bluuebunny/crossref_metadata_2025_split huggingface dataset:
Next-Generation Sequencing-Based Detection of Common Bean Viruses in Wild Plants from Tanzania and Their Mechanical Transmission to Common Bean Plants
Authors: Mwaipopo Beatrice , Rajamäki Minna-Liisa , Ngowi Neema , Nchimbi-Msolla Susan , Njau Paul J. R. , Valkonen Jari P. T. , Mbanzibwa Deusdedith R. 
Published: January 2021

Viral diseases are a major threat for common bean production. According to recent surveys, >15 different viruses belonging to 11 genera were shown to infect common bean (Phaseolus vulgaris L.) in Tanzania. Virus management requires an understanding of how viruses survive from one season to the next. During this study, we explored the possibility that alternative host plants have a central role in the survival of common bean viruses. We used next-generation sequencing (NGS) techniques to sequence virus-derived small interfering RNAs together with conventional reverse-transcription PCRs (RT-PCRs) to detect viruses in wild plants. Leaf samples for RNA extraction and NGS were collected from 1,430 wild plants around and within common bean fields in four agricultural zones in Tanzania. At least partial genome sequences of viruses potentially belonging to 25 genera were detected. The greatest virus diversity was detected in the eastern and northern zones, whereas wild plants in the Lake zone and especially in the southern highlands zone showed only a few viruses. The RT-PCR analysis of all collected plant samples confirmed the presence of yam bean mosaic virus and peanut mottle virus in wild legume plants. Of all viruses detected, only two viruses, cucumber mosaic virus and a novel bromovirus related to cowpea chlorotic mottle virus and brome mosaic virus, were mechanically transmitted from wild plants to common bean plants. The data generated during this study are crucial for the development of viral disease management strategies and predicting crop viral disease outbreaks in different agricultural regions in Tanzania and beyond. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Generalizability of the Ottawa Surgical Competency Operating Room Evaluation (O-SCORE) Scale to Assess Medical Student Performance on Core EPAs in the Workplace: Findings From One Institution
Authors: Ryan Michael S. , Richards Alicia , Perera Robert , Park Yoon Soo , Stringer J.K. , Waterhouse Elizabeth , Dubinsky Brieanne , Khamishon Rebecca , Santen Sally A. 
Published: January 2021

Purpose
Assessment of the Core Entrustable Professional Activities for Entering Residency (Core EPAs) requires direct observation of learners in the workplace to support entrustment decisions. The purpose of this study was to examine the internal structure validity evidence of the Ottawa Surgical Competency Operating Room Evaluation (O-SCORE) scale when used to assess medical student performance in the Core EPAs across clinical clerkships.

Method
During the 2018–2019 academic year, the Virginia Commonwealth University School of Medicine implemented a mobile-friendly, student-initiated workplace-based assessment (WBA) system to provide formative feedback for the Core EPAs across all clinical clerkships. Students were required to request a specified number of Core EPA assessments in each clerkship. A modified O-SCORE scale (1 = “I had to do” to 4 = “I needed to be in room just in case”) was used to rate learner performance. Generalizability theory was applied to assess the generalizability (or reliability) of the assessments. Decision studies were then conducted to determine the number of assessments needed to achieve a reasonable reliability.

Results
A total of 10,680 WBAs were completed on 220 medical students. The majority of ratings were completed on EPA 1 (history and physical) (n = 3,129; 29%) and EPA 6 (oral presentation) (n = 2,830; 26%). Mean scores were similar (3.5–3.6 out of 4) across EPAs. Variance due to the student ranged from 3.5% to 8%, with the majority of the variation due to the rater (29.6%–50.3%) and other unexplained factors. A range of 25 to 63 assessments were required to achieve reasonable reliability (Phi > 0.70).

Conclusions
The O-SCORE demonstrated modest reliability when used across clerkships. These findings highlight specific challenges for implementing WBAs for the Core EPAs including the process for requesting WBAs, rater training, and application of the O-SCORE scale in medical student assessment.
Leadership trends among orthopaedic trauma surgery fellowship directors: a cross-sectional demographic review
Authors: Sama Andrew J. , Schiller Nicholas C. , Ramirez Cody M. , Yong Taylor M. , Donnally Chester J. , Spielman Amanda F. , Gitajn Ida L. , Dodds Seth D. , Quinnan Stephen M. 
Published: January 2021

Background:
Fellowship directors in orthopaedic trauma surgery have an immense impact on the current and future trainees within orthopaedics. The purpose of our study was to evaluate and better understand the characteristics that are shared among current orthopaedic trauma surgery fellowship directors to provide a framework for aspiring leaders and to present a demographic snapshot.

Methods:
Orthopaedic trauma fellowship programs were identified using the Orthopaedic Trauma Association Directory for 2019 to 2020. Data for each fellowship director was gathered via online review, email, telephone, and curriculum vitae collection.

Results:
Demographic information was gathered for 72 fellowship directors. Of these, 93% of the leadership was male. Additionally, 40 (55%) fellowship directors responded to the racial classification question. Of those responding, 37 identified as Caucasian, one as Asian-American, one as Hispanic/Latino, and one as African American. The mean age of the current fellowship directors (51.4 yr), h-index (15.1), year of residency (2001) and fellowship (2003) graduation, time of employment at current institution (13.8 yr), time since training until fellowship director appointment (9.8 yr) were analyzed. The top residency and fellowship programs that produced future fellowship directors were University of Pittsburgh (n=4) and Harborview Medical Center (n=17).

Conclusions:
Our investigation highlighted the qualifications of orthopaedic trauma fellowship directors and can guide future leaders. A select few institutions train a disproportionate share of the current fellowship directors. Gender and racial diversity are limited in this population of leaders.

Level of Evidence:
Level III.
Histological and Immunohistochemical Changes of Congenital Melanocytic Nevi With Age
Authors: Gassenmaier Maximilian , Häfner Hans-Martin , Hahn Matthias , Kofler Lukas , Wagner Nikolaus B. , Forchhammer Stephan 
Published: January 2021

Abstract:
Clinical but not histological changes of congenital melanocytic nevi (CMN) with age are well characterized. Our objective was to analyze histological changes of CMN with age and discuss possible clinical implications of our findings. We investigated serial excisions of 21 patients with CMN and compared histological and immunohistochemical features over time. The median number of serial excisions was 6 [interquartile range (IQR) 5–7], the median age at the first excision was 12 months (IQR 5–98), and the median time between the first and last analyzed excision was 53 months (IQR 45–64). The projected adult size of the excised CMN was “large” or “giant” in 14 of the 21 CMN (67%) and “medium” in the remaining lesions (33%). Nineteen CMN (90%) involved the subcutaneous fat, and 16 of the 21 CMN (76%) reached the lower surgical margin. The histological pattern and depth did not change over time but the cellularity and HMB-45 expression of dermal melanocytes decreased in 16 of the 21 patients (76%) and in 15 of the 21 patients (71%), respectively (both P < 0.001). Patients with decreasing HMB-45 expression were significantly younger at the first excision (median 6 months, IQR 4–28) than patients with unchanged HMB-45 expression (median 176 months, IQR 12–186; P = 0.018). The expression of Ki-67 and p16 did not change significantly with age. Our study demonstrates that (1) the cellularity and pigment production of CMN decreases with age, (2) the histological pattern and extension in depth remain stable, and (3) clear resection margins can rarely be achieved in larger CMN.
Developing a Breast Reconstruction Program in a Resource-Constrained Ghanaian Teaching Hospital
Authors: Tieman Joshua T. , Nourian Maziar Mohsen , Agbenorku Pius , Hoyte-Williams Paa Ekow , Farhat Boutros , Goodwin Isak A. , Swistun Lukasz , Foreman Kenneth Bo , Rockwell William Bradford 
Published: January 2021

Abstract
As the detection of breast cancer in Ghana improves, the incidence of mastectomy has increased and the outcomes have improved. As a secondary result, the need for breast reconstruction is increasing. The cultural hesitation to undergo a mastectomy and live without a breast can be decreased by making breast reconstruction available, cost-effective, and acceptable. Cultural, economic, and technical factors were considered in choosing the best method of breast reconstruction. Discussions, lectures, and cadaver dissections investigated the various reconstructive options. Operative cases were performed using a latissimus musculocutaneous flap, a lower abdominal transverse rectus abdominis myocutaneous (TRAM) flap, and a midabdominal TRAM flap. The midabdominal TRAM was found to be the best choice at Komfo Anokye Teaching Hospital. It is a reliable, robust, well-perfused, single-stage flap that produced excellent patient satisfaction.
Bilateral Ethmoidal Mucocele Causing Proptosis in a Child
Authors: Sen Comert , Aydemir Levent , Comoglu Senol , Sonmez Said , Ozturk Ilker Erdinc , Deger Kemal 
Published: January 2021

Objectives:
Paranasal sinus mucocele is a benign cystic lesion, lined with respiratory epithelium and filled with mucoid secretions, which is generally seen in the ethmoid or frontal sinuses. Inflammation, trauma, fibrosis, neoplasm, and previous surgery play a role in etiology. Treatment of this condition requires marsupialization and drainage. Endoscopic surgery is the gold standard procedure.

Methods:
A 2-year-old boy was referred to our clinic with a diagnosis of bilateral ethmoid mucocele causing proptosis in the right eye. General clinical examinations and routine blood analysis revealed normal health condition of the patient and comorbidities such as cystic fibrosis (CF) and/or ciliary dysfunction were excluded. The patient was operated with an endoscopic endonasal approach.

Results:
As far as we know, our article reports the first case of bilateral ethmoidal sinus mucocele with no underlying comorbidity, such as cystic fibrosis or ciliary dyskinesia.

Conclusions:
Children are rarely affected by mucocele and if present at early age, there is usually an underlying cause. In pediatric patients with signs and symptoms suggestive of a mucocele, it is important to rule out other benign and malignant paranasal sinus pathologies. Marsupialization and drainage via endoscopic endonasal approach is the preferred treatment modality.
Initial Manifestation of Orbital Lymphomas: The Role of Early Diagnosis
Authors: Torres Luiz Henrique Soares , Gabrielli Marisa Aparecida Cabrini , Pererira Filho Valfrido Antônio 
Published: January 2021

Abstract
Orbital lymphoma is a rare condition with non-specific and variable clinical course. This features are the main obstacle for diagnosis and treatment. A 43-year-old female patient complaining of vision loss and hemiface paresthesia, Proptosis was noted associated with an expansive lesion involving the right temporal lobe and orbital region. Craniotomy was performed to allow orbital decompression and anatomopathogical analysis. Final diagnosis was Burkitt Lymphoma. Patient evolved to death after seven days. A 40-year-old male patient complaining excessive tearing and sight disturbance. Proptosis on the right eye was noticed. Extra-conal expansive lesion was observed. Final diagnosis was mucosa-associated lymphoid tissue lymphoma. Radio and chemotherapy protocol was initiated. In a 3 year follow-up, there are no signs of recurrence or ocular/orbital impairment. Maxillofacial surgeons should be aware of the initial clinical presentation and always include lymphoid neoplasms as a differential diagnosis in cases which acute functional alterations are present.
Photobiomodulation to Treat Necrotizing Fasciitis
Authors: de Mendonça Maria Patrícia Rogério , Andrade Ana Karisse de Carvalho , Gomes Vinícius Rodrigues , Carvalho Abrahão Cavalcante Gomes de Souza 
Published: January 2021

Abstract
The spread of odontogenic infections associated with comorbidities, such as diabetes mellitus, can result in a potentially lethal complication, with rapid necrosis of the superficial fascia, necrotizing fasciitis. In this case report, a female patient, 52 years old, fasting blood glucose of 303 mg/dL with necrotizing fasciitis associated with type 2 diabetes mellitus in the left cervical-thoracic region. She was treated with antibiotics, cervicotomy, abscess drainage, and underwent 10 photobiomodulation sessions with 2 weekly applications of the red wavelength laser to correct tissue loss in the left cervical region. With the development of tissue healing, the formation of granulation tissue increased, absence of necrotic areas, contraction of the edges, and total wound repair. This case emphasizes the effectiveness of photobiomodulation to optimize healing and modulate the inflammatory pattern in the treatment of necrotizing fasciitis sequelae.
Effectiveness of Different Surgical Flap Delay Methods and Their Systemic Toxicities
Authors: Yildiz Kemalettin , Mirapoglu Semih Lutfi , Kilic Ulkan , Guneren Ethem , Kocyigit Abdurrahim , Kirazoglu Ahmet , Sagir Haci Omer , Yesiloglu Nebil , Canter Halil Ibrahim , Cay Ali 
Published: January 2021

Objective:
The surgical flap delaying has been shown to be effective in preventing partial flap loss or in preparing larger flaps. However, there is no gold standard flap delay method in the literature. In this study, the authors aimed to compare 3 types of surgical delay methods to determine which model would increase more flap survival. The authors also investigated the effect of delay methods on circulating mononuclear leukocytes as a parameter of DNA damage.

Methods:
Twenty-four Sprague-Dawley male rats were divided into 4 groups. All subjects had a 10 × 3 cm modified McFarlane flap. Surface area measurements, biopsies, and blood samples were taken on the day of sacrification; 7th day for the control group and 14th day for delay groups.

Results:
Between incisional surgery delay groups, a significant difference was found in necrosis and apoptosis in the bipedicled group, and only necrosis in the tripedicled group compared to the control. In terms of DNA damage, it was found higher in all experimental groups than in the control group.

Conclusions:
Both incisional surgical delay procedures’ results were meaningfully effective when only incisions were made without the elevation of flaps. In conclusion, bipedicled incisional surgical delay seems to be the most effective method in McFarlane experimental flap model whereas two-staged surgeries may increase the risk of systemic toxicity.
Modelling the effect of lockdown
Authors: Kamei Hideto , Sato Akihiro 
Published: January 2021

1AbstractThis note models the effect of the lockdown during the first wave of COVID-19. We use SEIR type of model with a certain time lag between infection and becoming infectious. Firstly we compare the timing of the change of the coefficient of infection, growth rate of confirmed cases corresponds to the change of mobility index, and secondly we assume the change of the coefficient of infection, activity index β (analogous to R0) and fit the parameter to reproduce the actual number of confirmed cases. Finally, we assume that the activity index β is proportional to the square of the mobility and fit the parameters. The curves in various cuontries fits reasonably well in any cases, but estimating β from various parameters (including temperature) remains as an important task.
Deep RNA Sequencing of Intensive Care Unit Patients with COVID-19
Authors: Monaghan Sean F. , Fredericks Alger M. , Jentzsch Maximilian S. , Cioffi William G. , Cohen Maya , Fairbrother William G. , Gandhi Shivam J. , Harrington Elizabeth O. , Nau Gerard J. , Reichner Jonathan S. , Ventetuolo Corey E. , Levy Mitchell M. , Ayala Alfred 
Published: January 2021

PurposeCOVID-19 has impacted millions of patients across the world. Molecular testing occurring now identifies the presence of the virus at the sampling site: nasopharynx, nares, or oral cavity. RNA sequencing has the potential to establish both the presence of the virus and define the host’s response in COVID-19.MethodsSingle center, prospective study of patients with COVID-19 admitted to the intensive care unit where deep RNA sequencing (>100 million reads) of peripheral blood with computational biology analysis was done. All patients had positive SARS-CoV-2 PCR. Clinical data was prospectively collected.ResultsWe enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. Entropy calculated from alternative RNA splicing and transcription start/end predicted mortality in these patients.ConclusionsCurrent upper respiratory tract testing for COVID-19 only determines if the virus is present. Deep RNA sequencing with appropriate computational biology may provide important prognostic information and point to therapeutic foci to be precisely targeted in future studies.Take Home MessageDeep RNA sequencing provides a novel diagnostic tool for critically ill patients. Among ICU patients with COVID-19, RNA sequencings can identify gene expression, pathogens (including SARS-CoV-2), and can predict mortality.TweetDeep RNA sequencing is a novel technology that can assist in the care of critically ill COVID-19 patients & can be applied to other disease
Elevated 11-oxygenated androgens are not a major contributor to HPG-axis disturbances in adults with congenital adrenal hyperplasia due to 21-hydroxylase deficiency
Authors: Auer Matthias K. , Paizoni Luisa , Neuner Meike , Lottspeich Christian , Schmidt Heinrich , Bidlingmaier Martin , Hawley James , Keevil Brian , Reisch Nicole 
Published: January 2021

AbstractContextHypothalamus-pituitary-gonadal (HPG)-axis disturbances are a common phenomenon in patients with classic congenital adrenal hyperplasia (CAH). 11-oxygenated androgens have been suggested to play a role in this context.DesignCross-sectional single center study including 89 patients (N=42 men, N=55 women) with classic CAH.Main Outcome MeasuresIndependent predictors for hypogonadism in men and secondary amenorrhea in women with CAH with a special focus on 11-ketotestosterone (11KT) and 11β-hydroxyandrostenedione (11OHA4).ResultsHypogonadotropic hypogonadism was present in 23% of men and 61% of those women currently not on contraceptives suffered from irregular menstrual cycles or amenorrhea. Testicular adrenal rest tumor (TART) was documented in 28% of men. While 11KT (3.5x) and 11OHA4 (5.7x) among other adrenal steroids were significantly elevated in men with hypogonadism, in stepwise logistic regression, the only significant independent predictor for hypogonadism were elevated 17-OHP levels (B = 0.006; p = 0.039). Although 11KT (5.2x) and 11OHA4 (3.7x) levels were also significantly higher in women with amenorrhea in comparison to those with a regular cycle, the only significant predictor for amenorrhea were elevated total testosterone levels (B = 1.806; p = 0.040). 11-oxygenated androgens were not different in those with TART and those without. Of note, there were no significant differences in 11OHA4 or 11KT between those with a regular cycle and those currently on hormonal contraceptives.Conclusions11-oxygenated androgens do not seem to add additional information for explaining menstrual disturbances and hypogonadism in patients with CAH in comparison to established marker of disease control.HighlightsThe 11-oxygenated androgens 11-ketotestosterone and 11β-hydroxyandrostenedione are significantly elevated in men with CAH with hypogonadotropic hypogonadism and women with amenorrhea.Elevated 17-OHP levels in male patients and elevated testosterone levels in female patients are however the dominant predictor of HPG-axis disturbances.11-oxygenated androgens are not predictive for testicular adrenal rest tumors in men with CAH11-ketotestosterone and 11β-hydroxyandrostenedione levels do not seem to be influenced by intake of oral contraceptives.
Muscle-specific Cavin4 interacts with Bin1 to promote T-tubule formation and stability in developing skeletal muscle
Authors: Lo Harriet P. , Lim Ye-Wheen , Xiong Zherui , Martel Nick , Ferguson Charles , Ariotti Nicholas R. , Giacomotto Jean , Rae James A. , Floetenmeyer Matthias , Moradi Shayli Varasteh , Gao Ya , Tillu Vikas A. , Xia Di , Wang Huang , Rahnama Samira , Nixon Susan J. , Bastiani Michele , Day Ryan D. , Smith Kelly A. , Palpant Nathan J. , Johnston Wayne A. , Alexandrov Kirill , Collins Brett M. , Hall Thomas E. , Parton Robert G. 
Published: January 2021

SummaryThe cavin proteins are essential for caveola biogenesis and function. Here, we identify a role for the muscle-specific component, Cavin4, in skeletal muscle T-tubule development by analyzing two vertebrate systems: mouse and zebrafish. In both models Cavin4 localized to T-tubules and loss of Cavin4 resulted in aberrant T-tubule maturation. In zebrafish, which possess duplicatedcavin4paralogs, Cavin4b was shown to directly interact with the T-tubule-associated BAR domain protein, Bin1. Loss of both Cavin4a and Cavin4b caused aberrant accumulation of interconnected caveolae within the T-tubules, a fragmented T-tubule network enriched in Caveolin-3, and an impaired Ca2+response upon mechanical stimulation. We propose a role for Cavin4 in remodeling the T-tubule membrane early in development by recycling caveolar components from the T-tubule to the sarcolemma. This generates a stable T-tubule domain lacking caveolae that is essential for T-tubule function.