaluation of only the microscopy negative sand flies fed to those 47 PKDL cases estimated an even greater proportion of infectious cases (51.06%). In overall estimation of the infectious cases in retrospective manner, discordance in positivity rate was observed (p < 0.05) between LD-RPA (59.57%) assay and microscopy (46.81%), while LD-RPA had slightly better positivity rate than LD-qPCR (55.32%) as well.

Conclusions
Considering the sensitivity, cost, detection time, and field applicability, RPA assay can be considered as a promising single molecular detection tool for investigations pertaining to LD infections in sand flies and/or host infectiousness in PKDL, while it can also be useful in confirmation of microscopy negative sand fly samples.

Graphical abstract
Vector competence of human-biting ticks Ixodes scapularis, Amblyomma americanum and Dermacentor variabilis for Powassan virus
Authors: Sharma Rohit , Cozens Duncan W. , Armstrong Philip M. , Brackney Douglas E. 
Published: September 2021

Abstract
Background
Powassan virus (POWV; genus Flavivirus) is the sole North American member of the tick-borne encephalitis sero-complex and an increasing public health threat in the USA. Maintained in nature by Ixodes spp. ticks, POWV has also been isolated from species of other hard tick genera, yet it is unclear if these species can serve as vectors. Dermacentor variabilis and Amblyomma americanum share geographic and ecologic overlap with Ixodes spp. ticks and POWV transmission foci, raising the possibility that POWV could become established in these tick species and leading to range expansion and increased human risk. Therefore, we assessed the competency of Ixodes scapularis, D. variabilis and A. americanum for POWV lineage II (POWV II).

Methods
Larvae from all three species were co-infested on POWV-infected Balb/c mice. The engorged larvae were allowed to molt to nymphs and screened for the presence of POWV II RNA by reverse transcription-qPCR. Eight infected nymphs from each species were allowed to individually feed on a naïve mouse. Mice were screened for the presence of POWV II RNA to determine infection status.

Results
The results demonstrated that larvae from all three tick species were able to efficiently acquire POWV II via feeding on viremic mice, maintain infection through molting and successively transmit POWV to naïve mice at the nymphal stage at comparable rates across all three species.

Conclusions
Our findings reveal that non-Ixodes tick species can serve as competent vectors for POWV and highlight the potential role of these species in the ecology and epidemiology of POWV. Future studies examining the possible implications of these findings on POWV epidemiology and the adaptability of POWV in these new vectors are warranted.

Graphical abstract
An experimental approach to microbial carbonate precipitation in improving the engineering properties of sandy soils
Authors: Bagriacik Baki , Sani Zahraddeen Kabir , Uslu Fatima Masume , Yigittekin Esra Sunduz , Dincer Sadik 
Published: September 2021

Abstract
Purpose
Stabilization of weak soil can be achieved through different methods, some of which include jet column, cement stabilization and fly ash stabilization. Unfortunately, the use of the aforementioned methods of soil improvement affects the environment negatively thereby leading to environmental degradation. With the aforesaid impediment in mind, the need for devising methods of weak soil improvement becomes pertinent.

Methods
Bacillus sp. — a non-pathogenic organism found abundantly in soil — was investigated in this study as a potential agent of soil improvement. The usability of Bacillus sp. in soil improvement was investigated with direct shear tests and permeability tests under optimum conditions in this study.

Result
Time-dependent study on the effect of the ureolytic bacteria Bacillus sp.-induced calcium carbonate precipitation shows reduction in permeability and increase in the strength of the soil under study. On exhaustion of the available nutrients in the soil, however, the strength of the soil is not negatively impacted.

Conclusion
Microbially induced calcium precipitation by Bacillus sp. is effective in soil improvement as such it may serve as substitute for conventional soil stabilization techniques. The ability of the bacteria to precipitate calcium carbonate in the soil leads to reduction in the permeability and increase in the shear strength of the soil.
Acute pancreatitis associated with severe acute respiratory syndrome coronavirus-2 infection: a case report and review of the literature
Authors: Eldaly Abdullah S. , Fath Ayman R. , Mashaly Sarah M. , Elhadi Muhammed 
Published: September 2021

Abstract
Introduction
We report a case of Severe acute respiratory syndrome coronavirus-2 infection with acute pancreatitis as the only presenting symptom. To the best of our knowledge, there are few case reports of the same presentation.

Case presentation
An otherwise healthy 44-year-old white male from Egypt presented to the hospital with severe epigastric pain and over ten attacks of nonprojectile vomiting (first, gastric content, then bilious). Acute pancreatitis was suspected and confirmed by serum amylase, serum lipase, and computed tomography scan that showed mild diffuse enlargement of the pancreas. The patient did not have any risk factor for acute pancreatitis, and extensive investigations did not reveal a clear etiology. Given a potential occupational exposure, a nasopharyngeal swab for polymerase chain reaction testing for severe acute respiratory syndrome coronavirus 2 was done, which was positive despite the absence of the typical symptoms of severe acute respiratory syndrome coronavirus 2 such as fever and respiratory symptoms. The patient was managed conservatively. For pancreatitis, he was kept nil per os for 2 days and received intravenous lactated Ringer’s (10 ml per kg per hour), nalbuphine, alpha chymotrypsin, omeprazole, and cyclizine lactate. For severe acute respiratory syndrome coronavirus 2, he received a 5-day course of intravenous azithromycin (500 mg per day). He improved quickly and was discharged by the fifth day. We know that abdominal pain is not a rare symptom of severe acute respiratory syndrome coronavirus 2, and we also know that elevated levels of serum amylase and lipase were reported in severe acute respiratory syndrome coronavirus-2 patients, especially those with severe symptoms. However, the association between severe acute respiratory syndrome coronavirus-2 infection and idiopathic acute pancreatitis is rare and has been reported only a few times.

Conclusion
We believe further studies should be conducted to determine the extent of pancreatic involvement in severe acute respiratory syndrome coronavirus-2 patients and the possible causality between severe acute respiratory syndrome coronavirus 2 and acute pancreatitis. We reviewed the literature regarding the association between severe acute respiratory syndrome coronavirus 2 and acute pancreatitis patients. Published data suggest that severe acute respiratory syndrome coronavirus 2 possibly could be a risk factor for acute pancreatitis.
Human Wharton's jelly-derived mesenchymal stem cells alleviate concanavalin A-induced fulminant hepatitis by repressing NF-κB signaling and glycolysis
Authors: Pan Lijie , Liu Chang , Liu Qiuli , Li Yanli , Du Cong , Kang Xinmei , Dong Shuai , Zhou Zhuowei , Chen Huaxin , Liang Xiaoqi , Chu Jiajie , Xu Yan , Zhang Qi 
Published: September 2021

Abstract
Background
Fulminant hepatitis is a severe life-threatening clinical condition with rapid progressive loss of liver function. It is characterized by massive activation and infiltration of immune cells into the liver and disturbance of inflammatory cytokine production. Mesenchymal stem cells (MSCs) showed potent immunomodulatory properties. Transplantation of MSCs is suggested as a promising therapeutic approach for a host of inflammatory conditions.

Methods
In the current study, a well-established concanavalin A (Con A)-induced fulminant hepatitis mouse model was used to investigate the effects of transplanting human umbilical cord Wharton's jelly-derived MSCs (hWJ-MSCs) on fulminant hepatitis.

Results
We showed that hWJ-MSCs effectively alleviate fulminant hepatitis in mouse models, primarily through inhibiting T cell immunity. RNA sequencing of liver tissues and human T cells co-cultured with hWJ-MSCs showed that NF-κB signaling and glycolysis are two main pathways mediating the protective role of hWJ-MSCs on both Con A-induced hepatitis in vivo and T cell activation in vitro.

Conclusion
In summary, our data confirmed the potent therapeutic role of MSCs-derived from Wharton's jelly of human umbilical cord on Con A-induced fulminant hepatitis, and uncovered new mechanisms that glycolysis metabolic shift mediates suppression of T cell immunity by hWJ-MSCs.
Exposure to interparental violence and justification of intimate partner violence among women in sexual unions in sub-Saharan Africa
Authors: Aboagye Richard Gyan , Seidu Abdul-Aziz , Asare Bernard Yeboah-Asiamah , Peprah Prince , Addo Isaac Yeboah , Ahinkorah Bright Opoku 
Published: September 2021

Abstract
Background
Justification of intimate partner violence (IPV) is one of the critical factors that account for the high prevalence of IPV among women. In this study, we examined the association between exposure to interparental violence and IPV justification among women in sexual unions in sub-Saharan Africa (SSA).

Methods
Data for this study were obtained from the most recent Demographic and Health Surveys (DHS) of 26 countries in SSA conducted between 2010 and 2020. A total of 112,953 women in sexual unions were included in this study. A multivariable binary logistic regression analysis was carried out. The results of the regression analysis were presented using crude odds ratios (cOR) and adjusted odds ratios (aOR) with their respective 95% confidence intervals (CIs).

Results
The prevalence of interparental violence in the countries considered in this study was 23.8%, with the highest (40.8%) and lowest (4.9%) in Burundi and Comoros, respectively. IPV justification was 45.8%, with the highest and lowest prevalence in Mali (80.9%) and South Africa (4.6%) respectively. Women who were exposed to interparental violence were more likely to justify IPV compared to those who were not exposed [aOR = 1.53, 95% CI = 1.47–1.59]. We found higher odds of justification of IPV among women who were exposed to interparental violence compared to those who were not exposed in all the countries, except Burkina Faso, Comoros, Gambia, and Rwanda.

Conclusion
The findings call for several strategies for addressing interparental violence. These may include empowerment services targeting both men and women, formation of stronger social networks to improve women’s self-confidence, and the provision of evidence-based information and resources at the community level. These interventions should pay critical attention to young people exposed to interparental violence. Public health education and messaging should emphasise on the negative health and social implications of interparental violence and IPV.
577-nm high-power optically pumped semiconductor laser is safe and effective in the treatment of inflammatory acne: a prospective, single-center, split-face comparative study
Authors: Mohamed E. M. , Tawfik K. M. , Elsayed I. B. , Bölke E. , Gerber P. A. 
Published: September 2021

Abstract
Objective
This study aimed to appraise the efficacy of a 577-nm high-power optically pumped semiconductor laser (HOPSL) for the treatment of inflammatory acne.

Methods
The study included 50 patients with acne vulgaris (inflammatory type), 14 men, and 36 women; patient ages ranged from 16 to 35 years. The left side of the face was treated with a single pass of a 577-nm high-power optically pumped semiconductor laser (HOPSL) every 2 weeks for 3 sessions. The severity of acne examined prior to the first session and 4 weeks after the last session (Investigator's Global Assessment of acne severity, IGA; single lesion count).

Results
At baseline, no statistically significant difference in the severity of inflammatory acne lesions between both sides was observed. One month after the final session, a significant improvement (IGA reduction of > 50%) of the overall severity of acne was observed in 49 patients (98%) on the laser-treated side versus 41 (82%) the control side of the face (P < .05). Hence, we found a significant reduction in the mean percentage of inflammatory papules, pustules, and nodules on the laser-treated versus the control side (79.33 vs 56.92, 78.04 vs 43.33, 64.85 vs 21.93%, respectively) (P < 0.05). Side effects in the form of erythema and irritation during sessions were transient and tolerated by the patients.

Conclusion
The 577-nm high-power optically pumped semiconductor laser is effective and safe for the treatment of inflammatory lesions (papules, pustules, and nodules) in acne patients.
Synaptic tau: A pathological or physiological phenomenon?
Authors: Robbins Miranda , Clayton Emma , Kaminski Schierle Gabriele S. 
Published: September 2021

AbstractIn this review, we discuss the synaptic aspects of Tau pathology occurring during Alzheimer’s disease (AD) and how this may relate to memory impairment, a major hallmark of AD. Whilst the clinical diagnosis of AD patients is a loss of working memory and long-term declarative memory, the histological diagnosis is the presence of neurofibrillary tangles of hyperphosphorylated Tau and Amyloid-beta plaques. Tau pathology spreads through synaptically connected neurons to impair synaptic function preceding the formation of neurofibrillary tangles, synaptic loss, axonal retraction and cell death. Alongside synaptic pathology, recent data suggest that Tau has physiological roles in the pre- or post- synaptic compartments. Thus, we have seen a shift in the research focus from Tau as a microtubule-stabilising protein in axons, to Tau as a synaptic protein with roles in accelerating spine formation, dendritic elongation, and in synaptic plasticity coordinating memory pathways. We collate here the myriad of emerging interactions and physiological roles of synaptic Tau, and discuss the current evidence that synaptic Tau contributes to pathology in AD.