bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking of long-read assemblers for prokaryote whole genome sequencing
Authors: Wick Ryan R. , Holt Kathryn E. 
Published: February 2021

Background: Data sets from long-read sequencing platforms (Oxford Nanopore Technologies and Pacific Biosciences) allow for most prokaryote genomes to be completely assembled – one contig per chromosome or plasmid. However, the high per-read error rate of long-read sequencing necessitates different approaches to assembly than those used for short-read sequencing. Multiple assembly tools (assemblers) exist, which use a variety of algorithms for long-read assembly. Methods: We used 500 simulated read sets and 120 real read sets to assess the performance of eight long-read assemblers (Canu, Flye, Miniasm/Minipolish, NECAT, NextDenovo/NextPolish, Raven, Redbean and Shasta) across a wide variety of genomes and read parameters. Assemblies were assessed on their structural accuracy/completeness, sequence identity, contig circularisation and computational resources used. Results: Canu v2.1 produced reliable assemblies and was good with plasmids, but it performed poorly with circularisation and had the longest runtimes of all assemblers tested. Flye v2.8 was also reliable and made the smallest sequence errors, though it used the most RAM. Miniasm/Minipolish v0.3/v0.1.3 was the most likely to produce clean contig circularisation. NECAT v20200803 was reliable and good at circularisation but tended to make larger sequence errors. NextDenovo/NextPolish v2.3.1/v1.3.1 was reliable with chromosome assembly but bad with plasmid assembly. Raven v1.3.0 was reliable for chromosome assembly, though it did not perform well on small plasmids and had circularisation issues. Redbean v2.5 and Shasta v0.7.0 were computationally efficient but more likely to produce incomplete assemblies. Conclusions: Of the assemblers tested, Flye, Miniasm/Minipolish, NextDenovo/NextPolish and Raven performed best overall. However, no single tool performed well on all metrics, highlighting the need for continued development on long-read assembly algorithms.
Journal editors: How do their editing incomes compare?
Authors: Lee Janice C. L. , Watt Jennifer , Kelsall Diane , Straus Sharon 
Published: February 2021

Background:The work of journal editors is essential to producing high-quality literature, and editing can be a very rewarding career; however, the profession may not be immune to gender pay gaps found in many professions and industries, including academia and clinical medicine. Our study aimed to quantify remuneration for journal editors from core clinical journals, determine if a gender pay gap exists, and assess if there are remuneration differences across publishing models and journal characteristics.Methods:We completed an online survey of journal editors with substantial editing roles including section editors and editors-in-chief, identified from the Abridged Index Medicus “Core Clinical” journals in MEDLINE. We analyzed information on demographics, editing income, and journal characteristics using a multivariable partial proportional odds model for ordinal logistic regression.Results:There were 166 survey respondents (response rate of 9%), which represented editors from 69 of 111 journals (62%). A total of 140 fully completed surveys were analyzed (95 males and 45 females); 50 (36%) editors did not receive remuneration for editorial work. No gender pay gap and no difference in remuneration between editors who worked in subscription-based publishing vs. open access journals were detected. Editors who were not primarily health care providers were more likely to have higher editing incomes (adjusted odds ratio [OR] 2.96, 95% confidence interval [CI] 1.18-7.46). Editors who worked more than 10 hours per week editing earned more than those who worked 10 hours or less per week (adjusted OR 16.7, 95%CI 7.02-39.76).Conclusions:We were unable to detect a gender pay gap and a difference in remuneration between editors who worked in subscription-based publishing and those in open access journals. More than one third of editors surveyed from core clinical journals did not get remunerated for their editing work.
Clarifying Optimal Sodium InTake In Cardiovasular and Kidney (COSTICK) Diseases: a study protocol for two randomised controlled trials
Authors: Smyth Andrew , Yusuf Salim , Kerins Claire , Corcoran Colette , Dineen Roisin , Alvarez-Iglesias Alberto , Ferguson John , McDermott Suzanne , Hernon Orlaith , Ranjan Ritika , Nolan Aoife , Griffin Matthew , O'Shea Paula , Canavan Michelle , O'Donnell Martin 
Published: February 2021

Background: While low sodium intake (<2.3g/day) is recommended for all, there is uncertainty about feasibility and net cardiovascular effects. In COSTICK, we evaluated the effects of a dietary counselling intervention (reduced sodium intake) on intermediate cardiorenal outcomes in patients with (STICK) and without (COSIP) mild/moderate kidney disease. Methods: This is a protocol for two phase IIb randomised, two-group, parallel, open-label, controlled, single centre trials. Participants were aged >40 years with stable blood pressure, unchanged anti-hypertensive medications, willing to modify diet and provided written informed consent. Participants were excluded for abnormal sodium handling, heart failure, high dose diuretics, immunosuppression, pregnancy/lactation, postural hypotension, cognitive impairment, high or low body mass index (BMI) or inclusion in another trial. STICK participants had estimated glomerular filtration rate (eGFR) 30-60ml/min/1.73m2 and were excluded for acute kidney Injury, rapidly declining eGFR; known glomerular disease or current use of non-steroidal anti-inflammatory drugs. For COSIP, participants were excluded for known kidney or cardiovascular disease. Participants were randomized to usual care only (healthy eating) or an additional sodium lowering intervention (target <100mmol/day) through specific counseling (sodium use in foods, fresh over processed foods, sodium content of foods and eating outside of home). In STICK the primary outcome is change in 24-hour urinary creatinine clearance. In COSIP, the primary outcome is change in five biomarkers (renin, aldosterone, high sensitivity troponin T, pro-B-type natriuretic peptide and C-reactive protein). Our primary report (COSTICK), reports six biomarker outcome measures in the entire population at 2 years follow-up. Discussion: These Phase II trials will explore uncertainty about low sodium intake and cardiovascular and kidney biomarkers, and help determine the feasibility of low sodium intake. Trial results will also provide preliminary information to guide a future definitive clinical trial, if indicated. Trial registration: STICK: ClinicalTrials.gov NCT02738736 (04/04/2016); COSIP: ClinicalTrials.gov NCT02458248 (15/05/2016)
Co-prevalent infections in adults with HIV-associated cryptococcal meningitis are associated with an increased risk of death: a nested analysis of the Advancing Cryptococcal meningitis Treatment for Africa (ACTA) cohort
Authors: Ellis Jayne , Kalata Newton , Dziwani Eltas , Matope Agnes , Wang Duolao , Molloy Síle F. , Harrison Thomas S. , Lalloo David G. , Sloan Derek , Heyderman Robert S. 
Published: February 2021

Background: HIV-associated cryptococcal meningitis accounts for 15% of AIDS related deaths globally. In sub-Saharan Africa, acute mortality ranges from 24% to 100%. In addition to the mortality directly associated with cryptococcosis, patients with HIV-associated cryptococcal meningitis are at risk of a range of opportunistic infections (OIs) and hospital acquired nosocomial infections (HAIs). The attributable mortality associated with co-prevalent infections in cryptococcal meningitis has not been evaluated. Methods: As part of the Advancing Cryptococcal meningitis Treatment for Africa (ACTA) trial, consecutive HIV-positive adults with cryptococcal meningitis were randomised to one of five anti-fungal regimens and followed up until 10-weeks. We conducted a retrospective case note review of ACTA participants recruited from Queen Elizabeth Central Hospital in Blantyre, Malawi to describe the range and prevalence of OIs and HAIs diagnosed, and the attributable mortality associated with these infections. Results: We describe the prevalence of OIs and HAIs in 226 participants. Baseline median CD4 count was 29 cell/mm3, 57% (129/226) were on anti-retroviral therapy. 56% (127/226) had at least one co-prevalent infection during the 10-week study period. Data were collected for 187 co-prevalent infection episodes. Suspected blood stream infection was the commonest co-prevalent infection diagnosed (34/187, 18%), followed by community-acquired pneumonia (32/187, 17%), hospital-acquired pneumonia (13/187, 7%), pulmonary tuberculosis (12/187, 6%) and confirmed blood stream infections (10/187, 5%). All-cause mortality at 10-weeks was 35% (80/226), diagnosis of an OI or HAI increased the risk of death at 10 weeks by nearly 50% (HR 1.48, 95% CI 1.01-2.17, p=0.04). Conclusion: We demonstrate the high prevalence and broad range of OIs and HAIs occurring in patients with HIV-associated cryptococcal meningitis. These co-prevalent infections are associated with a significantly increased risk of death. Whether a protocolised approach to improve surveillance and proactive treatment of co-prevalent infections would improve cryptococcal meningitis outcomes warrants further investigation.
Comparative evaluation of ten lateral flow immunoassays to detect SARS-CoV-2 antibodies
Authors: Garrod Gala , Owen Sophie I. , Baillie J. Kenneth , Baldwin Lisa , Brown Lottie , Byrne Rachel L. , Cubas-Atienzar Ana I. , Cuevas Luis E. , Fraser Alice J. , Fletcher Thomas , Goodwin Lynsey , Kay Grant A. ,   ISARIC4C Investigators, Kontogianni Konstantina , Mason Jenifer , Openshaw Peter J.M. , Menzies Stefanie , Moore Shona C. , Semple Malcolm G. , Taylor Joseph , Turtle Lance C.W. , Williams Christopher T. , Adams Emily R. 
Published: February 2021

Background: Rapid mobilisation from industry and academia following the outbreak of the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), led to the development and availability of SARS-CoV-2 lateral flow immunoassays (LFAs). High quality LFAs are urgently needed at the point of care to add to currently available diagnostic tools. In this study, we provide evaluation data for ten LFAs suitable for use at the point of care. Methods: COVID-19 positive patients (N=45), confirmed by reverse transcription – quantitative polymerase chain reaction (RT-qPCR), were recruited through the International Severe Acute Respiratory and Emerging Infection Consortium - Coronavirus Clinical Characterisation Consortium (ISARIC4C) study. Sera collected from patients with influenza A (N=20), tuberculosis (N=5), individuals with previous flavivirus exposure (N=21), and healthy sera (N=4), collected pre-pandemic, were used as negative controls. Ten LFAs manufactured or distributed by ASBT Holdings Ltd, Cellex, Fortress Diagnostics, Nantong Egens Biotechnology, Mologic, NG Biotech, Nal von Minden and Suzhou Herui BioMed Co. were evaluated. Results: Compared to RT-qPCR, sensitivity of LFAs ranged from 87.0-95.7%. Specificity against pre-pandemic controls ranged between 92.0-100%. Compared to IgG ELISA, sensitivity and specificity ranged between 90.5-100% and 93.2-100%, respectively. Percentage agreement between LFAs and IgG ELISA ranged from 89.6-92.7%. Inter-test agreement between LFAs and IgG ELISA ranged between kappa=0.792-0.854. Conclusions: LFAs may serve as a useful tool for rapid confirmation of ongoing or previous infection in conjunction with clinical suspicion of COVID-19 in patients attending hospital. Impartial validation prior to commercial sale provides users with data that can inform best use settings.
Cast immobilization is non-inferior to volar locking plates in relation to QuickDASH after one year in patients aged 65 years and older: a randomized controlled trial of displaced distal radius fractures
Authors: Hassellund Sondre Stafsnes , Williksen John Håkon , Laane Marit Mjelde , Pripp Are , Rosales Carina Paulsen , Karlsen Øyvind , Madsen Jan Erik , Frihagen Frede 
Published: February 2021

Aims To compare operative and nonoperative treatment for displaced distal radius fractures in patients aged over 65 years. Methods A total of 100 patients were randomized in this non-inferiority trial, comparing cast immobilization with operation with a volar locking plate. Patients with displaced AO/OTA A and C fractures were eligible if one of the following were found after initial closed reduction: 1) dorsal angulation > 10°; 2) ulnar variance > 3 mm; or 3) intra-articular step-off > 2 mm. Primary outcome measure was the abbreviated version of the Disabilities of the Arm, Shoulder and Hand questionnaire (QuickDASH) after 12 months. Secondary outcome measures were the Patient-Rated Wrist and Hand Evaluation (PRWHE), EuroQol-5 dimensions 5-level questionnaire (EQ-5D-5L), range of motion (ROM), grip strength, “satisfaction with wrist function” (score 0 to 10), and complications. Results In all, 89 women and 11 men were included. Mean age was 74 years (65 to 91). Nonoperative treatment was non-inferior to operation with a five-point difference in median QuickDASH after 12 months (p = 0.206). After three and six months QuickDASH favoured the operative group (p = 0.010 and 0.030). Median values for PRWHE were 19 (interquartile range (IRQ) 10 to 32) in the operative group versus ten (IQR 1 to 31) in the nonoperative group at three months (p = 0.064), nine (IQR 2 to 20) versus five (IQR 0 to 13) (p = 0.020) at six months, and two (IQR 0 to 12) versus zero (IQR 0 to 8) (p = 0.019) after 12 months. Range of motion was similar between the groups. The EQ-5D-5L index score was better (mean difference 0.07) in the operative group at three and 12 months (p = 0.008 and 0.020). The complication rate was similar (p = 0.220). The operated patients were more satisfied with wrist function (median 8 (IQR 6 to 9) vs 6 (IQR 5 to 7) at three months, p = 0.002; 9 (IQR 7 to 9) vs 8 (IQR 6 to 8) at six months, p = 0.002; and 10 (IQR 8 to 10) vs 8 (IQR 7 to 9) at 12 months, p < 0.001). Conclusion Nonoperative treatment was non-inferior to operative treatment based on QuickDASH after one year. Patients in the operative group had a faster recovery and were more satisfied with wrist function. Results from previous trials comparing operative and nonoperative treatment for displaced distal radius fractures in the elderly vary between favouring the operative group and showing similar results between the treatments. This randomized trial suggests that most elderly patients may be treated nonoperatively. Cite this article: Bone Joint J 2021;103-B(2):247–255.
What constitutes a clinically important change in Mayo Elbow Performance Index and range of movement after open elbow arthrolysis?
Authors: Sun Ziyang , Li Juehong , Luo Gang , Wang Feiyan , Hu Yuehao , Fan Cunyi 
Published: February 2021

AimsThis study aimed to determine the minimal detectable change (MDC), minimal clinically important difference (MCID), and substantial clinical benefit (SCB) under distribution- and anchor-based methods for the Mayo Elbow Performance Index (MEPI) and range of movement (ROM) after open elbow arthrolysis (OEA). We also assessed the proportion of patients who achieved MCID and SCB; and identified the factors associated with achieving MCID.MethodsA cohort of 265 patients treated by OEA were included. The MEPI and ROM were evaluated at baseline and at two-year follow-up. Distribution-based MDC was calculated with confidence intervals (CIs) reflecting 80% (MDC 80), 90% (MDC 90), and 95% (MDC 95) certainty, and MCID with changes from baseline to follow-up. Anchor-based MCID (anchored to somewhat satisfied) and SCB (very satisfied) were calculated using a five-level Likert satisfaction scale. Multivariate logistic regression of factors affecting MCID achievement was performed.ResultsThe MDC increased substantially based on selected CIs (MDC 80, MDC 90, and MDC 95), ranging from 5.0 to 7.6 points for the MEPI, and from 8.2° to 12.5° for ROM. The MCID of the MEPI were 8.3 points under distribution-based and 12.2 points under anchor-based methods; distribution- and anchor-based MCID of ROM were 14.1° and 25.0°. The SCB of the MEPI and ROM were 17.3 points and 43.4°, respectively. The proportion of the patients who attained anchor-based MCID for the MEPI and ROM were 74.0% and 94.7%, respectively; furthermore, 64.2% and 86.8% attained SCB. Non-dominant arm (p = 0.022), higher preoperative MEPI rating (p < 0.001), and postoperative visual analogue scale pain score (p < 0.001) were independent predictors of not achieving MCID for the MEPI, while atraumatic causes (p = 0.040) and higher preoperative ROM (p = 0.005) were independent risk factors for ROM.ConclusionIn patients undergoing OEA, the MCID for the increased MEPI is 12.2 points and 25° increased ROM. The SCB is 17.3 points and 43.3°, respectively. Future studies using the MEPI and ROM to assess OEA outcomes should report not only statistical significance but also clinical importance. Cite this article: Bone Joint J 2021;103-B(2):366–372.
Influence of curve morphology and location on the efficacy of rigid conservative treatment in patients with adolescent idiopathic scoliosis
Authors: Strube Patrick , Gunold Maria , Müller Tanja , Leimert Mario , Sachse André , Pumberger Matthias , Putzier Michael , Zippelius Timo 
Published: February 2021

Aims The aim of the present study was to answer the question whether curve morphology and location have an influence on rigid conservative treatment in patients with adolescent idiopathic scoliosis (AIS). Methods We retrospectively analyzed AIS in 127 patients with single and double curves who had been treated with a Chêneau brace and physiotherapeutic specific exercises (B-PSE). The inclusion criteria were the presence of structural major curves ≥ 20° and < 50° (Risser stage 0 to 2) at the time when B-PSE was initiated. The patients were divided into two groups according to the outcome of treatment: failure (curve progression to ≥ 45° or surgery) and success (curve progression < 45° and no surgery). The main curve type (MCT), curve magnitude, and length (overall, above and below the apex), apical rotation, initial curve correction, flexibility, and derotation by the brace were compared between the two groups. Results In univariate analysis treatment failure depended significantly on: 1) MCT (p = 0.008); 2) the apical rotation of the major curve before (p = 0.007) and during brace treatment (p < 0.001); 3) the initial and in-brace Cobb angles of the major (p = 0.001 and p < 0.001, respectively) and minor curves (p = 0.015 and p = 0.002); 4) major curve flexibility (p = 0.005) and the in-brace curve correction rates (major p = 0.008, minor p = 0.034); and 5) the length of the major curve (LoC) above (p < 0.001) and below (p = 0.002) the apex. Furthermore, MCT (p = 0.043, p = 0.129, and p = 0.017 in MCT comparisons), LoC (upper length p = 0.003, lower length p = 0.005), and in-brace Cobb angles (major p = 0.002, minor p = 0.027) were significant in binary logistic regression analysis. Conclusion Curve size, location, and morphology were found to influence the outcome of rigid conservative treatment of AIS. These findings may improve future brace design and patient selection for conservative treatment. Cite this article: Bone Joint J 2021;103-B(2):373–381.
Mid-term foot function and pedobarographic analysis of 52 feet after polydactyly resection in childhood
Authors: Farr Sebastian , Jauker Fridolin , Ganger Rudolf , Kranzl Andreas 
Published: February 2021

Aims The aims of this study is to report the clinical and radiological outcomes after pre-, central-, and postaxial polydactyly resection in children from a tertiary referral centre. Methods All children who underwent resection of a supernumerary toe between 2001 and 2013 were prospectively enrolled and invited for a single re-assessment. Clinical parameters and several dedicated outcome scores (visual analogue scale (VAS), Paediatric Outcomes Data Collection Instrument (PODCI), Activities Scale for Kids (ASK), and American Orthopaedic Foot and Ankle Society Score (AOFAS)) were obtained, as were radiographs of the operated and non-operated feet along with pedobarographs. Results In all, 39 children (52 feet) with a mean follow-up of 7.2 years (3.1 to 13.0) were included in the study. Resection of a duplicated great toe was performed in ten children, central polydactyly in four, and postaxial polydactyly in 26. The mean postoperative VAS (0.7; 0 to 7), ASK (93.7; 64.2 to 100), and AOFAS range (85.9 to 89.0) indicated excellent outcomes among this cohort and the PODCI global functioning scale (95.7; 75.5 to 100) was satisfactory. No significant differences were found regarding outcomes of pre- versus postaxial patients, nor radiological toe alignment between the operated and non-operated sides. Minor complications were observed in six children (15%). There were seven surgical revisions (18%), six of whom were in preaxial patients. In both groups, below the operation area, a reduced mean and maximum force was observed. Changes in the hindfoot region were detected based on the prolonged contact time and reduced force in the preaxial group. Conclusion Excellent mid-term results can be expected after foot polydactyly resection in childhood. However, parents and those who care for these children need to be counselled regarding the higher risk of subsequent revision surgery in the preaxial patients. Also, within the study period, the plantar pressure distribution below the operated part of the foot did not return to completely normal. Cite this article: Bone Joint J 2021;103-B(2):415–420.
An update about molecular biology techniques to detect orthopaedic implant-related infections
Authors: Esteban Jaime , Gómez-Barrena Enrique 
Published: February 2021

Despite different criteria to diagnose a prosthetic joint infection (PJI), aetiological diagnosis of the causing microorganism remains essential to guide treatment. Molecular-biology-based PJI diagnosis is progressing (faster, higher specificity) in different techniques, from the experimental laboratory into clinical use. Multiplex polymerase chain reaction techniques (custom-made or commercial) provide satisfactory results in clinical series of cases, with specificity close to 100% and sensitivity over 70–80%. Next-generation metagenomics may increase sensitivity while maintaining high specificity. Molecular biology techniques may represent, in the next five years, a significant transformation of the currently available microbiological diagnosis in PJI. Cite this article: EFORT Open Rev 2021;6:93-100. DOI: 10.1302/2058-5241.6.200118