bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo genome assembly and functional annotation for Fusarium langsethiae
Authors: Zuo Ya , Verheecke-Vaessen Carol , Molitor Corentin , Medina Angel , Magan Naresh , Mohareb Fady 
Published: February 2022

Abstract
Background
Fusarium langsethiae is a T-2 and HT-2 mycotoxins producing species firstly characterised in 2004. It is commonly isolated from oats in Northern Europe. T-2 and HT-2 mycotoxins exhibit immunological and haemotological effects in animal health mainly through inhibition of protein, RNA and DNA synthesis. The development of a high-quality and comprehensively annotated assembly for this species is therefore essential in providing the molecular understanding and the mechanism of T-2 and HT-2 biosynthesis in F. langsethiae to help develop effective control strategies.

Results
The F. langsethiae assembly was produced using PacBio long reads, which were then assembled independently using Canu, SMARTdenovo and Flye. A total of 19,336 coding genes were identified using RNA-Seq informed ab-initio gene prediction. Finally, predicting genes were annotated using the basic local alignment search tool (BLAST) against the NCBI non-redundant (NR) genome database and protein hits were annotated using InterProScan. Genes with blast hits were functionally annotated with Gene Ontology.

Conclusions
We developed a high-quality genome assembly of a total length of 59 Mb and N50 of 3.51 Mb. Raw sequence reads and assembled genome is publicly available and can be downloaded from: GenBank under the accession JAFFKB000000000.
All commands used to generate this assembly are accessible via GitHub: https://github.com/FadyMohareb/fusarium_langsethiae.
HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly
Authors: Sim Sheina B. , Corpuz Renee L. , Simmonds Tyler J. , Geib Scott M. 
Published: February 2022

Abstract
Background
Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows.

Results
Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies.

Conclusions
Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.
HPV prevalence among young adult women living with and without HIV in Botswana for future HPV vaccine impact monitoring
Authors: McClung Nancy , Mathoma Anikie , Gargano Julia W. , Nyepetsi Naledi Gape , Querec Troy D. , Onyekwuluje Juanita , Mine Madisa , Morroni Chelsea , Luckett Rebecca , Markowitz Lauri E. , Ramogola-Masire Doreen 
Published: February 2022

Abstract
Introduction
In 2015, Botswana introduced quadrivalent human papillomavirus (HPV) vaccine for girls aged 9–13 years. To establish a baseline HPV prevalence for future HPV vaccine impact monitoring, we evaluated HPV prevalences among the youngest unvaccinated women in Botswana and compared HPV prevalences among women living with HIV (WLHIV) and without HIV.

Methods
Women aged 18–22 years were recruited from the University of Botswana and HIV clinics in Gaborone from October 2019–January 2021. Demographic and behavioral characteristics were self-reported during structured interviews; HIV clinical characteristics were abstracted from medical charts. Self-collected vaginal swabs were tested for 28 HPV types using Seegene Anyplex II HPV28. We compared prevalence of any HPV, high risk (HR)-HPV, and quadrivalent HPV vaccine types (HPV6/11/16/18) among WLHIV and women without HIV and evaluated risk factors for prevalence of HR-HPV.

Results
A total of 306 WLHIV and 500 women without HIV were recruited. Compared to women without HIV, WLHIV were more likely to be sexually experienced (86.6% versus 74.4%) and have ≥ 3 lifetime sex partners (55.3% versus 27.8%). All HPV type prevalences were significantly higher among WLHIV compared to women without HIV, including prevalence of any HPV (82.7% versus 63.0%), HR-HPV (72.9% versus 53.8%), and quadrivalent vaccine HPV types (34.3% versus 21.0%). Among WLHIV, there were no differences between those perinatally and non-perinatally infected for HPV prevalences, number of HPV types detected, CD4 count, or viral load.

Conclusions
Over one-third of WLHIV and nearly a quarter of those without HIV had vaccine-type HPV detected. This study supports need for the national HPV vaccination program in Botswana and provides important baseline data for future evaluation of impact of the program.
Socio-demographic characteristics associated with the dietary diversity of Thai community-dwelling older people: results from the national health examination survey
Authors: Chalermsri Chalobol , Rahman Syed Moshfiqur , Ekström Eva-Charlotte , Muangpaisan Weerasak , Aekplakorn Wichai , Satheannopakao Warapone , Ziaei Shirin 
Published: February 2022

Abstract
Background
Dietary diversity (DD) is an indicator of nutrient intake and is related to health outcomes in older people. Currently, limited research exists regarding factors associated with DD in older people in developing countries, such as Thailand, despite rapid growth in this population. Therefore, this study aims to examine the association between socio-demographic characteristics and DD in Thai older people.

Methods
A cross-sectional study based on the fifth Thai National Health Examination Survey (NHES-V) conducted between 2013 and 2015 was performed. A total of 7,300 nationally representative older participants aged ≥ 60 years were included. The individual-level dietary diversity score (DDS) was assessed as the frequency of consumption of eight food groups using food frequency questionnaires. Each food group was scored from 0 to 4 according to the frequency of consumption. The DDS was calculated as the sum of the scores, ranging from 0 to 32. Socio-demographic characteristics, including age, sex, highest education level, wealth index, living conditions, and residential area, were assessed. Data were analyzed using multiple linear regression and adjusted for complex survey design.

Results
The participants had a mean age of 69.7 (SD 7.6) years. The mean DDS of participants was 18.4 (SD 3.9). In the adjusted model, a higher educational level, a higher wealth index, and living in an urban area were positively associated with DDS, with adjusted β (95% CI) values of 1.37 (1.04, 1.70) for secondary education or higher, 0.81 (0.55, 1.06) for the richest group, and 0.24 (0.10, 0.44) for living in an urban area. Nevertheless, living alone had negative associations with DDS, with a β (95% CI) of - 0.27 (- 0.53, - 0.00).

Conclusions
This study showed that a higher educational level, a higher wealth index, and living in an urban area had a positive association, whereas living alone had a negative association with DD among Thai older participants. Interventions aiming to improve dietary diversity among older people might benefit from targeting more vulnerable groups, particularly those with less education and wealth, those living alone, or those in rural areas.
Associations between adipokines gene polymorphisms and knee osteoarthritis: a meta-analysis
Authors: Wang Yuqing , Meng Fanqiang , Wu Jing , Long Huizhong , Li Jiatian , Wu Ziying , He Hongyi , Wang Haochen , Wang Ning , Xie Dongxing 
Published: February 2022

Abstract
Background
Adipokines gene polymorphisms are speculated to be associated with the risk of knee osteoarthritis (OA), but evidence remains conflicting. This study therefore aimed to examine whether associations exist between adipokines gene polymorphisms and knee OA by considering the evidence collected from eligible studies through a meta-analysis.

Methods
A systematic search was performed on PubMed, Embase, Web of Science, China National Knowledge Infrastructure (CNKI), and Wanfang up to March 31, 2020. Meta-analysis was carried out by focusing on the associations between adipokines gene polymorphisms and knee OA with the allele model, dominant model, and recessive model.

Results
The present meta-analysis included 5 eligible studies for ADIPOQ rs1501299 with 1,021 cases and 1,097 controls, 3 eligible studies for ADIPOQ rs2241766 with 549 cases and 544 controls, 3 eligible studies for LEPR rs1137101 with 808 cases and 856 controls, 2 eligible studies for VISFATIN rs4730153 with 339 cases and 680 controls and 2 eligible studies for VISFATIN rs16872158 with 339 cases and 680 controls. Significant association was observed between LEPR rs1137101 and knee OA in the overall population (recessive: OR = 0.40, 95% CI 0.21–0.79). Limited data revealed that associations may exist between ADIPOQ rs2241766 and knee OA in Asians (dominant: OR = 1.35, 95% CI 1.03–1.78), between VISFATIN rs4730153 and knee OA in Asians (allele: OR = 0.58, 95% CI 0.41–0.83; dominant: OR = 0.57, 95% CI 0.39–0.83), and between VISFATIN rs16872158 and knee OA in Asians (allele: OR = 1.84, 95% CI 1.26–2.68; dominant: OR = 1.94, 95% CI 1.31–2.89).

Conclusions
Adipokines gene polymorphisms may be associated with knee OA. The association was observed in LEPR rs1137101 in the present study. In addition, limited data revealed that associations may also exist in ADIPOQ rs2241766, VISFATIN rs4730153 and VISFATIN rs16872158.

Prospero registration
CRD42020187664.
Resection and reconstruction for radial polydactyly Type IV-D in 206 cases: a retrospective clinical analysis
Authors: Liu Yuzhou , Xu Xiuyue , Wang Le , Lao Jie , Zhuang Yongqing , Fang Yousheng 
Published: February 2022

Abstract
Background
Radial Polydactyly Type IV-D deformity is difficult to treat because of the most complex bone and soft tissue anomalies. Resection and reconstruction for one of the two thumbs was an option for treatment.

Objective
The study was to present our method of resection and reconstruction with a new incision for radial polydactyly Type IV-D and evaluate the clinical efficacy comprehensively using Rotterdam assessment system in a large sample.

Methods
206 cases of type IV-D thumb duplication underwent resection and reconstruction surgical treatment between 2010 and 2019. Two equal triangle flap incisions were designed around the radial thumb. The radial thumb was resected and the ulnar thumb was reconstructed in aspects of bone, tendons, ligaments and abductor pollicis brevis.
The clinical results were evaluated using Rotterdam assessment system.

Results
The mean follow–up period was 2.2 years (SD 1.5). The mean age of the patients was 9 months (SD 1.8) at the time of operation. The mean ranges of active IP and MP joint flexion and extension were 110° and 26°. The mean angulations for IP and MP joint instabilities were 3° and 11°, relatively. Angulation for palmar abduction was 58°. The mean appearance domain score was 8.9. The average parental satisfaction score was 2.5 and the average patient-reported pain score was 2.1. The mean functional domain score for all patients was 6.6. The average appearance domain score was 8.9. The mean patient-reported domain score was 4.5. The mean Rotterdam outcome score was 20.0, equivalent to 67% of the full score. The postoperative score of patients over two years old was significantly lower than that of patients under two years old.

Conclusion
Resection and reconstruction method with two equal triangle flap incisions was a recommended treatment for radial polydactyly Type IV-D.

Level of evidence
IV
Musculoskeletal care – at the confluence of data science, sensors, engineering, and computation
Authors: Kataria Suchitra , Ravindran Vinod 
Published: February 2022

AbstractData has always been integral to modern medicine in almost all aspects of patient care and the recent proliferation of data has opened up innumerable opportunities for all the stakeholders in trying to improve the quality of care and health outcomes including quality of life and rehabilitation. Greater usage and adoption of digital technologies have led to the convergence of health data in different forms – clinical, self-reported, electronic health records social media, etc. The application and utilization of patient data set continue to get broadened each day with greater availability and access. These are empowering newer cutting-edge solutions such as connected care and artificial intelligence, 3D printing and real-life mimicking prosthetics. The availability of data at micro and macro levels has the potential to act as a catalyst for personalized care based on behavioral, cultural, genetic, and psychological needs for patients with musculoskeletal disorders. Realistic algorithms coupled with biomarkers which can identify relevant interventions and alert the care providers regarding any deterioration. Although in the nascent stage currently, 3D printing, exoskeletons, and virtual rehabilitation hold tremendous potential of cost-effective, precise interventions for the patients.
Primary total knee arthroplasty assisted by computed tomography-free navigation for secondary knee osteoarthritis following massive calcium phosphate cement packing for distal femoral giant-cell bone tumor treatment: a case report
Authors: Takeuchi Akihiko , Yamamoto Norio , Ohmori Takaaki , Hayashi Katsuhiro , Miwa Shinji , Igarashi Kentaro , Higuchi Takashi , Abe Kensaku , Yonezawa Hirotaka , Morinaga Sei , Araki Yoshihiro , Asano Yohei , Saito Shiro , Tsuchiya Hiroyuki 
Published: February 2022

Abstract
Background
Giant cell tumor of bone (GCTB) is an intermediate tumor commonly arising from the epiphysis of the distal femur and proximal tibia. Standard GCTB treatment is joint-preserving surgery performed using thorough curettage and the filling of the cavity with allo-, auto-, polymethyl methacrylate (PMMA), or synthetic bone graft. Calcium phosphate cement (CPC) is an artificial bone substitute, which has the benefit of being able to adjust defects, consequently inducing immediate mechanical strength, and promoting biological healing. Secondary osteoarthritis may occur following GCTB treatment and may need additional surgery if severe. However, details regarding surgery for secondary osteoarthritis have not been fully elucidated. There are no reports on the use of total knee arthroplasty (TKA) for the treatment of secondary osteoarthritis following CPC packing. The insertion of an alignment rod is a standard procedure in TKA; however, it was difficult to perform in this case due to CPC. Therefore, we used a computed tomography (CT)-free navigation system to assist the distal femur cut. This study presents a knee joint secondary osteoarthritis case following CPC packing for GCTB curettage that was treated with standard TKA.

Case presentation
A 67-year-old Japanese woman, who was previously diagnosed with left distal femur GCTB and was treated by curettage and CPC packing 7 years ago, complained of severe knee pain. Left knee joint plain radiography revealed Kellgren and Lawrence (K-L) grade 4 osteoarthritis without evidence of tumor recurrence. Therefore, she was scheduled for TKA. There are no reports on the cutting of a femoral condyle surface with massive CPC with accurate alignment. Because it is difficult to insert the alignment rod intramedullary and cut the femoral condyle with CPC, we planned CT-free navigation-guided surgery for accurate bone cutting using an oscillating tip saw system to prevent CPC cracks. We performed standard TKA without complications, as planned. Postoperative X-ray showed normal alignment. Knee Society Knee Score (KSKS) and Knee Society Function Score (KSFS) ameliorated from 27 and 29 to 64 and 68, respectively The patient can walk without a cane postoperatively.

Conclusion
There was no report about the surface TKA guided by CT-free navigation after primary GCT surgery with CPC. We believe that this case report will help in planning salvage surgery for secondary osteoarthritis after CPC packing.
In correspondence to “Spontaneous common bile duct perforation in full term pregnancy: a rare case report and review of literature”
Authors: Augustin Goran 
Published: February 2022

Abstract
Aim
The correspondence letter aims to correct the historical perspective on common bile duct perforations (CBD) during pregnancy and complete the number of published cases.

Findings
Instead of declared article by Piotrowski et al., from 1990, and according to available English language literature, the first two descriptions of maternal spontaneous CBD perforation in pregnancy were by JT Hogan Jr in 1957 and then Maurice Abitbol in 1958. Additional six cases of this condition were found, which is an increase of 50% of published cases.

Purpose
The purpose of this correspondence letter is to correct the historical perspective on CBD perforation during pregnancy. Also, only all published cases in English language literature can shed new light on incidence, diagnosis, treatment, and maternal and fetal prognosis from maternal CBD perforation in pregnancy.
Development of a list of competencies and entrustable professional activities for resident physicians during death pronouncement: a modified Delphi study
Authors: Kessoku Takaomi , Uneno Yu , Urushibara-Miyachi Yuka , Oya Kiyofumi , Kusakabe Akihiko , Nakajima Atsushi , Kobayashi Noritoshi , Ichikawa Yasushi , Miyashita Mitsunori , Muto Manabu , Mori Masanori , Morita Tatsuya 
Published: February 2022

AbstractBackgroundThe appropriate delivery of death pronouncements potentially affects bereaved families’ wellbeing positively. Although younger physicians need to learn the competencies and entrustable professional activities (EPAs) to conduct death pronouncement independently, both of which have not been clarified. Therefore, this study aimed to develop a list of competencies and EPAs necessary for death pronouncement practice, which resident physicians need to acquire by the end of their residency training (postgraduate year 2).MethodsAn anonymous modified Delphi study was conducted with a panel of 31 experts. The experts were invited online from general wards in hospitals with resident physicians across Japan to participate in the study using the purposive and snowball sampling method. A non-anonymous web conference was held with three additional external evaluators to finalize the item list. The consensus criterion was defined as a mean response of at least 4 points on a 5-point Likert scale for each competency and EPA item and a rating of 4 or 5 points by at least 80% of the participants.ResultsConsensus was achieved, with consistently high levels of agreement across panel members, on 11 competencies and 9 EPA items. Additionally, a correspondence matrix table between competencies and EPAs was developed.ConclusionsThis study clarified the standardized educational outcomes as competencies in death pronouncement practice and the unit of professional practice of physicians who can perform this independently (EPAs), serving as a blueprint to aid the development of an educational model and evaluation method for clinical educational institutions and developers of medical school curriculums.
An electronic medical records study of population obesity prevalence in El Paso, Texas
Authors: Salinas Jennifer J. , Sheen Jon , Shokar Navkiran , Wright Justin , Vazquez Gerardo , Alozie Ogechika 
Published: February 2022

Abstract
Background
In this study, we determine the feasibility of using electronic medical record (EMR) data to determine obesity prevalence at the census tract level in El Paso County, Texas, located on the U.S.-Mexico border.

Methods
2012–2018 Body Mass Index (BMI kg/m2) data from a large university clinic system in was geocoded and aggregated to a census tract level. After cleaning and removing duplicate EMR and unusable data, 143,524 patient records were successful geocoded. Maps were created to assess representativeness of EMR data across census tracts, within El Paso County. Additionally, maps were created to display the distribution of obesity across the same geography.

Results
EMR data represented all but one El Paso census tract. Representation ranged from 0.7% to 34.9%. Greatest representation were among census tracts in and around clinics. The mean EMR data BMI (kg/m2) was 30.1, this is approximately 6% less than the 36.0% estimated for El Paso County using the Behavioral Risk Factor Surveillance Study (BRFSS) estimate. At the census tract level, obesity prevalence ranged from 26.6 to 57.6%. The highest obesity prevalence were in areas that tended to be less affluent, with a higher concentration of immigrants, poverty and Latino ethnic concentration.

Conclusions
EMR data use for obesity surveillance is feasible in El Paso County, Texas, a U.S.-Mexico border community. Findings indicate substantial obesity prevalence variation between census tracts within El Paso County that may be associated with population distributions related to socioeconomics.
Overall performance of a drug–drug interaction clinical decision support system: quantitative evaluation and end-user survey
Authors: Van De Sijpe Greet , Quintens Charlotte , Walgraeve Karolien , Van Laer Eva , Penny Jens , De Vlieger Greet , Schrijvers Rik , De Munter Paul , Foulon Veerle , Casteels Minne , Van der Linden Lorenz , Spriet Isabel 
Published: February 2022

Abstract
Background
Clinical decision support systems are implemented in many hospitals to prevent medication errors and associated harm. They are however associated with a high burden of false positive alerts and alert fatigue. The aim of this study was to evaluate a drug–drug interaction (DDI) clinical decision support system in terms of its performance, uptake and user satisfaction and to identify barriers and opportunities for improvement.

Methods
A quantitative evaluation and end-user survey were performed in a large teaching hospital. First, very severe DDI alerts generated between 2019 and 2021 were evaluated retrospectively. Data collection comprised alert burden, override rates, the number of alert overrides reviewed by pharmacists and the resulting pharmacist recommendations as well as their acceptance rate. Second, an e-survey was carried out among prescribers to assess satisfaction, usefulness and relevance of DDI alerts as well as reasons for overriding.

Results
A total of 38,409 very severe DDI alerts were generated, of which 88.2% were overridden by the prescriber. In 3.2% of reviewed overrides, a recommendation by the pharmacist was provided, of which 79.2% was accepted. False positive alerts were caused by a too broad screening interval and lack of incorporation of patient-specific characteristics, such as QTc values. Co-prescribing of a non-vitamin K oral anticoagulant and a low molecular weight heparin accounted for 49.8% of alerts, of which 92.2% were overridden. In 88 (1.1%) of these overridden alerts, concurrent therapy was still present. Despite the high override rate, the e-survey revealed that the DDI clinical decision support system was found useful by prescribers.

Conclusions
Identified barriers were the lack of DDI-specific screening intervals and inclusion of patient-specific characteristics, both leading to a high number of false positive alerts and risk for alert fatigue. Despite these barriers, the added value of the DDI clinical decision support system was recognized by prescribers. Hence, integration of DDI-specific screening intervals and patient-specific characteristics is warranted to improve the performance of the DDI software.