bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Adoption of Oncoplastic Surgery Using Breast Reduction or Mastopexy Techniques in an Academic Breast Cancer Center Program Can Increase Breast Conservation Rates
Authors: Sekigami Yurie , Chowdhury Ritam , Char Sydney , Radparvar Jacob , Chen Lilian , Parsons Susan K. , Chatterjee Abhishek 
Published: April 2020

Background
Interest in oncoplastic surgery (OPS), a form of breast conservation surgery (BCS), has grown in the United States over the last decade. Oncoplastic surgery allows for the removal of larger tumors without compromising esthetic outcome or oncologic safety. One of the quality measures on which breast cancer centers in the United States are evaluated is rate of BCS. The purpose of this study was to investigate whether the adoption of OPS increases BCS rates and decreases mastectomy rates at the institutional level.

Methods
Clinicopathologic data were retrospectively collected for breast cancer patients in a single institution database. Rates of BCS vs mastectomy and partial mastectomy versus OPS were measured between 2012 and 2018 to capture 3 years before and 3 years after the hiring of an oncoplastic surgeon in 2015 with subsequent practice adoption of oncoplastic techniques. We compared the 2 periods using χ2 and Fisher exact test for categorical variables. Rates of breast conservation and mastectomy were further stratified by tumor stage.

Results
Four hundred sixty-eight patients underwent breast cancer surgery at Tufts Medical Center between 2012 and 2018.
Patients who underwent surgery between 2012–2015 and 2016–2018 were similar in terms of age, histological type, tumor size, receipt of neoadjuvant therapy, receptor status, and Charlson Comorbidity Index. There was a statistically significant (P < 0.0001) increase in BCS rate after 2015 attributable to the practice adoption of OPS. The proportion of patients who were recommended reexcision did not significantly increase with the introduction of OPS suggesting an appropriate and safe patient selection process for patients undergoing these breast conservation techniques. When stratified by T stage (tumor size), rates of mastectomy for T2 tumors (greater than 2 cm but less than 5 cm) decreased precipitously after 2015 and BCS increased proportionately. The rate of BCS for T1 tumors also increased but less drastically.

Conclusions
The adoption of OPS in an academic breast cancer center can result in significantly higher rates of BCS, particularly for those with larger tumors (T2). Academic breast cancer centers should strongly consider incorporating OPS to their treatment paradigm to provide patients with the option to avoid mastectomy.
Clinical Outcomes After Hematoma Development
Authors: Rogoff Hunter , Marquez Jocellie E. , Ghosh Kanad , Jou Christopher , McAuliffe Phoebe , Rathi Sourish , Monroig Kaitlin , Medrano Christopher , Marmor William A. , Ferrier Austin , Kapadia Kailash , Klein Gabriel , Huston Tara L. , Ganz Jason , Dagum Alexander B. , Khan Sami , Bui Duc 
Published: April 2020

Background
Hematomas after tissue expander immediate breast reconstruction (TE-IBR) pose a significant challenge during the recovery period. In this study, we aim to evaluate whether hematoma formation leads to subsequent complications and how management can impact final reconstructive goals.

Methods
A single-institution retrospective review of TE-IBRs from 2001 to 2018 was performed using an established breast reconstruction database. Demographics, medications, comorbidities, and complications were identified. Implant loss was defined as removal of the tissue expander/implant without immediate reimplantation during that operation. Hematoma size, management, transfusion requirement, reoperations, and final outcome were recorded. Reconstructive failure was defined as an implant loss that was not replaced with another implant or required secondary autologous reconstruction.

Results
Six hundred twenty-seven TE-IBR patients were analyzed. Postoperative hematoma (group 1) occurred in 4.1% (n = 26) of TE-IBRs and did not develop in 95.9% (group 2: n = 601). Group 2 had a higher mean body mass index (24.5 vs 27.3 kg/m2, P = 0.018); however, there were no significant differences in smoking status, preoperative/postoperative radiation/chemotherapy, or other comorbidities. Group 1 was found to have increased rates of implant loss (15.4% vs 3.7%, P = 0.0033) and reconstructive failure (11.5% vs 2.8%, P = 0.0133) compared with group 2.
Eighteen hematomas (69.2%) underwent surgical intervention (group 1a) compared with 30.8% (n = 8) that were clinically managed (group 1b). Group 1a had statistically significant lower rates of subsequent complications (22.2% vs 62.5%, P = 0.046) and reoperations (5.6% vs 27.5%, P = 0.037) than did group 1b, respectively.
Lastly, 23.1% (n = 6) of patients who developed a hematoma were on home antithrombotics (group 1c) compared with 76.9% (n = 20) of patients with no antithrombotics (group 1d). There were statistically significant differences in transfusion rates (50% vs 0%, P = 0.001) between groups 1c and 1d, respectively. Differences in hematoma volume (330 vs 169.3 mL, P = 0.078) and reconstructive failure (33.3% vs 5%, P = 0.057) approached significance between both groups.

Conclusions
Hematoma after TE-IBR should be monitored closely, as it may play a role in jeopardizing reconstruction success. Patients on home antithrombotic medication may be at increased risk of larger-volume hematomas and reconstruction failure. Plastic surgeons should consider aggressive surgical evacuation of postoperative TE-IBR hematomas to reduce subsequent complications and reoperations, thus optimizing reconstructive outcomes.
Repair of Massive Bone Defects of the Proximal Femur Using Iliac Bone Flaps of the Ascending Branch of the Lateral Circumflex Femoral Artery
Authors: Li Zonghuan , Yu Aixi , Yu Guorong , Tao Shengxiang , Qi Baiwen 
Published: April 2020

Background and Objective
The management of bone defects is still a difficult problem. Local vascularized bone grafts represent an efficient and widely used method. In this retrospective report, iliac bone flaps of the ascending branch of the lateral circumflex femoral artery were used for the management of proximal femur bone defects.

Patients and Methods
The hospital information system and clinical data collected by surgeons were retrospectively reviewed. Patients with massive bone defects of the proximal femur reconstructed with iliac bone flaps of the ascending branch of the lateral circumflex femoral artery were included. Relevant data, including general information, perioperative treatment, and imaging data during follow-up, were retrieved for analysis. Five patients (4 males and 1 female) aged 18 to 42 years were included in this report. All patients were diagnosed with proximal femoral bone defects. The sizes of the bone defects ranged from 5 ×4 cm to 8 × 5 cm. Harris hip score was adopted to evaluate the functional outcomes. The adverse events were recorded. The mean follow-up time was 6.3 years.

Results
Iliac bone flaps of the ascending branch of the lateral circumflex femoral artery were transferred locally for the 5 patients. Bone flaps were fixed with plates in 4 cases and Kirschner wires in 1 case. The hospital stay was 12 to 27 days, with an average of 19.4 days. All cases achieved bony healing after 3 to 6 months postoperatively. The Harris hip scores ranged from 87 to 95 at final follow-up. All patients achieved good to excellent functional outcomes. One superficial infection occurred. No other adverse events or serious adverse events were noted.

Conclusions
Local transfer of iliac bone flaps of the ascending branch of the lateral circumflex femoral artery represents a safe and effective method for the reconstruction of massive bone defects of the proximal femur.
Comparing Prepectoral Versus Subpectoral Tissue Expander Placement Outcomes in Delayed-Immediate Autologous Breast Reconstruction
Authors: Patel Ashraf A. , Borrelli Mimi R. , Cai Lawrence , Moshrefi Shawn , Sando Ian C. , Lee Gordon K. , Nazerali Rahim S. 
Published: April 2020

Background
Delayed-immediate breast reconstruction has traditionally involved placement of tissue expanders (TE) in the subpectoral (SP) position. Development of acellular dermal matrices has renewed interest in the prepectoral (PP) pocket, which avoids extensive muscle manipulation. We compare complication rates between PP and SP TE placement in autologous delayed-immediate breast reconstruction.

Methods
A retrospective chart review of patients undergoing autologous, delayed-immediate breast reconstruction at our institution (June 2009 to December 2018) was performed. Demographics, comorbidities, perioperative information, and complication incidence ≤12 months' follow-up were collected from first- and second-stage surgeries. Complications were modeled using univariable and multivariable binary logistic regressions.

Results
A total of 89 patients met the inclusion criteria, and data from 125 breast reconstructions were evaluated. Complication rates following TE placement trended lower in the PP cohort (28.8% vs 37%, P = 0.34). Overall complication rates following autologous reconstruction were significantly lower for PP reconstructions (7.7% vs 23.3%, P = 0.02). Multivariable regression showed TE position (P = 0.01) was a significant predictor of ≥1 complication following autologous reconstruction. Time delay between first- and second-stage surgeries was greater for SP reconstructions (199.7 vs 324.8 days, P < 0.001). Postoperative drains were removed earlier in the PP cohort (8.6 vs 12.0 days, P < 0.001). Mean follow-up time was 331.3 days.

Conclusions
Prepectoral reconstruction in the delayed-immediate autologous reconstruction patient leads to significantly lower complication rates, shorter duration between first- and second-stage surgeries, and shorter times before removal of breast drains compared with SP reconstructions.
A systematic, unbiased mapping of CD8+and CD4+T cell epitopes in Yellow Fever vaccinees
Authors: Stryhn Anette , Kongsgaard Michael , Rasmussen Michael , Harndahl Mikkel Nors , Østerbye Thomas , Bassi Maria Rosaria , Thybo Søren , Gabriel Mette , Hansen Morten Bagge , Nielsen Morten , Christensen Jan Pravsgaard , Thomsen Allan Randrup , Buus Soren 
Published: April 2020

1.AbstractExamining CD8+and CD4+T cell responses after primary Yellow Fever vaccination in a cohort of 210 volunteers, we have identified and tetramer-validated 92 CD8+and 50 CD4+T cell epitopes, many inducing strong and prevalent (i.e. immunodominant) T cell responses. Restricted by 40 and 14 HLA-class I and II allotypes, respectively, these responses have wide population coverage and might be of considerable academic, diagnostic and therapeutic interest. The broad coverage of epitopes and HLA overcame the otherwise confounding effects of HLA diversity and non-HLA background providing the first evidence of T cell immunodomination in humans. Also, double-staining of CD4+T cells with tetramers representing the same HLA-binding core, albeit with different flanking regions, demonstrated an extensive diversification of the specificities of many CD4+T cell responses. We suggest that this could reduce the risk of pathogen escape, and that multi-tetramer staining is required to reveal the true magnitude and diversity of CD4+T cell responses. Our T cell epitope discovery approach uses a combination of 1) overlapping peptides representing the entire Yellow Fever virus proteome to search for peptides containing CD4+and/or CD8+T cell epitopes, 2) predictors of peptide-HLA binding to suggest epitopes and their restricting HLA allotypes, 3) generation of peptide-HLA tetramers to identify T cell epitopes, and 4) analysis ofex vivoT cell responses to validate the same. This approach is systematic, exhaustive, and can be done in any individual of any HLA haplotype. It is all-inclusive in the sense that it includes all protein antigens and peptide epitopes, and encompasses both CD4+and CD8+T cell epitopes. It is efficient and, importantly, reduces the false discovery rate. The unbiased nature of the T cell epitope discovery approach presented here should support the refinement of future peptide-HLA class I and II predictors and tetramer technologies, which eventually should cover all HLA class I and II isotypes. We believe that future investigations of emerging pathogens (e.g. SARS-CoV-2) should include population-wide T cell epitope discovery using blood samples from patients, convalescents and/or long-term survivors, who might all hold important information on T cell epitopes and responses.
Entraining movement-related brain oscillations using rhythmic median nerve stimulation
Authors: Maiquez Barbara Morera , Jackson Georgina M. , Jackson Stephen R. 
Published: April 2020

SummaryNon-invasive brain stimulation techniques delivered to cortical motor areas have been shown previously to: modulate cortical motor excitability; entrain brain oscillations; and influence motor behavior; and have therefore attracted considerable interest as potential therapeutic approaches targeted for the treatment of movement disorders. However, these techniques are most often not suitable for treatment outside of the clinic, or for use with young children. We therefore investigated directly whether rhythmic pulses of median nerve stimulation (MNS) could be used to entrain brain oscillations linked to the suppression of movement. Using electroencephalography techniques together with concurrent MNS we demonstrate that 10 pulses of rhythmic MNS, delivered at 19Hz, is sufficient to entrain Beta-band brain oscillations within the contralateral sensorimotor cortex, whereas 10-pulse trains of arrhythmic MNS does not. This approach has potential in our view to be developed into a non-drug therapeutic device suitable for use outside of the research laboratory or the clinic with brain health conditions associated by excessive movements.
Post-transcriptional regulation of human endogenous retroviruses by RNA-Binding Motif Protein 4, RBM4
Authors: Foroushani Amir K. , Chim Bryan , Wong Madeline , Rastegar Andre , Barbian Kent , Martens Craig , Hafner Markus , Muljo Stefan A. 
Published: April 2020

AbstractThe human genome encodes for over 1,500 RNA-binding proteins (RBPs), which coordinate regulatory events on RNA transcripts (Gerstbergeret al., 2014). Most studies of RBPs concentrate on their action on mRNAs that encode protein, which constitute a minority of the transcriptome. A widely neglected subset of our transcriptome derives from integrated retroviral elements termed endogenous retroviruses (ERVs) that comprise ~8% of the human genome. Some ERVs have been shown to be transcribed under physiological and pathological conditions suggesting that sophisticated regulatory mechanisms to coordinate and prevent their ectopic expression exist. However, it is unknown whether RBPs and ERV transcripts directly interact to provide a post-transcriptional layer of regulation. Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). We used PAR-CLIP to demonstrate that RBM4 indeed bound ERV transcripts at CGG consensus elements. Loss of RBM4 resulted in elevated transcript level of bound ERVs of the HERV-K and -H families, as well as increased expression of HERV-K envelope protein. We pinpointed RBM4 regulation of HERV-K to a CGG-containing element that is conserved in the long terminal repeats (LTRs) of HERV-K-10 and -K-11, and validated the functionality of this site using reporter assays. In summary, we identified RBPs as potential regulators of ERV function and demonstrate a new role for RBM4 in controlling ERV expression.Significance StatementThe expression of endogenous retroviruses (ERVs) appears to have broad impact on human biology. Nevertheless, only a handful of transcriptional regulators of ERV expression are known and to our knowledge no RNA-binding proteins (RBPs) were yet implicated in positive or negative post-transcriptional regulation of ERVs. We implemented a computational pipeline that allowed us to identify RBPs that modulate ERV expression levels. Experimental validation of one of the prime candidates we identified, RBM4, showed that it indeed bound RNAs made from ERVs and negatively regulated the levels of those RNAs. We hereby identify a new layer of ERV regulation by RBPs.
Covid-19 Outbreak Progression in Italian Regions: Approaching the Peak by March 29th
Authors: Distante Cosimo , Piscitelli Prisco , Miani Alessandro 
Published: April 2020

AbstractBackgroundItaly and especially the Lombardy region is experiencing a heavy burden of Covid-19 infection. The peak of the epidemics has not yet been reached and it is expected to be delayed in Central and Southern Italian regions compared to Northern ones. We have modeled the Covid-19 outbreak progression in Italian Regions vs. Lombardy.MethodsIn our models, we have estimated the basic reproduction number (R0) -which represents the average number of people that can be infected by a person who has already acquired the infection - both by fitting the exponential growth rate of the infection across a 1-month period and also by using day by day assessment, based on single observations. We used the susceptible–exposed–infected–removed (SEIR) compartment model to predict the spreading of the pandemic in Italy.ResultsThe two methods provide agreements of values, although the first method based on exponential fit should provide a better estimation, being computed on the entire time series. Taking into account the growth rate of the infection across a 1-month period, in Lombardy each infected person has involved other 5 people (4.94 base on data of March 22nd vs. 5.07 based on data of March 19th) compared to a value of R0 = 2.68 reported in the Chinese city of Whuan. According to our model and Piedmont, Veneto, Emilia Romagna, Tuscany and Marche reach an R0 value up to 4. The R0 is 3.7 for Lazio and 3.6 for Campania region, where this latter shows the highest value among the Southern Italian regions, followed by Apulia (3.5), Sicily (3.4), Abruzzo (3.4), Calabria (3.1), Basilicata (2.5) and Molise (2.4). The value of R0 is decreasing in Lombardy and Northern Regions, while it is increasing in Central and Southern Regions.ConclusionThe expected peak of SEIR model can be forecast by the last week of March at national level, and by the first weeks of April in Southern Italian Regions. These kind of models can be useful for adoption of all the possible preventive measures, and to assess the epidemics progression across Southern regions as opposed to the Northern ones.
Population based estimates of comorbidities affecting risk for complications from COVID-19 in the US
Authors: Adams Mary L. , Katz David L. , Grandpre Joseph 
Published: April 2020

AbstractWe used 2017 Behavioral Risk Factor Surveillance System (BRFSS) data (N=444,649) to estimate the proportion of US adults who report comorbidities that suggest heightened risk of complications from COVID-19. Co-morbidities included cardiovascular disease, chronic obstructive pulmonary disease (COPD), diabetes, asthma, hypertension, and/or cancer other than skin, based on data from China. Overall 45.4% (95% CI 45.1-45.7) of adults reported any of the 6 comorbidities, increasing from 19.8% (19.1-20.4) for ages 18-29 years to 80.7% (79.5-81.8) for ages 80+ years. State rates ranged from 37.3% (36.2-38.5) in Utah to 58.7% (57.0-60.4) in West Virginia. Rates also varied by race/ethnicity, health insurance status, and employment. Excluded were residents of nursing homes or assisted living facilities. Although almost certainly an underestimate of all adults at risk due to these exclusions, these results should help in estimating healthcare needs for adults with COVID-19 complications living in the community.Article Summary LineOverall, 45.4% of US adults were estimated to be at heightened risk of COVID-19 complications due to co-morbidities, increasing from 19.8% for ages 18-29 years to 80.7% for ages 80+ years, with state-to-state variation.
Growth rate and acceleration analysis of the COVID-19 pandemic reveals the effect of public health measures in real time
Authors: Utsunomiya Yuri Tani , Utsunomiya Adam Taiti Harth , Torrecilha Rafaela Beatriz Pintor , de Cássia Paula Silvana , Milanesi Marco , Garcia José Fernando 
Published: April 2020

ABSTRACTBackgroundEnding the COVID-19 pandemic is arguably one of the most prominent challenges in recent human history. Following closely the growth dynamics of the disease is one of the pillars towards achieving that goal.ObjectiveWe aimed at developing a simple framework to facilitate the analysis of the growth rate (cases/day) and growth acceleration (cases/day2) of COVID-19 cases in real-time.MethodsThe framework was built using the Moving Regression (MR) technique and a Hidden Markov Model (HMM). The dynamics of the pandemic was initially modeled via combinations of four different growth stages: lagging (beginning of the outbreak), exponential (rapid growth), deceleration (growth decay) and stationary (near zero growth). A fifth growth behavior, namely linear growth (constant growth above zero), was further introduced to add more flexibility to the framework. AnR Shinyapplication was developed, which can be accessed athttp://www.theguarani.com.br/covid-19or downloaded fromhttps://github.com/adamtaiti/SARS-CoV-2. The framework was applied to data from the European Center for Disease Prevention and Control (ECDC), which comprised 853,200 cases reported worldwide as of April 2nd2020.ResultsWe found that the impact of public health measures on the prevalence of COVID-19 could be perceived in seemingly real-time by monitoring growth acceleration curves. Restriction to human mobility produced detectable decline in growth acceleration within few days, deceleration within ∼2 weeks and near-stationary growth within ∼6 weeks. Countries exhibiting different permutations of the five growth stages indicated that the evolution of COVID-19 prevalence is more complex and dynamic than previously appreciated.ConclusionsThese results corroborate that mass social isolation is a highly effective measure against the dissemination of SARS-CoV-2, as previously suggested. Apart from the analysis of prevalence partitioned by country, the proposed framework is easily applicable to city, state, region and arbitrary territory data, serving as an asset to monitor the local behavior of COVID-19 cases.
Molecular Basis for ADP-ribose Binding to the Macro-X Domain of SARS-CoV-2 Nsp3
Authors: Frick David N. , Virdi Rajdeep S. , Vuksanovic Nemanja , Dahal Narayan , Silvaggi Nicholas R. 
Published: April 2020

ABSTRACTThe virus that causes COVID-19, SARS-CoV-2, has a large RNA genome that encodes numerous proteins that might be targets for antiviral drugs. Some of these proteins, such as the RNA-dependent RNA polymers, helicase and main protease, are well conserved between SARS-CoV-2 and the original SARS virus, but several others are not. This study examines one of the proteins encoded by SARS-CoV-2 that is most different, a macrodomain of nonstructural protein 3 (nsp3). Although 26% of the amino acids in this SARS-CoV-2 macrodomain differ from those seen in other coronaviruses, biochemical and structural data reveal that the protein retains the ability to bind ADP-ribose, which is an important characteristic of beta coronaviruses, and potential therapeutic target.