bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary Resection of the Ulnar Slip of Flexor Digitorum Superficialis in the Persistently Triggering Patient After A1 Pulley Release
Authors: Polatsch Daniel B. , Rabinovich Remy V. , Casden Michael A. , Beldner Steven , Rahman Omar F. 
Published: February 2022

Background: The purpose of this study was to determine the occurrence of patients undergoing primary trigger finger release (TFR) that underwent ulnar superficialis slip resection (USSR) for decompression and to determine which digit was most commonly affected. Methods: A retrospective chart review was conducted of all cases of open TFR performed by a single surgeon. The following data were obtained: age, sex, laterality, affected digit, and consideration for USSR. All patients failed nonoperative treatment of at least 1 steroid injection. The occurrence of patients who underwent TFR and USSR and which digit(s) most commonly underwent USSR were determined. The average patient age that underwent USSR, frequency by sex, and relative occurrence of USSR in each digit were computed. Statistical calculations were conducted using χ2 analysis ( P < .05). Results: A total of 911 primary open TFRs were performed in 631 patients over a 16-year period. A total of 20 TFRs in 20 patients underwent USSR (2.2%). The long finger was the most commonly affected digit (40%) that required simple decompression. Within all USSR cases, the long finger was the most commonly affected digit. The index finger was the second most affected (30%), and there were no cases in the small finger. Conclusions: This study determined the occurrence of primary TFR cases that underwent USSR, with the long finger being the most commonly affected digit. Surgeons may consider this additional procedure to perform a larger decompression than simple A1 pulley release alone.
An intermittent outbreak of Burkholderia cepacia contaminating hematopoietic stem cells resulting in infusate-related blood stream infections
Authors: Raddaoui Anis , Ben Tanfous Farah , Chebbi Yosra , Mabrouk Aymen , Achour Wafa 
Published: February 2022

Microbial contamination of hematopoietic stem cells (HSC), used for autologous and allogenic transplantations, is rare but could cause serious blood stream infection in transplanted patients. These infections occur immediately, or later following the formation of biofilm on the catheter lumen. The present study describes an intermittent B. cepacia HSC contamination associated with nosocomial bacteremia: from October 2011 to April 2015, 17 B. cepacia strains were isolated in HSC bags ( n = 14) and blood cultures ( n = 3) in patients hospitalized in the National Bone Marrow Transplant Center. Two epidemiologic investigations in the National Blood Transfusion Center, allowing the isolation of three strains in hygiene samples, and four interventions in this institution were done. To identify the source of this contamination, a molecular investigation was done on 23 B. cepacia strains isolated in our center from 2007 to 2015. PFGE analysis revealed five clusters. The major cluster included 18 strains isolated from HSC bags ( n = 14), blood culture ( n = 1), and water cans and bath ( n = 3). The second cluster (B) including only two and the remaining clusters (C, D, and E) contained single strains isolated before the epidemic period. These findings confirmed that the origin of the outbreak was the contaminated water used in the water bath during the thawing step of HSC bags. Based on this result, new sterile water was used for every defrosting, but HSC bags contamination persisted. In May 2015, the water bath was replaced with a dry bath and no B. cepacia strain was isolated from that date to April 2020.
Effects of Blood Flow Restriction Training on Clinical Outcomes for Patients With ACL Reconstruction: A Systematic Review
Authors: Colapietro Mark , Portnoff Brandon , Miller Sayers John , Sebastianelli Wayne , Vairo Giampietro L. 
Published: February 2022

Context: Knee muscle atrophy and weakness are common impairments after anterior cruciate ligament (ACL) reconstruction. Blood flow restriction (BFR) training represents a new approach to treat such impairments. However, limited evidence currently exists to support this intervention in related patients. Objective: To appraise literature comparing the effects of BFR training with conventional therapy on knee muscle morphological and strength properties in ACL-reconstructed patients. Data Sources: PubMed, SPORTDiscus, CINAHL, and Cochrane Central Register databases were searched for relevant articles from January 1991 through April 2021. Study Selection: Articles were minimum Level 3 evidence focusing on knee muscle morphologic as well as extensor and flexor strength outcomes in ACL-reconstructed patients of all graft types. Study Design: Systematic review. Level of Evidence: Level 2. Data Extraction: Critical appraisal instruments (Downs and Black checklist, Cochrane Collaboration tool, ROBINS-1 tool) were used to evaluate study quality. We independently calculated effect sizes (ESs) (Cohen d) between groups in each study. The Strength of Recommendation Taxonomy grading scale was used for clinical recommendations. Results: Six articles (4 randomized control studies, 1 nonrandomized study, and 1 case-control study) met inclusion criteria. Exercises paired with BFR training included open kinetic chain, closed kinetic chain, and passive applications. Diverse assessments and time of intervention were observed across studies. ESs ranged from trivial to large in favor of BFR training for muscle morphological ( d = 0.06 to 0.81) and strength assessments ( d = −0.12 to 1.24) with CIs spanning zero. Conclusion: At this time, grade B or inconsistent and limited-quality patient-oriented evidence exists to support using BFR training to improve or maintain thigh muscle size as well as knee extensor and flexor strength in ACL-reconstructed patients. ESs indicated no consistent clinically meaningful differences when compared with conventional therapy. Subsequent analyses should be repeated as new evidence emerges to update practice guidelines.
Donor-derived multiple leukemia antigen–specific T-cell therapy to prevent relapse after transplant in patients with ALL
Authors: Naik Swati , Vasileiou Spyridoula , Tzannou Ifigeneia , Kuvalekar Manik , Watanabe Ayumi , Robertson Catherine , Lapteva Natalia , Tao Wang , Wu Mengfen , Grilley Bambi , Carrum George , Kamble Rammurti T. , Hill LaQuisa , Krance Robert A. , Martinez Caridad , Tewari Priti , Omer Bilal , Gottschalk Stephen , Heslop Helen E. , Brenner Malcom K. , Rooney Cliona M. , Vera Juan F. , Leen Ann M. , Lulla Premal D. 
Published: February 2022

Abstract
Hematopoietic stem cell transplant (HSCT) is a curative option for patients with high-risk acute lymphoblastic leukemia (ALL), but relapse remains a major cause of treatment failure. To prevent disease relapse, we prepared and infused donor-derived multiple leukemia antigen–specific T cells (mLSTs) targeting PRAME, WT1, and survivin, which are leukemia-associated antigens frequently expressed in B- and T-ALL. Our goal was to maximize the graft-versus-leukemia effect while minimizing the risk of graft-versus-host disease (GVHD). We administered mLSTs (dose range, 0.5 × 107 to 2 × 107 cells per square meter) to 11 patients with ALL (8 pediatric, 3 adult), and observed no dose-limiting toxicity, acute GVHD or cytokine release syndrome. Six of 8 evaluable patients remained in long-term complete remission (median: 46.5 months; range, 9-51). In these individuals we detected an increased frequency of tumor-reactive T cells shortly after infusion, with activity against both targeted and nontargeted, known tumor-associated antigens, indicative of in vivo antigen spreading. By contrast, this in vivo amplification was absent in the 2 patients who experienced relapse. In summary, infusion of donor-derived mLSTs after allogeneic HSCT is feasible and safe and may contribute to disease control, as evidenced by in vivo tumor-directed T-cell expansion. Thus, this approach represents a promising strategy for preventing relapse in patients with ALL.
G6b-B regulates an essential step in megakaryocyte maturation
Authors: Becker Isabelle C. , Nagy Zoltan , Manukjan Georgi , Haffner-Luntzer Melanie , Englert Maximilian , Heib Tobias , Vögtle Timo , Gross Carina , Bharti Richa , Dietrich Sascha , Mott Kristina , Heck Johannes , Stegmaier Sebastian , Baranowsky Anke , Schinke Thorsten , Schlegel Nicolas , Heckel Tobias , Stegner David , Pleines Irina , Ignatius Anita , Schulze Harald , Nieswandt Bernhard 
Published: February 2022

Abstract
G6b-B is a megakaryocyte lineage-specific immunoreceptor tyrosine-based inhibition motif–containing receptor, essential for platelet homeostasis. Mice with a genomic deletion of the entire Mpig6b locus develop severe macrothrombocytopenia and myelofibrosis, which is reflected in humans with null mutations in MPIG6B. The current model proposes that megakaryocytes lacking G6b-B develop normally, whereas proplatelet release is hampered, but the underlying molecular mechanism remains unclear. We report on a spontaneous recessive single nucleotide mutation in C57BL/6 mice, localized within the intronic region of the Mpig6b locus that abolishes G6b-B expression and reproduces macrothrombocytopenia, myelofibrosis, and osteosclerosis. As the mutation is based on a single-nucleotide exchange, Mpig6bmut mice represent an ideal model to study the role of G6b-B. Megakaryocytes from these mice were smaller, displayed a less-developed demarcation membrane system, and had a reduced expression of receptors. RNA sequencing revealed a striking global reduction in the level of megakaryocyte-specific transcripts, in conjunction with decreased protein levels of the transcription factor GATA-1 and impaired thrombopoietin signaling. The reduced number of mature MKs in the bone marrow was corroborated on a newly developed Mpig6b-null mouse strain. Our findings highlight an unexpected essential role of G6b-B in the early differentiation within the megakaryocytic lineage.
Fludarabine exposure predicts outcome after CD19 CAR T-cell therapy in children and young adults with acute leukemia
Authors: Dekker Linde , Calkoen Friso G. , Jiang Yilin , Blok Hilly , Veldkamp Saskia R. , De Koning Coco , Spoon Maike , Admiraal Rick , Hoogerbrugge Peter , Vormoor Britta , Vormoor H. Josef , Visscher Henk , Bierings Marc , Van Der Vlugt Marieke , Van Tinteren Harm , Nijstad A. Laura , Huitema Alwin D. R. , Van Der Elst Kim C. M. , Pieters Rob , Lindemans Caroline A. , Nierkens Stefan 
Published: February 2022

Abstract
The addition of fludarabine to cyclophosphamide as a lymphodepleting regimen prior to CD19 chimeric antigen receptor (CAR) T-cell therapy significantly improved outcomes in patients with relapsed/refractory (r/r) B-cell acute lymphoblastic leukemia (B-ALL). Fludarabine exposure, previously shown to be highly variable when dosing is based on body surface area (BSA), is a predictor for survival in allogeneic hematopoietic cell transplantation (allo-HCT). Hence, we hypothesized that an optimal exposure of fludarabine might be of clinical importance in CD19 CAR T-cell treatment. We examined the effect of cumulative fludarabine exposure during lymphodepletion, defined as concentration-time curve (AUC), on clinical outcome and lymphocyte kinetics. A retrospective analysis was conducted with data from 26 patients receiving tisagenlecleucel for r/r B-ALL. Exposure of fludarabine was shown to be a predictor for leukemia-free survival (LFS), B-cell aplasia, and CD19-positive relapse following CAR T-cell infusion. Minimal event probability was observed at a cumulative fludarabine AUCT0−∞ ≥14 mg*h/L, and underexposure was defined as an AUCT0−∞ &lt;14 mg*h/L. In the underexposed group, the median LFS was 1.8 months, and the occurrence of CD19-positive relapse within 1 year was 100%, which was higher compared with the group with an AUCT0−∞ ≥14 mg*h/L (12.9 months; P &lt; .001; and 27.4%; P = .0001, respectively). Furthermore, the duration of B-cell aplasia within 6 months was shorter in the underexposed group (77.3% vs 37.3%; P = .009). These results suggest that optimizing fludarabine exposure may have a relevant impact on LFS following CAR T-cell therapy, which needs to be validated in a prospective clinical trial.
Genomewide transcriptional response of Escherichia coli O157:H7 to norepinephrine
Authors: Sharma Vijay K. , Akavaram Suryatej , Bayles Darrell O. 
Published: February 2022

Abstract
Background
Chemical signaling between a mammalian host and intestinal microbes is health and maintenance of ‘healthy’ intestinal microbiota. Escherichia coli O157:H7 can hijack host- and microbiota-produced chemical signals for survival in a harsh and nutritionally competitive gastrointestinal environment and for intestinal colonization. Norepinephrine (NE) produced by sympathetic neurons of the enteric nervous system has been shown in vitro to induce expression of genes controlling E. coli O157:H7 swimming motility, acid resistance, and adherence to epithelial cells. A previous study used a microarray approach to identify differentially expressed genes in E. coli O157:H7 strain EDL933 in response to NE. To elucidate a comprehensive transcriptional response to NE, we performed RNA-Seq on rRNA-depleted RNA of E. coli O157:H7 strain NADC 6564, an isolate of a foodborne E. coli O157:H7 strain 86–24. The reads generated by RNA-Seq were mapped to NADC 6564 genome using HiSat2. The mapped reads were quantified by htseq-count against the genome of strain NADC 6564. The differentially expressed genes were identified by analyzing quantified reads by DESeq2.

Results
Of the 585 differentially expressed genes (≥ 2.0-fold; p < 0.05), many encoded pathways promoting ability of E. coli O157:H7 strain NADC 6564 to colonize intestines of carrier animals and to produce disease in an incidental human host through increased adherence to epithelial cells and production of Shiga toxins. In addition, NE exposure also induced the expression of genes encoding pathways conferring prolonged survival at extreme acidity, controlling influx/efflux of specific nutrients/metabolites, and modulating tolerance to various stressors. A correlation was also observed between the EvgS/EvgA signal transduction system and the ability of bacterial cells to survive exposure to high acidity for several hours. Many genes involved in nitrogen, sulfur, and amino acid uptake were upregulated while genes linked to iron (Fe3+) acquisition and transport were downregulated.

Conclusion
The availability of physiological levels of NE in gastrointestinal tract could serve as an important cue for E. coli O157:H7 to engineer its virulence, stress, and metabolic pathways for colonization in reservoir animals, such as cattle, causing illness in humans, and surviving outside of a host.
Evaluation of methods to detect circular RNAs from single-end RNA-sequencing data
Authors: Nguyen Manh Hung , Nguyen Ha-Nam , Vu Trung Nghia 
Published: February 2022

Abstract
Background
Circular RNA (circRNA), a class of RNA molecule with a loop structure, has recently attracted researchers due to its diverse biological functions and potential biomarkers of human diseases. Most of the current circRNA detection methods from RNA-sequencing (RNA-Seq) data utilize the mapping information of paired-end (PE) reads to eliminate false positives. However, much of the practical RNA-Seq data such as cross-linking immunoprecipitation sequencing (CLIP-Seq) data usually contain single-end (SE) reads. It is not clear how well these tools perform on SE RNA-Seq data.

Results
In this study, we present a systematic evaluation of six advanced RNA-based methods and two CLIP-Seq based methods for detecting circRNAs from SE RNA-Seq data. The performances of the methods are rigorously assessed based on precision, sensitivity, F1 score, and true discovery rate. We investigate the impacts of read length, false positive ratio, sequencing depth and PE mapping information on the performances of the methods using simulated SE RNA-Seq simulated datasets. The real datasets used in this study consist of four experimental RNA-Seq datasets with ≥100bp read length and 124 CLIP-Seq samples from 45 studies that contain mostly short-read (≤50bp) RNA-Seq data. The simulation study shows that the sensitivities of most of the methods can be improved by increasing either read length or sequencing depth, and that the levels of false positive rates significantly affect the precision of all methods. Furthermore, the PE mapping information can improve the method’s precision but can not always guarantee the increase of F1 score. Overall, no method is dominant for all SE RNA-Seq data. The RNA-based methods perform better for the long-read datasets but are worse for the short-read datasets. In contrast, the CLIP-Seq based methods outperform the RNA-Seq based methods for all the short-read samples. Combining the results of these methods can significantly improve precision in the CLIP-Seq data.

Conclusions
The results provide a systematic evaluation of circRNA detection methods on SE RNA-Seq data that would facilitate researchers’ strategies in circRNA analysis.
Airway management in a Helicopter Emergency Medical Service (HEMS): a retrospective observational study of 365 out-of-hospital intubations
Authors: Pietsch Urs , Müllner Raphael , Theiler Lorenz , Wenzel Volker , Meuli Lorenz , Knapp Jürgen , Sollid Stephen J. M. , Albrecht Roland 
Published: February 2022

AbstractBackgroundAirway management is a key skill in any helicopter emergency medical service (HEMS). Intubation is successful less often than in the hospital, and alternative forms of airway management are more often needed.MethodsRetrospective observational cohort study in an anaesthesiologist-staffed HEMS in Switzerland. Patient charts were analysed for all calls to the scene (n = 9,035) taking place between June 2016 and May 2017 (12 months). The primary outcome parameter was intubation success rate. Secondary parameters included the number of alternative techniques that eventually secured the airway, and comparison of patients with and without difficulties in airway management.ResultsA total of 365 patients receiving invasive ventilatory support were identified. Difficulties in airway management occurred in 26 patients (7.1%). Severe traumatic brain injury was the most common indication for out-of-hospital Intubation (n = 130, 36%). Airway management was performed by 129 different Rega physicians and 47 different Rega paramedics. Paramedics were involved in out-of-hospital airway manoeuvres significantly more often than physicians: median 7 (IQR 4 to 9) versus 2 (IQR 1 to 4),p < 0.001.ConclusionDespite high overall success rates for endotracheal intubation in the physician-staffed service, individual physicians get only limited real-life experience with advanced airway management in the field. This highlights the importance of solid basic competence in a discipline such as anaesthesiology.
Long-term clinical outcomes of patients with nonsignificant transplanted renal artery stenosis
Authors: Barteczko Manoela Linhares Machado , Orellana Henry Campos , Santos Gustavo Rocha Feitosa , Galhardo Attílio , Kanhouche Gabriel , Faccinetto Ana Carolina Buso , Júnior Hélio Tedesco , Pestana José Osmar Medina , de Paola Ângelo Amato Vincenzo , Barbosa Adriano Henrique Pereira 
Published: February 2022

Abstract
Background
Transplant renal artery stenosis (TRAS) is the main vascular complication of kidney transplantation. For research and treatment purposes, several authors consider critical renal artery stenosis to be greater than 50%, and percutaneous intervention is indicated in this scenario. However, there are no reports in the current literature on the evolution of patients with less than 50% stenosis.

Method
This retrospective study included data from all patients who underwent kidney transplantation and were suspected of having TRAS after transplantation with stenosis under 50% independent of age and were referred for angiography at a single centre between January 2007 and December 2014.

Results
During this period, 6,829 kidney transplants were performed at Hospital do Rim, 313 of whom had a clinical suspicion of TRAS, and 54 of whom presented no significant stenosis. The average age was 35.93 years old, the predominant sex was male, and most individuals (94.4%) underwent dialysis before transplantation. In most cases in this group, transplants occurred from a deceased donor (66.7%). The time between transplantation and angiography was less than one year in 79.6% of patients, and all presented nonsignificant TRAS. Creatinine levels, systolic blood pressure, diastolic blood pressure and glomerular filtration rate improved over the long term. The outcomes found were death and allograft loss.

Conclusion
Age, sex and ethnic group of patients were factors that did not interfere with the frequency of renal artery stenosis. The outcomes showed that in the long term, most patients evolve well and have improved quality of life and kidney function, although there are cases of death and kidney loss.
Massive digital gene expression analysis reveals different predictive profiles for immune checkpoint inhibitor therapy between adenocarcinoma and squamous cell carcinoma of advanced lung cancer
Authors: Kaneda Toshihiko , Kurata Takayasu , Yoshida Tomoko , Kibata Kayoko , Yoshioka Hiroshige , Yanagimoto Hiroaki , Takeda Kazuhiko , Yoshida Takao , Tsuta Koji 
Published: February 2022

AbstractBackgroundImmune checkpoint inhibitors prolong the survival of non-small cell lung cancer (NSCLC) patients. Although it has been acknowledged that there is some correlation between the efficacy of anti-programmed cell death-1 (PD-1) antibody therapy and immunohistochemical analysis, this technique is not yet considered foolproof for predicting a favorable outcome of PD-1 antibody therapy. We aimed to predict the efficacy of nivolumab based on a comprehensive analysis of RNA expression at the gene level in advanced NSCLC.MethodsThis was a retrospective study on patients with NSCLC who were administered nivolumab at the Kansai Medical University Hospital. To identify genes associated with response to anti-PD-1 antibodies, we grouped patients into responders (complete and partial response) and non-responders (stable and progressive disease) to nivolumab therapy. Significant genes were then identified for these groups using Welch’s t-test.ResultsAmong 42 analyzed cases (20 adenocarcinomas and 22 squamous cell carcinomas), enhanced expression ofMAGE-A4,BBC3,andOTOAgenes was observed in responders with adenocarcinoma, and enhanced expression ofDAB2,HLA-DPB,1andCDH2genes was observed in responders with squamous cell carcinoma.ConclusionsThis study predicted the efficacy of nivolumab based on a comprehensive analysis of mRNA expression at the gene level in advanced NSCLC. We also revealed different gene expression patterns as predictors of the effectiveness of anti PD-1 antibody therapy in adenocarcinoma and squamous cell carcinoma.