bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of Prochloraz Resistance in Fusarium fujikuroi from Heilongjiang Province in China
Authors: Peng Qin , Waqas Younas Muhammad , Yang Jikun , Zhu Hongwei , Miao Jianqiang , Gu Biao , Liu Xili
Published: August 2021

Prochloraz is widely used to control rice bakanae disease caused by Fusarium fujikuroi. The current study was aimed at monitoring the development of F. fujikuroi resistance to prochloraz in the Heilongjiang Province and analyzing the fitness of F. fujikuroi strains with different resistance levels. The results indicated that most of the 89 F. fujikuroi strains collected from the Heilongjiang Province were resistant to prochloraz, with resistance frequency reaching 92.1%. To assess the field resistance risk of prochloraz, 21 F. fujikuroi strains with different resistance levels were selected to investigate their biological characteristics and assess their fitness. Mycelial growth, sporulation, and germination rates were significantly different among the tested strains. However, when grouped into two subpopulations, no significant difference was tested between prochloraz-resistant and prochloraz-sensitive strains. Pathogenicity assays revealed that the disease severity index of prochloraz-resistant strains was higher than that of prochloraz-sensitive strains. Cross-resistance assays showed no cross-resistance between prochloraz and five other fungicides, namely phenamacril, ipconazole, tebuconazole, carbendazim, and fluopyram. Ffcyp51A gene overexpression was observed in the prochloraz-resistant F. fujikuroi strains after exposure to prochloraz. Collectively, these results indicated that F. fujikuroi resistance against prochloraz was severe. Furthermore, prochloraz-resistant strains were highly fit and could potentially become a dominant population in rice fields, consequently resulting in yield loss.
Effect of Intensive Glucose Control on Outcomes of Hyperglycemic Stroke Patients Receiving Mechanical Thrombectomy: Secondary Analysis of the SHINE Trial
Authors: Asaithambi Ganesh , Tipps Megan E.
Published: August 2021

Background:

Hyperglycemia is common among patients presenting with acute ischemic stroke (AIS) and is associated with poor clinical outcomes. We studied the effects of intensive blood glucose control among AIS patients presenting with hyperglycemia treated with mechanical thrombectomy (MT).

Methods:

We analyzed publicly available data from the Stroke Hyperglycemia Insulin Network Effort trial. In this nonpreplanned secondary analysis, we compared hyperglycemic AIS patients treated with MT who received intensive blood glucose control (80 to 130 mg/dL) with those who received standard blood glucose control (80 to 179 mg/dL). Outcomes included rates of favorable 90-day outcome (modified Rankin Scale score ≤2) and death.

Results:

This analysis included 146 patients (74 in the intensive treatment group and 72 in the standard treatment group). Intensive blood glucose was not associated with higher rates of 90-day favorable outcomes (intensive 31.1% vs. standard 30.6%, P=1.0; odds ratio 1.025, 95% confidence interval 0.51 to 2.07) or a decrease in rates of death (intensive 20.3% vs. standard 22.2%, P=0.84; odds ratio 0.98, 95% confidence interval 0.40 to 1.97).

Conclusions:

Intensive blood glucose control among AIS patients presenting with hyperglycemia and treated with MT was not associated with lower rates of death or higher rates of long-term favorable outcomes when compared with standard treatment.
Interaction Between Chronic Bronchitis and Blood Cadmium Levels on the Prevalence of Myocardial Infarction in US Adults
Authors: Ibrahimou Boubakari , Sun Ning , Azim Syeda Ishra , Aliyu Muktar H. , Guilarte Tomas R.
Published: August 2021

Objective:

To explore the interaction between chronic bronchitis and blood cadmium on the prevalence of myocardial infarction.

Methods:

We used weighted US-NHANES data. Multivariate survey logistic regression was used to examine the associations between myocardial infarction, cadmium concentration and chronic bronchitis. Adjusted odds ratios, 95% confidence intervals were computed.

Results:

There was a significant interaction (OR=1.33, CI = [1.01, 1.74]) between chronic bronchitis and blood cadmium level on the presence of myocardial infarction. For 1 μg/L increase in cadmium level, people with chronic bronchitis had 1.65 (1.24 × 1.33) times the odds of having myocardial infarction, while those without chronic bronchitis would be only 1.24 times as likely having the outcome (OR = 1.24, CI = [1.05, 1.46]).

Conclusion:

Findings highlights the role of chronic bronchitis on the relationship between blood cadmium concentration and myocardial infarction. Prospective cohort designs are needed to confirm these findings.
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.

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.
Papillary Renal Neoplasm With Reverse Polarity Is Often Cystic
Authors: Wei Shuanzeng , Kutikov Alexander , Patchefsky Arthur S. , Flieder Douglas B. , Talarchek Jacqueline N. , Al-Saleem Tahseen , Dulaimi Essel , Uzzo Robert G. , Testa Joseph R. , Pei Jianming
Published: August 2021

Papillary renal neoplasm with reverse polarity (PRNRP) is a newly proposed entity with distinct histology and frequent KRAS mutations. To date, 93 cases of PRNRPs have been reported. In this study, we present 7 new cases of PRNRP and review the literature. Most of the pathologic features in our 7 cases are similar to those previously reported cases. However, all 7 of our cases showed at least partial cystic changes, which was not stressed in prior studies. Single-nucleotide polymorphism–microarray based chromosomal analysis demonstrated no trisomy or other alteration of chromosomes 7 or 17; and no loss or other alteration of chromosome Y was detected in all 7 cases. Next-generation sequencing detected KRAS missense mutations in 4 of 7 cases. No fusion genes were detected. In summary, PRNRP is a small, well-circumscribed often encapsulated and cystic neoplasm with loose papillary formations. Cuboidal tumor cells always have eosinophilic cytoplasm and nuclei located at the pole opposite the basement membrane with a low World Health Organization (WHO)/International Society of Urologic Pathologists (ISUP) nuclear grade. The fibrovascular cores can be hyalinized or edematous. Macrophage aggregates and intracellular hemosiderin are uncommon, and no psammoma bodies or necrosis should be seen. Immunophenotypically, this tumor is always positive for CK7 and GATA3, and negative for CD117 and vimentin. CD10 and AMACR can be positive, but often weakly and focally. PRNRP often has KRAS mutations, however, only 32% of cases have chromosomal abnormalities in chromosomes 7, 17, and Y. No recurrences, metastases, or tumor-related deaths have been reported following complete resection.
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

Abstract

COVID-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

India 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

Aims

Increased 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 results

We 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).

Conclusions

We 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

Rapid 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

The 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

Spatial 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

Transport 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

Nucleolus 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.
A Bayesian Analysis of Steady–State Enzyme Data leads to Estimates of Rate Constants and Uncertainties in a Multi-Step Reaction, along with Free Energy Profiles†
Authors: Barr Ian
Published: August 2021

The microscopic rate constants that govern an enzymatic reaction are only directly measured under certain experimental set-ups, such as stopped flow, quenched flow, or temperaturejump assays; the majority of enzymology proceeds from steady state conditions which leads to a set of more easily–observable parameters such askcat,KM, and observed Kinetic Isotope Effects. This paper further develops a model from Toney (2013) to estimate microscopic rate constants from steady-state data for a set of reversible, four–step reactions. This paper uses the Bayesian modeling software Stan, and demonstrates the benefits of Bayesian data analysis in the estimation of these rate constants. In contrast to the optimization methods employed often in the estimation of kinetic constants, a Bayesian treatment is more equipped to estimate the uncertainties of each parameter; sampling from the posterior distribution using Hamiltonian Monte Carlo immediately gives parameter estimates as mean or median of the posterior, and also confidence intervals that express the uncertainty of each parameter.
Response to nitrogen and salinity in Rhizophora mangle propagules varies by maternal family and population of origin
Authors: Richards Christina L. , Langanke Kristen L. , Mounger Jeannie , Fox Gordon A. , Lewis David B.
Published: August 2021

Many coastal foundation plant species thrive across a range of environmental conditions, often displaying dramatic phenotypic variation in response to environmental variation. We characterized the response of propagules from six populations of the foundation species Rhizophora mangle L. to full factorial combinations of two levels of salt (15 ppt and 45 ppt) reflecting the range of salinity measured in the field populations, and two levels of nitrogen (N; no addition and amended at approximately 3 mg N per pot each week) equivalent to comparing ambient N to a rate of addition of 75 kg per hectare per year. The response to increasing salt included significant plasticity in succulence. Propagules also showed plasticity in maximum photosynthetic rate in response to N amendment, but the responses depended on the level of salt and varied by population of origin. Generally, survival was lower in high salt and high N, but the impact varied among populations. Overall, this study revealed significant phenotypic plasticity in response to salt and N level. Propagules from different populations differed in all traits measured. Variation in phenotypic plasticity and propagule survival in R. mangle may contribute to adaptation to a complex mosaic of environmental conditions and response to climate change.
GEPSi: A Python Library to Simulate GWAS Phenotype Data
Authors: Reidenbach Daniel A. , Lal Avantika , Slim Lotfi , Mosafi Ohad , Israeli Johnny
Published: August 2021

Motivation

Many computational methods aim to identify genetic variants associated with diseases and complex traits. Due to the absence of ground truth data, simulated genotype and phenotype data is needed to benchmark these methods. However, phenotypes are frequently simulated as an additive function of randomly selected variants, neglecting biological complexity such as non-random occurrence of causal SNPs, epistatic effects, heritability and dominance. Including such features would improve benchmarking studies and accelerate the development of methods for genetic analysis.

Results

Here, we describe GEPSi (GWAS Epistatic Phenotype Simulator), a user-friendly python package to simulate phenotype data based on user-supplied genotype data for a population. GEPSi incorporates diverse biological parameters such as heritability, dominance, population stratification and epistatic interactions between SNPs. We demonstrate the use of this package to compare machine learning methods for GWAS analysis.

Availability and Implementation

GEPSi is freely available under an Apache 2.0 license, and can be downloaded from https://github.com/clara-parabricks/GEPSi.

Supplementary information

Supplementary data are available online.
Sex-dependent development of Kras-induced anal squamous cell carcinoma in mice
Authors: Walcheck Morgan T. , Matkowskyj Kristina A. , Turco Anne , Blaine-Sauer Simon , Nukaya Manabu , Noel Jessica , Ronnekleiv Oline K. , Ronnekleiv-Kelly Sean M.
Published: August 2021

Anal squamous cell carcinoma (SCC) will be diagnosed in an estimated 9,080 adults in the United States this year, and rates have been rising over the last several decades. Most people that develop anal SCC have associated human papillomavirus (HPV) infection (∼85-95%), with approximately 5-15% of anal SCC cases occurring in HPV-negative patients from unknown etiology. This study identified and characterized a Kras-driven, female sex hormone-dependent development of anal squamous cell carcinoma (SCC) in the LSL-KrasG12D ; Pdx1-Cre (KC) mouse model that is not dependent on papillomavirus infection. One hundred percent of female KC mice develop anal SCC, while no male KC mice develop tumors. Both male and female KC anal tissue express Pdx1 and Cre-recombinase mRNA, and the activated mutant KrasG12D gene. Although the driver gene mutation KrasG12D is present in anus of both sexes, only female KC mice develop Kras-mutant induced anal SCC. To understand the sex-dependent differences, KC male mice were castrated and KC female mice were ovariectomized. Castrated KC males displayed an unchanged phenotype with no anal tumor formation. In contrast, ovariectomized KC females demonstrated a marked reduction in anal SCC development, with only 15% developing anal SCC. Finally, exogenous administration of estrogen rescued the tumor development in ovariectomized KC female mice and induced tumor development in castrated KC males. These results confirm that the anal SCC is estrogen mediated. The delineation of the role of female sex hormones in mediating mutant Kras to drive anal SCC pathogenesis highlights a subtype of anal SCC that is independent of papillomavirus infection. These findings may have clinical applicability for the papillomavirus-negative subset of anal SCC patients that typically respond poorly to standard of care chemoradiation.
Gadolinium-free Magnetic Resonance Imaging of the Liver using an Oatp1-targeted Manganese(III) Porphyrin
Authors: Nyström Nivin N. , Liu Hanlin , Martinez Francisco M. , Zhang Xiao-an , Scholl Timothy J. , Ronald John A.
Published: August 2021

Controversy surrounding gadolinium-based contrast agents (GBCAs) have rendered their continued utility highly contentious, but the liver-specific GBCA Gd(III) ethoxybenzyl-diethylene triamine pentaacetic acid (Gd(III)-EOB-DTPA) remains in use because it provides unique diagnostic information that could not be obtained by any other means. To address the need for an alternative liver-specific MRI contrast agent, we synthesized Mn(III) 20-(4-ethoxyphenyl) porphyrin-5,10,15-tricarboxylate (Mn(III)TriCP-PhOEt), which exhibited significantly higher r1 relaxivity than Gd(III)-EOB-DTPA, and targeted organic anion-transporting polypeptide 1 (Oatp1) channels as a biomarker of hepatocyte viability. Mn(III)TriCP-PhoEt increased the r1 relaxation rate of cells expressing rodent Oatp1a1 and human Oatp1b3, relative to control cells not expressing these liver channels. In mice, Mn(III)TriCP-PhoEt resulted in significant and specific increases in liver signal intensity on T1-weighted images, and significant decreases in liver T1 time relative to precontrast measurements. Our findings suggest that Mn(III)TriCP-PhOEt operates as a specific and sensitive MR contrast agent for in vivo liver imaging.
Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region
Authors: Turkahia Yatish , Thornlow Bryan , Hinrichs Angie , McBroome Jakob , Ayala Nicolas , Ye Cheng , De Maio Nicola , Haussler David , Lanfear Robert , Corbett-Detig Russell
Published: August 2021

Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses. During the SARS-CoV-2 pandemic, genomic data generation has exceeded the capacities of existing analysis platforms, thereby crippling real-time analysis of viral recombination. Low SARS-CoV-2 mutation rates make detecting recombination difficult. Here, we develop and apply a novel phylogenomic method to exhaustively search a nearly comprehensive SARS-CoV-2 phylogeny for recombinant lineages. We investigate a 1.6M sample tree, and identify 606 recombination events. Approximately 2.7% of sequenced SARS-CoV-2 genomes have recombinant ancestry. Recombination breakpoints occur disproportionately in the Spike protein region. Our method empowers comprehensive real time tracking of viral recombination during the SARS-CoV-2 pandemic and beyond.
Virucidal activity of CPC-containing oral rinses against SARS-CoV-2 variants and are active in the presence of human saliva
Authors: Anderson Enyia R , Patterson Edward I , Richards Siobhan , Green Alison , Mukherjee Sayandip , Hoptroff Michael , Hughes Grant L
Published: August 2021

The role of human saliva in aerosol-based transmission of SARS-CoV-2 has highlighted the need to understand the potential of oral hygiene products to inactivate the virus. Here we examined the efficacy of mouthwashes containing cetylpyridinium chloride (CPC) or chlorhexidine (CHX) in inactivating SARS-CoV-2. After 30 seconds contact under standard aqueous conditions CPC mouthwashes achieved a ≥4.0log10PFU/mL reduction in SARS-CoV-2 (USA-WA1/2020) titres whereas comparable products containing CHX achieved <2.0log10PFU/mL reduction. Further testing with CPC mouthwashes demonstrated efficacy against multiple SARS-CoV-2 variants, with inactivation below the limit of detection observed against the Alpha (B.1.1.7), Beta (B.1.351) and Gamma (P.1) variants. Virucidal efficacy of CPC mouthwash was also observed in the presence of human saliva with the product delivering ≥4.0log10PFU/mL reduction in SARS-CoV-2 titres after 30 seconds providing additional evidence for the virucidal efficacy of CPC mouthwashes under simulated physiological conditions. Together these data suggest CPC-based mouthwashes are effective at inactivating SARS-CoV-2 and further supports the use of mouthwash to mitigate the risk of transmission during dentistry procedures.
Th1/17 Cells Infiltrate Murine Cytomegalovirus-Infected Renal Allografts via Virus-Induced CCL20 and Promote Th1 Cells through IL-17A
Authors: Dhital Ravi , Anand Shashi , Zeng Qiang , Velazquez Victoria M. , Boddeda Srinivasa R. , Fitch James R. , Minz Ranjana W. , Minz Mukut , Sharma Ashish , Cianciolo Rachel , Shimamura Masako
Published: August 2021

Cytomegalovirus (CMV) infection is associated with renal allograft failure by unknown mechanisms. In a murine renal transplant model, murine CMV (MCMV) induces intragraft infiltration of Th17 cells co-expressing Th1 cytokines, IFN-γ and TNF-α, but only a minority of intragraft Th17 cells are specific for MCMV antigens. Instead, MCMV promotes viral antigen-independent Th17 cell recruitment via CCL20-CCR6 and CXCL10-CXCR3 interactions. Th17 cells correlate directly with Th1 cell frequencies and inversely with Tregs in MCMV infected grafts. Pharmacologic inhibition of IL-17A reduces intragraft Th17 cells and neutrophils, increases Tregs, and reduces total but not MCMV-specific Th1 cells. Among a clinical renal transplant cohort with acute rejection, patients with CMV DNAemia had significantly higher serum IL-17A quantities compared to those without CMV DNAemia. Together, these findings indicate that CMV infection upregulates Th17 cell activity during acute rejection and suggests that inhibition of IL-17A may ameliorate CMV-associated allograft injury without impairing antiviral Th1 cells.
Rapid assessment of SARS-CoV-2 evolved variants using virus-like particles
Authors: Syed Abdullah M. , Taha Taha Y. , Khalid Mir M. , Tabata Takako , Chen Irene P. , Sreekumar Bharath , Chen Pei-Yi , Hayashi Jennifer M. , Soczek Katarzyna M. , Ott Melanie , Doudna Jennifer A.
Published: August 2021

Newly evolved SARS-CoV-2 variants are driving ongoing outbreaks of COVID-19 around the world. Efforts to determine why these viral variants have improved fitness are limited to mutations in the viral spike (S) protein and viral entry steps using non-SARS-CoV-2 viral particles engineered to display S. Here we show that SARS-CoV-2 virus-like particles can package and deliver exogenous transcripts, enabling analysis of mutations within all structural proteins and rapid dissection of multiple steps in the viral life cycle. Identification of an RNA packaging sequence was critical for engineered transcripts to assemble together with SARS-CoV-2 structural proteins S, nucleocapsid (N), membrane (M) and envelope (E) into non-replicative SARS-CoV-2 virus-like particles (SC2-VLPs) that deliver these transcripts to ACE2- and TMPRSS2-expressing cells. Using SC2-VLPs, we tested the effect of 30 individual mutations within the S and N proteins on particle assembly and entry. While S mutations unexpectedly did not affect these steps, SC2-VLPs bearing any one of four N mutations found universally in more-transmissible viral variants (P199L, S202R, R203M and R203K) showed increased particle production and up to 10-fold more reporter transcript expression in receiver cells. Our study provides a platform for rapid testing of viral variants outside a biosafety level 3 setting and identifies viral N mutations and viral particle assembly as mechanisms to explain the increased spread of current viral variants, including Delta (N:R203M).

One-Sentence Summary

R203M substitution within SARS-CoV-2 N, found in delta variant, improves RNA packaging into virus-like particles by 10-fold.
Precision dynamical mapping using topological data analysis reveals a unique hub-like transition state at rest
Authors: Saggar Manish , Shine James M. , Liégeois Raphaël , Dosenbach Nico U. F. , Fair Damien
Published: August 2021

Even in the absence of external stimuli, neural activity is both highly dynamic and organized across multiple spatiotemporal scales. The continuous evolution of brain activity patterns during rest is believed to help maintain a rich repertoire of possible functional configurations that relate to typical and atypical cognitive phenomena. Whether these transitions or “explorations” follow some underlying arrangement or instead lack a predictable ordered plan remains to be determined. Here, using a precision dynamics approach, we aimed at revealing the rules that govern transitions in brain activity at rest at the single participant level. We hypothesized that by revealing and characterizing the overall landscape of whole brain configurations (or states) we could interpret the rules (if any) that govern transitions in brain activity at rest. To generate the landscape of whole-brain configurations we used Topological Data Analysis based Mapper approach. Across all participants, we consistently observed a rich topographic landscape in which the transition of activity from one state to the next involved a central hub-like “transition state.” The hub topography was characterized as a shared attractor-like basin where all canonical resting-state networks were represented equally. The surrounding periphery of the landscape had distinct network configurations. The intermediate transition state and traversal through it via a topographic gradient seemed to provide the underlying structure for the continuous evolution of brain activity patterns at rest. In addition, differences in the landscape architecture were more consistent within than between subjects, providing evidence of idiosyncratic dynamics and potential utility in precision medicine.
Dystrophin modulates focal adhesion tension and YAP-mediated mechanotransduction
Authors: Ramirez Maria Paz , Anderson Michael J.M. , Sundby Lauren J. , Hagerty Anthony R. , Wenthe Sophia J. , Ervasti James M. , Gordon Wendy R.
Published: August 2021

Dystrophin is an essential muscle protein that contributes to cell membrane stability by linking the actin cytoskeleton to the extracellular matrix. The absence or impaired function of dystrophin causes muscular dystrophy. Focal adhesions are mechanosensitive adhesion complexes that also connect the cytoskeleton to the extracellular matrix. However, the interplay between dystrophin and focal adhesion force transmission has not been investigated. Using a bioluminescent tension sensor, we measured focal adhesion tension in transgenic C2C12 myoblasts expressing wild type (WT) dystrophin, a non-pathogenic SNP (I232M), or two missense mutations associated with Duchenne (L54R), or Becker muscular dystrophy (L172H). We found that myoblasts expressing WT or nonpathogenic I232M dystrophin showed increased focal adhesion tension compared to non-transgenic myoblasts, while myoblasts expressing L54R or L172H dystrophin presented with decreased focal adhesion tension. Moreover, myoblasts expressing L54R or L172H dystrophin showed decreased YAP activation and exhibited slower and less directional migration compared to cells expressing WT or I232M dystrophin. Our results suggest that disease-causing missense mutations in dystrophin may disrupt a cellular tension sensing pathway in dystrophic skeletal muscle.