bluuebunny/crossref_metadata_2025_split huggingface dataset:
MitoFish, MitoAnnotator, and MiFish Pipeline: Updates in 10 Years
Authors: Zhu Tao , Sato Yukuto , Sado Tetsuya , Miya Masaki , Iwasaki Wataru 
Published: March 2023

AbstractMitoFish, MitoAnnotator, and MiFish Pipeline are comprehensive databases of fish mitochondrial genomes (mitogenomes), accurate annotation software of fish mitogenomes, and a web platform for metabarcoding analysis of fish mitochondrial environmental DNA (eDNA), respectively. The MitoFish Suite currently receives over 48,000 visits worldwide every year; however, the performance and usefulness of the online platforms can still be improved. Here, we present essential updates on these platforms, including an enrichment of the reference data sets, an enhanced searching function, substantially faster genome annotation and eDNA analysis with the denoising of sequencing errors, and a multisample comparative analysis function. These updates have made our platform more intuitive, effective, and reliable. These updated platforms are freely available at http://mitofish.aori.u-tokyo.ac.jp/.
Evolution is not Uniform Along Coding Sequences
Authors: Bricout Raphaël , Weil Dominique , Stroebel David , Genovesio Auguste , Roest Crollius Hugues 
Published: March 2023

AbstractAmino acids evolve at different speeds within protein sequences, because their functional and structural roles are different. Notably, amino acids located at the surface of proteins are known to evolve more rapidly than those in the core. In particular, amino acids at the N- and C-termini of protein sequences are likely to be more exposed than those at the core of the folded protein due to their location in the peptidic chain, and they are known to be less structured. Because of these reasons, we would expect that amino acids located at protein termini would evolve faster than residues located inside the chain. Here we test this hypothesis and found that amino acids evolve almost twice as fast at protein termini compared with those in the center, hinting at a strong topological bias along the sequence length. We further show that the distribution of solvent-accessible residues and functional domains in proteins readily explain how structural and functional constraints are weaker at their termini, leading to the observed excess of amino acid substitutions. Finally, we show that the specific evolutionary rates at protein termini may have direct consequences, notably misleading in silico methods used to infer sites under positive selection within genes. These results suggest that accounting for positional information should improve evolutionary models.
Circulating thrombospondin-2 level for identifying individuals with rapidly declining kidney function trajectory in type 2 diabetes: a prospective study of the Hong Kong West Diabetes Registry
Authors: Lee Chi-Ho , Lui David Tak-Wai , Cheung Chloe Yu-Yan , Fong Carol Ho-Yi , Yuen Michele Mae-Ann , Chow Wing-Sun , Xu Aimin , Lam Karen Siu-Ling 
Published: March 2023

ABSTRACT

Background
Thrombospondin-2 (TSP2) is a matricellular protein with tissue expression induced by hyperglycaemia. TSP2 has been implicated in non-diabetic renal injury in preclinical studies and high circulating levels were associated with worse kidney function in cross-sectional clinical studies. Therefore, we investigated the prospective associations of circulating TSP2 level with kidney function decline and the trajectories of estimated glomerular filtration rate (eGFR) in type 2 diabetes.

Methods
Baseline serum TSP2 level was measured in 5471 patients with type 2 diabetes to evaluate its association with incident eGFR decline, defined as ≥40% sustained eGFR decline, using multivariable Cox regression analysis. Among participants with relatively preserved kidney function (baseline eGFR ≥60 mL/min/1.73 m2), joint latent class modelling was employed to identify three different eGFR trajectories. Their associations with baseline serum TSP2 were evaluated using multinomial logistic regression analysis. The predictive performance of serum TSP2 level was examined using time-dependent c-statistics and calibration statistics.

Results
Over a median follow-up of 8.8 years, 1083 patients (19.8%) developed eGFR decline. Baseline serum TSP2 level was independently associated with incident eGFR decline [hazard ratio (HR) 1.21, 95% confidence interval (CI) 1.07–1.37, P = .002]. With internal validation, incorporating serum TSP2 to a model of clinical risk factors including albuminuria led to significant improvement in c-statistics from 83.9 to 84.4 (P &lt; .001). Among patients with eGFR ≥60 mL/min/1.73 m2, baseline serum TSP2 level was independently associated with a rapidly declining eGFR trajectory (HR 1.63, 95% CI 1.26–2.10, P &lt; .001).

Conclusion
Serum TSP2 level was independently associated with incident eGFR decline, particularly a rapidly declining trajectory, in type 2 diabetes.
Respiratory Syncytial Virus Disease Burden in Community-Dwelling and Long-Term Care Facility Older Adults in Europe and the United States: A Prospective Study
Authors: Narejos Pérez Sílvia , Ramón Torrell Josep María , Põder Airi , Leroux-Roels Isabel , Pérez-Breva Lina , Steenackers Katie , Vandermeulen Corinne , Meisalu Sandra , McNally Damien , Bowen Jordan S T , Heer Amardeep , Beltran Martinez Adrian , Helman Laura L , Arora Amit , Feldman Robert G , Patel Rajul , Shah Amit , Devadiga Raghavendra , Damaso Silvia , Matthews Sean , Pirçon Jean-Yves , Luyts Dominique 
Published: March 2023

AbstractBackgroundData on respiratory syncytial virus (RSV) disease burden in adults remain scarce. We assessed the burden of confirmed RSV-acute respiratory infections (cRSV-ARIs) in community-dwelling (CD) adults and those in long-term care facilities (LTCFs).MethodsIn this prospective cohort study covering 2 RSV seasons (October 2019–March 2020 and October 2020–June 2021), RSV-ARIs were identified through active surveillance, in medically stable CD-adults ≥50 years (Europe) or adults ≥65 years in LTCFs (Europe and the United States). RSV infection was confirmed by polymerase chain reaction from combined nasal and throat swabs.ResultsOf 1981 adults enrolled, 1251 adults in CD and 664 LTCFs (season 1) and 1223 adults in CD and 494 LTCFs (season 2) were included in the analyses. During season 1, overall incidence rates ([IRs] cases/1000 person-years) and attack rates (ARs) for cRSV-ARIs were 37.25 (95% confidence interval [CI], 22.62–61.35) and 1.84% in adults in CD and 47.85 (CI, 22.58–101.4) and 2.26% in adults in LTCFs. Complications occurred for 17.4% (CD) and 13.3% (LTCFs) of cRSV-ARIs. One cRSV-ARI occurred in season 2 (IR = 2.91 [CI, 0.40–20.97]; AR = 0.20%), without complications. No cRSV-ARIs led to hospitalization or death. Viral pathogens were codetected in ≤17.4% of cRSV-ARIs.ConclusionsRSV is an important cause of disease burden in adults in CD and LTCFs. Despite the observed low severity of cRSV-ARI, our results support the need for RSV prevention strategies among adults ≥50 years old.
How to plug the leaky pipeline in clinical rheumatology across Europe—lessons to be learned from experiences in business
Authors: Sautner Judith , Grabner Isabella , Posch Arthur , Duftner Christina 
Published: March 2023

Abstract

Objectives
While &gt;50% of medical students and residents are women, their proportion drastically diminishes within higher ranks and leadership roles; this is known as the ‘leaky pipeline’. We aimed to evaluate the leaky pipeline among rheumatologists across Europe and to assess determinants inducing rheumatologists to leave hospitals.

Methods
Experts in the field of economics developed a questionnaire with scientific focus on the leaky pipeline among rheumatologists, which was distributed electronically by national scientific societies of EULAR countries and by individual contacts. We performed common factor analysis, univariate t-tests and multivariate regression analyses to appraise our dataset.

Results
A total of 311 hospital-based rheumatologists from 23/45 EULAR countries (52.7% females, 47.3% males) answered the questionnaire. The presence of the leaky pipeline was evident for the entire sample. Of 64% female rheumatologists only 34.2% of departments’ directors were female, with noteworthy regional differences. Female doctors reported higher intentions to leave their hospital (β = 0.28, P &lt; 0.05) and lower commitment towards their current organization (β = –0.34, P &lt; 0.05) when compared with males. Women reported lower levels of job satisfaction (β = –0.26, P &lt; 0.10), promotion justice (β = –0.55, P &lt; 0.01) and career perspectives (β = –0.26, P &lt; 0.10, one-tailed) than men, explaining their lower organizational commitment.

Conclusion
Female rheumatologists perceive worse job opportunities and satisfaction than males. Many reasons for the leaky pipeline are beyond the control of organizations. Based on our results, organizations should be encouraged to reconsider and adjust their performance management practices to enable an equitable work environment.
Obstructive sleep apnea in aboriginal Australians: polysomnographic outcomes and symptom perception post-continuous positive airway pressure implementation
Authors: Lindfield Matthew , Howarth Timothy P , Perez Ara J , Crespo Jessie , Atos Charmain B , Huang Hsin-Chia C , Heraganahally Subash S 
Published: March 2023

AbstractStudy ObjectivesObstructive sleep apnea (OSA) is reported to be highly prevalent among Aboriginal Australians. However, no studies have assessed the implementation and efficacy of continuous positive airway pressure (CPAP) therapy in this population. Hence, we compared the clinical, self-reported perception of sleep quality and polysomnographic (PSG) characteristics among Aboriginal patients with OSA.MethodsAdult Aboriginal Australians who underwent both diagnostic (Type 1 and 2) and in-lab CPAP implementation studies were included.ResultsTotal of 149 patients were identified (46% female, median age 49 years, body mass index 35 kg/m2). The OSA severity was 6% mild, 26% moderate, and 68% severe on the diagnostic PSG. On application of CPAP, there were significant improvements in; total arousal index (diagnostic 29 to 17/h on CPAP), total apnea–hypopnea index (AHI) (diagnostic 48 to 9/h on CPAP), non-rapid eye movement AHI (diagnostic 47 to 8/h on CPAP), rapid eye movement (REM) AHI (diagnostic 56 to 8/h on CPAP) and oxygen saturation (SpO2) nadir (diagnostic 77% to 85% on CPAP) (p &lt; 0.001 for each). Following a single night of CPAP, 54% of patients reported sleeping “better than normal” compared to 12% following the diagnostic study (p = 0.003). In multivariate regression models, males had a significantly lesser change in REM AHI than females (5.7 events/hour less change (IQR 0.4, 11.1), p = 0.029).ConclusionsThere is substantial improvement in several sleep-related domains on the application of CPAP among Aboriginal patients with a good initial acceptance of treatment. Whether the positive impact observed in this study translates to better sleep health outcomes with long-term adherence to CPAP therapy is yet to be assessed.
Erectile dysfunction from mechanisms to medicines with a focus on the application of topical Minoxidil
Authors: Tavakoli Marziye Ranjbar , Faraji Maryam , Sam Sanaz , Ghasempour Ali , Rezaei Masoud , Langarizadeh Mohammad Amin , Karami-Mohajeri Somayyeh 
Published: March 2023

AbstractIntroductionErectile dysfunction (ED), for multifactorial reasons, is one of the biggest current quandaries among men worldwide and results in other complications such as reduced quality of life of the patient and his sexual partner, impotence, and psychiatric problems.ObjectivesUnderstanding of disease etiology, penile anatomy, erectile physiology, therapeutic mechanisms, and effective molecular pathways all play key roles in determining a therapeutic approach. This project is based on the study of topical minoxidil’s effectiveness in treating ED.MethodsTo perform a comprehensive overview of the subject, we performed a triple-keyword combination search to assess recent studies of ED.ResultsThe most common formulation used in these studies was 2% minoxidil solution. Except for cases studied in paralytic patients, topical treatment with minoxidil appears to elicit a mild erectile response; however, this finding is insufficient to confirm the effectiveness of this topical treatment.ConclusionsAlthough evidence to confirm the therapeutic properties of minoxidil in ED is limited, combination therapy and the use of modern formulations of minoxidil are promising options for treating ED in the future.
Analysis of human rabies deaths reported at two hospitals in Karachi, Pakistan: a call to save lives by reforming rabies prevention facilities
Authors: Salahuddin N , Gohar M A , Jamali S , Qureshi M A , Baig-Ansari N 
Published: March 2023

ABSTRACT

Background
Rabies is endemic in low- and middle-income countries. It is caused mainly by the bite of a rabid dog and is fatal if not treated effectively and in a timely manner with quality post-exposure prophylaxis. Despite a profusion of private and public healthcare centres in Sindh province, most are ill-equipped to treat dog bites.

Methods
We analysed 129 human deaths from rabies who presented at the emergency departments of two tertiary care hospitals in Karachi over 10 y. Demographic data, time, location of the bite and distance travelled to report symptoms of rabies were recorded.

Results
Most victims were male, and children were more often affected; almost none had received post-exposure prophylaxis. A total of 12% of bites were on the face, head or neck. The mean incubation period was 56 d. Most (60%) of the rabies victims travelled long distances, hoping to receive treatment.

Conclusions
Rabies deaths were either due to a lack of awareness or the non-availability of rabies immunobiologicals within easy reach. Public health services must raise awareness, conduct surveillance and provide appropriately spaced centres for free treatment of dog bites. This lethal disease must be prevented at all costs.
In-Hospital Mortality Following Traumatic Injury in South Africa
Authors: Storm Erik , Smith Michelle , Kong Victor , Laing Grant L. , Bruce John L. , Bekker Wanda , Svensson Johan , Manchev Vassil , Franklin Karl A. , Clarke Damian L. 
Published: March 2023

Objectives:
Trauma is a leading cause of death worldwide and in South Africa. We aimed to quantify the in-hospital trauma mortality rate in Pietermaritzburg, South Africa.

Background:
The in-hospital trauma mortality rate in South Africa remains unknown, and it is unclear whether deficits in hospital care are contributing to the high level of trauma-related mortality.

Methods:
All patients hospitalized because of trauma at the Department of Surgery at Grey’s Hospital, Pietermaritzburg Metropolitan Trauma Service, were prospectively entered in an electronic database starting in 2013 and the data were retrospectively analyzed. The trauma service adheres to Advanced Trauma Life Support and the doctors have attended basic and advanced courses in trauma care. The primary outcome was in-hospital mortality.

Results:
Of 9795 trauma admissions, 412 (4.2%) patients died during hospital care between January 2013 and January 2019. Forty-six percent died after road traffic accidents, 19% after gunshot wounds, 13% after stab wounds, and 10% after assaults. Sixteen percent were classified as avoidable deaths due to inappropriate care and resource limitations. Fifty percent died because of traumatic brain injury and 80% of them were unavoidable.

Conclusions:
In conclusion, the in-hospital trauma mortality rate at a South African trauma center using systematic trauma care is lower than that reported from other trauma centers in the world during the past 20 years. Nevertheless, 16% of death cases were assessed as avoidable if there had been better access to intensive care, dialysis, advanced respiratory care, blood for transfusion, and improvements in surgery and medical care.
Prognostic Nomogram and Competing Risk Analysis of Death for Primary Thyroid Lymphoma
Authors: Zhang Kun , Peng Xue , Wei Tao , Li Zhihui , Zhu Jingqiang , Chen Ya-Wen 
Published: March 2023

Background:
Primary thyroid lymphoma (PTL) is such a rare malignancy that there are no large-scale prognostic proofs to create a consensus on optimal management. This study aimed to determine the survival outcomes of PTL and specify associated factors by building a prognostic nomogram and to analyze competing risks of death to balance the hazards and benefits of different therapeutic approaches.

Method:
A total of 1638 PTL patients from 2000 to 2018 were identified from the Surveillance, Epidemiology, and End Results (SEER) database. Cox proportional hazard regression and competing risk analysis were applied.

Results:
We have identified through Cox analysis that age in years, diffuse large B-cell lymphoma (DLBCL) pathology, lymph node dissection, radiation, and chemotherapy were independent prognostic factors for disease-specific survival (DSS). Based on these findings, we built a nomogram for predicting 5- and 10-year DSS and analyzed the overall survival (OS) by calculating cumulative incidence of death. The overall cumulative incidences of the 5- and 10-year PTL-specific cumulative death probabilities were 14.0% (95% CI: 12.3%–15.9%) and 16.3% (95% CI: 14.4%–18.4%), respectively, while the 5- and 10-year cumulative death probabilities from other causes were 12.4% (95% CI: 10.6%–12.3%) and 24.7% (95% CI: 22.1%–27.4%). Results from the competing risk hazards regression analysis revealed that older age and Ann Arbor grading were associated with a greater probability of death from other causes and death from PTL. Radioactive therapy by external beam radiation was associated with death from other causes only. DLBCL histology, lymph node dissection, and chemotherapy were correlated with death from PTL. Cumulative incidence curves demonstrated that the pathological type of lymphoma is the factor determining the likelihood of dying from PTL versus other causes.

Conclusion:
Patients’ age, Ann Arbor stage, pathological type of lymphoma, and the use of specific therapy regimen should all be taken into consideration when devising individualized treatment strategies for PTL. Decision models based on our findings may help clinicians make better decisions by taking into account the competing risk of death from causes other than PTL.
Telemedicine in Spine Patients
Authors: Bovonratwet Patawut , Chen Aaron Z. , Song Junho , Morse Kyle W. , Shafi Karim A. , Amen Troy B. , Dowdell James E. , Sheha Evan D. , Qureshi Sheeraz A. , Iyer Sravisht 
Published: March 2023

Study Design.
Retrospective cohort study.

Objective.
The objectives of the present study were to 1) define telemedicine utilization rates during and after the initial height of the COVID-19 lockdown period and 2) determine patient satisfaction with telemedicine during and after the initial height of the COVID-19 lockdown period for spine patients at an orthopedic specialty hospital.

Summary of Background Data.
Previous studies have shown high patient satisfaction with telemedicine during the initial height of the COVID-19 pandemic. However, there exists limited data about spine telemedicine utilization and patient satisfaction after the reopening of in-person office visits and easing of restrictions on elective surgical care.

Methods.
All patients who had an in-person or telemedicine visit at an urban tertiary specialty hospital from April 1, 2020 to April 15, 2021 were identified. Rates of overall telemedicine utilization over time were delineated. Patient satisfaction with telemedicine, as assessed through a series of questionnaires, was also evaluated over time.

Results.
Overall, 60,368 patients were identified. Of these, 19,568 patients (32.4%) had a telemedicine visit. During the peak initial coronavirus lockdown period, rate of overall telemedicine utilization on average was greater than 90%. After the peak period, the rate of overall telemedicine utilization on average was at approximately 29% of all visits per month. The percentage of patients who would have been definitely comfortable if the telemedicine visit had been in-person increased over the entire study period (P<0.001). Despite this, patient satisfaction based on survey responses remained statistically similar throughout the study period (P>0.05).

Conclusion.
The rate of telemedicine utilization in spine patients remains high, at approximately 1/3 of all visits, even after the initial peak coronavirus lockdown period. In addition, patient satisfaction with telemedicine remained consistent throughout the study period, regardless of pandemic restrictions on in-person visits.

Level of Evidence.
III
Local Recurrence Rates After Excision of Desmoplastic Melanoma: A Systematic Review and Meta-Analysis
Authors: Ran Nina A. , Veerabagu Surya , Miller Christopher J. , Elenitsas Rosalie , Chu Emily Y. , Krausz Aimee E. 
Published: March 2023

BACKGROUND
Few prospective studies have evaluated local recurrence rates (LRR) after excision of desmoplastic melanoma (DM); however, several retrospective studies have reported high LRR.

OBJECTIVE
To determine LRR after excision of DM and evaluate factors affecting LRR.

MATERIALS AND METHODS
Systematic review of the PubMed, Embase, and Web of Science databases was performed to identify studies reporting local recurrence after excision of DM with conventional wide local excision (WLE), Mohs micrographic surgery (MMS), or staged excision (SE). Meta-analysis was performed to calculate summary LRR and pooled risk ratios (RR).

RESULTS
Literature search identified 4 studies evaluating MMS or SE (total n = 61 DM). 53 studies assessed WLE (n = 3,080) and were analyzed quantitatively. The overall LRR after WLE of DM was 21% (95% CI, 0.16–0.28; n = 2,308). Local recurrence rate was higher with positive/unknown histologic excision margins (49%, 95% CI, 0.25–0.74; n = 91) versus negative histologic margins (11%, 95% CI, 0.07–0.17; n = 1,075; [p < .01]). Neurotropism was also associated with increased LRR (RR, 1.79; 95% CI, 1.34–2.38, p < .01; n = 644).

CONCLUSION
DM has high LRR after WLE. Local recurrence risk was greatest with positive excision margins, indicating the importance of achieving negative microscopic margins. Greater study of MMS and SE for DM is required.
18F-FDOPA PET/CT of Paraganglioma in the Spermatic Cord
Authors: Goujon Anna , Pop Gabriel , Hissier Julien , Moreau Benjamin , Palard-Novello Xavier 
Published: March 2023

Abstract
A 53-year-old man with chronic kidney failure was referred to perform an 18F-FDOPA PET/CT to characterize a mass located on the right spermatic cord. Previously, the pathological analysis of CT-guided biopsies suggested paraganglioma or metastatic lesion of pheochromocytoma. Serum normetanephrine and serum metanephrine values were respectively 2- and 1.5-fold greater than the normal upper limit, which could be explained by the chronic kidney failure. PET/CT images revealed intense 18F-FDOPA uptake of the mass without any other pathological findings, suggesting the diagnosis of paraganglioma. Pathological examination of surgical specimen confirmed the diagnosis of paraganglioma of the spermatic cord, which is exceptional.