bluuebunny/crossref_metadata_2025_split huggingface dataset:
Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions
Authors: Ghaffari Pouyan , Shoaie Saeed , Nielsen Lars K. 
Published: April 2022

AbstractThe human microbiome has been linked to several diseases. Gastrointestinal diseases are still one of the most prominent area of study in host-microbiome interactions however the underlying microbial mechanisms in these disorders are not fully established. Irritable bowel syndrome (IBS) remains as one of the prominent disorders with significant changes in the gut microbiome composition and without definitive treatment. IBS has a severe impact on socio-economic and patient’s lifestyle. The association studies between the IBS and microbiome have shed a light on relevance of microbial composition, and hence microbiome-based trials were designed. However, there are no clear evidence of potential treatment for IBS. This review summarizes the epidemiology and socioeconomic impact of IBS and then focus on microbiome observational and clinical trials. At the end, we propose a new perspective on using data-driven approach and applying computational modelling and machine learning to design microbiome-aware personalized treatment for IBS.
A novel rat model for cerebral venous sinus thrombosis: verification of similarity to human disease via clinical analysis and experimental validation
Authors: Mu Shuwen , Lin Yinghong , Xu Yongjun , Wei Xianqing , Zeng Zihuan , Lin Kunzhe , Zhu Linghua , Liu Qinghong , Qi Xingfeng , Wei Liangfeng , Liang Shengxiang , Wang Shousen 
Published: April 2022

Abstract
Background
Cerebral venous sinus thrombosis (CVST) is a rare neurovascular disorder with highly variable manifestations and clinical courses. Animal models properly matched to the clinical form of CVST are necessary for elucidating the pathophysiology of the disease. In this study, we aimed to establish a rat model that accurately recapitulates the clinical features of CVST in human patients.

Methods
This study consisted of a clinical analysis and animal experiments. Clinical data for two centres obtained between January 2016 and May 2021 were collected and analysed retrospectively. In addition, a Sprague–Dawley rat model of CVST was established by inserting a water-swellable rubber device into the superior sagittal sinus, following which imaging, histological, haematological, and behavioural tests were used to investigate pathophysiological changes. Principal component analysis and hierarchical clustering heatmaps were used to evaluate the similarity between the animal models and human patients.

Results
The imaging results revealed the possibility of vasogenic oedema in animal models. Haematological analysis indicated an inflammatory and hypercoagulable state. These findings were mostly matched with the retrospective clinical data. Pathological and serological tests further revealed brain parenchymal damage related to CVST in animal models.

Conclusions
We successfully established a stable and reproducible rat model of CVST. The high similarity between clinical patients and animal models was verified via cluster analysis. This model may be useful for the study of CVST pathophysiology and potential therapies.
Precision treatment of Singleton Merten syndrome with ruxolitinib: a case report
Authors: Broser Philip , von Mengershausen Ursula , Heldt Katrin , Bartholdi Deborah , Braun Dominique , Wolf Christine , Lee-Kirsch Min Ae 
Published: April 2022

Abstract
Background
Singleton-Merten syndrome 1 (SGMRT1) is a rare type I interferonopathy caused by heterozygous mutations in the IFIH1 gene. IFIH1 encodes the pattern recognition receptor MDA5 which senses viral dsRNA and activates antiviral type I interferon (IFN) signaling. In SGMRT1, IFIH1 mutations confer a gain-of-function which causes overactivation of type I interferon (IFN) signaling leading to autoinflammation.

Case presentation
We report the case of a nine year old child who initially presented with a slowly progressive decline of gross motor skill development and muscular weakness. At the age of five years, he developed osteoporosis, acro-osteolysis, alveolar bone loss and severe psoriasis. Whole exome sequencing revealed a pathogenic de novo IFIH1 mutation, confirming the diagnosis of SGMRT1. Consistent with constitutive type I interferon activation, patient blood cells exhibited a strong IFN signature as shown by marked up-regulation of IFN-stimulated genes. The patient was started on the Janus kinase (JAK) inhibitor, ruxolitinib, which inhibits signaling at the IFN-α/β receptor. Within days of treatment, psoriatic skin lesions resolved completely and the IFN signature normalized. Therapeutic efficacy was sustained and over the course muscular weakness, osteopenia and growth also improved.

Conclusions
JAK inhibition represents a valuable therapeutic option for patients with SGMRT1. Our findings also highlight the potential of a patient-tailored therapeutic approach based on pathogenetic insight.
Identification of a conserved neutralizing epitope in Seneca Valley virus VP2 protein: new insight for epitope vaccine designment
Authors: Wen Wei , Chen Xinghua , Lv Qiang , Chen Huanchun , Qian Ping , Li Xiangmin 
Published: April 2022

Abstract
Background
Seneca Valley virus (SVV) is a picornavirus that causes vesicular disease in swine. Clinical characteristics of the disease are similar to common viral diseases such as foot-and-mouth disease virus, porcine vesicular disease virus, and vesicular stomatitis virus, which can cause vesicles in the nose or hoof of pigs. Therefore, developing tools for detecting SVV infection is critical and urgent.

Methods
The neutralizing antibodies were produced to detect the neutralizing epitope.

Results
Five SVV neutralizing monoclonal antibodies (mAb), named 2C8, 3E4, 4C3, 6D7, and 7C11, were generated by immunizing mouses with ultra-purified SVV-LNSY01-2017. All five monoclonal antibodies exhibited high neutralizing titers to SVV. The epitopes targeted by these mAbs were further identified by peptide scanning using GST fusion peptides. The peptide 153QELNEE158 is defined as the smallest linear neutralizing epitope. The antibodies showed no reactivity to VP2 single mutants E157A. Furthermore, the antibodies showed no neutralizing activity with the recombinant virus (SVV-E157A).

Conclusions
The five monoclonal antibodies and identified epitopes may contribute to further research on the structure and function of VP2 and the development of diagnostic methods for detecting different SVV strains. Additionally, the epitope recognized by monoclonal antibodies against VP2 protein may provide insights for novel SVV vaccines and oncolytic viruses development.
Establishment and evaluation of a quadruple quantitative real-time PCR assay for simultaneous detection of human coronavirus subtypes
Authors: Zhao Mengchuan , Xu Yi , Zhang Dijun , Li Guixia , Gao Huixia , Zeng Xianping , Tie Yanqing , Wu Yong , Dai Erhei , Feng Zhishan 
Published: April 2022

Abstract
Background
The newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and four seasonal human coronaviruses (HCoVs) (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1) still circulate worldwide. The early clinical symptoms of SARS-CoV-2 and seasonal HCoV infections are similar, so rapid and accurate identification of the subtypes of HCoVs is crucial for early diagnosis, early treatment, prevention and control of these infections. However, current multiplex molecular diagnostic techniques for HCoV subtypes including SARS-CoV-2 are limited.

Methods
We designed primers and probes specific for the S and N genes of SARS-CoV-2, the N gene of severe acute respiratory syndrome coronavirus (SARS-CoV), and the ORF1ab gene of four seasonal HCoVs, as well as the human B2M gene product. We developed and optimized a quadruple quantitative real-time PCR assay (qq-PCR) for simultaneous detection of SARS-CoV-2, SARS-CoV and four seasonal HCoVs. This assay was further tested for specificity and sensitivity, and validated using 184 clinical samples.

Results
The limit of detection of the qq-PCR assay was in the range 2.5 × 101 to 6.5 × 101 copies/μL for each gene and no cross-reactivity with other common respiratory viruses was observed. The intra-assay and inter-assay coefficients of variation were 0.5–2%. The qq-PCR assay had a 91.9% sensitivity and 100.0% specificity for SARS-CoV-2 and a 95.7% sensitivity and 100% specificity for seasonal HCoVs, using the approved commercial kits as the reference. Compared to the commercial kits, total detection consistency was 98.4% (181/184) for SARS-CoV-2 and 98.6% (142/144) for seasonal HCoVs.

Conclusion
With the advantages of sensitivity, specificity, rapid detection, cost-effectiveness, and convenience, this qq-PCR assay has potential for clinical use for rapid discrimination between SARS-CoV-2, SARS-CoV and seasonal HCoVs.
Characteristics and productivity of the chiropractic workforce of the Veterans Health Administration
Authors: Corcoran Kelsey L. , Peterson Douglas R. , Zhao Xiwen , Moran Eileen A. , Lisi Anthony J. 
Published: April 2022

Abstract
Background
Increasingly, integrated healthcare systems such as the United States Veterans Health Administration (VHA) are employing chiropractors. However, little is known about chiropractor employee clinical productivity which may be important for resource planning and monitoring care delivery. With its history of delivering chiropractic care and its enterprise-level assessment metrics, the VHA is an ideal setting to study a chiropractic workforce. We aim to assess characteristics of chiropractors employed by the VHA and explore associations between these characteristics and clinical productivity.

Methods
This was a cross-sectional and serial analyses of VHA administrative data. Characteristics of the chiropractor workforce were evaluated from fiscal year (FY) 2016 to FY2019. Productivity was calculated using the VHA productivity measure, the quotient of an individual’s total work relative value units (wRVUs) per FY divided by the direct clinical full-time equivalent (FTE) worked. A multivariable regression model was used to analyze the association between productivity and characteristics of the chiropractor and VHA facility.

Results
From FY2016 to FY2019, the number of chiropractor employees increased from 102 to 167. In FY2019, the typical chiropractor employee was male, white, and 45.9 years old with 5.2 years of VHA experience. In FY2019, the VHA chiropractor workforce was 25.1% female, 79% white, and 20.4% Veteran. The productivity measure of a chiropractor was 3040 in FY2019. A higher facility complexity measure, presence of 3 chiropractor employees at a facility, and older age of the providers were the only characteristics studied that had a significant impact on productivity after adjusting for other covariates.

Conclusion
Provider characteristics and productivity metrics of the VHA chiropractor employee workforce are presented. The productivity measure provides an initial benchmarking that may be relevant to future modeling of chiropractor personnel in VHA and other healthcare systems.
Breastfeeding-friendly policies and programs in three public Universities in Ghana
Authors: Gbagbo Fred Yao , Nkrumah Jacqueline 
Published: April 2022

Abstract
Background
The United Nations through its Sustainable Development Goals (SDG) 3 and 5 has championed Women empowerment for exclusive breastfeeding through various action plans and expected the concept to be decentralized through locally mandatory implementation of various institutional policies and programs in member Countries. Using Kabeer’s empowerment concept, the authors in this paper assessed availability and implementation of breastfeeding policies and programs in three public universities in Ghana.

Methods
The study design was an exploratory-descriptive-case study involving university employees and student mothers from three public universities in Ghana. The universities were selected via simple random approach whilst selection of participants was purposive. Data were collected between April and July 2018 using an unstructured interview guide developed by the authors, audio recordings, field notes and desktop review of documents. Manual thematic analysis of data was done to present results descriptively. The University of Cape-Coast Ethics Review Board approved the study.

Results
Thirty-six respondents participated in the study. Three main themes (Breastfeeding policy and programs, Institutional support, and views on Breastfeeding/Childcare support) emerged. Despite being gender/child friendly, none of the universities in this study has a formal breastfeeding/childcare policy/program and there are no immediate policy plans for on-campus facilities to enhance breastfeeding. Financial cost emerged as a major challenge hindering the universities from implementing a policy/program in this regard. On the part of student mothers, lack of legal protection, lack of breastfeeding-friendly university policies, inadequate availability of breastfeeding facilities, and insufficient awareness of the importance of breastfeeding among nursing mothers has been a major setback for breastfeeding on campus, hence nursing mothers continue to make personal but challenging arrangements for breastfeeding on university campuses.

Conclusions
The study findings reflect negative implications for childcare as it affects optimal child nutrition, hence impacting on achieving the SDGs 3 and 5 in Ghana. The authors recommend introducing formal breastfeeding-friendly policies/programs as one of the criteria for accreditation of universities in Ghana to enhance optimal childcare and sound maternal mind for studies and/or work once there is an assurance of child safety and proximity to breastfeed on demand.
Predictive modeling of Persian walnut (Juglans regia L.) in vitro proliferation media using machine learning approaches: a comparative study of ANN, KNN and GEP models
Authors: Sadat-Hosseini Mohammad , Arab Mohammad M. , Soltani Mohammad , Eftekhari Maliheh , Soleimani Amanollah , Vahdati Kourosh 
Published: April 2022

AbstractBackgroundOptimizing plant tissue culture media is a complicated process, which is easily influenced by genotype, mineral nutrients, plant growth regulators (PGRs), vitamins and other factors, leading to undesirable and inefficient medium composition. Facing incidence of different physiological disorders such as callusing, shoot tip necrosis (STN) and vitrification (Vit) in walnut proliferation, it is necessary to develop prediction models for identifying the impact of different factors involving in this process. In the present study, three machine learning (ML) approaches including multi-layer perceptron neural network (MLPNN),k-nearest neighbors (KNN) and gene expression programming (GEP) were implemented and compared to multiple linear regression (MLR) to develop models for prediction of in vitro proliferation of Persian walnut (Juglans regiaL.). The accuracy of developed models was evaluated using coefficient of determination (R2), root mean square error (RMSE) and mean absolute error (MAE). With the aim of optimizing the selected prediction models, multi-objective evolutionary optimization algorithm using particle swarm optimization (PSO) technique was applied.ResultsOur results indicated that all three ML techniques had higher accuracy of prediction than MLR, for example, calculated R2of MLPNN, KNN and GEP vs. MLR was 0.695, 0.672 and 0.802 vs. 0.412 in Chandler and 0.358, 0.377 and 0.428 vs. 0.178 in Rayen, respectively. The GEP models were further selected to be optimized using PSO. The comparison of modeling procedures provides a new insight into in vitro culture medium composition prediction models. Based on the results, hybrid GEP-PSO technique displays good performance for modeling walnut tissue culture media, while MLPNN and KNN have also shown strong estimation capability.ConclusionHere, besides MLPNN and GEP, KNN also is introduced, for the first time, as a simple technique with high accuracy to be used for developing prediction models in optimizing plant tissue culture media composition studies. Therefore, selection of the modeling technique to study depends on the researcher’s desire regarding the simplicity of the procedure, obtaining clear results as entire formula and/or less time to analyze.
Direct comparison of low-dose-rate brachytherapy versus radical prostatectomy using the surgical definition of biochemical recurrence for patients with intermediate-risk prostate cancer
Authors: Tsumura Hideyasu , Tanaka Nobumichi , Oguchi Tomohiko , Owari Takuya , Nakai Yasushi , Asakawa Isao , Iijima Kazuyoshi , Kato Haruaki , Hashida Iwao , Tabata Ken-ichi , Satoh Takefumi , Ishiyama Hiromichi 
Published: April 2022

Abstract
Background
We compared the oncological outcomes of patients who received seed brachytherapy (SEED-BT) with those who received radical prostatectomy (RP) for intermediate-risk prostate cancer.

Methods
Candidates were patients treated with either SEED-BT (n = 933) or RP (n = 334). One-to-one propensity score matching was performed to adjust the patients’ backgrounds. We compared the biochemical recurrence (BCR)-free rate using the Phoenix definition (prostate-specific antigen [PSA] nadir plus 2 ng/mL) for SEED-BT and the surgical definition (PSA cut-off value of 0.2 ng/mL) for RP. We also directly compared the BCR-free rates using the same PSA cut-off value of 0.2 ng/mL for both SEED-BT and RP.

Results
In the propensity score-matched analysis with 214 pairs, the median follow-up treatment was 96 months (range 1–158 months). Fifty-three patients (24.7%) were treated with combined SEED-BT and external-beam radiotherapy. Forty-three patients (20.0%) received salvage radiotherapy after RP. Comparing the BCR-free rate using the above definitions for SEED-BT and RP showed that SEED-BT yielded a significantly better 8-year BCR-free rate than did RP (87.4% vs. 74.3%, hazard ratio [HR] 0.420, 95% confidence interval [CI] 0.273–0.647). Comparing the 8-year BCR-free rate using the surgical definition for both treatments showed no significant difference between the two treatments (76.7% vs. 74.3%, HR 0.913, 95% CI 0.621–1.341). SEED-BT had a significantly better 8-year salvage hormonal therapy-free rate than did RP (92.0% vs. 85.6%, HR 0.528, 95% CI 0.296–0.942, P = 0.030). The 8-year metastasis-free survival rates (98.5% vs. 99.0%, HR 1.382, 95% CI 0.313–6.083, P = 0.668) and overall survival rates (91.9% vs. 94.6%, HR 1.353, 95% CI 0.690–2.650) did not significantly differ between the treatments.

Conclusions
The BCR-free rates did not significantly differ between patients treated with SEED-BT and those treated with RP for intermediate-risk prostate cancer even when they were directly compared using the surgical definition for BCR. SEED-BT and RP can be adequately compared for oncological outcomes.
Robotics versus personalized 3D preoperative planning in total knee arthroplasty: a propensity score-matched analysis
Authors: Lei Kai , Liu LiMing , Yang PengFei , Xiong Ran , Yang Liu , He Rui , Guo Lin 
Published: April 2022

Abstract
Purpose
Lower limb alignment is crucial in total knee arthroplasty (TKA). Previous studies have shown that robotics and personalized three-dimensional (3D) preoperative planning could improve postoperative alignment accuracy compared with conventional TKA, but comparison between the above two techniques has never been reported. The authors hypothesized that robotics may be superior to personalized 3D preoperative planning in terms of postoperative alignment in primary TKA, with similar patient-reported outcome measures (PROMs) but higher cost and longer operative time.

Methods
A consecutive series of patients who received TKA in our center from September 2020 to January 2021 were enrolled retrospectively. After 1:2 matching, 52 and 104 patients were included and divided into study group for robotics and control group for personalized 3D preoperative planning, respectively. Multiple postoperative alignment angles were measured, and clinical features such as operation and tourniquet time, length of hospital stay and hemoglobin (Hb) were recorded. Knee Society Score (KSS) and Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) were used to evaluate clinical results.

Results
Compared with control group, robotics group had significantly lower frontal femoral component angle (FFC) and frontal tibial component angle (FTC) absolute deviation (P < 0.05). It also had less outliers in hip–knee–ankle angle (HKA), FTC, lateral femoral component angle (LFC) and lateral tibial component angle (LTC) (P < 0.05). Hb loss of robotics group was significantly lower than control group (P < 0.001), while the operation and tourniquet time were longer (P < 0.001). There was no significant difference in KSS and WOMAC scores between two groups.

Conclusion
Compared with control group, patients in robotics group had significantly less malalignment, malposition, Hb loss, but similar PROMs. The operations in robotics group spent longer operation time and cost more compared with control group.

Trial registration: The Chinese Clinical Trial Registry, ChiCTR2000036235. Registered 22 August 2020, http://www.chictr.org.cn/showproj.aspx?proj=59300.

Level of evidence
III.
Efficacy of CRP in combination with D-dimer in predicting adverse postoperative outcomes of patients with acute Stanford type A aortic dissection
Authors: Tang Zhiwei , Liu Hong , Shao Yongfeng 
Published: April 2022

Abstract
Purpose
The present study evaluated the efficacy of C-reactive protein (CRP) and D-dimer and the combination of them as prognostic indicators for patients with acute type A aortic dissection (ATAAD).

Methods
This is a retrospective cohort study. From January 2019 to December 2021, patients with ATAAD admitted to the emergency medicine center of our hospital within 24 h after symptoms (chest pain, back pain, abdominal pain and so on) onset were enrolled in our study. Serum concentration of CRP and D-dimer were measured during hospitalization. Logistic regression was used to evaluate the association between these two biomarkers and in-hospital adverse outcomes (IAO) by adjusting confounding factors. Predictive efficacy was assessed by area under the curve (AUC) of receiver operating characteristic curve.

Results
A total of 199 patients with ATAAD were finally enrolled. They were categorized as Non-IAO group (n = 146) and IAO group (n = 53) according to postoperative outcomes. After controlling for potentially confounding variables, we found categorized variables that admission CRP > 54.28 mg/L, admission D-dimer > 8.45 mg/L and peak D-dimer > 24.89 mg/L were independent predictors of in-hospital adverse outcomes. Multiple Logistic regression analysis revealed that the odd ratios were 2.9 for admission D-dimer > 8.45 [95% Confidence Interval (CI) 1.11–7.5, p = 0.03], 4.9 for admission CRP > 54.28 (95% CI 1.6–14.9, p = 0.005) and 5.7 for peak D-dimer > 24.89 (95% CI 2.49–13, p < 0.001). The predictive accuracy of the combination of three categorized variables (AUC: 0.867, 95% CI 0.813–0.921, p < 0.001) was superior to that of any other one alone.

Conclusion
Admission D-dimer > 8.45 mg/L, peak D-dimer > 24.89 mg/L and admission CRP > 54.28 mg/L are independent predictors of in-hospital adverse outcomes in patients with ATAAD. Combination of these three markers will improve the predictive efficacy.