bluuebunny/crossref_metadata_2025_split huggingface dataset:
Industry Payments to Plastic Surgeons, 2013 to 2018: Who’s Getting Paid?
Authors: Singerman Kyle W. , Moore Meredith G. , Kortlever Joost T. P. , Gobble Ryan M. 
Published: December 2021

Background:
The Physician Payments Sunshine Act of 2010 mandated that all industry payments to physicians be publicly disclosed. To date, industry support of plastic surgeons has not been longitudinally characterized. The authors seek to evaluate payment trends from 2013 to 2018 and characteristics across plastic surgeon recipients of industry payments.

Methods:
The authors cross-referenced those in the 2019 American Society of Plastic Surgeons member database with Centers for Medicare & Medicaid Services Open Payments database physician profile identification number indicating industry funds received within the study period. We categorized surgeons by years since American Board of Plastic Surgery certification, practice region, and academic affiliation.

Results:
A sum of $89,436,100 (247,614 payments) was received by 3855 plastic surgeons. The top 1 percent of earners (n = 39) by dollar amount received 52 percent of industry dollars to plastic surgeons; of these, nine (23 percent) were academic. Overall, 428 surgeons (11 percent) were academic and received comparable dollar amounts from industry as their nonacademic counterparts. Neither geographic location nor years of experience were independent predictors of payments received. The majority of individual transactions were for food and beverage, whereas the majority of industry dollars were typically for royalties or license.

Conclusions:
Over half of all industry dollars transferred went to just 1 percent of American Society of Plastic Surgeons members receiving payments between 2013 and 2018. Considerable heterogeneity exists when accounting for payment subcategories.
Superior Hemimastectomy with Inferior Pedicle Nipple-Bearing Flap: A Five-Step Surgical Technique
Authors: Morante Lea , El Hajj Houssein , Delecourt Camille , Sabiani Laura , Bannier Marie , Rua Sandrine , Barrou Julien , Lambaudie Eric , Houvenaeghel Gilles , Cohen Monique 
Published: December 2021

Summary:
Oncoplastic breast surgery is an evolving field combining both breast aesthetic surgery and oncologic breast surgery. It aims to optimize cosmetic outcomes without interfering with oncologic safety. The superior hemimastectomy is a technique that can be considered for large upper-quadrant breast tumors or multifocal and multicentric breast tumors localized in the upper quadrants. As with mastectomy, axillary procedures can be performed through the same incision. The nipple-areola complex can be preserved and reimplanted. Superior hemimastectomy allows wide excision of the breast tissue, but its main disadvantage is the increased risk of necrosis of the free grafted nipple-areola complex. In this article, the authors present the surgical technique of superior hemimastectomy with an inferior pedicle nipple-bearing flap. This technique is presented as a simple five-step algorithm. A modified superior hemimastectomy with nipple-areola complex preservation using an inferior pedicle nipple-bearing flap is an alternative to the classic superior hemimastectomy technique. This modified technique decreases the risk of nipple-areola complex necrosis and preserves better nipple-areola complex sensitivity.
High-Quality and Easy-to-Regenerate Personal Filter
Authors: Fraenkl Max , Krbal Milos , Houdek Jakub , Zmrhalova Zuzana Olmrova , Prokes Borivoj , Hejda Petr , Slang Stanislav , Prikryl Jan , Ondracek Jakub , Makes Otakar , Kostyk Juraj , Nasadil Petr , Malcik Pavel , Zdimal Vladimir , Vlcek Miroslav 
Published: December 2021

AbstractProper respiratory tract protection is the key factor to limiting the rate of COVID-19 spread and providing a safe environment for health care workers. Traditional N95 (FFP2) respirators are not easy to regenerate and thus create certain financial and ecological burdens; moreover, their quality may vary significantly. A solution that would overcome these disadvantages is desirable. In this study a commercially available knit polyester fleece fabric was selected as the filter material, and a total of 25 filters of different areas and thicknesses were prepared. Then, the size-resolved filtration efficiency (40–400 nm) and pressure drop were evaluated at a volumetric flow rate of 95 L/min. We showed the excellent synergistic effect of expanding the filtration area and increasing the number of filtering layers on the filtration efficiency; a filter cartridge with 8 layers of knit polyester fabric with a surface area of 900 cm2 and sized 25 × 14 × 8 cm achieved filtration efficiencies of 98 % at 95 L/min and 99.5 % at 30 L/min. The assembled filter kit consists of a filter cartridge (14 Pa) carried in a small backpack connected to a half mask with a total pressure drop of 84 Pa at 95 L/min. In addition, it is reusable, and the filter material can be regenerated at least ten times by simple methods, such as boiling. We have demonstrated a novel approach for creating high-quality and easy-to-breathe-through respiratory protective equipment that reduces operating costs and is a green solution because it is easy to regenerate.
Evaluation of the Roche SARS-CoV-2 Rapid Antibody Test in samples from vaccinated individuals
Authors: Hayer Johannes , Urlaub Eva 
Published: December 2021

AbstractObjectiveThe study aimed to establish the performance of the SARS-CoV-2 Rapid Antibody Test (IgG and IgM) and the Elecsys® Anti-SARS-CoV-2 S assay in vaccinated individuals.MethodsA panel of serum samples from Boca Biolistics was utilized to assess antibodies following vaccination, consisting of samples drawn prior to vaccination, after the first dose, or at least 14 days after the second dose of Moderna mRNA-1273 or Pfizer-BioNTech BNT162b2 COVID-19 vaccines. Agreement between the two methods was measured and stratified by test evaluator and assay lot.ResultsAgreement between the SARS-CoV-2 Rapid Antibody Test (IgG) and Elecsys Anti-SARS-CoV-2 S assay qualitative measurements at the different assessment points for both mRNA-1273 and BNT162b2 ranged between 97.06% (95% confidence interval [CI] 84.67, 99.93) to 100% (95% CI 82.35, 100). Agreement of the SARS-CoV-2 Rapid Antibody Test (IgG) with the Elecsys Anti-SARS-CoV-2 S assay was not highly influenced by either lot or evaluator. There was a medium-to-strong correlation between the semi-quantitative SARS-CoV-2 Rapid Antibody Test (IgG) result and quantitative Elecsys Anti-SARS-CoV-2 S assay in samples taken after both doses of the vaccines, with higher intensity bands being associated with higher total anti-S antibody titer (mRNA-1273, p=0.0019; BNT162b2, p<0.0001).ConclusionSemi-quantitative SARS-CoV-2 Rapid Antibody Test (IgG) and quantitative Elecsys Anti-SARS-CoV-2 S assay correlated well, suggesting that the SARS-CoV-2 Rapid Antibody Test (IgG) is helpful in understanding the immune response post-vaccination. The current data support the use of the SARS-CoV-2 Rapid Antibody Test (IgG) in the vaccinated population.ImportanceSerologic assays are an essential tool for seroprevalence surveys, for quality control of vaccines, and to determine the response to vaccination. Although a correlate of immunity has not yet been established for COVID-19 vaccines, antibody titers after natural infection and vaccination have been associated with protection from symptomatic SARS-CoV-2 infection. Rapid point-of-care assays can be of use in this context with advantages over centralized testing, such as speed and ease of use. The point-of-care SARS-CoV-2 Rapid Antibody Test (IgG) compared favorably to the Elecsys Anti-SARS-CoV-2 S assay with agreement rates above 97.06%, after one or two doses of Moderna mRNA-1273 or Pfizer-BioNTech BNT162b2. Semi-quantitative SARS-CoV-2 Rapid Antibody Test (IgG) and quantitative Elecsys Anti-SARS-CoV-2 S assay results correlated well, suggesting that SARS-CoV-2 Rapid Antibody Test (IgG) is helpful in understanding the immune response post-vaccination. The current data support the use of the SARS-CoV-2 Rapid Antibody Test (IgG) in the vaccinated population.
Outpatient therapies for COVID-19: How do we choose?
Authors: Lee Todd C. , Morris Andrew M. , Grover Steven A. , Murthy Srinivas , McDonald Emily G. 
Published: December 2021

AbstractBackgroundSeveral outpatient COVID-19 therapies have reduced hospitalization in randomized controlled trials. The choice of therapy may depend on drug efficacy, toxicity, pricing, availability, and access to administration infrastructure. To facilitate comparative decision making, we evaluated the efficacy of each treatment in clinical trials and then estimated the associated cost per hospitalization prevented.MethodsWherever possible, we obtained relative risk for hospitalization from published randomized controlled trials. Otherwise, we extracted data from press releases, conference abstracts, government submissions, or preprints. If more than one study was published, the results were meta-analyzed. Using relative risk, we estimated the number needed to treat (NNT), assuming a baseline hospitalization risk of 5%. Drug pricing was based on Canadian formularies, government purchases, or manufacturer estimates.Administrative and societal costs were not included. Results will be updated online as new studies emerge or final publication numbers become available.ResultsAt a 5% risk of hospitalization the estimated NNTs were: 87 for colchicine, 80 for fluvoxamine, 72 for inhaled corticosteroids, 24 for nirmatrelvir/ritonavir, 25 for sotrovimab, 24 for remdesivir, 29 for casirivimab/imdevimab, 29 for bamlanivimab/etesevimab and 52 for molnupiravir. Colchicine, fluvoxamine, inhaled corticosteroids, and nirmatrelvir/ritonavir had cost per hospitalization prevented point estimates below the CIHI estimated cost of hospitalization ($23000).InterpretationCanada is fortunate to have access to several effective outpatient therapies to prevent COVID-19 hospitalization. Given differences in efficacy, toxicity, cost and administration complexities, this assessment serves as one tool to help guide policy makers and clinicians in their treatment selection.
RESISTANCE CONFERRING MUTATIONS IN SARS-CoV-2 DELTA FOLLOWING SOTROVIMAB INFUSION
Authors: Rockett Rebecca J , Basile Kerri , Maddocks Susan , Fong Winkie , Agius Jessica E , Mackinnon Jessica Johnson , Arnott Alicia , Chandra Shona , Gall Mailie , Draper Jenny , Martinez Elena , Sim Eby M , Lee Clement , Ngo Christine , Ramsperger Marc , Ginn Andrew N , Wang Qinning , Fennell Michael , Ko Danny , Lim H Ling , Gilroy Nicky , O’Sullivan Matthew V N , Chen Sharon C-A , Kok Jen , Dwyer Dominic E , Sintchenko Vitali 
Published: December 2021

ABSTRACTSeveral Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) neutralising monoclonal antibodies (mAbs) have received emergency use authorisation by regulatory agencies for treatment and prevention of Coronavirus Disease 2019 (COVID-19), including in patients at risk for progression to severe disease. Here we report the persistence of viable SARS-CoV-2 in patients treated with sotrovimab and the rapid development of spike gene mutations that have been shown to confer high level resistance to sotrovimab in vitro. We highlight the need for SARS-CoV-2 genomic surveillance in at risk individuals to inform stewardship of mAbs use and prevent potential treatment failures.
Interleukin-10 knockout mice do not reliably exhibit macroscopic inflammation: a natural history endoscopic surveillance study
Authors: Kim Seung Young , Park Jaeho , Leite Gabriela , Pimentel Mark , Rezaie Ali 
Published: December 2021

AbstractBackgroundInterleukin (IL)-10 knockout (KO) mice, used as a model for inflammatory bowel disease (IBD), develop chronic enterocolitis. Endoscopy, the gold standard for evaluation of human mucosal health, is not widely available for murine models. We aimed to assess the natural history of left-sided colitis in IL-10 KO mice via serial endoscopies.MethodsBALB/cJ IL10 KO mice underwent regular endoscopic assessments from 2 up to 8 months of age. Procedures were recorded and blindly evaluated using a 4-component endoscopic score: mucosal wall transparency, intestinal bleeding, focal lesions and perianal lesions (0-3 points each). An endoscopic score ≥1 point was considered as the presence of colitis/flare.ResultsIL-10 KO mice (N=40, 9 female) were assessed. Mean age at first endoscopy was 62.5±2.5 days; average number of procedures per mouse was 6.0±1.3. A total of 238 endoscopies were conducted every 24.8±8.3 days, corresponding to 124.1±45.2 days of surveillance per mouse (13.6 years cumulative surveillance). Thirty-three endoscopies in 24 mice (60%) detected colitis, mean endoscopy score 2.5±1.3 (range: 1-6.3). Nineteen mice (47.5%) had one episode of colitis and 5 (12.5%) had 2-3 episodes. All exhibited complete spontaneous healing on subsequent endoscopies.ConclusionsIn this largest endoscopic surveillance study of IL-10 KO mice, 40% of mice did not develop endoscopic left-sided colitis. Furthermore, IL-10 KO mice did not exhibit persistent colitis and universally exhibited complete spontaneous healing without treatment. The natural history of colitis in IL-10 KO mice may not be comparable with that of IBD in humans and requires careful consideration.
Quantifying the patterns of metabolic plasticity and heterogeneity along the epithelial-hybrid-mesenchymal spectrum in cancer
Authors: Muralidharan Srinath , Sahoo Sarthak , Saha Aryamaan , Chandran Sanjay , Majumdar Sauma Suvra , Levine Herbert , Jolly Mohit Kumar 
Published: December 2021

AbstractCancer metastasis is the leading cause of cancer-related mortality and the process of Epithelial to Mesenchymal Transition (EMT) is crucial for cancer metastasis. Either a partial or complete EMT have been reported to influence the metabolic plasticity of cancer cells in terms of switching among oxidative phosphorylation, fatty acid oxidation and glycolysis pathways. However, a comprehensive analysis of these major metabolic pathways their associations with EMT across different cancers is lacking. Here, we analyse more than 180 cancer cell datasets and show diverse associations of these metabolic pathways with the EMT status of cancer cells. Our bulk data analysis shows that EMT generally positively correlates with glycolysis but negatively with oxidative phosphorylation and fatty acid metabolism. These correlations are also consistent at the level of their molecular master regulators, namely AMPK and HIF1α. Yet, these associations are shown to not be universal. Analysis of singlecell data of EMT induction shows dynamic changes along the different axes of metabolic pathways, consistent with general trends seen in bulk samples. Together, our results reveal underlying patterns of metabolic plasticity and heterogeneity as cancer cells traverse through the epithelial-hybrid-mesenchymal spectrum of states.
GRaNIE and GRaNPA: Inference and evaluation of enhancer-mediated gene regulatory networks applied to study macrophages
Authors: Kamal Aryan , Arnold Christian , Claringbould Annique , Moussa Rim , Servaas Nila H. , Kholmatov Maksim , Daga Neha , Nogina Daria , Mueller-Dott Sophia , Reyes-Palomares Armando , Palla Giovanni , Sigalova Olga , Bunina Daria , Pabst Caroline , Zaugg Judith B. 
Published: December 2021

AbstractAmong the biggest challenges in the post-GWAS (genome-wide association studies) era is the interpretation of disease-associated genetic variants in non-coding genomic regions. Enhancers have emerged as key players in mediating the effect of genetic variants on complex traits and diseases. Their activity is regulated by a combination of transcription factors (TFs), epigenetic changes and genetic variants. Several approaches exist to link enhancers to their target genes, and others that infer TF-gene connections. However, we currently lack a framework that systematically integrates enhancers into TF-gene regulatory networks. Furthermore, we lack an unbiased way of assessing whether inferred regulatory interactions are biologically meaningful. Here we present two methods, implemented as user-friendly R packages: GRaNIE (Gene Regulatory Network Inference including Enhancers) for building enhancer-based gene regulatory networks (eGRNs) and GRaNPA (Gene Regulatory Network Performance Analysis) for evaluating GRNs. GRaNIE jointly infers TF-enhancer, enhancer-gene and TF-gene interactions by integrating open chromatin data such as ATAC-Seq or H3K27ac with RNA-seq across a set of samples (e.g. individuals), and optionally also Hi-C data. GRaNPA is a general framework for evaluating the biological relevance of TF-gene GRNs by assessing their performance for predicting cell-type specific differential expression. We demonstrate the power of our tool-suite by investigating gene regulatory mechanisms in macrophages that underlie their response to infection and cancer, their involvement in common genetic diseases including autoimmune diseases, and identify the TF PURA as putative regulator of pro-inflammatory macrophage polarisation.Availability- GRaNIE:https://bioconductor.org/packages/release/bioc/html/GRaNIE.html- GRaNPA:https://git.embl.de/grp-zaugg/GRaNPAGraphical abstract
HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization
Authors: Lexa Matej , Cechova Monika , Nguyen Son Hoang , Jedlicka Pavel , Tokan Viktor , Kubat Zdenek , Hobza Roman , Kejnovsky Eduard 
Published: December 2021

AbstractThe role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA segments in nuclei. We combined Hi-C data, plant reference genome data and tools for the characterization of genomic repeats to build a Nextflow pipeline identifying and quantifying the contacts of specific repeats revealing the preferential homotypic interactions of ribosomal DNA, DNA transposons and some LTR retrotransposon families. We provide a novel way to analyze the organization of repetitive elements in the 3D nucleus.
The Place of Fluvoxamine in the Treatment of Non-critically ill Patients with COVID-19: A Living Systematic Review and Meta-analysis
Authors: Oussama Kacimi Salah Eddine , Greca Elona , Haireche Mohamed Amine , ElHawary Ahmed Sallam , Setti Mounir Ould , Caruana Rebecca , Rizwan Sahar , Benyettou Hidayet , Essar Mohammad Yasir , Shah Jaffer , Ghozy Sherief 
Published: December 2021

AbstractBackgroundFluvoxamine is a selective serotonin reuptake inhibitor that is known to be used as antidepressant. Repurposing of Fluvoxamine for the treatment of COVID-19 is theorized to help in the prevention of the clinical deterioration of SARS CoV-2 patients. In our systematic review and meta-analysis, we aim to assess the safety and efficacy of the drug under study in terms of its effect on the mortality and the risk of hospitalization and mechanical ventilation in non-critically ill COVID-19 patients.MethodsWe performed a systematic search of seven electronic databases. The search results were screened based on the previously determined inclusion and exclusion criteria. We determined the data related to our objectives. The mortality rates, rates of hospitalization, risk of mechanical ventilation and serious side effects were extracted from the studies that successfully met our inclusion and exclusion criteria. Then, the extracted data from the included studies was included in the meta-analysis.ResultsThree studies, two randomized clinical trials and one observational cohort study, with 1762 patients, were the final outcome of our search and screening processes. Among all participants, 886 patients received Fluvoxamine while 876 were controls. Follow up periods ranged from 7 days to 28 days. There was no significant difference in the intention-to-treat mortality rates between the two groups (RR = 0.66; 95% CI: 0.36 - 1.21, p-value = 0.18; I2 = 0%). However, Fluvoxamine decreased the per-protocol mortality compared to both placebo alone or placebo/standard care (RR = 0.09; 95% CI: 0.01 - 0.64, p-value = 0.02; I2 = 0% and RR = 0.09; 95% CI: 0.01 - 0.72, respectively). As compared to placebo or standard care, the all-cause hospitalization was significantly reduced in the fluvoxamine group (RR = 0.71; 95% CI: 0.54 - 0.93, p-value = 0.01; I2 = 61%). This risk reduction was not significant when compared to placebo alone (RR = 0.76; 95% CI: 0.57 - 1.00; p-value = 0.051; I2 = 48%). Furthermore, the risk of mechanical ventilation was not improved in the fluvoxamine group as compared to placebo (RR = 0.71; 95% CI: 0.43 - 1.16, p-value = 0.17; I2 = 0%). The serious adverse effects were almost the same in the treatment group and the control (13% and 12% respectively).ConclusionFluvoxamine does not significantly reduce the mortality rates or the risk of mechanical ventilation in SARS CoV-2 patients. Nonetheless, it was found to have a good impact on reducing all cause hospitalization among patients with COVID-19 disease. Therefore, further clinical studies are needed to determine the effectiveness of the drug and its mechanisms of action.
Variant-to-gene-mapping followed by cross-species genetic screening identifies GPI-anchor biosynthesis as novel regulator of sleep
Authors: Palermo Justin , Chesi Alessandra , Zimmerman Amber , Sonti Shilpa , Lasconi Chiara , Brown Elizabeth B. , Pippin James A. , Wells Andrew D. , Doldur-Balli Fusun , Mazzotti Diego R. , Pack Allan I. , Gehrman Phillip R. , Grant Struan F.A. , Keene Alex C. 
Published: December 2021

ABSTRACTSleep is nearly ubiquitous throughout the animal kingdom, with deficiencies in sleep having been linked to a wide range of human disorders and diseases. While genome wide association studies (GWAS) in humans have identified loci robustly associated with several heritable diseases or traits, little is known about the functional roles of the underlying causal variants in regulating sleep duration or quality. We applied an ATAC-seq/promoter focused Capture C strategy in human iPSC-derived neural progenitors to carry out a ‘variant-to-gene’ mapping campaign that identified 88 candidate sleep effector genes connected to relevant GWAS signals. To functionally validate the role of the implicated effector genes in sleep regulation, we performed a neuron-specific RNAi screen in the fruit fly,Drosophila melanogaster. This approach identified a number of genes that regulated sleep, including phosphatidylinositol N-acetylglucosaminyltransferase subunit Q (PIG-Q), a gene that encodes an enzyme involved in the first step of glycosylphosphatidylinositol (GPI)- anchor biosynthesis. We show that flies deficient forPIG-Qhave longer sleep during both day and night due to an increase in the total number of sleep bouts. Subsequent systematic investigation of other PIG-family genes identified increased sleep in flies for multiple different genes within the PIG pathway. We then mutated thePIG-Qlocus in zebrafish and identified similar increases in sleep to those observed inDrosophila, confirming deep homology ofPIG-Qmediated sleep regulation. These results provide the first physical variant-to-gene mapping of human sleep genes followed by a model organism-based prioritization, revealing a novel and conserved role for GPI-anchor biosynthesis in sleep regulation.