bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduction in Diameter of Hamstring Autograft With Additional Circumferential Preconditioning During ACL Reconstruction in a Pediatric Population
Authors: Weltsch Daniel , Chan Calvin , Dale Kevin M. , Koehler Ryan J. , Talwar Divya , Ganley Theodore J. , Lawrence J. Todd R. 
Published: August 2021

Background: Over 130,000 anterior cruciate ligament (ACL) reconstructions (ACLRs) are performed annually in the United States. Previous studies have shown that circumferential preconditioning reduces the diameter of fresh-frozen allografts, but no studies have described the effect in ACL autografts used during ACLR. Purpose: To characterize the changes in the hamstring autograft diameter as a result of preparatory circumferential preconditioning. Study Design: Case series; Level of evidence, 4. Methods: A total of 135 patients with ACLR, with a median age of 15 years (interquartile range, 14-16 years; 50.4% boys), were identified in 2 pediatric hospitals. Three orthopaedic surgeons recorded hamstring autograft diameters at 2 time points during graft preparation. Hamstring tendons were prepared using a standardized procedure, tensioned to 15 to 20 lbs, and measured using cylindrical sizing guides. The graft was left with passive compression in the smallest initial rigid sizing guide for 10 minutes on both the tibial and femoral sides and then measured again immediately before implantation. Tunnels were drilled based on the second measurement of graft size. Comparisons were made between the graft diameter before and after circumferential preconditioning. A random-effects regression model and a linear regression model were performed to capture any unexplained variance on the linear predictor scale and determine correlations between demographics and graft characteristics. Results: The median initial diameter for both femoral and tibial sides was 9.5 mm. After longitudinal tension and circumferential preconditioning, the median autograft diameter of both sides decreased by 1 mm ( P < .001) to 8.5 mm. In the random-effects model, decreased patient height was a significant predictor of greater reduction in graft diameter. Increased height was a significant predictor for greater initial graft diameter (average beta coefficient = 3.08; P < .01). No intraoperative complications were noted with implantation of the preconditioned grafts in smaller diameter tunnels. Conclusion: The median diameter of hamstring ACL autografts decreases by 1 mm after circumferential preconditioning within standard cylindrical sizing guides. This allowed for drilling of tunnels that were an average of 1 mm smaller without any noted intraoperative complications with graft insertion.
Neutrophil HIF-1α stabilization is augmented by mitochondrial ROS produced via the glycerol 3-phosphate shuttle
Authors: Willson Joseph A. , Arienti Simone , Sadiku Pranvera , Reyes Leila , Coelho Patricia , Morrison Tyler , Rinaldi Giulia , Dockrell David H. , Whyte Moira K. B. , Walmsley Sarah R. 
Published: August 2021

Abstract
Neutrophils are predominantly glycolytic cells that derive little ATP from oxidative phosphorylation; however, they possess an extensive mitochondrial network and maintain a mitochondrial membrane potential. Although studies have shown neutrophils need their mitochondria to undergo apoptosis and regulate NETosis, the metabolic role of the respiratory chain in these highly glycolytic cells is still unclear. Recent studies have expanded on the role of reactive oxygen species (ROS) released from the mitochondria as intracellular signaling molecules. Our study shows that neutrophils can use their mitochondria to generate ROS and that mitochondrial ROS release is increased in hypoxic conditions. This is needed for the stabilization of a high level of the critical hypoxic response factor and pro-survival protein HIF-1α in hypoxia. Further, we demonstrate that neutrophils use the glycerol 3-phosphate pathway as a way of directly regulating mitochondrial function through glycolysis, specifically to maintain polarized mitochondria and produce ROS. This illustrates an additional pathway by which neutrophils can regulate HIF-1α stability and will therefore be an important consideration when looking for treatments of inflammatory conditions in which HIF-1α activation and neutrophil persistence at the site of inflammation are linked to disease severity.
Helmet noninvasive ventilation compared to facemask noninvasive ventilation and high-flow nasal cannula in acute respiratory failure: a systematic review and meta-analysis
Authors: Chaudhuri Dipayan , Jinah Rehman , Burns Karen E.A. , Angriman Federico , Ferreyro Bruno L. , Munshi Laveena , Goligher Ewan , Scales Damon , Cook Deborah J. , Mauri Tommaso , Rochwerg Bram 
Published: August 2021

BackgroundAlthough small randomised controlled trials (RCTs) and observational studies have examined helmet noninvasive ventilation (NIV), uncertainty remains regarding its role. We conducted a systematic review and meta-analysis to examine the effect of helmet NIV compared to facemask NIV or high-flow nasal cannula (HFNC) in acute respiratory failure.MethodsWe searched multiple databases to identify RCTs and observational studies reporting on at least one of mortality, intubation, intensive care unit (ICU) length of stay, NIV duration, complications or comfort with NIV therapy. We assessed study risk of bias using the Cochrane Risk of Bias 2 tool for RCTs and the Ottawa–Newcastle Scale for observational studies, and rated certainty of pooled evidence using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) framework.ResultsWe separately pooled data from 16 RCTs (n=949) and eight observational studies (n=396). Compared to facemask NIV, based on low certainty of evidence, helmet NIV may reduce mortality (relative risk 0.56, 95% CI 0.33–0.95) and intubation (relative risk 0.35, 95% CI 0.22–0.56) in both hypoxic and hypercapnic respiratory failure, but may have no effect on duration of NIV. There was an uncertain effect of helmet NIV on ICU length of stay and development of pressure sores. Data from observational studies were consistent with the foregoing findings but of lower certainty. Based on low and very low certainty data, helmet NIV may reduce intubation compared to HFNC, but its effect on mortality is uncertain.ConclusionsCompared to facemask NIV, helmet NIV may reduce mortality and intubation; however, the effect of helmet NIV compared to HFNC remains uncertain.
Randomised trial of indwelling pleural catheters for refractory transudative pleural effusions
Authors: Walker Steven P. , Bintcliffe Oliver , Keenan Emma , Stadon Louise , Evison Matthew , Haris Mohammed , Nagarajan Thapas , West Alex , Ionescu Alina , Prudon Benjamin , Guhan Anur , Mustafa Rehan , Herre Jurgen , Arnold David , Bhatnagar Rahul , Kahan Brennan , Miller Robert F. , Rahman Najib M. , Maskell Nick A. 
Published: August 2021

ObjectiveRefractory symptomatic transudative pleural effusions are an indication for pleural drainage. There has been supportive observational evidence for the use of indwelling pleural catheters (IPCs) for transudative effusions, but no randomised trials. We aimed to investigate the effect of IPCs on breathlessness in patients with transudative pleural effusions when compared with standard care.MethodsA multicentre randomised controlled trial, in which patients with transudative pleural effusions were randomly assigned to either an IPC (intervention) or therapeutic thoracentesis (TT; standard care). The primary outcome was mean daily breathlessness score over 12 weeks from randomisation.Results220 patients were screened from April 2015 to August 2019 across 13 centres, with 33 randomised to intervention (IPC) and 35 to standard care (TT). Underlying aetiology was heart failure in 46 patients, liver failure in 16 and renal failure in six. In primary outcome analysis, the mean±sdbreathlessness score over the 12-week study period was 39.7±29.4 mm in the IPC group and 45.0±26.1 mm in the TT group (p=0.67). Secondary outcomes analysis demonstrated that mean±sddrainage was 17 412±17 936 mL and 2901±2416 mL in the IPC and TT groups, respectively. A greater proportion of patients had at least one adverse event in the IPC group (p=0.04).ConclusionWe found no significant difference in breathlessness over 12 weeks between IPCs or TT. TT is associated with fewer complications and IPCs reduced the number of invasive pleural procedures required. Patient preference and circumstances should be considered in selecting the intervention in this cohort.
Association of antinuclear antibody seropositivity with inhaled environmental exposures in patients with interstitial lung disease
Authors: Biblowitz Kathleen , Lee Cathryn , Zhu Daisy , Noth Imre , Vij Rekha , Strek Mary E. , Bellam Shashi K. , Adegunsoye Ayodeji 
Published: August 2021

BackgroundInterstitial lung diseases (ILDs) are diffuse parenchymal lung disorders that cause substantial morbidity and mortality. In patients with ILD, elevated antinuclear antibody (ANA) titres may be a sign of an autoimmune process. Inhalational exposures contribute to ILD pathogenesis and affect prognosis and may trigger autoimmune disease. The association of inhalational exposures with ANA seropositivity in ILD patients is unknown.MethodsThis was a retrospective cohort study of adult ILD patients from five centres in the United States. Exposures to tobacco, inhaled organic antigens and inhaled inorganic particles were extracted from medical records. A multivariable logistic regression model was used to analyse the effects of confounders including age, ILD diagnosis, gender and exposure type on ANA seropositivity.ResultsAmong 1265 patients with ILD, there were more ANA-seropositive (58.6%, n=741) than ANA-seronegative patients (41.4%, n=524). ANA-seropositive patients had lower total lung capacity (69%versus75%, p<0.001) and forced vital capacity (64%versus70%, p<0.001) than patients who were ANA-seronegative. Among patients with tobacco exposure, 61.4% (n=449) were ANA-positive compared to 54.7% (n=292) of those without tobacco exposure. In multivariable analysis, tobacco exposure remained independently associated with increased ANA seropositivity (OR 1.38, 95% CI 1.12–1.71). This significant difference was similarly demonstrated among patients with and without a history of inorganic exposures (OR 1.52, 95% CI 1.12–2.07).ConclusionPatients with ILD and inhalational exposure had significantly higher prevalence of ANA-seropositivity than those without reported exposures across ILD diagnoses. Environmental and occupational exposures should be systematically reviewed in patients with ILD, particularly those with ANA-seropositivity.
Evaluating the differences in the early laparoscopic donor nephrectomy learning curves of a Swiss high volume transplant program and a South African low volume transplant program after knowledge transfer
Authors: van der Merwe André , Ebinger Mundorf N. Nicole , van Heerden H. , Bonkat G. , van Deventer H. , Mantica G. , Keyser Z. , Bachmann A. 
Published: August 2021

Abstract
Background
To describe the retroperitoneoscopic donor nephrectomy learning curve differences between a high volume (training) hospital in Basel, Switzerland, and a low volume (trainee) hospital in Cape Town, South Africa, after knowledge transfer. The South African hospital is resource constraint in hospital and training equipment. Techniques for performing the surgery were near identical.

Methods
Both units maintained prospective databases. Comparisons were made of the first 74 cases in each database: Basel’s series were from 19 January 2001 until 28 June 2004, while the Cape Town Hospital were from 8 April 2008 until 15 July 2008. Four surgeons operated in the Basel group, while only one surgeon operated in the Cape Town group. Variables compared include operating time (first skin incision until kidney was extracted), warm ischaemic time (renal arterial occlusion until cold bench reperfusion), blood loss, graft function, and hospital stay. We also analysed the first and last 25 cases of each series. Subgroup analysis of a single Basel surgeon was conducted.

Results
Donor age (means: Basel vs. Cape Town 54 vs. 33 p < 0.0001) and gender (males vs. females Cape Town 57% male and Basel 31% male) differed widely. The Basel group did more left-sided operations (72% vs. 58%). Operative times, blood loss and donor creatinine did not differ. Warm ischaemic time was significantly shorter in the Basel group (Cape Town mean 204 s Basel mean 130 s P = 0.0023). There was double the number of early graft failures in the South African group (six vs. three)—not related to donor surgery. Both groups showed a decline in operating times, plateauing at 30–34 cases.

Conclusions
There are statistically significant differences in some aspects of the learning curves of the Swiss (training) and South African (trainee) hospitals. These differences are clinically not pronounced, and the knowledge transfer was worth the effort.
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts
Authors: Cole John J. , Faydaci Bekir A. , McGuinness David , Shaw Robin , Maciewicz Rose A. , Robertson Neil A. , Goodyear Carl S. 
Published: August 2021

Abstract
Background
Once bulk RNA-seq data has been processed, i.e. aligned and then expression and differential tables generated, there remains the essential process where the biology is explored, visualized and interpreted. Without the use of a visualisation and interpretation pipeline this step can be time consuming and laborious, and is often completed using R. Though commercial visualisation and interpretation pipelines are comprehensive, freely available pipelines are currently more limited.

Results
Here we demonstrate Searchlight, a freely available bulk RNA-seq visualisation and interpretation pipeline. Searchlight provides: a comprehensive statistical and visual analysis, focusing on the global, pathway and single gene levels; compatibility with most differential experimental designs irrespective of organism or experimental complexity, via three workflows; reports; and support for downstream user modification of plots via user-friendly R-scripts and a Shiny app. We show that Searchlight offers greater automation than current best tools (VIPER and BioJupies). We demonstrate in a timed re-analysis study, that alongside a standard bulk RNA-seq processing pipeline, Searchlight can be used to complete bulk RNA-seq projects up to the point of manuscript quality figures, in under 3 h.

Conclusions
Compared to a manual R based analysis or current best freely available pipelines (VIPER and BioJupies), Searchlight can reduce the time and effort needed to complete bulk RNA-seq projects to manuscript level. Searchlight is suitable for bioinformaticians, service providers and bench scientists. https://github.com/Searchlight2/Searchlight2.
Intratumoral regulatory T cells from colon cancer patients comprise several activated effector populations
Authors: Szeponik Louis , Ahlmanner Filip , Sundström Patrik , Rodin William , Gustavsson Bengt , Bexe Lindskog Elinor , Wettergren Yvonne , Quiding-Järbrink Marianne 
Published: August 2021

AbstractBackgroundIntratumoral regulatory T cells (Treg) in colon cancer are a heterogeneous cell population, with potential impact on patient outcome. Generally, a high Treg infiltration has been correlated to a worse patient outcome, but it is still unclear how the composition of different Treg subsets affects patient relapse and survival. In this study, we used mass and flow cytometry to characterize Treg in colon tumors and corresponding unaffected tissue, followed by a correlation to clinical parameters and patient outcome.ResultsUsing mass cytometry, we defined 13 clusters of intestinal Treg, three of which were enriched in the tumors. The two most enriched clusters were defined by their expression of the proliferation marker Ki67 and CD56, respectively. The Treg accumulating in the tumors expressed inducible T-cell co-stimulator (ICOS), OX-40, and CD39, indicating that they were effector Treg (eTreg). Intratumoral CD39+Treg also had a higher expression of Foxp3, suggesting a higher suppressive activity, and we subsequently used CD39 as a marker for eTreg. Our further studies showed that colon tumors can be divided into two tumor groups, based on the proportion of CD39+putative eTreg in the tumors. This property was independent of both tumor microsatellite status and tumor stage, which are important factors in predicting cancer disease progression. In a prospective study of forty-four colon cancer patients, we also showed that patients with a high CD39 expression on tumor-infiltrating Treg have a tendency towards a less favorable patient outcome in terms of cumulative cancer-specific survival.ConclusionsThis study uncovers novel subsets of tumor-infiltrating Treg in colon cancer, and suggests that CD39 may be a potential therapeutic target in patients with microsatellite stable colon tumors, which are usually refractory to checkpoint blockade therapy.
A cysteine-rich receptor-like protein kinase CaCKR5 modulates immune response against Ralstonia solanacearum infection in pepper
Authors: Mou Shaoliang , Meng Qianqian , Gao Feng , Zhang Tingting , He Weihong , Guan Deyi , He Shuilin 
Published: August 2021

Abstract
Background
Cysteine-rich receptor-like kinases (CRKs) represent a large subfamily of receptor-like kinases and play vital roles in diverse physiological processes in regulating plant growth and development.

Results
CaCRK5 transcripts were induced in pepper upon the infection of Ralstonia solanacearum and treatment with salicylic acid. The fusions between CaCRK5 and green fluorescence protein were targeted to the plasma membrane. Suppression of CaCRK5 via virus-induced gene silencing (VIGS) made pepper plants significantly susceptible to R. solanacearum infection, which was accompanied with decreased expression of defense related genes CaPR1, CaSAR8.2, CaDEF1 and CaACO1. Overexpression of CaCRK5 increased resistance against R. solanacearum in Nicotiana benthamiana. Furthermore, electrophoretic mobility shift assay and chromatin immunoprecipitation coupled with quantitative real-time PCR analysis revealed that a homeodomain zipper I protein CaHDZ27 can active the expression of CaCRK5 through directly binding to its promoter. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses suggested that CaCRK5 heterodimerized with the homologous member CaCRK6 on the plasma membrane.

Conclusions
Our data revealed that CaCRK5 played a positive role in regulating immune responses against R. solanacearum infection in pepper.
Plasma carbohydrate antigen-125 for prediction of atrial fibrillation recurrence after radiofrequency catheter ablation
Authors: Wang Qingya , Dang Chengjing , Liu Haoyu , Hui Jie 
Published: August 2021

Abstract
Background
Elevated plasma carbohydrate antigen-125 (CA-125) levels are strongly associated with new-onset atrial fibrillation (AF) and heart failure, but the relationship between plasma CA-125 level and AF recurrence following radiofrequency catheter ablation (RFCA) remains poorly investigated. We aimed to assess whether elevated CA-125 levels are related to long-term AF recurrence following RFCA.

Methods
Preoperative CA-125 levels were determined in AF patients undergoing initial RFCA. Multivariate-adjusted Cox models were constructed to determine the relationship between CA-125 levels and AF recurrence. Multivariate logistic regression analyses were performed to determine predictors of AF recurrence.

Results
Of the 353 enrolled patients, 85 patients (24.1%) had AF recurrence at the 12-month follow-up. These patients had significantly higher baseline CA-125 levels than those without AF recurrence [(18.71 ± 12.63) vs. (11.27 ± 5.40) U/mL, P < 0.001]. The incidence of AF recurrence across quartiles 1–4 of CA-125 was 11.5%, 13.3%, 21.6% and 50.0%, respectively (P-trend < 0.001). The adjusted hazard ratios (aHRs) for AF recurrence across quartiles 1–4 of CA-125 were 1.00 (reference), 1.085 (95% CI, 0.468–2.520), 1.866 (95% CI, 0.867–4.019), and 4.246 (95% CI, 2.113–8.533), respectively (P-trend < 0.001). A similar effect was obtained when CA-125 was studied as continuous data (aHR per unit increase in LnCA-125, 3.225, 95% CI, 2.258–4.606; P < 0.001). When a predefined CA-125 cut-off of 13.75 U/mL was established, patients with CA-125 ≥ 13.75 U/mL had a higher risk of recurrent AF than those with CA-125 < 13.75 U/mL (aHR, 3.540, 95% CI, 2.268–5.525, P < 0.001). Multivariate analysis revealed CA-125, high-sensitivity C-reactive protein, and left atrium anteroposterior diameter as independent risk factors for AF recurrence.

Conclusions
Elevated preoperative CA-125 levels are related to a higher risk of AF recurrence and can independently predict AF recurrence following RFCA.
Isolation of Brucella abortus biovar 1 from human lumbar disc bulging: a case report of brucellar discitis
Authors: Alamian Saeed , Etemadi Afshar , Samiee Mohammad Reza , Dadar Maryam 
Published: August 2021

Abstract
Background
Brucellosis is an endemic zoonotic disease with rising health and economic concerns in many areas worldwide. Musculoskeletal pains are among the main complications of human brucellosis, which are often difficult to diagnose due to the variability of clinical symptoms. Brucellar discitis is a very disabling problem in some chronic forms of the disease which may lead to serious vertebral and neurological consequences.

Case presentation
In this case report, we reported the isolation of Brucella abortus from lumbar disc bulging in a woman who had rheumatoid arthritis and diabetes mellitus as underlying conditions. The patient had several negative brucellosis serological tests and dorsolumbar pains with urinary incontinence over a 2-month period. The diagnosis was confirmed by magnetic resonance imaging (MRI) examination of lumbar spine as well as disc culture. MRI examination was performed without intravenous contrast and revealed the presence of disc bulging, left foraminal narrowing at L5-S1, left foraminal narrowing, anterolisthesis grade II at L4-L5. The diagnosis was also confirmed by isolation of B. abortus biovar 1 from bulging disc culture. The isolate was characterized by AMOS PCR, Bruce-ladder PCR and biotyping, resulting in the identification of B. abortus from L4-L5 and L5-S1 disc bulging regions. The patient was treated with two drugs i.e. doxycycline and rifampin for 3 months. In the follow-up, in addition to improving the patient’s general condition, low-back pain was also significantly reduced.

Conclusions
MRI, serology, cultural and molecular test along with patient history are important to make a rapid diagnosis of brucellosis’ discitis, thereby decreasing the delay for the brucellosis treatment. The present report suggests that the infection by Brucella spp. should be fundamentally considered among the causative agents of back pain especially in the endemic areas of Brucella infections.