bluuebunny/crossref_metadata_2025_split huggingface dataset:
Not All Breast Explants Are Equal: Contemporary Strategies in Breast Explantation Surgery
Authors: Tanna Neil , Calobrace M. Bradley , Clemens Mark W. , Hammond Dennis C. , Nahabedian Maurice Y. , Rohrich Rod J. , Zhang Ben H. , Bregman Dana , Perry Adam D. 
Published: March 2021

Summary:
Breast implant removal and replacement has been a common secondary breast procedure in the long-term maintenance of breast augmentation, but more recently growing concerns about silicone-related systemic illness, breast implant-associated anaplastic large cell lymphoma (BIA-ALCL), and changing perceptions of aesthetic beauty have seen breast implant removal without replacement become increasingly requested by patients. Explantation can be challenging, especially when performed with a total capsulectomy. Currently, there is no evidence regarding whether a partial or total capsulectomy has any effect on BIA-ALCL risk mitigation in patients that have textured implants without disease. Total capsulectomy with incomplete resection of a mass can contribute to hyperprogression of BIA-ALCL and death. There have also been cases of BIA-ALCL diagnosed years after removal of the textured device and “total capsulectomy.” Therefore, the common practice of simple prophylactic capsulectomy in a textured implant to mitigate future disease has not been established and at the current time should be discouraged. In addition, aesthetic outcomes can be quite variable, and patients should have appropriate preoperative counseling regarding the indications and contraindications for explantation, associated risks, financial implications, and postoperative appearance. The authors review salient aspects related to the planning and management of breast implant removal.
Uncertainty quantification of dynamic earthquake rupture simulations
Authors: Daub Eric G. , Arabnejad Hamid , Mahmood Imran , Groen Derek 
Published: March 2021

We present a tutorial demonstration using a surrogate-model based uncertainty quantification (UQ) approach to study dynamic earthquake rupture on a rough fault surface. The UQ approach performs model calibration where we choose simulation points, fit and validate an approximate surrogate model or emulator, and then examine the input space to see which inputs can be ruled out from the data. Our approach relies on themogp_emulatorpackage to perform model calibration, and the FabSim3 component from the VECMA toolkit to streamline the workflow, enabling users to manage the workflow using the command line to curate reproducible simulations on local and remote resources. The tools in this tutorial provide an example template that allows domain researchers that are not necessarily experts in the underlying methods to apply them to complex problems. We illustrate the use of the package by applying the methods to dynamic earthquake rupture, which solves the elastic wave equation for the size of an earthquake and the resulting ground shaking based on the stress tensor in the Earth. We show through the tutorial results that the method is able to rule out large portions of the input parameter space, which could lead to new ways to constrain the stress tensor in the Earth based on earthquake observations.This article is part of the theme issue ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantificationin silico’.
The case for free and open source software in research and scholarship
Authors: Fortunato Laura , Galassi Mark 
Published: March 2021

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today.This article is part of the theme issue ‘Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantificationin silico’.
Multifocal vascular affection in a patient with angina pectoris - rationale and design of a clinical study
Authors: Pintova M. , Simova I. , Dimitrov N. , Krasnaliev J. , Kornovski V. , Vekov T. 
Published: March 2021

AbstractAtherosclerosis is a disease of the large and middle arteries and is characterized mainly by endothelial dysfunction, inflammation of the vascular wall and the accumulation of lipids, cholesterol, calcium and cell debris in the intima of the vascular wall. This accumulation leads to plaque formation, vascular remodeling, acute and chronic obstruction of the vessel lumen, blood flow abnormalities, and reduced oxygen supply to target organs. As a result, blood vessels become harder and their lumen shrinks, which increases the risk of obstruction and thrombosis. Depending on the affected area, the corresponding symptoms appear - angina or myocardial infarction when affecting the coronary circulation; transient ischemic attack (TIA) or stroke affecting cerebral circulation; claudication or gangrene when affecting the limbs; aneurysm or dissection affecting the aorta. Various risk factors are known to affect the onset of the disease. They are divided into adjustable (dyslipoproteinemia, hypertension, diabetes mellitus, smoking, obesity, inactivity, emotional stress, etc.) and unadjustable (gender, age, family predisposition). The risk of developing atherosclerosis increases significantly in the presence of several risk factors. For example, the presence of 2 risk factors increases the risk of developing atherosclerosis 4 times.The atherosclerotic process is multifocal - it develops everywhere in the body - affecting the cardiac, cerebral and peripheral arteries almost simultaneously or sequentially. Its isolated manifestations in only one area are an exception.
The recombinant Link module of human TSG-6 suppresses cartilage damage in models of osteoarthritis: a potential disease-modifying OA drug
Authors: Drummond Sheona P , Bartnik Eckart , Kouvatsos Nikolaos , Scott Jenny L , Dyer Douglas P , Thomson Jennifer M , Price Andrew J , Anand Sanjay , Biant Leela C , Leeuw Thomas , Herrmann Matthias , Milner Caroline M , Day Anthony J 
Published: March 2021

ABSTRACTObjectivesTo investigate the role of endogenous TSG-6 in human osteoarthritis (OA) and assess the disease-modifying potential of a TSG-6-based biological treatment in cell, explant and animal models of OA.MethodsKnee articular cartilages from OA patients were analysed for TSG-6 protein and mRNA expression using immunohistochemistry and RNAscope, respectively. The inhibitory activities of TSG-6 and its isolated Link module domain (Link_TSG6) on cytokine-induced glycosaminoglycan loss in OA cartilage explants were compared. Mesenchymal stem/stromal cell (MSC)-derived chondrocyte pellet cultures were used to determine the effects of Link_TSG6 and full-length TSG-6 on IL-1α-, IL-1β- or TNF-stimulated ADAMTS4, ADAMTS5 and MMP13 mRNA expression. Link_TSG6 was administered i.a. to the rat ACLTpMMx model and cartilage damage and tactile allodynia were assayed.ResultsTSG-6 is predominantly associated with chondrocytes in regions of cartilage damage and its expression is negatively correlated with MMP13, the major collagenase implicated in OA progression. Link_TSG6 is more potent than full-length TSG-6 at dose-dependently inhibiting cytokine-mediated matrix breakdown in human OA cartilage explants; about 50% of donor cartilages, from 59 tested, were responsive to Link_TSG6 treatment. Similarly, Link_TSG6 displayed more potent effects in 3D pellet cultures, suppressing aggrecanase and collagenase gene expression. Link_TSG6 treatment reduced touch-evoked pain and dose-dependently inhibited cartilage damage in a rodent model of surgically-induced OA.ConclusionsNative TSG-6 is associated with a low catabolic chondrocyte phenotype in OA cartilage. Link_TSG6, which has enhanced chondroprotective activity compared to the full-length TSG-6 protein, demonstrates potential as a disease modifying OA drug (DMOAD) and warrants further investigation and development.KEY MESSAGESWhat is already known about this subject?TSG-6, a protein with anti-inflammatory and protective effects in other tissues, is expressed in joints affected by osteoarthritis – a condition for which there are no disease-modifying drugs.What does this study add?A novel protective mechanism has been identified, whereby TSG-6 inhibits inflammatory cytokine-induced catabolic pathways in cartilage.The Link module of TSG-6 (Link_TSG6) has been shown to have greater potency than TSG-6 as an inhibitor of cartilage damage and is efficacious in a rat model of osteoarthritis.Data from cartilage explants indicate that OA patients can be stratified for Link_TSG6 responsiveness.How might this impact on clinical practice or future developments?Link_TSG6 has been identified as potential disease-modifying OA drug that mimics an intrinsic protective process.
Emergence and spread of SARS-CoV-2 lineages B.1.1.7 and P.1 in Italy
Authors: Di Giallonardo Francesca , Puglia Ilaria , Curini Valentina , Cammà Cesare , Mangone Iolanda , Calistri Paolo , Cobbin Joanna C.A. , Holmes Edward C. , Lorusso Alessio 
Published: March 2021

AbstractItaly’s second wave of SARS-CoV-2 has hit hard, with more than 3 million cases and over 100,000 deaths, representing an almost ten-fold increase on the numbers reported by August 2020. Herein, we present the analysis of 6,515 SARS-CoV-2 sequences sampled in Italy between 29th January 2020 and 1st March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern – lineage P.1 – from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.
De novo Powered Air-Purifying Respirator Design and Fabrication for Pandemic Response
Authors: Kothakonda Akshay , Atta Lyla , Plana Deborah , Ward Ferrous , Davis Chris , Cramer Avilash , Moran Robert , Freake Jacob , Tian Enze , Mazor Ofer , Gorelik Pavel , Van Christopher , Hansen Christopher , Yang Helen , Sinha Michael S. , Li Ju , Yu Sherry H. , LeBoeuf Nicole R. , Sorger Peter K. 
Published: March 2021

SUMMARYThe rapid spread of COVID-19 and disruption of normal supply chains resulted in severe shortages of personal protective equipment (PPE), particularly devices with few suppliers such as powered air-purifying respirators (PAPRs). A scarcity of information describing design and performance criteria represents a substantial barrier to new approaches to address these shortages. We sought to apply open-source product development to PAPRs to enable alternative sources of supply and further innovation. We describe the design, prototyping, validation, and user testing of locally manufactured, modular, PAPR components, including filter cartridges and blower units, developed by the Greater Boston Pandemic Fabrication Team (PanFab). Two designs, one with a fully custom-made filter and blower unit housing, and the other with commercially available variants (the “Custom” and “Commercial” designs respectively) were developed. Engineering performance of the prototypes was measured and safety validated using NIOSH-equivalent tests on apparatus available under pandemic conditions, at university laboratories. Feedback on designs was obtained from four individuals, including two clinicians working in an ambulatory clinical setting and two research technical staff for whom PAPR use is a standard part of occupational PPE. Respondents rated the PanFab Custom PAPR a 4 to 5 on a 5 Likert-scale 1) as compared to current PPE options, 2) for the sense of security with use in a clinical setting, and 3) for comfort. The three other versions of the designs (with a commercial blower unit, filter, or both) performed favorably, with survey responses consisting of scores ranging from 3-5. Engineering testing and clinical feedback demonstrate that the PanFab designs represents favorable alternative PAPRs in terms of user comfort, mobility, and sense of security. A nonrestrictive license promotes innovation in respiratory protection for current and future medical emergencies.
Plasma lipids and growth faltering: a longitudinal cohort study in rural Gambian children
Authors: Gonzales Gerard Bryan , Brals Daniella , Sonko Bakary , Sosseh Fatou , Darboe Momodou , Prentice Andrew M. , Moore Sophie E. , Koulman Albert 
Published: March 2021

AbstractGrowth faltering in children arises from metabolic and endocrine dysfunction driven by complex interactions between poor diet, persistent infections and immunopathology. Here, we determined the progression of the plasma lipidome among Gambian children and assessed its influence on growth faltering over the first 2 years of life using panel vector autoregression modelling. We further investigated temporal associations among lipid clusters. We observed that measures of stunting, wasting and underweight significantly influence each other, and that lipid groups containing PUFA and phosphatidylcholines significantly influence growth outcomes. Linear growth was influenced by the majority of lipids, indicating a higher nutritional demand to improve height compared to weight among growth-restricted children. Our results indicate a critical role for PUFAs and choline in early life dietary interventions to combat the child growth faltering still so prevalent in low-income settings.Abstract Figure
Early experiences of rehabilitation for patients post-COVID to improve fatigue, breathlessness exercise capacity and cognition
Authors: Daynes E , Gerlis C , Chaplin E , Gardiner N , Singh S 
Published: March 2021

AbstractPatients with lasting symptoms of COVID-19 should be offered a comprehensive recovery programme. Patients that completed a six week, twice supervised adapted pulmonary rehabilitation programme demonstrated statistically significant improvements in exercise capacity, respiratory symptoms, fatigue and cognition. Participants improved by 112m on the Incremental Shuttle Walking Test and 544 seconds on the Endurance Shuttle Walking Test. There were no serious adverse events recorded, and there were no dropouts related to symptom worsening. COVID-19 rehabilitation appears feasible and significantly improves clinical outcomes.
Integrative genetic and immune cell analysis of plasma proteins in healthy donors identifies novel associations involving primary immune deficiency genes
Authors: Caron Barthelemy , Patin Etienne , Rotival Maxime , Charbit Bruno , Albert Matthew L , Quintana-Murci Lluis , Duffy Darragh , Rausell Antonio ,   Milieu Intérieur Consortium†
Published: March 2021

AbstractBlood plasma proteins play an important role in immune defense against pathogens, including cytokine signaling, the complement system and the acute-phase response. Recent large-scale studies have reported genetic (i.e. quantitative trait loci, pQTLs) and non-genetic factors, such as age and sex, as major determinants to inter-individual variability in immune response variation. However, the contribution of blood cell composition to plasma protein heterogeneity has not been fully characterized and may act as a confounding factor in association studies. Here, we evaluated plasma protein levels from 400 unrelated healthy individuals of western European ancestry, who were stratified by sex and two decades of life (20-29 and 60-69 years), from the Milieu Intérieur cohort. We quantified 297 proteins by Luminex in a clinically certified laboratory and their levels of variation were analysed together with 5.2M single-nucleotide polymorphisms. With respect to non-genetic variables, we included more than 700 lifestyle and biochemical factors, as well as counts of seven circulating immune cell populations measured by hemogram and standardized flow cytometry. Collectively, we found 152 significant associations involving 49 proteins and 20 non-genetic variables. Consistent with previous studies, age and sex showed a global, pervasive impact on plasma protein heterogeneity, while body mass index and other health status variables were among the non-genetic factors with the highest number of associations. After controlling for these covariates, we identified 100 and 12 pQTLs acting in cis and trans, respectively, collectively associated with 87 plasma proteins and including 30 novel genetic associations. Genetic factors explained the largest fraction of the variability of plasma protein levels, as compared to non-genetic factors. In addition, blood cell fractions, including leukocytes, lymphocytes and three types of polymorphonuclear cells, had a larger contribution to inter-individual variability than age and sex, and appeared as confounders of specific genetic associations. Finally, we identified new genetic associations with plasma protein levels of eight monogenic Mendelian disease genes including three primary immunodeficiency genes (Ficolin-3, Interleukine-2 Receptor alpha and FAS). Our study identified novel genetic and non-genetic factors associated to plasma protein levels which may inform health status and disease management.
Recent trends in postoperative mortality after liver resection- A systemic review and metanalysis of studies published in last 5 years and metaregression of various factors affecting 90 days mortality
Authors: Vasavada Bhavin , Patel Hardik 
Published: March 2021

AbstractAimThe aim of this systemic review and meta-analysis was to analyse 90 days mortality after liver resection, and also study various factors associated with mortality via univariate and multivariate metaregression.MethodsPubMed, Cochrane library, Embase, google scholar, web of science with keywords like ‘liver resection”; “mortality”;” hepatectomy”. Weighted percentage 90 days mortalities were analysed. univariate metaregression was done by DerSimonian-Liard methods. Major hepatectomy, open surgery, cirrhotic livers, blood loss, hepatectomy for hepatocellular carcinoma, hepatectomy for colorectal liver metastasis were taken as moderators in metaregression analysis. We decided to enter all co-variants in multivariate model to look for mixed effects. Heterogeneity was assessed using the Higgins I2 test, with values of 25%, 50% and 75% indicating low, moderate and high degrees of heterogeneity. Cohort studies were assessed for bias using the Newcastle-Ottawa Scale to assess for the risk of bias. Publication bias was assessed using funnel plot. Funnel plot asymmetry was evaluated by Egger’s test.ResultsTotal 29931 patients’ data who underwent liver resections for various etiologies were pooled from 41 studied included1257 patients died within 90 days post operatively. Weighted 90 days mortality was 3.6% (95% C.I 2.8% −4.4%). However, heterogeneity of the analysis was high with I2 94.625%.(p<0.001). We analysed various covariates like major hepatectomy, Age of the patient, blood loss, open surgery, liver resections done for hepatocellular carcinoma or colorectal liver metastasis and cirrhotic liver to check for their association with heterogeneity in the analysis and hence 90 days mortality. On univariate metaregression analysis major hepatectomy (p<0.001), Open hepatectomy (p<0.001), blood loss (p=0.002) was associated with heterogeneity in the analysis and 90 days mortality. On multivariate metaregression Major hepatectomy(p=0.003) and Open surgery (p=0.012) was independently associated with higher 90 days mortality, and liver resection for colorectal liver metastasis was independently associated with lesser 90 days mortality (z= −4.11,p<0.01). Residual heterogeneity after all factor multivariate metaregression model was none (I2=0,Tau2=0, H2=1) and nonsignificant (p=0.49).ConclusionMajor hepatectomy, open hepatectomy, and cirrhotic background is associated with higher mortality rates and colorectal liver metastasis is associated with lower peri operative mortality rates.
Analyzing the Global Impact of COVID-19 Vaccination Progress: A Result-oriented Storytelling Approach
Authors: Dey Samrat Kumar , Rahman Md. Mahbubur , Siddiqi Umme Raihan , Howlader Arpita , Tushar Arifuzzaman 
Published: March 2021

AbstractThe next big step in combating the coronavirus disease 2019 (COVID-19) pandemic will be gaining widespread acceptance of a vaccination campaign for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but achieving high uptake need proper understandings. Many health professionals, researchers, statisticians, and programmers to track the viruses spread in different parts of the world have used various methods. However, the proliferation of vaccines produced by talented scientists around the world has sparked a strong desire to extract meaningful insights from available data. Until now, several vaccines against coronavirus disease (COVID-19) have been approved and are being distributed worldwide in various regions. This study aims to report the detailed data analysis and result-oriented storytelling of the COVID-19 vaccination program of different countries across the globe. To analyze the vaccination trend globally this research utilized two different open datasets provided by ourworldindata.org and worldometers.info. An exploratory data analysis (EDA) with interactive data visualization using various python libraries was conducted, and the results are presented in this article to better understand the impact of ongoing vaccination programs around the world. Apart from the valuable insights gained from the data of various countries, this investigation also included a comparison of the number of confirmed and death cases before and after vaccination to determine the efficacy of each vaccine in each country. The results show that a large number of people are still undecided about whether or not to get a COVID-19 vaccine, despite the virus’s continued devastating effects on communities. Overall, our findings contribute to ongoing research aimed at informing policy on how to persuade the unvaccinated to be vaccinated.