bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bus Operators’ Body Weight Changes During Their First 2 Years of Work
Authors: Olson Ryan , Rice Sean P.M. , Mansfield Layla R. , Wipfli Brad , Bodner Todd , Anger W. Kent , Bauer Talya N. 
Published: August 2021

Objective:
To empirically assess retrospective reports of weight changes during bus operators’ first years on the job, and to investigate experienced and desired training topics for new operators.

Methods:
Bus operators (n = 261) completed an online survey on topics of early weight changes and training experiences.

Results:
Operators reported gaining an average of 7.64 lb (SD = 16.36) during their first year. Further weight gain was not reported during the second year. Most operators reported that health-related topics were not addressed during their initial training. Stress management and healthy eating were the operators’ two most desired topics to be included in their initial training.

Conclusion:
Bus operators reported medically meaningful weight gain during their first year of work and a desire for more health-related training. Objective research to document the magnitude of this hazard, and contributing working conditions, is needed.
Characteristics of and Prognosis for Facial Palsy in Patients With Otitis Media With ANCA-Associated Vasculitis (OMAAV)
Authors: Fujiwara Keishi , Morita Shinya , Fukuda Atsushi , Yanagi Hiroko , Hoshino Kimiko , Nakamaru Yuji , Furuta Yasushi , Homma Akihiro 
Published: August 2021

Objectives:
The aim of the present study was to investigate the characteristics and prognosis of facial palsy in patients with otitis media with antineutrophil cytoplasmic antibody (ANCA)-associated vasculitis (OMAAV).

Study Design:
Retrospective case review.

Setting:
Tertiary referral center.

Patients:
Thirty-seven patients with OMAAV.

Main Outcome Measures:
The patients were divided into the facial palsy group and non-palsy group. The severity of and prognosis for facial palsy were evaluated using the House–Brackmann facial grading system (HB). Characteristics were compared between the facial palsy group and non-palsy group.

Results:
Facial palsy was observed in eight patients. The last HB grade for all patients was either grade I or II after treatment with a combination of corticosteroids and immunosuppressant therapy. There were no cases in which palsy relapsed. Facial palsy in OMAAV was significantly more common in female patients, and patients with facial palsy demonstrated significantly higher rates of hypertrophic pachymeningitis than did those without facial palsy.

Conclusions:
Facial palsy in patients with OMAAV was detected in 21.6% and a good prognosis was obtained by use of the appropriate treatment. Facial palsy is one of the most important symptoms by which to diagnose OMAAV. When encountering the patients with intractable otitis media complicated with facial palsy, appropriate examination including ANCA titer should be performed.
Access to liver transplantation for minority populations in the United States
Authors: McClinton Aneesah , Gullo Joy , Martins Paulo N. , Serrano Oscar K. 
Published: August 2021

Purpose of review
Racial disparities in access to liver transplantation have been known since the National Transplant Act of 1980. Since the inception of the Final Rule in 2000, the United Network of Organ Sharing has sought to ensure the equitable distribution of donor livers. Despite several measures aimed to improve access for vulnerable populations, disparities in outcomes are still prevalent throughout the liver transplant (LT) evaluation, while on the waitlist, and after liver transplantation.

Recent findings
Blacks and Hispanics are underrepresented on the LT list and have an increased waitlist mortality rate compared to Whites. Additionally, Blacks have a significantly higher risk of posttransplant mortality.

Summary
Ongoing efforts are necessary to eliminate inequities in transplant access. Strategies such as policy implementation and increasing diversity in the healthcare workforce may prove efficacious in creating change.
The Impact of Neoadjuvant Treatment on Survival in Patients Undergoing Pancreatoduodenectomy With Concomitant Portomesenteric Venous Resection: An International Multicenter Analysis
Authors: Machairas Nikolaos , Raptis Dimitri A , Velázquez Patricia Sánchez , Sauvanet Alain , Rueda de Leon Alexandra , Oba Atsushi , Koerkamp Bas Groot , Lovasik Brendan , Chan Carlos , Yeo Charles J. , Bassi Claudio , Ferrone Cristina R. , Kooby David , Moskal David , Tamburrino Domenico , Yoon Dong-Sup , Barroso Eduardo , de Santibañes Eduardo , Kauffmann Emanuele F. , Vigia Emanuel , Robin Fabien , Casciani Fabio , Burdío Fernando , Belfiori Giulio , Malleo Giuseppe , Lavu Harish , Hartog Hermien , Hwang Ho-Kyoung , Han Ho-Seong , Marques Hugo P. , Poves Ignasi , Domínguez-Rosado Ismael , Park Joon-Seong , Lillemoe Keith D. , Roberts Keith , Sulpice Laurent , Besselink Marc G. , Abuawwad Mahmoud , Del Chiaro Marco , de Santibañes Martin , Falconi Massimo , D'Silva Mizelle , Silva Michael , Hilal Mohammed Abu , Qadan Motaz , Sell Naomi M. , Beghdadi Nassiba , Napoli Niccolò , Busch Olivier R. C. , Mazza Oscar , Muiesan Paolo , Müller Philip C. , Ravikumar Reena , Schulick Richard , Powell-Brett Sarah , Abbas Syed Hussain , Mackay Tara M. , Stoop Thomas F. , Gallagher Tom K. , Boggi Ugo , van Eijck Casper , Clavien Pierre-Alain , Conlon Kevin C. P. , Fusai Giuseppe Kito 
Published: August 2021

Objective:
The aim of this study was to evaluate whether neoadjuvant therapy (NAT) critically influenced microscopically complete resection (R0) rates and long-term outcomes for patients with pancreatic ductal adenocarcinoma who underwent pancreatoduodenectomy (PD) with portomesenteric vein resection (PVR) from a diverse, world-wide group of high-volume centers.

Summary of Background Data:
Limited size studies suggest that NAT improves R0 rates and overall survival compared to upfront surgery in R/BR-PDAC patients.

Methods:
This multicenter study analyzed consecutive patients with R/BR-PDAC who underwent PD with PVR in 23 high-volume centers from 2009 to 2018.

Results:
Data from 1192 patients with PD and PVR were collected and analyzed. The median age was 68 [interquartile range (IQR) 60-73] years and 52% were males. Some 186 (15.6%) and 131 (10.9%) patients received neoadjuvant chemotherapy (NAC) alone and neoadjuvant chemoradiotherapy, respectively. The R0/R1/R2 rates were 57%, 39.3%, and 3.2% in patients who received NAT compared to 46.6%, 49.9%, and 3.5% in patients who did not, respectively (P =0.004). The 1-, 3-, and 5-year OS in patients receiving NAT was 79%, 41%, and 29%, while for those that did not it was 73%, 29%, and 18%, respectively (P <0.001). Multivariable analysis showed no administration of NAT, high tumor grade, lymphovascular invasion, R1/R2 resection, no adjuvant chemotherapy, occurrence of Clavien-Dindo grade 3 or higher postoperative complications within 90 days, preoperative diabetes mellitus, male sex and portal vein involvement were negative independent predictive factors for OS.

Conclusion:
Patients with PDAC of the pancreatic head expected to undergo venous reconstruction should routinely be considered for NAT.
UNOS/OPTN Data-guided Assessment of Focal Segmental Glomerulosclerosis After Kidney Transplantation and Evaluation of Immunosuppressive Protocols in a Steroid-free Center
Authors: Kurian Sunil M. , Spierling Bagsic Samantha R. , Case Jamie , Barrick Bethany L. , Schaffer Randolph , Rice James C. , Marsh Christopher L. 
Published: August 2021

Background.
Focal segmental glomerulosclerosis (FSGS) is a common recurrent glomerulopathy associated with graft loss and patient survival after kidney transplantation (KT). However, its natural history, clinical predictors, and treatment response are still poorly understood. Steroid withdrawal regimens in KT have been associated with improvements in cardiovascular risk and patient outcomes. The Scripps Center for Organ Transplantation (SCOT) uses a rapid low-dose steroid withdrawal immunosuppression (IS) protocol for KT maintenance.

Methods.
We assessed the impact of our protocol on FSGS disease recurrence over a 10-y period to reassess our steroid and IS protocols and to evaluate if our patient outcomes diverge from published data. We compared 4 groups: steroids always, steroid free, steroid switch on, and steroid weaned off. We used IS and induction-matched retrospective data from United Network for Organ Sharing (UNOS) to investigate patient and graft survival for FSGS at SCOT.

Results.
Our analysis results differ from earlier studies showing that FSGS was associated with a higher risk of graft loss, perhaps because of selection of a UNOS data set filtered to match the SCOT IS protocol for making direct comparisons. Overall outcomes of graft failure and recipient death did not differ between SCOT patients and steroid-free transplant patient data from the UNOS data for FSGS. SCOT recurrence rate for FSGS was 7.5%, which was lower than in most published single-center studies.

Conclusions.
Based on our results, we believe that it is safe to continue the steroid avoidance protocols at SCOT and the steroid-free protocol may not be detrimental when the adverse effects and toxicities associated with steroid use are considered.
Data-driven Testing Program Improves Detection of COVID-19 Cases and Reduces Community Transmission
Authors: Krieg Steven J. , Avendano Carolina , Grantham-Brown Evan , Asbun Aaron Lilienfeld , Schnur Jennifer J. , Miranda Marie Lynn , Chawla Nitesh V. 
Published: August 2021

AbstractCOVID-19 remains a global threat in the face of emerging SARS-CoV-2 variants and gaps in vaccine administration and availability, and organizations must be prepared to detect and mitigate its risk to their people and activities. In this report we share key lessons learned from an adaptive COVID-19 testing program implemented at a mid-sized university in the Midwest. The program utilized two simple, diverse, and easily interpretable machine learning models to quickly and accurately predict which students were at elevated risk for contracting COVID-19 and should be called proactively for testing. Our adaptive testing cohorts produced positivity rates that were 26% higher than the random cohort: 0.58% positivity (95% CI 0.47% to 0.68%) from 19,171 tests, and 0.46% positivity (95% CI 0.41% to 0.51%) from 64,003 tests, respectively. Within 14 days of their selection, 2.94% of the adaptive cohort tested positive, compared to 1.27% of the random cohort. Close contacts who were predicted by the adaptive testing models received a COVID-19 test within an average of 0.94 days (95% CI 0.78 to 1.11) of the source testing positive, while those who were manually contact traced were tested in an average of 1.92 days (95% CI 1.81 to 2.02). These results suggest that machine learning strategies can improve surveillance testing effectiveness, especially in a university setting, by effectively distributing testing resources and potentially reducing community transmission.
Dynamics of COVID-19 pandemic in India and Pakistan: A metapopulation modelling approach
Authors: Brozak Samantha J. , Pant Binod , Safdar Salman , Gumel Abba B. 
Published: August 2021

AbstractIndia has been the latest global epicenter for COVID-19, a novel coronavirus disease that emerged in China in late 2019. We present a base mathematical model for the transmission dynamics of COVID-19 in India and its neighbour, Pakistan. The base model, which takes the form of a deterministic system of nonlinear differential equations, is parameterized using cumulative COVID-19 mortality data from each of the two countries. The model was used to assess the population-level impact of the control and mitigation strategies implemented in the two countries (notably community lockdowns, use of face masks, and social-distancing). Numerical simulations of the basic model indicate that, based on the current baseline levels of the control and mitigation strategies implemented, the pandemic trajectory in India is on a downward trend (as characterized by the reproduction number of the disease dynamics in India below, but close to, unity). This downward trend will be reversed, and India will be recording mild outbreaks (i.e., pandemic waves), if the control and mitigation strategies are relaxed from their current levels (e.g., relaxed to the extent that the associated community transmission parameters are increased by 20% or 40% from their current baseline values). Our simulations suggest that India could record up to 460,000 cumulative deaths by early September 2021 under the baseline levels of the control strategies implemented (up to 25,000 of the projected deaths could be averted if the control and mitigation measures are strengthened to the extent that the associated community transmission parameters are reduced by 20% from their baseline values). Our simulations show that the pandemic in Pakistan is much milder, with an estimated projected cumulative mortality of about 24,000 by early September 2021 under the baseline scenario. The basic model was extended to assess the impact of back-and-forth mobility between the two countries. Simulations of the resulting metapopulation model show that the burden of the COVID-19 pandemic in Pakistan increases with increasing values of the average time residents of India spend in Pakistan. In particular, it is shown that the India- to-Pakistan mobility pattern may trigger a fourth wave of the pandemic in Pakistan (under certain mobility scenarios), with daily mortality peaking in mid-August to mid-September of 2021. Under the respective baseline control scenarios, our simulations show that the back-and-forth mobility between India and Pakistan could delay the time-to-elimination of the COVID-19 pandemic in the two countries by three to five months (specifically, under the respective baseline scenarios, elimination could be delayed in India and Pakistan to November 2022 and July 2022, respectively).
Deep Learning of Left Atrial Structure and Function Provides Link to Atrial Fibrillation Risk
Authors: Pirruccello James P. , Di Achille Paolo , Choi Seung Hoan , Khurshid Shaan , Nekoui Mahan , Jurgens Sean J. , Nauffal Victor , Ng Kenney , Friedman Samuel F. , Lunetta Kathryn L. , Philippakis Anthony A. , Ho Jennifer E. , Lubitz Steven A. , Ellinor Patrick T. 
Published: August 2021

AbstractAimsIncreased left atrial (LA) volume is a known risk factor for atrial fibrillation (AF). There is also emerging evidence that alterations in LA function due to an atrial cardiomyopathy are associated with an increased risk of AF. The availability of large-scale cardiac MRI data paired with genetic data provides a unique opportunity to assess the joint genetic contributions of LA structure and function to AF risk.Methods and resultsWe developed deep learning models to measure LA traits from cardiovascular magnetic resonance imaging (MRI) in 40,558 UK Biobank participants and integrated these data to estimate LA minimum (LAmin), maximum (LAmax), and stroke volume (LASV), as well as emptying fraction (LAEF). We conducted a genome-wide association study (GWAS) in 35,049 participants without pre-existing cardiovascular disease, identifying 20 common genetic loci associated with LA traits. Eight of the loci associated with LA traits were previously associated with AF: the AF risk alleles were associated with an increased LA minimum volume (LAmin) and a decreased LAEF. A Mendelian randomization analysis confirmed that AF causally affects LA volume (IVW P = 6.2E-06), and provided evidence that LAmin causally affects AF risk (IVW P = 4.7E-05). In UK Biobank participants, a polygenic prediction of LAmin was significantly associated with risk for AF (HR 1.09 per SD; P = 1.6E-36) and ischemic stroke (HR 1.04 per SD; P = 4.7E-03).ConclusionsWe performed the largest and highest resolution assessment of LA structure and function to date. We then identified 20 common genetic variants associated with LA volumes or LAEF, 19 of which were novel. We found that a polygenic prediction of the minimal LA volume was associated with AF and stroke. Finally, we found an inverse relation between genetic variants associated with AF risk and LAEF. Our findings provide evidence of a causal relation between LA contractile function and AF.
Sensitive and multiplexed RNA detection with Cas13 droplets and kinetic barcoding
Authors: Son Sungmin , Lyden Amy , Shu Jeffrey , Stephens Stephanie I. , Fozouni Parinaz , Knott Gavin J. , Smock Dylan C. J. , Liu Tina Y. , Boehm Daniela , Simoneau Camille , Kumar G. Renuka , Doudna Jennifer A. , Ott Melanie , Fletcher Daniel A. 
Published: August 2021

SUMMARYRapid and sensitive quantification of RNA is critical for detecting infectious diseases and identifying disease biomarkers. Recent direct detection assays based on CRISPR-Cas13a1–4 avoid reverse transcription and DNA amplification required of gold-standard PCR assays5, but these assays have not yet achieved the sensitivity of PCR and are not easily multiplexed to detect multiple viruses or variants. Here we show that Cas13a acting on single target RNAs loaded into droplets exhibits stochastic nuclease activity that can be used to enable sensitive, rapid, and multiplexed virus quantification. Using SARS-CoV-2 RNA as the target and combinations of CRISPR RNA (crRNA) that recognize different parts of the viral genome, we demonstrate that reactions confined to small volumes can rapidly achieve PCR-level sensitivity. By tracking nuclease activity within individual droplets over time, we find that Cas13a exhibits rich kinetic behavior that depends on both the target RNA and crRNA. We demonstrate that these kinetic signatures can be harnessed to differentiate between different human coronavirus species as well as SARS-CoV-2 variants within a single droplet. The combination of high sensitivity, short reaction times, and multiplexing makes this droplet-based Cas13a assay with kinetic barcoding a promising strategy for direct RNA identification and quantification.
Quantitative SARS-CoV-2 tracking of variants Delta, Delta plus, Kappa and Beta in wastewater by allele-specific RT-qPCR
Authors: Lee Wei Lin , Gu Xiaoqiong , Armas Federica , Chandra Franciscus , Chen Hongjie , Wu Fuqing , Leifels Mats , Xiao Amy , Desmond Chua Feng Jun , Kwok Germaine WC , Jolly Shreshtha , Lim Claire YJ , Thompson Janelle , Alm Eric J 
Published: August 2021

ABSTRACTThe Delta (B.1.617.2) variant has caused major devastation in India and other countries around the world. First detected in October 2020, it has now spread to more than 100 countries, prompting WHO to declare it as a global variant of concern (VOC). The Delta (B.1.617.2), Delta plus (B.1.617.2.1) and Kappa (B.1.617.1) variants are all sub-lineages of the original B.1.617 variant. Prior to the inception of B.1.617, vaccine rollout, safe-distancing and timely lockdowns greatly reduced COVID-19 hospitalizations and deaths. However, the Delta variant, allegedly more infectious and for which existing vaccines seemed less effective, has catalyzed the resurgence of cases. Therefore, there is an imperative need for increased surveillance of the B.1.617 variants. While the Beta variant is increasingly outpaced by the Delta variant, the spread of the Beta variant remains of concern due to its vaccine resistance. Efforts have been made to utilize wastewater-based surveillance for community-based tracking of SARS-CoV-2 variants, however wastewater with its low SARS-CoV-2 viral titers and mixtures of viral variants, requires assays to be variant-specific yet accurately quantitative for meaningful interpretation. Following on the design principles of our previous assays for the Alpha variant, here we report allele-specific and multiplex-compatible RT-qPCR assays targeting mutations T19R, D80A, K417N, T478K and E484Q, for quantitative detection and discrimination of the Delta, Delta plus, Kappa and Beta variants in wastewater. This method is open-sourced and can be implemented using commercially available RT-qPCR protocols, and would be an important tool for tracking the spread of B.1.617 and the Beta variants in communities.
Localization of T cell clonotypes using spatial transcriptomics
Authors: Hudson William H. , Sudmeier Lisa J. 
Published: August 2021

AbstractSpatial transcriptomics is an emerging technology that measures gene expression while preserving spatial information. Here, we present a method to determine localization of specific T cell clones by obtaining T cell receptor (TCR) sequences from spatial transcriptomics assays. Our method uses an existing commercial spatial transcriptomics platform and open-source software for analysis, allowing simple and inexpensive integration with archived samples and existing laboratory workflows. Using human brain metastasis samples, we show that TCR sequences are readily obtained from human tumor tissue and that these sequences are recapitulated by single-cell sequencing methods. This technique will permit detailed studies of the spatial organization of the human T cell repertoire, such as the identification of tumor-infiltrating and tumor-excluded T cell clones.
Quantitative phase velocimetry measures bulk intracellular transport of cell mass during the cell cycle
Authors: Pradeep Soorya , Zangle Thomas A. 
Published: August 2021

ABSTRACTTransport of mass within cells helps maintain homeostasis and is disrupted by disease and stress. Here, we develop quantitative phase velocimetry (QPV) as a label-free approach to make the invisible flow of mass within cells visible and quantifiable. We benchmark our approach against alternative image registration methods, a theoretical error model, and synthetic data. Our method tracks not just individual labeled particles or molecules, but the entire flow of bulk material through the cell. This enables us to measure diffusivity within distinct cell compartments using a single approach, which we use here for direct comparison of nuclear and cytoplasmic diffusivity. As a label-free method, QPV can be used for long-term tracking to capture dynamics through the cell cycle.
rRNA Biogenesis Regulates Mouse 2C-like State by 3D Structure Reorganization of Peri-Nucleolar Heterochromatin
Authors: Yu Hua , Sun Zhen , Tan Tianyu , Pan Hongru , Zhao Jing , Zhang Ling , Chen Jiayu , Lei Anhua , Zhu Yuqing , Chen Lang , Xu Yuyan , Chen Ming , Gao Shaorong , Daley George Q. , Zhang Jin 
Published: August 2021

AbstractNucleolus is the organelle for ribosome biogenesis and for sensing various types of stress. Its role in regulating stem cell fate is unclear. Here, we present multiple lines of evidence that nucleolar stress induced by interfering rRNA biogenesis can drive 2-cell stage embryo-like (2C-like) transcriptional program and induce an expanded 2C-like cell population in mouse embryonic stem (mES) cells. Mechanistically, the nucleolar integrity mediated by rRNA biogenesis maintains the normal liquid-liquid phase separation (LLPS) of nucleolus and the formation of peri-nucleolar heterochromatin (PNH). Upon rRNA biogenesis defect, the natural LLPS of nucleolus is disrupted, causing dissociation of NCL/TRIM28 complex from PNH and changes of epigenetic states and reorganization of the 3D structure of PNH, which leads to Dux, a 2C program transcription factor gene, to be released from the PNH region and activation of 2C-like program. Correspondingly, embryos with rRNA biogenesis defect are incompatible to develop from 2-cell (2C) to 4-cell embryos, with delayed repression of 2C/ERV genes and a transcriptome skewed toward earlier cleavage embryo signatures. Our results highlight that rRNA-mediated nucleolar integrity and 3D structure reshaping of PNH compartment regulates the fate transition of mES cells to 2C-like cells, and that rRNA biogenesis is a critical regulator during the 2-cell-to-4-cell transition of murine pre-implantation embryo development.