bluuebunny/crossref_metadata_2025_split huggingface dataset:
vcfView: An Extensible Data Visualization and Quality Assurance Platform for Integrated Somatic Variant Analysis
Authors: O’Sullivan Brian , Seoighe Cathal 
Published: November 2020

Motivation: Somatic mutations can have critical prognostic and therapeutic implications for cancer patients. Although targeted methods are often used to assay specific cancer driver mutations, high throughput sequencing is frequently applied to discover novel driver mutations and to determine the status of less-frequent driver mutations. The task of recovering somatic mutations from these data is nontrivial as somatic mutations must be distinguished from germline variants, sequencing errors, and other artefacts. Consequently, bioinformatics pipelines for recovery of somatic mutations from high throughput sequencing typically involve a large number of analytical choices in the form of quality filters. Results: We present vcfView, an interactive tool designed to support the evaluation of somatic mutation calls from cancer sequencing data. The tool takes as input a single variant call format (VCF) file and enables researchers to explore the impacts of analytical choices on the mutant allele frequency spectrum, on mutational signatures and on annotated somatic variants in genes of interest. It allows variants that have failed variant caller filters to be re-examined to improve sensitivity or guide the design of future experiments. It is extensible, allowing other algorithms to be incorporated easily. Availability: The shiny application can be downloaded from GitHub ( https://github.com/BrianOSullivanGit/vcfView ). All data processing is performed within R to ensure platform independence. The app has been tested on RStudio, version 1.1.456, with base R 3.6.2 and Shiny 1.4.0. A vignette based on a publicly available data set is also available on GitHub.
Occurrence and microstructural features of slowly expanding lesions on fingolimod or natalizumab treatment in multiple sclerosis
Authors: Preziosa Paolo , Pagani Elisabetta , Moiola Lucia , Rodegher Mariaemma , Filippi Massimo , Rocca Maria A 
Published: November 2020

Background: In multiple sclerosis (MS), up to 57% of white matter lesions are chronically active. These slowly expanding lesions (SELs) contribute to disability progression. Objective: The aim of this study is to compare fingolimod and natalizumab effects on progressive linearly enlarging lesions (i.e. SELs), a putative biomarker of smouldering inflammation. Methods: Relapsing-remitting MS patients starting fingolimod ( n = 24) or natalizumab ( n = 28) underwent 3T brain magnetic resonance imaging (MRI) at baseline, months 6, 12 and 24. SELs were identified among baseline-visible lesions showing ⩾ 12.5% of annual increase, calculated by linearly fitting the Jacobian of the nonlinear deformation field between timepoints obtained combining T1- and T2-weighted scans. SEL burden, magnetization transfer ratio (MTR) and T1 signal intensity were compared using linear models. Results: The prevalences of fingolimod (75%) and natalizumab patients (46%) with ⩾ 1 SEL were not significantly different (adjusted- p = 0.08). Fingolimod group had higher SEL number and volume (adjusted- p ⩽ 0.047, not false discovery rate (FDR) survived). In both groups, SELs versus non-SELs showed lower MTR and T1 signal intensity (adjusted- p ⩽ 0.01, FDR-survived). Longitudinally, non-SEL MTR increased in both treatment groups (adjusted- p ⩽ 0.005, FDR-survived). T1 signal intensity decreased in SELs with both treatments (adjusted- p ⩽ 0.049, FDR-survived in fingolimod group) and increased in natalizumab non-SELs (adjusted- p = 0.03, FDR-survived). Conclusion: The effects of natalizumab and fingolimod on SEL occurrence seem modest, with natalizumab being slightly more effective. Both treatments may promote reparative mechanisms in stable or chronic inactive lesions.
Where has vulnerability gone?
Authors: Phillips Catherine R 
Published: November 2020

During Covid-19, health care workers have been vulnerable to death, and at the same time, in response to their vulnerability, heroic. Heroism is one of the most ubiquitous narratives during this pandemic. In this article, I am interested in the juncture between vulnerability and heroism, the discursive privileging of a hero and the implications of this for social workers in health and social care. I use the writings of Judith Butler to ask, where has vulnerability gone? I argue that it is not that vulnerability is erased or suppressed, or comes second in the public imaginary, but rather, vulnerability is reconstituted as heroic and becomes unrecognisable. Vulnerability is an under-examined concept in social work and an analysis of its cultural representation during the outbreak of Covid-19, can contribute to our knowledge about how vulnerability operates in health and social care, as well as how vulnerability conditions the cultural spaces we operate within. Can new insights, provoked by the cultural responses to this pandemic, lead to a reorientation for social work politics and the politics of vulnerability?
Stent-assisted coil embolization for an unruptured vertebral artery–posterior inferior cerebellar artery aneurysm with retrograde access via type 1 persistent primitive proatlantal artery: A case report
Authors: Nariai Yasuhiko , Takigawa Tomoji , Suzuki Ryotaro , Hyodo Akio , Suzuki Kensuke 
Published: November 2020

Vertebral artery (VA)-posterior inferior cerebellar artery (PICA) aneurysms are rare lesions that are difficult to treat with both endovascular and surgical techniques. Tight angulation of the PICA from VA may make access to the PICA difficult from ipsilateral VA if adjunctive techniques are needed. Recently, the safety and efficacy of retrograde access have been reported. We report a case of endovascular treatment for a VA-PICA aneurysm with a stent-assisted technique using retrograde access via contralateral persistent primitive proatlantal artery (PPA). The patient was a 76-year-old woman with an unruptured VA-PICA aneurysm on the dominant VA side. Coil embolization with a stent-assisted technique using retrograde access seemed appropriate. However, the origin of the left VA was not confirmed. Left common carotid artery angiography demonstrated that the PPA (type 1) branching from external carotid artery joined the VA V4 segment. Retrograde access via the PPA for stenting was performed. A microcatheter for stenting was retrogradely advanced to the right PICA at ease. After deploying the stent, coil insertion was completed from the right VA, and the final angiogram showed adequate occlusion of the aneurysm with preservation of the PICA. Thus, PPA may be an approach route in the treatment of VA-PICA aneurysms with unconfirmed contralateral VA orifice and apparent PPA on angiography, when retrograde access is needed.
Physician-modified fenestrated endovascular repair of type 1A endoleaks from polymer-based low-profile endografts
Authors: Zhang Louis , Magee Gregory A , Ziegler Kenneth R , Weaver Fred A , Han Sukgu M 
Published: November 2020

Purpose There have been increasing number of endovascular aortic aneurysm repair performed in hostile necks using newer generation technology including polymer-based proximal sealing devices such as the Ovation system. Unique design features of the device can pose challenges during endovascular salvage of type 1A endoleak. We describe two cases of successful application of physician-modified fenestrated endografting, in order to repair type 1A endoleaks following endovascular aortic aneurysm repair with ovation system. Technique In both cases, multi-fenestrated endografts were custom-modified using preloaded wire technique on Cook Zenith Alpha thoracic stent grafts at the back table. Under general anesthesia, left brachial cut down and a single percutaneous femoral access were performed. Staggered deployment of fenestrated endograft, accompanied by sequential catheterization of target vessels, facilitated correct alignment of fenestrated endograft. Infolding of fenestrated endograft inside the Ovation main body resulted in leg claudication, and repaired with balloon expandable covered tent. Prophylactic deployment of balloon expandable covered stent was performed in the second case. Both cases showed resolution of type 1A endoleak. Conclusion Fenestrated endovascular repair is feasible for proximal failure of Ovation endografts. Careful planning and advanced skill set in complex endovascular aortic repair are required, as well as detailed knowledge of the failed endografts.
Slowing of brain atrophy with teriflunomide and delayed conversion to clinically definite MS
Authors: Zivadinov Robert , Dwyer Michael G. , Carl Ellen , Poole Elizabeth M. , Cavalier Steve , Briassouli Paraskevi , Bergsland Niels 
Published: November 2020

Background: We explored the effect of teriflunomide on cortical gray matter (CGM) and whole brain (WB) atrophy in patients with clinically isolated syndrome (CIS) from the phase III TOPIC study and assessed the relationship between atrophy and risk of conversion to clinically definite MS (CDMS). Methods: Patients (per McDonald 2005 criteria) were randomized 1:1:1 to placebo, teriflunomide 7 mg, or teriflunomide 14 mg for ⩽108 weeks (core study). In the extension, teriflunomide-treated patients maintained their original dose; placebo-treated patients were re-randomized 1:1 to teriflunomide 7 mg or 14 mg. Brain volume was assessed during years 1–2. Results: Teriflunomide 14 mg significantly slowed annualized CGM and WB atrophy versus placebo during years 1–2 [percent reduction: month 12, 61.4% (CGM; p = 0.0359) and 28.6% (WB; p = 0.0286); month 24, 40.2% (CGM; p = 0.0416) and 43.0% (WB; p < 0.0001)]. For every 1% decrease in CGM or WB volume during years 1–2, risk of CDMS conversion increased by 14.5% ( p =  0.0004) and 47.3% ( p < 0.0001) during years 1–2, respectively, and 6.6% ( p =  0.0570) and 35.9% ( p = 0.0250) during years 1–5. In patients with the least (bottom quartile) versus most (top quartile) atrophy during years 1–2, risk of CDMS conversion was reduced by 58% (CGM; p = 0.0024) and 58% (WB; p = 0.0028) during years 1–2, and 42% (CGM; p = 0.0138) and 29% (WB; p = 0.1912) during years 1–5. Conclusion: These findings support the clinical relevance of CGM and WB atrophy and early intervention with teriflunomide in CIS.
Emerging treatment options for patients with high-risk myelodysplastic syndrome
Authors: Bewersdorf Jan Philipp , Carraway Hetty , Prebet Thomas 
Published: November 2020

Myelodysplastic syndromes (MDS) are clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis with peripheral blood cytopenias, dysplastic cell morphology, and a variable risk of progression to acute myeloid leukemia (AML). The hypomethylating agents (HMA) azacitidine and decitabine have been used for over a decade in MDS treatment and lead to a modest survival benefit. However, response rates are only around 40% and responses are mostly transient. For HMA-refractory patients the prognosis is poor and there are no therapies approved by the United States Food and Drug Administration. Combinations of HMAs, especially along with immune checkpoint inhibitors, have shown promising signals in both the frontline and HMA-refractory setting. Several other novel agents including orally available and longer acting HMAs, the BCL-2 inhibitor venetoclax, oral agents targeting driver mutations ( IDH1/2, FLT3), immunotherapies, and new options for intensive chemotherapy have been studied with variable success and will be reviewed herein. Except for the minority of patients with targetable driver mutations, HMAs – likely as part of combination therapies – will remain the backbone of frontline MDS treatment. However, the wider use of genetic testing may enable a more targeted and individualized therapy of MDS patients.
Managing Diabetes in the Workplace
Authors: McCarthy Margaret , Vorderstrasse Allison , Yan Joeyee , Portillo Angie , Dickson Victoria Vaughan 
Published: November 2020

Background: Although many adults with diabetes are productive members of the workforce, loss of work productivity has been associated with diabetes. The purpose of this study was to explore the interrelationship between work-related factors and current work ability in adults with type 1 diabetes (T1D) and type 2 diabetes (T2D). Methods: This study used a convergent mixed-method design. We assessed the relationship between work-related factors and work ability using bivariate statistics and logistic regression. Work ability was measured using the Work Ability Index and Karasek’s Job Content Questionnaire (JCQ) was employed to measure job demands. Qualitative interviews ( n = 30) explored the relationship between diabetes and work. Findings: The sample ( n =101) was mostly female (65%) and White (74%). Most worked full-time (65%), had T2D (87%), an elevated glycated hemoglobin A1c ≥ 7% (56%), and were overweight (22%) or obese (68%). Only 33% of subjects self-reported their work ability as excellent. Four of the JCQ subscales (skill discretion, psychological demands, supervisor support, and coworker support), and work–life balance were significantly associated with work ability (all p < .05). In adjusted models, better coworker support (OR = 1.4; 95% CI = [1.04, 1.9]) and better work–life balance (OR = 1.3; 95% CI = [1.1, 1.5]) were associated with excellent work ability. Many stated their diabetes impacted them at work and spoke of the effects of stress. Few engaged in workplace wellness programs. Conclusion/Application to Practice: Social support and work–life balance were associated with excellent work ability. Engaging workers with diabetes in workplace educational programs may take strategic efforts by occupational health staff.
Clinical and Radiological Outcomes of Meniscal Repair Versus Partial Meniscectomy for Medial Meniscus Root Tears: A Systematic Review and Meta-analysis
Authors: Ro Kyung-Han , Kim Jun-Ho , Heo Jae-Won , Lee Dae-Hee 
Published: November 2020

Background: Given the superiority of meniscal repair over partial meniscectomy according to biomechanical data, the clinical outcomes of meniscal repair are likely to be better than those of partial meniscectomy for a medial meniscus root tear (MMRT). Purpose/Hypothesis: This review was designed to compare the clinical and radiological results between meniscal repair and partial meniscectomy for MMRTs. It was hypothesized that meniscal repair would result in better clinical and radiological results compared with partial meniscectomy. Study Design: Systematic review; Level of evidence, 4. Methods: Studies were included in the review if they (1) included patients with MMRTs who underwent primary arthroscopic meniscal repair or partial meniscectomy and (2) analyzed validated patient-reported outcomes and/or radiological evaluations. Summary odds ratios (ORs) with 95% CIs were calculated to compare partial meniscectomy with meniscal repair for each outcome. Results: A total of 13 studies were included. The mean duration of follow-up was 33.5 and 47.2 months in the meniscal repair group and partial meniscectomy group, respectively. The change in the Lysholm score from preoperatively to postoperatively was statistically significantly in favor of meniscal repair (OR, 2.20 [95% CI, 1.55-3.12]), while no difference was found with respect to the change in the Tegner score between the 2 surgical approaches (OR, 1.21 [95% CI, 0.65-2.24]). The prevalence of postoperative severe knee osteoarthritis (OR, 0.31 [95% CI, 0.17-0.54]) as well as that of reoperations (OR, 0.05 [95% CI, 0.01-0.19]) were significantly in favor of meniscal repair. Conclusion Better outcomes were seen after meniscal repair compared with partial meniscectomy for MMRTs, with greater improvements in Lysholm scores, and lower rates of progression to knee osteoarthritis, and lower reoperation rate.
Neural Tube Defects and Associated Factors among Neonates Admitted to the Neonatal Intensive Care Units in Hiwot Fana Specialized University Hospital, Harar, Ethiopia
Authors: Edris Yunus , Abdurahman Hanan , Desalew Assefa , Weldegebreal Fitsum 
Published: November 2020

Background: Neural tube defects are a major public health problem and substantially contribute to morbidity and mortality, particularly in low-income countries, including Ethiopia. There are a paucity of data on the magnitude and associated factors of neural tube defects in Ethiopia, particularly in the study setting. Objective: This study aimed to assess the magnitude of neural tube defects and associated factors among neonates admitted to the neonatal intensive care unit in Hiwot Fana Specialized University Hospital, Harar, Ethiopia. Methods: A hospital-based cross-sectional study was employed from October 2019 to January 2020. A total of 420 newborn-mother pairs were included consecutively. Data were collected using a face-to-face interviewer-administered questionnaire and clinical examination. Data were entered into Epi Data version 3.1 and analyzed using the statistical package for Social Sciences version 20.0 software. An adjusted odds ratio (AOR) with 95% confidence interval (CI) was used to identify the associated factors. A p-value <.05 was considered statistically significant. Results: The magnitude of neural tube defects was 5.71% (95% CI: 3.5-7.9). Approximately 83.5% of infants had spinal bifida and 16.5% anencephaly. In multivariable logistic regression analyses, preterm birth (32-34 weeks) (AOR= 3.84; 95% CI: 2.1,10.7), low birth weight (1000-1500 g) (AOR = 4.74; 95% CI: 1.8, 9.1), 1500-2500 g (AOR = 3.01; 95% CI: 2. 1, 13.2), maternal coffee consumption (AOR = 11.2; 95% CI: 3.1, 23.7), a history of abortion or stillbirth (AOR = 9.6; 95% CI:7.6,19.4), radiation exposure (AOR = 5.0; 95% CI:1.6,14.3), and intake of anticonvulsant drugs during pregnancy (AOR = 4.75; 95% CI: 1.5,16.2) were factors associated with neural tube defects. Conclusion: In this study, the burden of neural tube defects was 5.71% among neonates admitted to the neonatal intensive care unit, which was a public health concern. Increased attention to the monitoring of neural tube defects in eastern Ethiopia is crucial to improve birth outcomes in the study setting.
Renal trauma: a 5-year retrospective review in single institution
Authors: Syarif  , Palinrungi Achmad M. , Kholis Khoirul , Palinrungi Muhammad Asykar , Syahrir Syakri , Sunggiardi Reinaldo , Faruk Muhammad 
Published: November 2020

Abstract
Background
Renal trauma occurs in up to 5% of all trauma cases and accounts for 24% of abdominal solid organ injuries. Renal trauma management has evolved over the past decades, and current management is transitioning toward more conservative approaches for the majority of hemodynamically stable patients. The objective of this study was to analyze the mechanism of injury, management, and outcome in renal trauma.

Methods
Patients diagnosed with renal trauma in Makassar, Indonesia, from January 2014 to December 2018 were identified retrospectively by the ICD-10 code. Data were collected from medical records. Imaging was classified by radiologists. Variables analyzed included age, sex, mechanism of injury, degree of renal trauma, related organ injury, management, and outcome.

Results
Out of the 68 patients identified, the average age was 23.9 ± 0.6 years, and most were male (83.8%). Blunt trauma accounted for 89.7% of all cases. The most common renal injuries were grade IV (42.6%), and 14% of the cases had no hematuria. Most patients were treated with non-operative management (NOM). Nephrectomy was performed in 16.2% of cases, and 5.9% of cases underwent renorrhaphy. It was found that 58.8% of cases had isolated renal trauma, and the overall mortality rate (2.9%) was due to related injuries.

Conclusions
The majority of blunt and penetrating renal trauma cases that are hemodynamically stable have a good outcome when treated with NOM. The presence of injury in other important organs both intra- and extra-abdominally aggravates the patient’s condition and affects the prognosis.
Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa
Authors: Zhao Zhongning , Heideman Neil , Bester Phillip , Jordaan Adriaan , Hofmeyr Margaretha D. 
Published: November 2020

AbstractBackgroundClimatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world’s tortoise genera. The distribution ofPsammobates tentorius(Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly divergedP. tentoriusrepresents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa.ResultsWe investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in thePsammobates tentoriusspecies complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis inP. tentoriusstarted in the late Miocene (11.63–5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group.ConclusionClimatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of theP. tentoriusspecies complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution ofP. tentoriussubstantially. We found the taxonomic diversify of theP. tentoriusspecies complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B–Ptr, Ptt-A and Pv-A.