bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of Retinopathy and Systemic Vascular Comorbidities on All-Cause Mortality
Authors: Zhu Zhuoting , Shang Xianwen , Wang Wei , Ha Jason , Chen Yifan , He Jingyi , Hu Wenyi , Yang Xiaohong , He Mingguang
Published: January 2021

Aims/hypothesis

To investigate the joint effects of retinopathy and systemic vascular comorbidities on mortality.

Methods

This study included 5703 participants (≥40 years old) from the 2005-2008 National Health and Nutrition Examination Survey. The Early Treatment Diabetic Retinopathy Study grading scale was used to evaluate the retinopathy status. Systemic vascular comorbidities included diabetes mellitus (DM), high blood pressure (HBP), chronic kidney disease (CKD) and cardiovascular disease (CVD). Time to death was calculated as the time from baseline to either the date of death or censoring (December 31st, 2015), whichever came first. Risks of mortality were estimated using Cox proportional hazards models.

Results

After adjusting for confounders, the presence of retinopathy predicted higher all-cause mortality (hazard ratio [HR], 1.40; 95% confidence interval [CI], 1.09-1.81). The all-cause mortality among participants with both retinopathy and systemic vascular comorbidities including DM (HR, 1.63; 95% CI, 1.06-2.50), HBP (HR, 1.46; 95% CI, 1.03-2.08), CKD (HR, 1.71; 95% CI, 1.24-2.35) and CVD (HR, 1.88; 95% CI, 1.19-2.96) was significantly higher than that among those without either condition.

Conclusions/interpretation

In this prospective study, individuals with retinopathy had increased all-cause mortality. The joint effects of retinopathy and major systemic vascular comorbidities increased the all-cause mortality further, suggesting that more extensive vascular risk factor assessment and management are needed to detect the burden of vascular pathologies and improve long-term survival in individuals with retinopathy.

Research in context

What is already known about this subject?

Retinopathy has been recognized as an independent risk factor for mortality.

What is the key question?

What are the joint effects of retinopathy and systemic vascular comorbidities (including diabetes mellitus, hypertension and chronic kidney disease and cardiovascular disease) on mortality?

What are the new findings?

Consistent evidence on the increased risk of mortality among individuals with retinopathy was noted in a large sample of middle-aged and older adults.

The co-occurrence of retinopathy and systemic vascular conditions (diabetes mellitus, hypertension and chronic kidney disease and cardiovascular disease) further increased all-cause mortality independent of other covariates.

How might this impact on clinical practice in the foreseeable future?

Individuals with retinopathy may benefit from a comprehensive vascular assessment.

Intensive vascular risk reduction is needed in the management of patients with retinopathy and and micro- or macrovascular disorders.

Highlighted the importance of retinopathy screening using retinal imaging for identifying individuals at high risk of mortality, particularly among individuals with systemic vascular comorbidities.
Performance of intensive care unit severity scoring systems across different ethnicities
Authors: Sarkar Rahuldeb , Martin Christopher , Mattie Heather , Gichoya Judy Wawira , Stone David J. , Celi Leo Anthony
Published: January 2021

Background

Despite wide utilisation of severity scoring systems for case-mix determination and benchmarking in the intensive care unit, the possibility of scoring bias across ethnicities has not been examined. Recent guidelines on the use of illness severity scores to inform triage decisions for allocation of scarce resources such as mechanical ventilation during the current COVID-19 pandemic warrant examination for possible bias in these models. We investigated the performance of three severity scoring systems (APACHE IVa, OASIS, SOFA) across ethnic groups in two large ICU databases in order to identify possible ethnicity-based bias.

Method

Data from the eICU Collaborative Research Database and the Medical Information Mart for Intensive Care were analysed for score performance in Asians, African Americans, Hispanics and Whites after appropriate exclusions. Discrimination and calibration were determined for all three scoring systems in all four groups.

Findings

While measurements of discrimination -area under the receiver operating characteristic curve (AUROC) -were significantly different among the groups, they did not display any discernible systematic patterns of bias. In contrast, measurements of calibration -standardised mortality ratio (SMR) -indicated persistent, and in some cases significant, patterns of difference between Hispanics and African Americans versus Asians and Whites. The differences between African Americans and Whites were consistently statistically significant. While calibrations were imperfect for all groups, the scores consistently demonstrated a pattern of over-predicting mortality for African Americans and Hispanics.

Interpretation

The systematic differences in calibration across ethnic groups suggest that illness severity scores reflect bias in their predictions of mortality.

Funding

LAC is funded by the National Institute of Health through NIBIB R01 EB017205. There was no specific funding for this study.
CoAI: Cost-Aware Artificial Intelligence for Health Care
Authors: Erion Gabriel , Janizek Joseph D. , Hudelson Carly , Utarnachitt Richard B. , McCoy Andrew M. , Sayre Michael R. , White Nathan J. , Lee Su-In
Published: January 2021

The recent emergence of accurate artificial intelligence (AI) models for disease diagnosis raises the possibility that AI-based clinical decision support could substantially lower the workload of healthcare providers. However, for this to occur, the input data to an AI predictive model, i.e., the patient’s features, must themselves be low-cost, that is, efficient, inexpensive, or low-effort to acquire. When time or financial resources for gathering data are limited, as in emergency or critical care medicine, modern high-accuracy AI models that use thousands of patient features are likely impractical. To address this problem, we developed the CoAI (Cost-awareAI) framework to enable any kind of AI predictive model (e.g., deep neural networks, tree ensemble models, etc.) to make accurate predictions given a small number of low-cost features. We show that CoAI dramatically reduces the cost of predicting prehospital acute traumatic coagulopathy, intensive care mortality, and outpatient mortality relative to existing risk scores, while improving prediction accuracy. It also outperforms existing state-of-the-art cost-sensitive prediction approaches in terms of predictive performance, model cost, and training time. Extrapolating these results to all trauma patients in the United States shows that, at a fixed false positive rate, CoAI could alert providers of tens of thousands more dangerous events than other risk scores while reducing providers’ data-gathering time by about 90 percent, leading to a savings of 200,000 cumulative hours per year across all providers. We extrapolate similar increases in clinical utility for CoAI in intensive care. These benefits stem from several unique strengths: First, CoAI uses axiomatic feature attribution methods that enable precise estimation of feature importance. Second, CoAI is model-agnostic, allowing users to choose the predictive model that performs the best for the prediction task and data at hand. Finally, unlike many existing methods, CoAI finds high-performance models within a given budget without any tuning of the cost-vs-performance tradeoff. We believe CoAI will dramatically improve patient care in the domains of medicine in which predictions need to be made with limited time and resources.
Leveraging fine-mapping and non-European training data to improve cross-population polygenic risk scores
Authors: Weissbrod Omer , Kanai Masahiro , Shi Huwenbo , Gazal Steven , Peyrot Wouter J. , Khera Amit V. , Okada Yukinori ,   The Biobank Japan Project, Martin Alicia R. , Finucane Hilary , Price Alkes L.
Published: January 2021

Polygenic risk scores (PRS) based on European training data suffer reduced accuracy in non-European target populations, exacerbating health disparities. This loss of accuracy predominantly stems from LD differences, MAF differences (including population-specific SNPs), and/or causal effect size differences. PRS based on training data from the non-European target population do not suffer from these limitations, but are currently limited by much smaller training sample sizes. Here, we propose PolyPred, a method that improves cross-population polygenic prediction by combining two complementary predictors: a new predictor that leverages functionally informed fine-mapping to estimate causal effects (instead of tagging effects), addressing LD differences; and BOLT-LMM, a published predictor. In the special case where a large training sample is available in the non-European target population (or a closely related population), we propose PolyPred+, which further incorporates the non-European training data, addressing MAF differences and causal effect size differences. PolyPred and PolyPred+ require individual-level training data (for their BOLT-LMM component), but we also propose analogous methods that replace the BOLT-LMM component with summary statistic-based components if only summary statistics are available. We applied PolyPred to 49 diseases and complex traits in 4 UK Biobank populations using UK Biobank British training data (averageN=325K), and observed statistically significant average relative improvements in prediction accuracy vs. BOLT-LMM ranging from +7% in South Asians to +32% in Africans (and vs. LD-pruning + P-value thresholding (P+T) ranging from +77% to +164%), consistent with simulations. We applied PolyPred+ to 23 diseases and complex traits in UK Biobank East Asians using both UK Biobank British (averageN=325K) and Biobank Japan (averageN=124K) training data, and observed statistically significant average relative improvements in prediction accuracy of +24% vs. BOLT-LMM and +12% vs. PolyPred. The summary statistic-based analogues of PolyPred and PolyPred+ attained similar improvements. In conclusion, PolyPred and PolyPred+ improve cross-population polygenic prediction accuracy, ameliorating health disparities.
The Role of Disease Severity and Demographics in the Clinical Course of COVID-19 Patients Treated with Convalescent Plasma
Authors: Ma Tengfei , Wiggins Chad C. , Kornatowski Breanna M. , Hailat Ra’ed S. , Clayburn Andrew C. , Guo Winston , Johnson Patrick W. , Senefeld Jonathon W. , Klassen Stephen A. , Baker Sarah E. , Bruno Katelyn A. , Fairweather DeLisa , Wright R. Scott , Carter Rickey E. , Li Chenxi , Joyner Michael J. , Paneth Nigel
Published: January 2021

Treatment of patients with COVID-19 using convalescent plasma from recently recovered patients has been shown to be safe, but the time course of change in clinical status following plasma transfusion in relation to baseline disease severity has not yet been described. We analyzed short, descriptive daily reports of patient status in 7,180 hospitalized recipients of COVID-19 convalescent plasma in the Mayo Clinic Expanded Access Program. We assessed, from the day following transfusion, whether the patient was categorized by his or her physician as better, worse or unchanged compared to the day before, and whether, on the reporting day, the patient received mechanical ventilation, was in the ICU, had died or had been discharged. Most patients improved following transfusion, but clinical improvement was most notable in mild to moderately ill patients. Patients classified as severely ill upon enrollment improved, but not as rapidly, while patients classified as critically ill/end-stage and patients on ventilators showed worsening of disease status even after treatment with convalescent plasma. Patients age 80 and over showed little or no clinical improvement following transfusion. Clinical status at enrollment and age appear to be the primary factors in determining the therapeutic effectiveness of COVID-19 convalescent plasma among hospitalized patients.
COVID-19: making the best out of a forced transition to online medical teaching. A mixed methods study
Authors: Virumbrales Montserrat , Elorduy Marta , Graell Mariona , Mezquita Pau , Brotons Pedro , Balaguer Albert
Published: January 2021

Introduction

the COVID-19 pandemic resulted in a decreed confinement in our country from March until the end of term in June 2020. This forced a transition exclusively to distance learning. The aim of this study was to broaden the understanding of fully online distance learning from the experiences of undergraduate medical students and faculty members during confinement, and identify its key elements.

Methods

A convergent mixed methods study analyzing: (a) an online teaching follow- up program, (b) two focus groups and a nominal group with students and faculty, respectively, and (c) a survey with students from 1st to 5th year.

Results

Thirteen strongly interconnected categories were identified. Four played an organizational role: course planning, coordination, communication and pedagogical coherence. The remaining nine categories were: learning outcomes, teaching methodology, online resources, evaluation, time management, workload, student motivation, participation, and teacher-student relationship. Among the key aspects of learning were those that promoted rapport between faculty and students, such as synchronous sessions, especially those based on clinical cases.

Conclusion

the experiences from confinement allowed us to gain insight into some of the key aspects of online medical teaching. Promoting student motivation and participation at all levels was essential to distance learning in Medicine.
Identifying high-risk groups for change in weight and body mass index: population cohort of 11 million measurements in 2.3 million adults
Authors: Katsoulis Michail , Lai Alvina G , Diaz-Ordaz Karla , Gomes Manuel , Pasea Laura , Banerjee Amitava , Denaxas Spiros , Tsilidis Kostas , Lagiou Pagona , Misirli Gesthimani , Bhaskaran Krishnan , Wannamethee Goya , Dobson Richard , Batterham Rachel L , Kipourou DK , Lumbers R Thomas , Wareham Nick , Langenberg Claudia , Hemingway Harry
Published: January 2021

Background

Adult obesity prevention policies, which are largely untargeted, have met with limited success globally. Population groups with the highest risk of weight gain, if they could be reliably identified using readily available information, might benefit from targeted policy. The relative importance of age, sex, ethnicity, geographical region and social deprivation for weight gain is unknown.

Methods

We calculated longitudinal changes in BMI over one, five and ten years and investigated transition between BMI categories using 11,187,383 clinically recorded, repeated measures of BMI from population-based electronic health records of 2,328,477 adults in England (1998-2016). The influence of risk factors was tested using logistic regression.

Findings

The youngest adult age group (18-24 years) was more strongly associated with risk of weight gain than older age, male sex, socioeconomic deprivation, ethnicity or geographic region. Among the youngest adults, the top quartile gained 15.9kg in men and 12kg in women at 10 years. The odds of transitioning to a higher BMI category over 10 years were 4-6 times higher in the youngest (18-24 years) compared to oldest (65-74 years) individuals; odds ratio (95% confidence interval) 4.22 (3.85-4.62)) from normal weight to overweight or obesity, 4.60 (4.06-5.22) for overweight to obesity, and 5.87 (5.23-6.59) from obesity to severe obesity in multiple adjusted analyses. Among the youngest adults, socially deprived men were at greater risk of transitioning from normal weight to overweight (72%) and from overweight to obesity (68%) over 10 years. We provide an open access online risk calculator (https://pasea.shinyapps.io/bmi_shiny_app/) and present high resolution obesity risk charts over a 1-, 5- and 10-year follow-up.

Interpretation

A radical shift in policy is required to focus on those at highest risk of weight gain-young adults-for individual and population level prevention of obesity and its long-term consequences for health and health care.

Funding

BHF, HDR-UK, MRC
A comprehensive antigen production and characterization study for easy-to-implement, highly specific and quantitative SARS-CoV-2 antibody assays
Authors: Klausberger Miriam , Dürkop Mark , Haslacher Helmuth , Wozniak-Knopp Gordana , Cserjan-Puschmann Monika , Perkmann Thomas , Lingg Nico , Aguilar Patricia Pereira , Laurent Elisabeth , De Vos Jelle , Hofer Manuela , Holzer Barbara , Stadler Maria , Manhart Gabriele , Vierlinger Klemens , Egger Margot , Milchram Lisa , Gludovacz Elisabeth , Marx Nicolas , Köppl Christoph , Tauer Christopher , Beck Jürgen , Maresch Daniel , Grünwald-Gruber Clemens , Strobl Florian , Satzer Peter , Stadlmayr Gerhard , Vavra Ulrike , Huber Jasmin , Wahrmann Markus , Eskandary Farsad , Breyer Marie-Kathrin , Sieghart Daniela , Quehenberger Peter , Leitner Gerda , Strassl Robert , Egger Alexander E. , Irsara Christian , Griesmacher Andrea , Hoermann Gregor , Weiss Günter , Bellmann-Weiler Rosa , Loeffler-Ragg Judith , Borth Nicole , Strasser Richard , Jungbauer Alois , Hahn Rainer , Mairhofer Jürgen , Hartmann Boris , Binder Nikolaus B. , Striedner Gerald , Mach Lukas , Weinhäusl Andreas , Dieplinger Benjamin , Grebien Florian , Gerner Wilhelm , Binder Christoph J. , Grabherr Reingard
Published: January 2021

Antibody tests are essential tools to investigate humoral immunity following SARS-CoV-2 infection. While first-generation antibody tests have primarily provided qualitative results with low specificity, accurate seroprevalence studies and tracking of antibody levels over time require highly specific, sensitive and quantitative test setups. Here, we describe two quantitative ELISA antibody tests based on the SARS-CoV-2 spike receptor-binding domain and the nucleocapsid protein. Comparative expression in bacterial, insect, mammalian and plant-based platforms enabled the identification of new antigen designs with superior quality and high suitability as diagnostic reagents. Both tests scored excellently in clinical validations with multi-centric specificity and sensitivity cohorts and showed unprecedented correlation with SARS-CoV-2 neutralization titers. Orthogonal testing increased assay specificity to 99.8%, thereby enabling robust serodiagnosis in low-prevalence settings. The inclusion of a calibrator permits accurate quantitative monitoring of antibody concentrations in samples collected at different time points during the acute and convalescent phase of COVID-19.
City Reduced Probability of Infection (CityRPI) for Indoor Airborne Transmission of SARS-CoV-2 and Urban Building Energy Impacts
Authors: Katal Ali , Albettar Maher , Wang Liangzhu (Leon)
Published: January 2021

Airborne transmission of aerosols produced by asymptomatic individuals is a large portion of the SARS-CoV-2 spread indoors. Outdoor air ventilation rate, air filtration, room occupancy, exposure time, and mask-wearing are among the key parameters that affect its airborne transmission in indoor spaces. In this work, we developed a new web-based platform, City Reduced Probability of Infection - CityRPI, to calculate the indoor airborne transmission of COVID-19 in various buildings of a city scale. An archetype library of twenty-nine building types is developed based on several standards and references. Among the mitigation strategies recommended to reduce infection risk, some could result in significant energy impacts on buildings. To study the combined effects of energy consumption and reduced infection probability, we integrated CityRPI with City Building Energy Model. We applied the integrated model to Montreal City and studied the impact of six mitigation measures on the infection risk and peak energy demand in winter. It shows that the same strategy could perform quite differently, depending on building types and properties. In the winter season, increasing the outdoor air ventilation rate may cause massive building energy consumption. All strategies are shown to reduce the infection risk but wearing a mask and reducing exposure time are the most effective strategies in many buildings, with around 60% reduction. Doubling the outdoor air ventilation rate is not as effective as other strategies to reduce the risk with less than 35% reduction. It also significantly increases building peak heating demand with 10-60%.
Enhancing the Human Health Status Prediction: the ATHLOS Project
Authors: Anagnostou Panagiotis , Tasoulis Sotiris , Vrahatis Aristidis G. , Georgakopoulos Spiros , Prina Matthew , Ayuso-Mateos José Luis , Bickenbach Jerome , Bayes Ivet , Caballero Francisco Félix , Egea-Cortés Laia , García-Esquinas Esther , Leonardi Matilde , Scherbov Sergei , Tamosiunas Abdonas , Galas Aleksander , Haro Josep Maria , Sanchez-Niubo Albert , Plagianakos Vassilis , Panagiotakos Demosthenes
Published: January 2021

Preventive healthcare is a crucial pillar of health as it contributes to staying healthy and having immediate treatment when needed. Mining knowledge from longitudinal studies has the potential to significantly contribute to the improvement of preventive healthcare. Unfortunately, data originated from such studies are characterized by high complexity, huge volume and a plethora of missing values. Machine Learning, Data Mining and Data Imputation models are utilized as part of solving the aforementioned challenges, respectively. Towards this direction, we focus on the development of a complete methodology for the ATHLOS (Ageing Trajectories of Health: Longitudinal Opportunities and Synergies) Project - funded by the European Union’s Horizon 2020 Research and Innovation Program, which aims to achieve a better interpretation of the impact of aging on health. The inherent complexity of the provided dataset lie in the fact that the project includes 15 independent European and international longitudinal studies of aging. In this work, we particularly focus on the HealthStatus (HS) score, an index that estimates the human status of health, aiming to examine the effect of various data imputation models to the prediction power of classification and regression models. Our results are promising, indicating the critical importance of data imputation in enhancing preventive medicine’s crucial role.
Transspecies beak color polymorphism in the Darwin’s finch radiation
Authors: Enbody Erik D. , Sprehn C. Grace , Abzhanov Arhat , Bi Huijuan , Dobreva Mariya P. , Osborne Owen G. , Rubin Carl-Johan , Grant Peter R. , Grant B. Rosemary , Andersson Leif
Published: January 2021

Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles1, but little is known of how they affect fitness and are maintained as species multiply2. We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin’s finches. Beaks are pink or yellow, and yellow is recessive3. Here we show that the polymorphism arose in the Galápagos approximately half a million years ago through a regulatory mutation in theBCO2gene, and is shared by 14 descendant species. The frequency of the yellow genotype is associated with cactus flower abundance in cactus finches, and is altered by introgressive hybridization. The polymorphism is most likely a balanced polymorphism, maintained by ecological selection pressures associated with diet, and augmented by occasional interspecific introgression. Polymorphisms that are hidden as adults, as here, may contribute to evolutionary diversification in underappreciated ways in other systems.
Rapid protection from COVID-19 in nonhuman primates vaccinated intramuscularly but not intranasally with a single dose of a recombinant vaccine
Authors: Furuyama Wakako , Shifflett Kyle , Pinski Amanda N. , Griffin Amanda J. , Feldmann Friederike , Okumura Atsushi , Gourdine Tylisha , Jankeel Allen , Lovaglio Jamie , Hanley Patrick W. , Thomas Tina , Clancy Chad S. , Messaoudi Ilhem , O’Donnell Kyle L. , Marzi Andrea
Published: January 2021

The ongoing pandemic of Coronavirus disease 2019 (COVID-19) continues to exert a significant burden on health care systems worldwide. With limited treatments available, vaccination remains an effective strategy to counter transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent discussions concerning vaccination strategies have focused on identifying vaccine platforms, number of doses, route of administration, and time to reach peak immunity against SARS-CoV-2. Here, we generated a single dose, fast-acting vesicular stomatitis virus-based vaccine derived from the licensed Ebola virus (EBOV) vaccine rVSV-ZEBOV, expressing the SARS-CoV-2 spike protein and the EBOV glycoprotein (VSV-SARS2-EBOV). Rhesus macaques vaccinated intramuscularly (IM) with a single dose of VSV-SARS2-EBOV were protected within 10 days and did not show signs of COVID-19 pneumonia. In contrast, intranasal (IN) vaccination resulted in limited immunogenicity and enhanced COVID-19 pneumonia compared to control animals. While IM and IN vaccination both induced neutralizing antibody titers, only IM vaccination resulted in a significant cellular immune response. RNA sequencing data bolstered these results by revealing robust activation of the innate and adaptive immune transcriptional signatures in the lungs of IM-vaccinated animals only. Overall, the data demonstrates that VSV-SARS2-EBOV is a potent single-dose COVID-19 vaccine candidate that offers rapid protection based on the protective efficacy observed in our study.

One sentence summary

VSV vaccine protects NHPs from COVID-19 in 10 days
Coordinated action of RTBV and RTSV proteins suppress host RNA silencing machinery
Authors: Anand Abhishek , Pinninti Malathi , Tripathi Anita , Mangrauthia Satendra Kumar , Sanan-Mishra Neeti
Published: January 2021

RNA silencing is as an adaptive immune response in plants that limits accumulation or spread of invading viruses. Successful virus infection entails countering the RNA silencing for efficient replication and systemic spread in the host. The viruses encode proteins having the ability to suppress or block the host silencing mechanism, resulting in severe pathogenic symptoms and diseases. Tungro virus disease caused by a complex of two viruses provides an excellent system to understand these host and virus interactions during infection. It is known thatRice tungro bacilliform virus(RTBV) is the major determinant of the disease whileRice tungro spherical virus(RTSV) accentuates the symptoms. This study brings to focus the important role of RTBV ORF-IV in Tungro disease manifestation, by acting as both the victim and silencer of the RNA silencing pathway. The ORF-IV is a weak suppressor of the S-PTGS or pre-established stable silencing but its suppression activity is augmented in the presence of RTSV proteins. The RTBV and RTSV proteins interact to suppress localized silencing as well as spread of silencing, in the host plants.
(p)ppGpp inhibits 70S ribosome formation inStaphylococcus aureusby impeding GTPase-ribosome interactions
Authors: Bennison Daniel J. , Nakamoto Jose A. , Craggs Timothy D. , Milón Pohl , Rafferty John B. , Corrigan Rebecca M.
Published: January 2021

During nutrient limitation, bacteria produce the alarmones (p)ppGpp as effectors of the stress signalling network termed the stringent response. Screening for (p)ppGpp-binding targets withinStaphylococcus aureusidentified four ribosome-associated GTPases (RA-GTPases), RsgA, RbgA, Era and HflX, each of which are cofactors in ribosome assembly, where they cycle between the ON (GTP-bound) and OFF (GDP-bound) states. Entry into the OFF-state from the ON-state occurs upon hydrolysis of GTP, with GTPase activity increasing substantially upon ribosome association. When bound to (p)ppGpp, GTPase activity is inhibited, reducing 70S ribosome assembly. Here, we sought to determine how (p)ppGpp impacts RA-GTPase-ribosome interactions by examining the affinity and kinetics of binding between RA-GTPases and ribosomes in various nucleotide-bound states. We show that RA-GTPases preferentially bind to 5′-diphosphate-containing nucleotides GDP and ppGpp over GTP, which is likely exploited as a regulatory mechanism within the cell. Binding to (p)ppGpp reduces stable association of RA-GTPases to ribosomal subunits compared to the GTP-bound state bothin vitroand within bacterial cells by inducing the OFF-state conformation. We propose that in this conformation, the G2/switch I loop adopts a conformation incompatible with ribosome association. Altogether, we highlight (p)ppGpp-mediated inhibition of RA-GTPases as a major mechanism of stringent response-mediated growth control.
Intron-mediated induction of phenotypic heterogeneity
Authors: Lukačišin Martin , Espinosa-Cantú Adriana , Bollenbach Tobias
Published: January 2021

Introns are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns2–4. Despite recent findings on the role of RP introns under stress and starvation5–7, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling8with single-cell protein measurements9, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, mediated by an intron in the 5’ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to grow faster after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal a new role for introns in inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness10.
BRD2 inhibition blocks SARS-CoV-2 infection by reducing transcription of the host cell receptor ACE2
Authors: Samelson Avi J. , Tran Quang Dinh , Robinot Rémy , Carrau Lucia , Rezelj Veronica V. , Kain Alice Mac , Chen Merissa , Ramadoss Gokul N. , Guo Xiaoyan , Lim Shion A. , Lui Irene , Nunez James , Rockwood Sarah J. , Wang Jianhui , Liu Na , Carlson-Stevermer Jared , Oki Jennifer , Maures Travis , Holden Kevin , Weissman Jonathan S. , Wells James A. , Conklin Bruce R. , TenOever Benjamin R. , Chakrabarti Lisa A. , Vignuzzi Marco , Tian Ruilin , Kampmann Martin
Published: January 2021

SARS-CoV-2 infection of human cells is initiated by the binding of the viral Spike protein to its cell-surface receptor ACE2. We conducted a targeted CRISPRi screen to uncover druggable pathways controlling Spike protein binding to human cells. We found that the protein BRD2 is required forACE2transcription in human lung epithelial cells and cardiomyocytes, and BRD2 inhibitors currently evaluated in clinical trials potently block endogenousACE2expression and SARS-CoV-2 infection of human cells, including those of human nasal epithelia. Moreover, pharmacological BRD2 inhibition with the drug ABBV-744 inhibited SARS-CoV-2 replication in Syrian hamsters. We also found that BRD2 controls transcription of several other genes induced upon SARS-CoV-2 infection, including the interferon response, which in turn regulates the antiviral response. Together, our results pinpoint BRD2 as a potent and essential regulator of the host response to SARS-CoV-2 infection and highlight the potential of BRD2 as a novel therapeutic target for COVID-19.
UniverSC: a flexible cross-platform single-cell data processing pipeline
Authors: Kelly S. Thomas , Battenberg Kai , Hetherington Nicola A. , Hayashi Makoto , Minoda Aki
Published: January 2021

Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.
Bazooka/Par3 cooperates with Sanpodo for the assembly of Notch signaling clusters following asymmetric division ofDrosophilasensory organ precursor cells
Authors: Houssin Elise , Pinot Mathieu , Bellec Karen , Le Borgne Roland
Published: January 2021

In multiple cell lineages, Delta-Notch signaling regulates cell fate decisions owing to unidirectional signaling between daughter cells. InDrosophilapupal sensory organ lineage, Notch regulates pIIa/pIIb fate decision at cytokinesis. Notch and Delta that localize apically and basally at the pIIa-pIIb interface, are expressed at low levels and their residence time at the plasma membrane is in the order of the minute. How Delta can effectively interact with Notch to trigger signaling from a large plasma membrane remains poorly understood. Here, we report that the signaling interface possesses a unique apicobasal polarity with Par3/Bazooka localizing in the form of nano-clusters at the apical and basal level. Notch is preferentially targeted to the pIIa-pIIb interface where it co-clusters with Bazooka and the Notch cofactor Sanpodo. Clusters whose assembly relies on Bazooka and Sanpodo activities, are also positive for Neuralized, the E3 ligase required for Delta-activity. We propose that the nano-clusters act as snap buttons at the new pIIa-pIIb interface to allow efficient intra-lineage signaling.
freqpcr: estimation of population allele frequency using qPCR ΔΔCq measures from bulk samples
Authors: Sudo Masaaki , Osakabe Masahiro
Published: January 2021

PCR techniques, both quantitative (qPCR) and non-quantitative, have been used to estimate allele frequency in a population. However, the labor required to sample numerous individuals, and subsequently handle each sample, makes quantification of rare mutations, including pesticide resistance genes at the early stages of resistance development, challenging. Meanwhile, pooling DNA from multiple individuals as a “bulk sample” may reduce handling costs. The qPCR output for a bulk sample, however, contains uncertainty owing to variations in DNA yields from each individual, in addition to measurement errors. In this study, we developed a statistical model for the interval estimation of allele frequency using ΔΔCq-based qPCR analyses of multiple bulk samples collected from a population. We assumed a gamma distribution as the individual DNA yield and developed an R package for parameter estimation, which was verified with real DNA samples from acaricide-resistant spider mites, as well as a numerical simulation. Our model resulted in unbiased point estimates of the allele frequency compared with simple averaging of the ΔΔCq values, while their confidence intervals suggest that collecting and pooling additional samples from individuals may produce higher precision than individual PCR tests with moderate sample sizes.
Xanthomonastranscriptome inside cauliflower hydathodes reveals bacterial virulence strategies and physiological adaptation at early infection stages
Authors: Luneau Julien S. , Cerutti Aude , Roux Brice , Carrère Sébastien , Jardinaud Marie-Françoise , Gaillac Antoine , Gris Carine , Lauber Emmanuelle , Berthomé Richard , Arlat Matthieu , Boulanger Alice , Noël Laurent D.
Published: January 2021

Xanthomonas campestrispv.campestris(Xcc) bacterium is a seed-transmitted vascular pathogen causing black rot disease on cultivated and wildBrassicaceae. Xccenters the plant tissues preferentially via hydathodes which are organs localized at leaf margins. In order to decipher both physiological and virulence strategies deployed byXccduring early stages of infection, the transcriptomic profile ofXccwas analyzed three days after entry into cauliflower hydathodes. Despite the absence of visible plant tissue alterations and a bacterial biotrophic lifestyle, 18% ofXccgenes undergo a transcriptional reprogramming, including a striking repression of chemotaxis and motility functions.Xccfull repertoire of virulence factors was not yet activated but the expression of the 95-gene HrpG regulon, including genes coding for the type three secretion machinery important for suppression of plant immunity, was induced. The expression of genes involved in metabolic adaptations such as catabolism of plant compounds, transport functions, sulfur and phosphate metabolism was upregulated while limited stress responses were observed three days post infection. These transcriptomic observations give information about the nutritional and stress status of bacteria during the early biotrophic infection stages and help to decipher the adaptive strategy ofXccto the hydathode environment.
Pest control strategies after first signs of invasive black rat: case study in the Community of Madrid
Authors: Bermejo-Nogales Azucena , Navas José M.
Published: January 2021

Rodents are animals that provoke special concern in the rural and urban areas as may cause potential damage in facilities and infrastructures as well as social alarm. The control of rodent populations is based on prevention and on what it has been called an “Integrated Pest Management” strategy. The most important species affected by this strategy are brown rat (Rattus norvegicus), black rat (Rattus rattus L.) and mouse (Mus musculus). In the present work, our original objective was to monitor changes in status or range of rodent species in the Community of Madrid (Spain). We conducted in coordination with the professional organization of Pest Control Operators “ANECPLA” a procedure designed to obtain faecal samples in locations with rodenticide treatment. Determination of pest specie was based on cytochrome b (cytb) sequences and phylogenetic analysis. We received samples from a variety of locations in which a rodenticide treatment was applied due to infestation or to citizen notice. While we recorded a number of data about the distribution of brown rat the presence of black rat was unexpectedly discovered. The detection of this species implies changes in pest control strategies to improve the results in the application of rodenticides available in the market.

Key Message

Rodent pest control is a key issue but little is known about Spanish populations. We aimed to know how many rat species there are in Central Spain, specifically in the Community of Madrid. We found for the first time the presence of black rat and a new wild strain of brown rat in this area. These findings have change the strategies of rodent treatment and stresses the importance of population studies for a better control.
Transcripts switched off at the stop of phloem unloading highlight the energy efficiency of sugar import in the ripeningV. viniferafruit
Authors: Savoi Stefania , Torregrosa Laurent , Romieu Charles
Published: January 2021

Transcriptomic changes at the cessation of sugar accumulation in the pericarp ofVitis viniferawere addressed on single berries re-synchronized according to their individual growth patterns. The net rates of water, sugars and K+accumulation inferred from individual growth and solute concentration confirmed that these inflows stopped simultaneously in the ripe berry, while the small amount of malic acid remaining at this stage was still being oxidized at low rate. Re-synchronized individual berries displayed negligible variations in gene expression among triplicates. RNA-Seq studies revealed sharp reprogramming of cell wall enzymes and structural proteins at the stop of phloem unloading, associated with an 80% repression of multiple sugar transporters and aquaporins on the plasma or tonoplast membranes, with the noticeable exception of H+/sugar symporters, that were rather weakly and constitutively expressed. This was verified in three genotypes placed in contrasted thermo-hydric conditions. The prevalence of SWEET suggests that electrogenic transporters would play a minor role on the plasma membranes of SE/CC complex and the one of the flesh, while sucrose/H+exchangers dominate on its tonoplast.Cis-regulatory elements present in their promoters allowed to sort these transporters in different groups, also including specific TIPs and PIPs paralogs, and cohorts of cell wall related genes. Together with simple thermodynamic considerations, these results lead to propose that H+/sugar exchangers at the tonoplast, associated with a considerably acidic vacuolar pH, may exhaust cytosolic sugars in the flesh and alleviate the need for supplementary energization of sugar transport at the plasma membrane.
Piriformospora indica employs host’s putrescine for growth promotion in plants
Authors: Kundu Anish , Jogawat Abhimanyu , Mishra Shruti , Kundu Pritha , Vadassery Jyothilakshmi
Published: January 2021

Growth promotion by endosymbiont Piriformospora indica has been observed in various plants; however, specific functional metabolites involved in P. indica mediated growth promotion are unknown. A GC-MS based untargeted metabolite analysis was used to identify Solanum lycopersicum metabolites altered during P. indica mediated growth promotion. Metabolomic analysis showed primary metabolites altered and specifically putrescine to be maximally induced in roots during the interaction. P. indica induced putrescine biosynthetic gene SlADC1 in S. lycopersicum and acts via arginine decarboxylase (ADC) mediated pathway. P. indica did not promote growth in Sladc-VIGS (virus induced gene silencing of SlADC gene) lines of S. lycopersicum and when the ADC enzyme was inhibited with an inhibitor, DL-α-(Difluoromethyl) arginine. In Arabidopsis adc knock-out mutants, P. indica do not promote growth and this response was rescued upon exogenous application of putrescine. Putrescine promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4, GA7) levels in S. lycopersicum. Putrescine is also important for P. indica hyphal growth indicating that it is co-adapted by both host and microbe. Hence, we conclude that putrescine is an essential metabolite and its biosynthesis in plants is crucial for P. indica mediated growth promotion and fungal growth.
Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions
Authors: Hosni Nicole Dittrich , Anauate Ana Carolina , Boim Mirian Aparecida
Published: January 2021

Background

Real-time PCR remains currently the gold standard method for gene expression studies. Identification of the best reference gene is a key point in performing high quality qPCR, providing strong support for results, as well as performing as a source of bias when inappropriately chosen. Mesangial cells and podocytes, as essential cell lines to study diabetic kidney disease (DKD) physiopathology, demand accurate analysis of the reference genes used so far to enhance validity of gene expression studies, especially regarding high glucose (HG) and DKD treatments, with angiotensin II receptor blockers (e.g. Losartan) being the most commonly used. This study aimed to evaluate the suitability and define the most stable reference gene for mesangial cells and podocytes studies of anin vitroDKD model of disease and its treatment.

Methods

Five software packages (RefFinder, NormFinder, GeNorm, Bestkeeper, and DataAssist) and the comparative ΔCt method were selected to analyze six different candidate genes:HPRT, ACTB, PGAM-1, GAPDH, PPIA,andB2M.RNA was extracted and cDNA was synthesized from immortalized mouse mesangial cells and podocytes cultured in 4 groups: control (n=5; 5mM glucose), mannitol (n=5; 30mM, as osmotic control), HG (n=5; 30mM glucose), and HG + losartan (n=5; 30mM glucose and 10-4mM of losartan). Real-time PCR was performed according to MIQE guidelines.

Results

We identified that the use of 2 genes is the best combination for qPCR normalization for both mesangial cell and podocytes. For mesangial cells, the combination ofHPRTandACTBpresented higher stability values. For podocytes,HPRTandGAPDHshowed the best results.

Conclusion

This analysis provides support for the use ofHPRTandACTBas reference genes in mouse mesangial cell studies of gene expression via real-time PCR technique, while for podocytes,HPRTandGAPDHshould be chosen.
Integration of spatial transcriptomic and single cell sequencing identifies expression patterns underlying immune and epithelial cell cross-talk in acute kidney injury
Authors: Ferreira Ricardo Melo , Sabo Angela R. , Winfree Seth , Collins Kimberly S. , Janosevic Danielle , Gulbronson Connor , Cheng Ying-Hua , Casbon Lauren , Barwinska Daria , Ferkowicz Michael J. , Xuei Xiaoling , Zhang Chi , Dunn Kenneth W. , Kelly Katherine J. , Sutton Timothy A. , Hato Takashi , Dagher Pierre C. , El-Achkar Tarek M. , Eadon Michael T.
Published: January 2021

Despite important advances in studying experimental and clinical acute kidney injury (AKI), the pathogenesis of this disease remains incompletely understood. Single cell sequencing studies have closed this knowledge gap by characterizing the transcriptomic signature of different cell types within the kidney. However, the spatial distribution of injury can be regional and affect cells heterogeneously. We first optimized coordination of spatial transcriptomics and single nuclear sequencing datasets, mapping 30 dominant cell types to a human nephrectomy sample. The predicted cell type spots corresponded with the underlying hematoxylin and eosin histopathology. To study the implications of acute kidney injury on the distribution of transcript expression, we then characterized the spatial transcriptomic signature of two murine AKI models: ischemia reperfusion injury (IRI) and cecal ligation puncture (CLP). Localized regions of reduced overall expression were found associated with tissue injury pathways. Using single cell sequencing, we deconvoluted the signature of each spatial transcriptomic spot, identifying patterns of colocalization between immune and epithelial cells. As expected, neutrophils infiltrated the renal medullary outer stripe in the ischemia model. Atf3 was identified as a chemotactic factor in S3 proximal tubule cells. In the CLP model, infiltrating macrophages dominated the outer cortical signature and Mdk was identified as a corresponding chemotactic factor. The regional distribution of these immune cells was validated with multiplexed CO-Detection by inDEXing (CODEX) immunofluorescence. Spatial transcriptomic sequencing can aid in uncovering the mechanisms driving immune cell infiltration and allow detection of relevant subpopulations in single cell sequencing. The complementarity of these technologies facilitates the development of a transcriptomic kidney atlas in health and disease.