bluuebunny/crossref_metadata_2025_split huggingface dataset:
Digital manometry to measure cerebrospinal fluid pressure during lumbar puncture
Authors: Heider Robert , Kranz Peter G , Weant Erin Hope , Gray Linda , Amrhein Timothy J 
Published: December 2021

Rationale and Objectives Accurate cerebrospinal fluid (CSF) pressure measurements are critical for diagnosis and treatment of pathologic processes involving the central nervous system. Measuring opening CSF pressure using an analog device takes several minutes, which can be burdensome in a busy practice. The purpose of this study was to compare accuracy of a digital pressure measurement device with analog manometry, the reference gold standard. Secondary purpose included an assessment of possible time savings. Materials and Methods This study was a retrospective, cross-sectional investigation of 71 patients who underwent image-guided lumbar puncture (LP) with opening CSF pressure measurement at a single institution from June 2019 to September 2019. Exclusion criteria were examinations without complete data for both the digital and analog measurements or without recorded needle gauge. All included LPs and CSF pressures were measured with the patient in the left lateral decubitus position, legs extended. Acquired data included (1) digital and analog CSF pressures and (2) time required to measure CSF pressure. Results A total of 56 procedures were analyzed in 55 patients. There was no significant difference in mean CSF pressures between devices: 22.5 cm H2O digitally vs 23.1 analog ( p = .7). Use of the digital manometer resulted in a time savings of 6 min (438 s analog vs 78 s digital, p < .001). Conclusion Cerebrospinal fluid pressure measurements obtained with digital manometry demonstrate comparable accuracy to the reference standard of analog manometry, with an average time savings of approximately 6 min per case.
Practice Variation Research in Degenerative Lumbar Disc Surgery: A Literature Review on Design Characteristics and Outcomes
Authors: Van Munster Juliëtte J. C. M. , de Weerdt Vera , Halperin Ilan J. Y. , Zamanipoor Najafabadi Amir H. , van Benthem Peter Paul G. , Schoonman Guus G. , Moojen Wouter A. , van den Hout Wilbert B. , Atsma Femke , Peul Wilco C. 
Published: December 2021

Study Design Literature review. Objective To describe whether practice variation studies on surgery in patients with lumbar degenerative disc disease used adequate study methodology to identify unwarranted variation, and to inform quality improvement in clinical practice. Secondary aim was to describe whether variation changed over time. Methods Literature databases were searched up to May 4th, 2021. To define whether study design was appropriate to identify unwarranted variation, we extracted data on level of aggregation, study population, and case-mix correction. To define whether studies were appropriate to achieve quality improvement, data were extracted on outcomes, explanatory variables, description of scientific basis, and given recommendations. Spearman’s rho was used to determine the association between the Extreme Quotient (EQ) and year of publication. Results We identified 34 articles published between 1990 and 2020. Twenty-six articles (76%) defined the diagnosis. Prior surgery cases were excluded or adjusted for in 5 articles (15%). Twenty-three articles (68%) adjusted for case-mix. Variation in outcomes was analyzed in 7 articles (21%). Fourteen articles (41%) identified explanatory variables. Twenty-six articles (76%) described the evidence on effectiveness. Recommendations for clinical practice were given in 9 articles (26%). Extreme Quotients ranged between 1-fold and 15-fold variation and did not show a significant change over time (rho= −.33, P= .09). Conclusions Practice variation research on surgery in patients with degenerative disc disease showed important limitations to identify unwarranted variation and to achieve quality improvement by public reporting. Despite the availability of new evidence, we could not observe a significant decrease in variation over time.
Psychometric Properties of the Korean Version of the Perceived Therapeutic Efficacy Scale for Physical Activity in Adults With Type 2 Diabetes
Authors: Kim Moonsun , Kim Chun-Ja , Kim Dae Jung , Schlenk Elizabeth A. 
Published: December 2021

Purpose: The purpose of this study is to translate the Perceived Therapeutic Efficacy Scale (PTES) into Korean and investigate its validity and reliability. Methods: The authors conducted a cross-sectional survey using baseline data from a randomized controlled study to psychometrically validate the PTES-Korean (PTES-K) among 108 adults with type 2 diabetes from an outpatient clinic at a university-affiliated hospital in Korea. The original PTES was forward-translated and back-translated to ensure translation equivalence of the PTES-K. Structured questionnaires were used for psychometric evaluation; exploratory and confirmatory factor analysis assessed validity, and Cronbach’s alpha coefficient and intraclass correlation coefficient (ICC) were used for reliability. Results: The interitem correlation analyses revealed that 5 items were redundant; thus, the scale was reduced to 5 items. A 1-factor model explained 76.85% of the variance; confirmatory factor analysis showed that this model adequately fit the data. The ICC for test-retest reliability was .78; Cronbach’s alpha was .92. The PTES-K showed significant associations with the scores of diabetes self-care activities for physical activity, quality of life, and depressive symptoms. Participants with good glycemic control and regular physical activity tended to have a higher score on the PTES-K than their counterparts, demonstrating known-groups validity. Conclusions: The cross-cultural applicability, reliability, and validity of the PTES-K were confirmed. The PTES-K may be used in clinical settings to examine the potential role of perceived therapeutic efficacy for physical activity in enhanced glycemic control among patients with diabetes.
MicroRNA-148a-3p suppresses cell proliferation and migration of esophageal carcinoma by targeting CEP55
Authors: Lin Yong , Chen Yushan , Shen Rongqiang , Chen Dingzhu , Lin Yimin 
Published: December 2021

AbstractThis study evaluated microRNA-148a-3p in esophageal carcinoma cells. The prediction of bioinformatics analysis revealed that microRNA-148a-3p may target CEP55. qRT-PCR and western blot showed that CEP55 level in esophageal carcinoma cells and tissue was dramatically higher than that of normal cells and tissue, while microRNA-148a-3p was the opposite. Forced expression of microRNA-148a-3p restrained cell malignant behaviors of esophageal carcinoma, and repression of microRNA-148a-3p resulted in the converse results in terms of cell function. Dual-luciferase assay confirmed that microRNA-148a-3p targeted CEP55. CEP55 attenuated the suppressive effect of microRNA-148a-3p on proliferation and migration of esophageal carcinoma cells, demonstrating that microRNA-148a-3p regulated function of esophageal carcinoma cells via decreasing CEP55 level. Microscopy observation indicated that cell morphology was also affected by the microRNA-148a-3p/CEP55 axis. Furthermore, western blot analysis revealed that the PI3K/AKT signaling pathway could be suppressed by activating the microRNA-148a-3p/CEP55 axis. Finally, in vivo experiments confirmed the effects of microRNA-148a-3p on tumorigenesis. Thus, microRNA-148a-3p could act as a repressor in esophageal carcinoma via binding to CEP55.
cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries
Authors: Qi Meifang , Nayar Utthara , Ludwig Leif S. , Wagle Nikhil , Rheinbay Esther 
Published: December 2021

AbstractBackgroundExogenous cDNA introduced into an experimental system, either intentionally or accidentally, can appear as added read coverage over that gene in next-generation sequencing libraries derived from this system. If not properly recognized and managed, this cross-contamination with exogenous signal can lead to incorrect interpretation of research results. Yet, this problem is not routinely addressed in current sequence processing pipelines.ResultsWe present cDNA-detector, a computational tool to identify and remove exogenous cDNA contamination in DNA sequencing experiments. We demonstrate that cDNA-detector can identify cDNAs quickly and accurately from alignment files. A source inference step attempts to separate endogenous cDNAs (retrocopied genes) from potential cloned, exogenous cDNAs. cDNA-detector provides a mechanism to decontaminate the alignment from detected cDNAs. Simulation studies show that cDNA-detector is highly sensitive and specific, outperforming existing tools. We apply cDNA-detector to several highly-cited public databases (TCGA, ENCODE, NCBI SRA) and show that contaminant genes appear in sequencing experiments where they lead to incorrect coverage peak calls.ConclusionscDNA-detector is a user-friendly and accurate tool to detect and remove cDNA detection in NGS libraries. This two-step design reduces the risk of true variant removal since it allows for manual review of candidates. We find that contamination with intentionally and accidentally introduced cDNAs is an underappreciated problem even in widely-used consortium datasets, where it can lead to spurious results. Our findings highlight the importance of sensitive detection and removal of contaminant cDNA from NGS libraries before downstream analysis.
Immunological effects of convalescent plasma therapy for coronavirus: a scoping review
Authors: Esmaeili Behnaz , Esmaeili Shahnaz , Pourpak Zahra 
Published: December 2021

AbstractBackgroundPreliminary studies revealed the safety and effectiveness of convalescent plasma (CP) therapy for patients with coronavirus. In this study, we aimed to evaluate and summarize the available evidence on CP therapy, identify the research gap regarding the immunological response to CP therapy and pave the road for future studies.MethodsThis study was conducted according to the Hilary Arksey and Lisa O’Malley framework. To find out the relevant studies, we searched PubMed, Scopus and Embase databases up to 30th May 2021. Data have been extracted according to three categories: (1) patients’ characteristics, (2) clinical and immunological responses to CP therapy and (3) pre-infusion screening of the CP samples.ResultsA total of 12,553 articles were identified. One hundred fifty-four studies met the inclusion criteria for full-text review. More than half of the included studies (112 studies, (75.6%)) concluded satisfactory outcomes and or safety of CP infusion in patients. Results of studies showed the efficacy of CP therapy in clinical improvement (101 studies), decreasing in the level of inflammatory factors (62 studies), elimination or decreasing in viral load (60 studies), and induction or increase in antibody response (37 studies). Despite these promising results, the results of the 49 studies revealed that CP therapy was ineffective in the survival of patients, clinical improvement, viral infection elimination or decrease in the inflammatory factor levels. Furthermore, the adaptive immune response was evaluated in 3 studies. Information related to the pre-infusion screening for human leukocyte antigen/human neutrophil antigen (HLA/HNA) antibodies was not reported in most of the studies. Our gap analysis revealed that the influence of the CP infusion on the adaptive immune and inflammatory responses in patients with coronavirus needs further investigation.ConclusionsBased on the results of most included studies, CP infusion was safe and resulted in clinical improvement of patients and decreasing the viral load. The effect of the CP infusion on adaptive immune response and inflammatory cytokines in patients with coronavirus needs further investigation.
Pericytes as mediators of infiltration of macrophages in multiple sclerosis
Authors: Kaushik Deepak Kumar , Bhattacharya Anindita , Lozinski Brian Mark , Wee Yong V. 
Published: December 2021

Abstract
Background
Multiple sclerosis (MS) is a neurodegenerative condition of the central nervous system (CNS). It is associated with blood–brain barrier (BBB) breakdown and intravasation of leukocytes, particularly monocyte-derived macrophages, into the CNS. Pericytes are mural cells that are encased within the basement membrane of vasculature, and they contribute functionally to the neurovascular unit. These cells play an important role in maintaining BBB integrity and CNS homeostasis. However, the critical role of pericytes in mediating inflammation in MS or its models is unclear. Whether pericytes infiltrate into the CNS parenchyma in MS also needs clarification.

Methods
CNS samples from the experimental autoimmune encephalomyelitis (EAE) mouse model of MS were collected at different time points for immunohistochemical analysis of pericytes along the inflamed vasculature. These findings were validated using MS brain specimens, and further analysis of pericyte involvement in inflammation was carried out by culturing primary pericytes and macrophages. Multiplex ELISA, transmigration assay and real-time PCR were used to study the inflammatory potential of pericytes in cultures.

Results
We found that pericytes exhibit a heterogenous morphology, with notable elongation in the inflamed perivascular cuffs of EAE. This was manifested by a decrease in pericyte density but an increase in the coverage by pericytes along the vasculature. Chondroitin sulfate proteoglycans (CSPGs), a family of extracellular matrix proteins enriched within inflamed perivascular cuffs, elevated levels of pro-inflammatory chemokines/cytokines in pericytes in culture. Importantly, pericytes stimulated with CSPGs enhanced macrophage migration. We did not detect pericytes in the CNS parenchyma during EAE, and this was corroborated in MS brain samples.

Conclusions
Our data suggest that pericytes seek to restore the BBB through increased coverage, but that their exposure to CSPGs prompt their facilitation of macrophages to enter the CNS to elevate neuroinflammation in EAE and MS.
“COVID affected us all:” the birth and postnatal health experiences of resettled Syrian refugee women during COVID-19 in Canada
Authors: Stirling Cameron Emma , Ramos Howard , Aston Megan , Kuri Marwa , Jackson Lois 
Published: December 2021

Abstract
Background
Prior to COVID-19, postnatal resettled refugee women in Canada reported barriers to healthcare and low levels of social support, contributing to maternal health morbidities. The COVID-19 pandemic appears to be further exacerbating health inequities for marginalized populations. The experiences of resettled refugee women are not fully known.

Aim
To understand Syrian refugee women’s experiences accessing postnatal healthcare services and supports during the COVID-19 pandemic.

Methods
Semi-structured, virtual interviews were conducted with eight resettled Syrian refugee women living in Nova Scotia (Canada) who were postnatal between March and August 2020. Data analysis was informed by constructivist grounded theory.

Findings
Three themes emerged: “the impacts of COVID-19 on postnatal healthcare;” “loss of informal support;” and “grief and anxiety.” Women experienced difficult healthcare interactions, including socially and physically isolated deliveries, challenges accessing in-person interpreters, and cancelled or unavailable in-home services (e.g., public health nurse and doula visits). Increased childcare responsibilities and limited informal supports due to pandemic restrictions left women feeling overwhelmed and exhausted. Stay-at-home orders resulted in some women reporting feelings of isolation and loss, as they were unable to share in person postnatal moments with friends and family, ultimately impacting their mental wellness.

Conclusions
COVID-19 and associated public health restrictions had significant impacts on postnatal Syrian refugee women. Data presented in this study demonstrated the ways in which the pandemic environment and related restrictions amplified pre-existing barriers to care and postnatal health inequalities for resettled refugee women—particularly a lack of postnatal informal supports and systemic barriers to care.
Upright versus supine MRI: effects of body position on craniocervical CSF flow
Authors: Muccio Marco , Chu David , Minkoff Lawrence , Kulkarni Neeraj , Damadian Brianna , Damadian Raymond V. , Ge Yulin 
Published: December 2021

Abstract
Background
Cerebrospinal fluid (CSF) circulation between the brain and spinal canal, as part of the glymphatic system, provides homeostatic support to brain functions and waste clearance. Recently, it has been observed that CSF flow is strongly driven by cardiovascular brain pulsation, and affected by body orientation. The advancement of MRI has allowed for non-invasive examination of the CSF hydrodynamic properties. However, very few studies have addressed their relationship with body position (e.g., upright versus supine). It is important to understand how CSF hydrodynamics are altered by body position change in a single cardiac phase and how cumulative long hours staying in either upright or supine position can affect craniocervical CSF flow.

Methods
In this study, we investigate the changes in CSF flow at the craniocervical region with flow-sensitive MRI when subjects are moved from upright to supine position. 30 healthy volunteers were imaged in upright and supine positions using an upright MRI. The cranio-caudal and caudo-cranial CSF flow, velocity and stroke volume were measured at the C2 spinal level over one cardiac cycle using phase contrast MRI. Statistical analysis was performed to identify differences in CSF flow properties between the two positions.

Results
CSF stroke volume per cardiac cycle, representing CSF volume oscillating in and out of the cranium, was ~ 57.6% greater in supine (p < 0.0001), due to a ~ 83.8% increase in caudo-cranial CSF peak velocity during diastole (p < 0.0001) and extended systolic phase duration when moving from upright (0.25 ± 0.05 s) to supine (0.34 ± 0.08 s; p < 0.0001). Extrapolation to a 24 h timeframe showed significantly larger total CSF volume exchanged at C2 with 10 h spent supine versus only 5 h (p < 0.0001).

Conclusions
In summary, body position has significant effects on CSF flow in and out of the cranium, with more CSF oscillating in supine compared to upright position. Such difference was driven by an increased caudo-cranial diastolic CSF velocity and an increased systolic phase duration when moving from upright to supine position. Extrapolation to a 24 h timeframe suggests that more time spent in supine position increases total amount of CSF exchange, which may play a beneficial role in waste clearance in the brain.
Transcriptome analysis reveals the molecular mechanism of Yiqi Rougan decoction in reducing CCl4-induced liver fibrosis in rats
Authors: Xiong Yu , Hu Jinyuan , Xuan Chen , Tian Jiayu , Tan Kaiyue , Chen Zhiwei , Luo Yan , Du Xuqin , Cheng Junxiong , Zhang Lanyue , Cao Wenfu 
Published: December 2021

Abstract
Background
Liver fibrosis develops from various chronic liver diseases, and there is currently a lack of specific treatment strategies. Yiqi Rougan decoction (YQRG) is a traditional Chinese medicine that has shown durative effects in the treatment of liver fibrosis; however, the mechanism associated with YQRG-related improvements in liver fibrosis remains to be experimentally determined. This study evaluated the therapeutic effect of YQRG on carbon tetrachloride (CCl4)-induced liver fibrosis in rats and its molecular mechanism.

Methods
We used low-, medium-, and high-dose YQRG to treat CCl4-induced liver fibrosis in rats, followed by assessment of liver injury and fibrosis according to liver appearance, body weight, liver mass index, histopathologic examination, and serum testing. Additionally, we performed transcriptome analysis using RNA-sequencing (RNA-seq) technology, including cluster, Gene Ontology (GO), and pathway analyses, to identify differentially expressed genes (DEGs), and protein and gene expression were detected by immunofluorescence (IFC), western blot and real-time quantitative PCR.

Results
The results showed that YQRG effectively alleviated CCl4-induced liver injury and fibrosis in rats, including observations of improved liver function, decreased activity of hepatic stellate cells (HSCs), and decreased extracellular matrix (ECM) deposition. Moreover, we identified downregulated and upregulated DEGs in the model group relative to the control and YQRG-treated groups, with GO analysis revealing their enrichment in biological processes, such as endoplasmic reticulum stress (ERS), apoptosis, and autophagy. Furthermore, pathway analysis showed that YQRG treatment downregulated the mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase/Akt (PI3K/AKT) signalling pathways and upregulated other signalling pathways, including those related to peroxisome proliferator-activated receptors(PPAR) and AMP-activated protein kinase(AMPK), with these findings subsequently verified experimentally.

Conclusion
These findings showed that YQRG improved CCl4-induced liver fibrosis through multiple mechanisms and pathways, offering critical insight into the YQRG-related therapeutic mechanism and promoting further research into its potential application.
TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids
Authors: Ferro-Costas David , Mosquera-Lois Irea , Fernández-Ramos Antonio 
Published: December 2021

AbstractIn this work, we introduce , a user-friendly software written in Python 3 and designed to find all the torsional conformers of flexible acyclic molecules in an automatic fashion. For the mapping of the torsional potential energy surface, the algorithm implemented in combines two searching strategies: preconditioned and stochastic. The former is a type of systematic search based on chemical knowledge and should be carried out before the stochastic (random) search. The algorithm applies several validation tests to accelerate the exploration of the torsional space. For instance, the optimized structures are stored and this information is used to prevent revisiting these points and their surroundings in future iterations. operates with a dual-level strategy by which the initial search is carried out at an inexpensive electronic structure level of theory and the located conformers are reoptimized at a higher level. Additionally, the program takes advantage of conformational enantiomerism, when possible. As a case study, and in order to exemplify the effectiveness and capabilities of this program, we have employed to locate the conformers of the twenty proteinogenic amino acids in their neutral canonical form. has produced a number of conformers that roughly doubles the amount of the most complete work to date.
Graphical Abstract