bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fat embolism syndrome with cerebral fat embolism through a patent foramen ovale
Authors: Yang Lijuan , Wu Jiafang , Wang Baojun 
Published: June 2020

AbstractRationale:Fat embolism syndrome with cerebral fat embolism, rarely observed at our neurology department, is often associated with long bone fractures. Its diagnosis is based on medical history and supportive imaging data and is usually not difficult. However, its pathogenesis remains poorly understood.Patient concerns:A 46-year-old woman was urgently presented to a nearby hospital because of a femur fracture caused by an accident. She rapidly developed somnolence and was suspected to have fat embolism syndrome.Diagnoses:Due to patients history of trauma and supportive imaging data, she was diagnosed with fat embolism syndrome obviously. However, severe brain damage confused our understanding of the pathogenesis. The subsequent diagnosis of fat embolism syndrome with patent foramen ovale provided a reasonable explanation.Interventions:Initially, we did not consider the fact that the patient had developed fat embolism syndrome and thus designed a comprehensive treatment program for fat embolism syndrome. Then the routine cardiac and vascular ultrasound screening were followed up, but patent foramen ovale was diagnosed unexpectedly, which led to a more aggressive treatment of brain injury.Outcomes:After relevant symptomatic treatment continued for nearly 3 months, an overall improvement was observed. Patients consciousness was restored but language disorders were left.Lessons:Clinicians should consider patent foramen ovale as the embolization pathway, particularly in young and middle-aged patients with cerebral embolism because it is often mistaken for a rare situation.
Incidence, predictors, and outcome of prosthesis-patient mismatch after transcatheter aortic valve replacement
Authors: He Shixin , Fang Zhenfei 
Published: June 2020

Abstract

Background:
Prosthesis-patient mismatch (PPM) following transcatheter aortic valve replacement (TAVR) is common, but the incidence, predictors and outcome of PPM are still controversial.

Methods:
A total of 18 articles incorporating 72,016 patients were identified form PubMed and Embase online database.

Results:
The pooled incidences of overall, and severe PPM following TAVR were 32.0% and 10.0% separately. Comparing to surgical aortic valve replacement (SAVR), TAVR had lower incidence of overall (OR, 0.31, 95% CI, 0.20–0.50) and severe PPM (OR, 0.38, 95% CI, 0.28–0.52). PPM was associated with a larger body surface area (BSA), larger body mass index (BMI) and previous myocardial infarction in comparison with those patients without PPM. Although PPM was not rare after TAVR, no significant differences were observed both in short- and mid-term all-cause mortality (30 day: OR: 1.51, 95% CI, 0.79–2.87, 1 year: OR: 1.02, 95% CI, 0.96–1.08, and 2 years: OR: 0.99, 95% CI, 0.79–1.24) between patients with PPM and those without PPM.

Conclusions:
Despite the fact that the incidence of PPM was lower than that of SAVR, PPM was not seen to have an impact on short- and mid-term survival.
Transparent cap-assisted endoscopic injection sclerotherapy for the treatment of patients with esophageal varices
Authors: Wang Jing , Zhang Xiaohua , Zhao Shulei 
Published: June 2020

Abstract
The aim of this study was to compare the efficacy and safety of cap-assisted endoscopic injection sclerotherapy (EIS) versus direct EIS in the management of esophageal variceal bleeding in patients with cirrhosis.
This retrospective study included patients with cirrhosis and esophageal variceal bleeding who underwent EIS with or without the use of a transparent cap at Shandong Provincial Hospital between December 2014 and April 2017. Patients were divided into two groups: Group A (EIS with transparent cap, n = 50) and Group B (direct EIS, n = 45). Data collected included patients’ demographics, procedure details, and rates of variceal eradication, variceal rebleeding, variceal recurrence, and survival during the follow-up period. All data were expressed as mean ± SD. Quantitative variables were compared with Student t test; qualitative variables were compared with the Fisher exact test or chi-square test. P values less than .05 were considered significant.
The mean follow-up duration was similar in both groups (16.3 ± 10.2 mo in Group A and 15.5 ± 9.5 mo in Group B). The volume of sclerosant (64.86 ± 10.62 vs 104.73 ± 21.25 ml, P = .044), mean number of sessions (2.37 ± 1.15 vs 5.70 ± 1.57, P = .042), time required to perform endoscopic treatment (6.57 ± 1.50 vs 11.22 ± 2.29 minutes, P = .049), and time to initial esophageal varices eradication (5.43 ± 1.38 vs 8.93 ± 1.5 wk, P = .041) were significantly smaller in the cap-assisted EIS group than in the direct EIS group. The probability of variceal recurrence and rebleeding was significantly higher in the direct EIS group than in the cap-assisted EIS group (14% versus 35.6% and 20% versus 40%). Only 22 patients (44%) developed complications in the cap-assisted group versus 30 patients (66.7%) in the EIS group (P = .039). The probability of survival was similar in both groups (86% versus 75.6%, P = .133).
Modified EIS with the use of a transparent cap resulted in lower rates of esophageal variceal recurrence, rebleeding, and complications, compared with direct EIS.
The association of gene rearrangement and lymphoma diagnosis
Authors: He Xiaoyan , Xu Pei , Wang Xianwei , Jiang Shuming , Gong Daoyin , Wu Ning 
Published: June 2020

Abstract

Introduction:
To investigate the gene rearrangement and mutation of lymphoma biomarkers including (Immunoglobulin H (IgH), Immunoglobulin kappa (IGK), Immunoglobulin lambda (IGL), and TCR) in the lymphoma diagnosis.

Methods and analysis:
Paraffin tissue samples from 240 cases diagnosed as suspected lymphoma in the department of pathology, Deyang City People's Hospital from June 2020 to June 2021 will be enrolled. Deoxyribonucleic acid extraction and Polymerase Chain Reaction (PCR) amplification will be performed in these paraffin tissue samples. Immunoglobulin and T cell receptor (TCR) rearrangement will be analyzed by hetero-double chain gel electrophoresis and BioMed-2 standardized immunoglobulin gene rearrangement detection system. In this study protocol IGH gene rearrangement, IGK gene rearrangement, both IGH and IGL gene rearrangement, both IGH and IGK gene rearrangement, both IGK and IGL gene rearrangement, both IGH, IGK and IGL gene rearrangement, TCR gene rearrangement and positive Ig/TCR rearrangement will be analyzed.

Discussion:
In this study, we will use B and T cell lymphoma analysis focusing on IgH, IGK, IGL, and TCR gene rearrangement, so as to provide early guidance for the diagnosis of lymphoma. Second generation sequencing technology is helpful in the differential diagnosis of lymphoma.

Trial registration:
Chinese Clinical trial registry: ChiCTR2000032366.
Dose–response of rPMS for upper Limb hemiparesis after stroke
Authors: Kinoshita Shoji , Ikeda Kumi , Yasuno Shinji , Takahashi Sho , Yamada Naoki , Okuyama Yumi , Sasaki Nobuyuki , Hada Takuya , Kuriyama Chiaki , Suzuki Shin , Hama Midori , Ozaki Naoto , Watanabe Shu , Abo Masahiro 
Published: June 2020

Abstract

Introduction:
Repetitive peripheral magnetic stimulation (rPMS) therapy is an innovative and minimally invasive neurorehabilitative technique and has been shown to facilitate neural plasticity. However, there is at present no research that clarifies the dose–response of rPMS therapy on the recovery of upper limb hemiparesis after stroke. This trial aims to clarify the dose–response of rPMS therapy combined with intensive occupational therapy (OT) for chronic stroke patients with moderate to severe upper limb hemiparesis.

Methods and analysis:
This multicenter, prospective, assessor-blinded, randomized controlled study with 3 parallel groups will be conducted from January 20, 2020 to September 30, 2022. Fifty patients will be randomly assigned in a ratio of 1:2:2 to the control group, the group receiving daily 2400 pulses of rPMS, or the group receiving daily 4800 pulses of rPMS, respectively. From the day after admission (Day 1), rPMS therapy and intensive OT will be initiated. The primary outcome is the change in the motor function of the affected upper extremity (Fugl-Meyer Assessment) between the time of admission (Day 0) and the day after 2 weeks of treatment (Day 14). Secondary outcomes will include the changes in spasticity, active range of motion, motor evoked potential, and activity of daily living.

Ethics and dissemination:
The study was approved by the Jikei University Certified Review Board for all institutions (reference number: JKI19–020). Results of the primary and secondary outcomes will be published in a peer-reviewed journal and presented at international congresses. The results will also be disseminated to patients.

Trial registration number:
jRCTs032190191.
Nursing Students’ Academic Success Factors
Authors: Brown Janine , McDonald Meghan , Besse Cheryl , Manson Patti , McDonald Reid , Rohatinsky Noelle , Singh Madeline 
Published: June 2020

Background
Attrition from nursing programs is an ongoing concern. Capitalizing on nursing students' strengths and supporting areas for remediation will maximize student success.

Purpose
This study explored undergraduate nursing student strengths and areas for remediation at program entry and across all years of nursing education study.

Methods
We used a cross-sectional design and collected data via the Academic Success Inventory for College Students survey tool. Baseline data were collected on first-year students after program start, and data were collected for all years of study at the end of the academic terms.

Results
Compared with other undergraduate students, nursing students exhibited strengths in study skills, in self-organization strategies, in their certainty of progress toward career goals, in recognizing the importance of their studies, and in levels of socializing that did not hinder academic performance. At some data collection points, they had strengths in motivation, confidence, and concentration. Nursing students indicated areas for remediation in studying or test-taking anxiety and their perception of the educator's ability to organize, teach, and assess student progress.

Conclusion
Nurse educators' pedagogical approaches should augment nursing student strengths. Remediation is required to support student success relative to anxiety, and students need orientation to the process of learning.
Complementary and Alternative Medicine Use Among Pediatric Emergency Department Patients in Singapore
Authors: Sathiyan Jayapriya , Faeyza Noorul , Ramasamy Krishnapriya , Ng Wei Sheng , Ganapathy Sashikumar 
Published: June 2020

Objective
The aim of the study was to determine the prevalence and types of complementary and alternative medicine (CAM) use among pediatric emergency department (ED) patients and perceptions of CAM among the caregivers who administer CAM in Singapore.

Methods
A survey was administered in a Singapore ED (June 2016–June 2017). A convenience sample of parents/carers accompanying pediatric patients completed a self-administered questionnaire. The primary outcome measures were prevalence of CAM use and perceptions of CAM.

Results
Parents/carers of 610 patients participated. Four hundred seventy-five (78.0%, 95% confidence interval, 74.5–81.0) had taken a CAM within the previous 12 months and 110 (18.1%; 95% confidence interval, 14.8–21.0) had taken a CAM on the day of presentation. There were no sex differences between CAM users and nonusers (P = 0.691). The use of CAM was more common among preschool children and younger (62.9%). There was no difference in CAM use among those with and without chronic disease (P = 0.878). Vitamins/supplements, cod liver oil, and probiotics were the most commonly used CAM. A total of 0.7% of CAM use was reported to the ED doctor. There were no adverse effects reported. The perception that CAMs are safe was more common among parents or caregivers who had administered CAM (P = 0.008).

Conclusions
Complementary and alternative medicine use is very common among pediatric ED patients in Singapore and is more prevalent than in Australia and the United Kingdom. However, it is not always reported to the doctor. Parents or caregivers who administer CAM are more likely to perceive CAMs to be safe.
Simultaneous Dual-Contrast Imaging of Small Bowel With Iodine and Bismuth Using Photon-Counting-Detector Computed Tomography
Authors: Ren Liqiang , Rajendran Kishore , Fletcher Joel G. , McCollough Cynthia H. , Yu Lifeng 
Published: June 2020

Objectives
Dual-energy and multienergy computed tomography (DECT/MECT) has the potential to simultaneously visualize two contrast agents in the small bowel: arterial enhancement of iodine in the bowel wall and enteric enhancement of bismuth in the bowel lumen. The purpose of this study was to explore its feasibility in a swine study using a research whole-body photon-counting-detector (PCD) computed tomography (CT) system.

Materials and Methods
A phantom study was initially performed to evaluate the quantification accuracy of iodine and bismuth separation from a single PCD-CT scan, which also served as the calibration reference for material decomposition of in vivo swine PCD-CT data. In the animal study, a test bolus scan was first performed to determine the time-attenuation curve for the arterial enhancement, based on which the timing of the PCD-CT dual-contrast scan was determined. A 600 mL homogeneous bismuth-saline solution (180 mL Pepto-Bismol + 420 mL normal saline) was orally administered to the pig using esophageal intubation. Approximately 1 hour after bismuth administration, 40 mL iodine contrast (Omnipaque 350, 5 mL/s) was injected intravenously. A PCD-CT scan was performed 13 seconds after the initiation of the contrast injection to simultaneously capture the arterial enhancement of iodine and the enteric enhancement of bismuth. To provide optimal material separation and quantification, all PCD-CT scans in both phantom and animal studies were operated at 140 kV with 4 energy thresholds of 25, 50, 75, and 90 keV.

Results
Using a generic image-based material decomposition method, the iodine and bismuth samples were successfully delineated and quantified in the phantom images with a root-mean-square-error of 1.32 mg/mL in iodine measurement and 0.64 mg/mL in bismuth measurement. In the pig study, the enhancing bowel wall containing iodine and the small bowel loop containing bismuth were not differentiable in the original PCD-CT images. However, they were clearly distinctive from each other in the iodine- and bismuth-specific images after material decomposition, as reviewed by an abdominal radiologist. In addition, quantitative analysis showed that the misclassification between the two contrast materials was less than 1.0 mg/mL.

Conclusions
Our study demonstrated the feasibility of simultaneous imaging of iodine and bismuth in small bowel of swine using PCD-CT.
Deciding between one-step and two-step irreversible inhibition mechanisms on the basis of “kobs” data: A statistical approach
Authors: Kuzmič Petr 
Published: June 2020

AbstractThis paper describes an objective statistical approach that can be used to decide between two alternate kinetic mechanisms of covalent enzyme inhibition from kinetic experiments based on the standard “kobs” method. The two alternatives are either a two-step kinetic mechanism, which involves a reversibly formed noncovalent intermediate, or a one-step kinetic mechanism, proceeding in a single bimolecular step. Recently published experimental data [Hopperet al.(2020)J. Pharm. Exp. Therap.372, 331–338] on the irreversible inhibition of Bruton tyrosine kinase (BTK) and tyrosine kinase expressed in hepatocellular carcinoma (TEC) by ibrutinib (PCI-32765) and acalabrutinib are used as an illustrative example. The results show that the kinetic mechanism of inhibition was misdiagnosed in the original publication for at least one of the four enzyme/inhibitor combinations. In particular, based on the availablekobsdata, ibrutinib behaves effectively as a one-step inhibitor of the TEC enzyme, which means that it is not possible to reliably determine either the inhibition constantKior the inactivation rate constantkinact, but only the covalent efficiency constantkeff=kinact/Ki. Thus, the published values ofKiandkinactfor this system are not statistically valid.
SARS-CoV-2 sequence typing, evolution and signatures of selection using CoVa, a Python-based command-line utility
Authors: Ali Farhan , Sharda Mohak , Seshasayee Aswin Sai Narain 
Published: June 2020

AbstractThe current global pandemic COVID-19, caused by SARS-CoV-2, has resulted in millions of infections worldwide in a few months. Global efforts to tackle this situation have produced a tremendous body of genomic data, which can be used for tracing transmission routes, characterization of isolates, and monitoring variants with potential for unusual virulence. Several groups have analyzed these genomes using different approaches. However, as new data become available, the research community needs a pipeline to perform a set of routine analyses, that can quickly incorporate new genome sequences and update the analysis reports. We developed a programmatic tool, CoVa, with this objective. It is a fast, accurate and user-friendly utility to perform a variety of genome analyses on hundreds of SARS-CoV-2 sequences. Using CoVa, we define a modified sequence typing nomenclature and identify sites under positive selection. Further analysis identified some peptides and sites showing geographical patterns of selection. Specifically, we show differences in sequence type distribution between sequences from India and those from the rest of the world. We also show that several sites show signatures of positive selection uniquely in sequences from India. Preliminary evolutionary analysis, using features that will be incorporated into CoVa in the near future, show a mutation rate of 7.4 × 10−4substitutions/site/year, confirm a temporal signal with a November 2019 origin of SARS-CoV-2, and a heterogeneity in the geographical distribution of Indian samples.
A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein
Authors: Riojas Marco A. , Frank Andrew M. , Puthuveetil Nikhita P. , Flores Beth , Parker Michael , King Stephen P. , Peiris Malik , Chu Daniel K. W. , Benton Briana , Bradford Rebecca , Hazbón Manzour Hernando , Rashid Sujatha 
Published: June 2020

AbstractThe function of the SARS-CoV-2 accessory protein p6, encoded by ORF6, is not fully known. Based upon its similarity to p6 from SARS-CoV, it may play a similar role, namely as an antagonist of type I interferon (IFN) signaling. Here we report the sequencing of a SARS-CoV-2 strain passaged six times after original isolation from a clinical patient in Hong Kong. The genome sequence shows a 27 nt in-frame deletion (Δ27,264-27,290) within ORF6, predicted to result in a 9 aa deletion (ΔFKVSIWNLD) from the central portion of p6. This deletion is predicted to result in a dramatic alteration in the three-dimensional structure of the resultant protein (p6Δ22-30), possibly with significant functional implications. Analysis of the original clinical sample indicates that the deletion was not present, while sequencing of subsequent passages of the strain identifies the deletion as a majority variant. This suggests that the deletion originatedab initioduring passaging and subsequently propagated into the majority, possibly due to the removal of selective pressure through the IFN-deficient Vero E6 cell line. The specific function of the SARS-CoV-2 p6 N-terminus, if any, has not yet been determined. However, this deletion is predicted to cause a shift from N-endo to N-ecto in the transmembrane localization of the SARS-CoV-2 p6Δ22-30N-terminus, possibly leading to the ablation of its native function.
Diversification of fungal chitinases and their functional differentiation inHistoplasma capsulatum
Authors: Goughenour Kristie D. , Whalin Janice , Slot Jason C. , Rappleye Chad A. 
Published: June 2020

ABSTRACTChitinases enzymatically hydrolyze chitin, a highly abundant biomolecule with many potential industrial and medical uses in addition to their natural biological roles. Fungi are a rich source of chitinases, however the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase family 18 (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C). The chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade in this larger phylogenetic analysis. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin binding domains (CBD) including the LysM domain do not define specific clades but instead are found more broadly across clades of chitinase enzymes. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus,Histoplasma capsulatum:six A clade (3 A-V, 1 A-IV, and two A-II), one B clade (B-I), and one formerly classified C clade (C-I) chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression ofCTS3in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. This suggests chitinase activity is variable even within sub-clades and that predictions of functionality require more sophisticated models.
Potent neutralization of clinical isolates of SARS-CoV-2 D614 and G614 variants by a monomeric, sub-nanomolar affinity Nanobody
Authors: Nieto Guillermo Valenzuela , Jara Ronald , Watterson Daniel , Modhiran Naphak , Amarilla Alberto A , Himelreichs Johanna , Khromykh Alexander A. , Salinas Constanza , Pinto Teresa , Cheuquemilla Yorka , Margolles Yago , González del Rey Natalia López , Miranda-Chacon Zaray , Cuevas Alexei , Berking Anne , Deride Camila , González-Moraga Sebastián , Mancilla Héctor , Maturana Daniel , Langer Andreas , Toledo Juan Pablo , Müller Ananda , Uberti Benjamín , Krall Paola , Ehrenfeld Pamela , Blesa Javier , Chana-Cuevas Pedro , Rehren German , Schwefel David , Fernandez Luis Ángel , Rojas-Fernandez Alejandro 
Published: June 2020

AbstractDespite unprecedented global efforts to rapidly develop SARS-CoV-2 treatments, in order to reduce the burden placed on health systems, the situation remains critical. Effective diagnosis, treatment, and prophylactic measures are urgently required to meet global demand: recombinant antibodies fulfill these requirements and have marked clinical potential. Here, we describe the fast-tracked development of an alpaca Nanobody specific for the receptor-binding-domain (RBD) of the SARS-CoV-2 Spike protein with therapeutic potential applicability. We present a rapid method for nanobody isolation that includes an optimized immunization regimen coupled with VHH library E. coli surface display, which allows single-step selection of high-affinity nanobodies using a simple density gradient centrifugation of the bacterial library. The selected single and monomeric Nanobody, W25, binds to the SARS-CoV-2 S RBD with sub-nanomolar affinity and efficiently competes with ACE-2 receptor binding. Furthermore, W25 potently neutralizes SARS-CoV-2 wild type and the D614G variant with IC50 values in the nanomolar range, demonstrating its potential as antiviral agent.