bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels as compared with therapy based on protease inhibitors
Authors: Pasternak Alexander O. , Vroom Jelmer , Kootstra Neeltje A. , Wit Ferdinand W.N.M. , Bruin Marijn de , Francesco Davide De , Bakker Margreet , Sabin Caroline A , Winston Alan , Prins Jan M. , Reiss Peter , Berkhout Ben
Published: March 2021

BACKGROUND

It remains unclear whether combination antiretroviral therapy (ART) regimens differ in their ability to fully suppress HIV replication. Here, we report the results of two cross-sectional studies that compared levels of cell-associated (CA) HIV markers between individuals receiving suppressive ART containing either a non-nucleoside reverse transcriptase inhibitor (NNRTI) or a protease inhibitor (PI).

METHODS

CA HIV unspliced RNA and total HIV DNA were quantified in two cohorts (n=100, n=124) of individuals treated with triple ART regimens consisting of two nucleoside reverse transcriptase inhibitors (NRTIs) plus either a NNRTI or a PI. To compare CA HIV RNA and DNA levels between the regimens, we built multivariable models adjusting for age, gender, current and nadir CD4+ count, plasma viral load zenith, duration of virological suppression, NRTI backbone composition, low-level plasma HIV RNA detectability, and electronically-measured adherence to ART.

RESULTS

In both cohorts, levels of CA HIV RNA and DNA strongly correlated (rho=0.70 and rho=0.54) and both markers were lower in NNRTI-treated than in PI-treated individuals. In the multivariable analysis, CA RNA in both cohorts remained significantly reduced in NNRTI-treated individuals (padj=0.02 in both cohorts), with a similar but weaker association between the ART regimen and total HIV DNA (padj=0.048 and padj=0.10). No differences in CA HIV RNA or DNA levels were observed between individual NNRTIs or individual PIs, but CA HIV RNA was lower in individuals treated with either nevirapine or efavirenz, compared to PI-treated individuals.

CONCLUSIONS

All current classes of antiretroviral drugs only prevent infection of new cells but do not inhibit HIV RNA transcription in long-lived reservoir cells. Therefore, these differences in CA HIV RNA and DNA levels by treatment regimen suggest that NNRTIs are more potent in suppressing HIV residual replication than PIs, which may result in a smaller viral reservoir size.
Virtual peer role-play during COVID-19 pandemic for teaching medical students how to break bad news
Authors: Bouaoud Jebrane , Saintigny Pierre
Published: March 2021

In order to cope with the SARS-CoV-2 pandemic and meet with the educational needs of medical students, we have evaluated the virtual peer role-plays (VPRP), an innovative approach to teach breaking bad news communication skills to medical students. Three scenarios of relational simulation were successively proposed to 237 medical students divided in 10 groups, each supervised by two teachers. Pre- and post-VPRP questionnaires were submitted to evaluate students’ satisfaction. The response rate of the pre- and post-VPRP questionnaires were 89% and 52% respectively. Two-thirds of the students had never participated in a peer role-play session. Most students had low level of confidence in breaking bad news communication and were motivated to participate to the VPRP session. Students’ satisfaction on VPRP session regarding quality (realism, organization), interest, perceived benefits was very positive. In conclusion, VPRP are feasible, of low cost (no material is required), applicable to other healthcare students and is relevant to the growth of teleconsultation.
Is the vitamin D status of patients with COVID-19 associated with reduced mortality?
Authors: Bignardi Paulo R , de Andrade Castello Paula , de Matos Aquino Bruno , Alvares Delfino Vinicius Daher
Published: March 2021

Objective

A systematic review with meta-analysis was performed to assess a possible association between plasma vitamin D levels and mortality in patients with COVID – 19.

Methods

PubMed, EMBASE, and Cochrane Library databases were searched. Studies involving COVID-19 patients that reported an association between plasma vitamin D levels and COVID-19 mortality published until February 5, 2021, were included. The risk ratio (RR) and confidence interval (CI) were pooled using a fixed-effects or random-effects model.

Results

A total of 11 studies that measured plasma vitamin D levels at admission were included in the meta-analysis, ten cohorts and one case-controls. Low plasma vitamin D levels (25(OH)D) in patients with COVID-19 were not associated with mortality (RR=1.35, 95%CI 0.84–1.86). Subgroup analysis by vitamin D cut-off (<20 or 25 ng/ml and <10 or 12 ng/ml) showed were not associated with mortality. When the RR in mortality analysis was calculated included four studies that did not perform adjusted analysis for confounding factors, the result was 1.43 (95% CI 1.18-1.69), suggesting that confounders may have led many observational studies to incorrectly estimate the association between vitamin D status and mortality in COVID-19 patients.

Conclusion

Deficient vitamin D levels were not associated with a higher mortality rate in patients with COVID-19. Randomized clinical trials are needed to assess this association.
Diagnostic accuracy of cerebrospinal fluid and blood biomarkers for the differential diagnosis of sporadic Creutzfeldt-Jakob disease: a (network) meta-analysis
Authors: Rübsamen Nicole , Pape Stephanie , Konigorski Stefan , Zapf Antonia , Rücker Gerta , Karch André
Published: March 2021

Objective

To conduct a systematic review of cerebrospinal fluid (CSF) and blood biomarkers as diagnostic tests for sporadic Creutzfeldt-Jakob disease (sCJD) in a specialised care setting and to compare diagnostic accuracies in a network meta-analysis (NMA).

Methods

We searched Medline, Embase, and the Cochrane Library for diagnostic studies of sCJD biomarkers. Risk of bias was assessed with the QUADAS-2 tool. We used a generalised bivariate model to conduct individual biomarker meta-analyses, and to estimate between-study variability. To investigate sources of heterogeneity, we performed subgroup analyses based on QUADAS-2 quality and clinical criteria. For the NMA, we applied a Bayesian beta-binomial ANOVA model. The study protocol was registered at PROSPERO (CRD42019118830).

Results

Out of 2,976 publications screened, we included 16 studies, which investigated 14-3-3β Western blot (n=13), 14-3-3γ ELISA (n=3), NfL (n=1), NSE (n=1), p-tau181/t-tau ratio (n=2), RT-QuIC (n=6), S100B (n=3), t-tau (n=12), and t-tau/Aβ42 ratio (n=1) in CSF. No included study investigated blood biomarkers. Many diagnostic studies excluded had strong limitations in study design. In the NMA, RT-QuIC (0.93; 95% CI [0.87, 0.96]) and NfL (0.94 [0.81, 0.99]) were the most sensitive biomarkers. RT-QuIC was the most specific biomarker (0.96 [0.86, 0.99]), and had the highest balanced accuracy (0.94). Heterogeneity in accuracy estimates was high between studies, especially for specificity.

Conclusions

Our NMA identified RT-QuIC as the overall most accurate biomarker, partially confirming current guidelines. The severe shortcomings identified in many diagnostic studies for sCJD biomarkers need to be addressed in future studies in the field.
Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 using Data Mining and Natural Language Processing
Authors: Schöning Verena , Liakoni Evangelia , Drewe Jürgen , Hammann Felix
Published: March 2021

Objectives

Several risk factors have been identified for severe clinical outcomes of COVID-19 caused by SARS-CoV-2. Some can be found in structured data of patients’ Electronic Health Records. Others are included as unstructured free-text, and thus cannot be easily detected automatically. We propose an automated real-time detection of risk factors using a combination of data mining and Natural Language Processing (NLP).

Material and methods

Patients were categorized as negative or positive for SARS-CoV-2, and according to disease severity (severe or non-severe COVID-19). Comorbidities were identified in the unstructured free-text using NLP. Further risk factors were taken from the structured data.

Results

6250 patients were analysed (5664 negative and 586 positive; 461 non-severe and 125 severe). Using NLP, comorbidities, i.e. cardiovascular and pulmonary conditions, diabetes, dementia and cancer, were automatically detected (error rate ≤2%). Old age, male sex, higher BMI, arterial hypertension, chronic heart failure, coronary heart disease, COPD, diabetes, insulin only treatment of diabetic patients, reduced kidney and liver function were risk factors for severe COVID-19. Interestingly, the proportion of diabetic patients using metformin but not insulin was significantly higher in the non-severe COVID-19 cohort (p<0.05).

Discussion and conclusion

Our findings were in line with previously reported risk factors for severe COVID-19. NLP in combination with other data mining approaches appears to be a suitable tool for the automated real-time detection of risk factors, which can be a time saving support for risk assessment and triage, especially in patients with long medical histories and multiple comorbidities.
Increasing Trust in Real-World Evidence Through Evaluation of Observational Data Quality
Authors: Blacketer Clair , Defalco Frank J , Ryan Patrick B , Rijnbeek Peter R
Published: March 2021

Advances in standardization of observational healthcare data have enabled methodological breakthroughs, rapid global collaboration, and generation of real-world evidence to improve patient outcomes. Standardizations in data structure, such as use of Common Data Models (CDM), need to be coupled with standardized approaches for data quality assessment. To ensure confidence in real-world evidence generated from the analysis of real-world data, one must first have confidence in the data itself. The Data Quality Dashboard is an open-source R package that reports potential quality issues in an OMOP CDM instance through the systematic execution and summarization of over 3,300 configurable data quality checks. We describe the implementation of check types across a data quality framework of conformance, completeness, plausibility, with both verification and validation. We illustrate how data quality checks, paired with decision thresholds, can be configured to customize data quality reporting across a range of observational health data sources. We discuss how data quality reporting can become part of the overall real-world evidence generation and dissemination process to promote transparency and build confidence in the resulting output. Transparently communicating how well CDM standardized databases adhere to a set of quality measures adds a crucial piece that is currently missing from observational research. Assessing and improving the quality of our data will inherently improve the quality of the evidence we generate.
Task-related excitatory/inhibitory ratios in the fronto-striatal circuitry predict attention control deficits in attention-deficit/hyperactivity disorder
Authors: Mamiya Ping C. , Richards Todd L. , Edden Richard A.E. , Lee Adrian K.C. , Stein Mark A. , Kuhl Patricia K.
Published: March 2021

Reduced GABA concentrations at rest in the fronto-striatal circuitry are repeatedly implicated in cognitive symptoms of ADHD. However, recent evidence has suggested that GABA and its precursor, glutamate, are capable of undergoing dynamic modifications in response to environments. Yet, it remains unclear how the dynamics between glutamate and GABA may change when people are exerting their control of attention, and whether they would predict attention control deficits in ADHD. To study this question, we used MR spectroscopy to quantify GABA and glutamate+glutamine (Glx) concentrations in the anterior cingulate cortex (ACC) and the caudate nucleus in the fronto-striatal circuitry while subjects were performing attention control tasks. We studied 19 adults with ADHD (31-51 years) and 16 adults without ADHD (28-54). We found GABA and Glx concentrations during the tasks increased in both subjects with or without ADHD, but the extent of increases was significantly reduced in subjects with ADHD. Notably, E/I ratios (Glx/GABA) also increased and significantly predicted error rates while subjects with or without ADHD performed the Stroop and Flanker tasks. Critically, regression models including E/I ratios, GABA concentrations, and the ADHD diagnosis significantly predicted task performance in these tasks. Furthermore, clear interactions among these factors predicted the impaired attention control in the Flanker task in subjects with ADHD. These findings demonstrate for the first time that E/I ratios in the ACC and the caudate nucleus increased when people exerted their control of attention, and suggest that reduced GABA contribution to E/I ratio in these two brain regions may account for cognitive deficits in ADHD.
A differential regulatory T cell signature distinguishes the immune landscape of COVID-19 hospitalized patients from those hospitalized with other respiratory viral infections
Authors: Vick Sarah C. , Frutoso Marie , Mair Florian , Konecny Andrew J. , Greene Evan , Wolf Caitlin R. , Logue Jennifer K. , Boonyaratanakornkit Jim , Gottardo Raphael , Schiffer Joshua T. , Chu Helen Y. , Prlic Martin , Lund Jennifer M.
Published: March 2021

SARS-CoV-2 infection has caused a lasting global pandemic costing millions of lives and untold additional costs. Understanding the immune response to SARS-CoV-2 has been one of the main challenges in the past year in order to decipher mechanisms of host responses and interpret disease pathogenesis. Comparatively little is known in regard to how the immune response against SARS-CoV-2 differs from other respiratory infections. In our study, we compare the peripheral blood immune signature from SARS-CoV-2 infected patients to patients hospitalized pre-pandemic with Influenza Virus or Respiratory Syncytial Virus (RSV). Our in-depth profiling indicates that the immune landscape in patients infected by SARS-CoV-2 is largely similar to patients hospitalized with Flu or RSV. Similarly, serum cytokine and chemokine expression patterns were largely overlapping. Unique to patients infected with SARS-CoV-2 who had the most critical clinical disease state were changes in the regulatory T cell (Treg) compartment. A Treg signature including increased frequency, activation status, and migration markers was correlated with the severity of COVID-19 disease. These findings are particularly relevant as Tregs are being discussed as a therapy to combat the severe inflammation seen in COVID-19 patients. Likewise, having defined the overlapping immune landscapes in SARS-CoV-2, existing knowledge of Flu and RSV infections could be leveraged to identify common treatment strategies.

Highlights

The immune landscapes of hospitalized pre-pandemic RSV and influenza patients are similar to SARS-CoV-2 patients

Serum cytokine and chemokine expression patterns are largely similar between patients hospitalized with respiratory virus infections, including SARS-CoV-2, versus healthy donors

SARS-CoV-2 patients with the most critical disease displayed unique changes in the Treg compartment

advances in understanding and treating SARS-CoV-2 could be leveraged for other common respiratory infections

Graphical Abstract
Acoustic Remote Control of Bacterial Immunotherapy
Authors: Abedi Mohamad H. , Yao Michael S. , Mittelstein David R. , Bar-Zion Avinoam , Swift Margaret , Lee-Gosselin Audrey , Shapiro Mikhail G.
Published: March 2021

Rapid advances in synthetic biology are driving the development of genetically engineered microbes as therapeutic agents for a multitude of human diseases, including cancer. In particular, the immunosuppressive microenvironment of solid tumors creates a favorable niche for systemically administered bacteria to engraft in the tumor and release therapeutic payloads. However, such payloads can be harmful if released in healthy tissues where the bacteria also engraft in smaller numbers. To address this limitation, we engineer therapeutic bacteria to be controlled by focused ultrasound, a form of energy that can be applied noninvasively to specific anatomical sites such as solid tumors. This control is provided by a temperature-actuated genetic state switch that produces lasting therapeutic output in response to briefly applied focused ultrasound hyperthermia. Using a combination of rational design and high-throughput screening we optimized the switching circuits of engineered cells and connected their activity to the release of immune checkpoint inhibitors. In a clinically relevant cancer model, ultrasound-activated therapeutic microbes successfully turned onin situand induced a marked suppression of tumor growth. This technology provides a critical tool for the spatiotemporal targeting of potent bacterial therapeutics in a variety of biological and clinical scenarios.
A UVB-responsive common variant at chr7p21.1 confers tanning response and melanoma risk via regulation of the aryl hydrocarbon receptor gene (AHR)
Authors: Xu Mai , Mehl Lindsey , Zhang Tongwu , Thakur Rohit , Sowards Hayley , Myers Timothy , Jessop Lea , Chesi Alessandra , Johnson Matthew E , Wells Andrew D , Michael Helen T , Bunda Patricia , Jones Kristine , Higson Herbert , Hennessey Rebecca C , Jermusyk Ashley , Kovacs Michael A , Landi Maria Teresa , Iles Mark M , Goldstein Alisa M ,   Melanoma Meta-Analysis Consortium, Choi Jiyeon , Chanock Stephen J , Grant Struan F A , Chari Raj , Merlino Glenn , Law Matthew H , Brown Kevin M
Published: March 2021

Genome-wide association studies have identified a melanoma-associated locus on chromosome band 7p21.1 with rs117132860 as the lead SNP, and a secondary independent signal marked by rs73069846. rs117132860 is also associated with tanning ability and cutaneous squamous cell carcinoma (cSCC). As ultraviolet radiation (UVR) is a key environmental exposure for all three traits, we investigated the mechanisms by which this locus contributes to melanoma risk, focusing on cellular response to UVR. Fine-mapping of melanoma GWAS identified four independent sets of candidate causal variants. A GWAS region-focused Capture-C study of primary melanocytes identified physical interactions between two causal sets and the promoter of the aryl hydrocarbon receptor gene (AHR). Subsequent chromatin state annotation, eQTL, and luciferase assays identified rs117132860 as a functional variant and reinforcedAHRas a likely causal gene. As AHR plays critical roles in cellular response to dioxin and UVR, we explored links between this SNP andAHRexpression after both 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and ultraviolet B (UVB) exposure. Allele-specific AHR binding to rs117132860-G was enhanced following both, consistent with predicted weakened AHR binding to the risk/poor-tanning rs117132860-A allele, and allele-preferentialAHRexpression driven from the protective rs117132860-G allele was observed following UVB exposure. Small deletions surrounding rs117132860 via CRISPR abrogates AHR binding, reduces melanocyte cell growth, and prolongs growth arrest following UVB exposure. These data suggestAHRis a melanoma susceptibility gene at the 7p21.1 risk locus, and rs117132860 is a functional variant within a UVB-responsive element, leading to allelicAHRexpression, and altering melanocyte growth phenotypes upon exposure.
Protein degradation sets the fraction of active ribosomes at vanishing growth
Authors: Calabrese Ludovico , Grilli Jacopo , Osella Matteo , Kempes Christopher P , Lagomarsino Marco Cosentino , Ciandrini Luca
Published: March 2021

Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data fromE. coliandS. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms.

Author summary

The idea that simple quantitative relationships relate cell physiology to cellular composition dates back to the 1950s, but the recent years saw a leap in our understanding of such “growth laws”, with relevant implications regarding the interdependence between growth, metabolism and biochemical networks. However, recent works on nutrient-limited growth mainly focused on laboratory conditions that are favourable to growth. Thus, our current mathematical understanding of the growth laws neglects protein degradation, under the argument that it occurs slowly compared to the timescale of the cell cycle. Instead, at slow growth the timescales of mass loss from protein degradation and dilution become comparable. In this work, we propose that protein degradation shapes the quantitative relationships between ribosome allocation and growth rate, and determines a fraction of ribosomes that do not contribute to growth and need to remain active to balance degradation.
Integrating diverse data sources to predict disease risk in dairy cattle
Authors: Lasser Jana , Matzhold Caspar , Egger-Danner Christa , Fuerst-Waltl Birgit , Steininger Franz , Wittek Thomas , Klimek Peter
Published: March 2021

Livestock farming is currently undergoing a digital revolution and becoming increasingly data-driven. Yet, such data often reside in disconnected silos making it impossible to leverage their full potential to improve animal well-being. Here, we introduce a precision medicine approach, bringing together information streams from a variety of life domains of dairy cattle to predict eight common and economically important diseases. Dairy cows are part of a highly industrialised environment. The animals and their surroundings are closely monitored and environmental, behavioural and physiological observations are readily accessible yet seldomly integrated. We use random forest classifiers trained on data from 5,828 animals in 166 herds in Austria to predict occurrences of lameness, acute and chronic mastitis, anoestrus, ovarian cysts, metritis, ketosis (hyperketonemia) and periparturient hypocalcemia (milk fever). To assess the importance of specific cattle life domains and individual features for these predictions, we use multivariate logistic regression and feature permutation approaches. We show that disease in dairy cattle is a product of the complex interplay between a multitude of life domains such as housing, nutrition or climate, and identify a range of features that were previously not associated with increased disease risk. For example, we can predict anoestrus with high sensitivity and specificity (F1=0.72) and find that housing, feed and husbandry variables such as barn design and time on pasture are most predictive of this disease. We also find previously unknown associations of features with disease risk, for example humid conditions, which significantly decrease the odds for ketosis. Our findings pave the way towards data-driven point-of-care interventions and demonstrate the added value of integrating all available data in the dairy industry to improve animal well-being and reduce disease risk.
Spatiotemporal Control of Actomyosin Contractility by MRCKβ Signaling Drives Phagocytosis
Authors: Zihni Ceniz , Georgiadis Anastasios , Ramsden Conor M. , Sanchez-Heras Elena , Nommiste Britta , Semenyuk Olha , Bainbridge James W.B. , Coffey Peter J. , Smith Alexander J. , Ali Robin R. , Balda Maria S. , Matter Karl
Published: March 2021

Phagocytosis requires myosin-generated contractile force to regulate actin dynamics. However, little is known about the molecular mechanisms that guide this complex morphodynamic process. Here we show that particle binding to Mer Tyrosine Kinase (MerTK), a widely expressed phagocytic receptor, stimulates phosphorylation of the Cdc42 GEF Dbl3 in the retinal pigment epithelium (RPE), triggering activation of MRCKβ and its co-effector N-WASP that cooperate to deform the membrane into cups. Continued MRCKβ activity then drives recruitment of a mechanosensing bridge enabling transmission of the cytoskeletal force required for cup closure and particle internalization. MRCKβ is also required for Fc receptor-mediated phagocytosis by macrophages.In vivo, MRCKβ is essential for RPE phagocytosis of photoreceptor debris and, hence, retinal integrity. MerTK-independent activation of MRCKβ signaling by a phosphomimetic Dbl3 mutant rescues phagocytosis in retinitis pigmentosa RPE cells lacking functional MerTK. Thus, conserved MRCKβ signaling controls spatiotemporal regulation of actomyosin contractility to guide actomyosin dynamics-driven phagocytosis and represents the principle phagocytic effector pathway downstream of MerTK.
Strength of interactions in the Notch gene regulatory network determines patterning and fate in the notochord
Authors: Sánchez-Iranzo Héctor , Halavatyi Aliaksandr , Diz-Muñoz Alba
Published: March 2021

Development of multicellular organisms requires the generation of gene expression patterns that determines cell fate and organ shape. Groups of genetic interactions known as Gene Regulatory Networks (GRNs) play a key role in the generation of such patterns. However, how the topology and parameters of GRNs determine patterningin vivoremains unclear due to the complexity of most experimental systems. To address this, we use the zebrafish notochord, an organ where coin-shaped precursor cells are initially arranged in a simple unidimensional geometry. These cells then differentiate into vacuolated and sheath cells. Using newly developed transgenic tools together with in vivo imaging, we identifyjag1aandher6/her9as the main components of a Notch GRN that generates a lateral inhibition pattern and determines cell fate. Making use of this experimental system and mathematical modeling we show that lateral inhibition patterning requires that ligand-receptor interactions are stronger within the same cell than in neighboring cells. Altogether, we establish the zebrafish notochord as an experimental system to study pattern generation, and identify and characterize how the properties of GRNs determine self-organization of gene patterning and cell fate.
Dual TCR-alpha expression on MAIT cells as a potential confounder of TCR interpretation
Authors: Suliman Sara , Kjer-Nielsen Lars , Iwany Sarah K. , Tamara Kattya Lopez , Loh Liyen , Grzelak Ludivine , Kedzierska Katherine , Ocampo Tonatiuh A. , Corbett Alexandra J. , McCluskey James , Rossjohn Jamie , León Segundo R , Calderon Roger , Garcia Leonid Lecca , Murray Megan B. , Moody D. Branch , Van Rhijn Ildiko
Published: March 2021

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant T cell receptor (TCR) α chain that uses TRAV1-2 joined to TRAJ33/20/12 and recognize metabolites from bacterial riboflavin synthesis bound to the antigen-presenting molecule, MR1. Recently, our attempts to identify alternative MR1-presented antigens led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered antigen specificity is likely to lead to altered affinity for the most potent known antigen, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRα and β chain sequencing, and single cell-based paired TCR sequencing, on T cells that bound the MR1-5-OP-RU tetramer, but with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlowcells. Whereas we initially interpreted these as diverse MR1-restricted TCRs, single cell TCR sequencing revealed that cells expressing atypical TCRα chains also co-expressed an invariant MAIT TCRα chain. Transfection of each non-TRAV1-2 TCRα chain with the TCRβ chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα chain expression in human T cells and competition for the endogenous β chain explains the existence of some MR1-5-OP-RU tetramerlowT cells. The discovery of simultaneous expression of canonical and non-canonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of antigen specificity.
Thermal Fogging with Disinfectant Didecyl Dimethyl Ammonium Bromide Effectively Kills A Coronavirus, An Influenza Virus and Two Indicator Bacteria in Subzero Cold-Chain Environment
Authors: Hu Qiaoyun , Ma Pei , Hong Junyi , Wang Yulong , Huang Dong , Tan Yadi , Yu Zhengjun
Published: March 2021

Background

The origin of several local COVID-19 outbreaks in China in 2020 were confirmed to be frozen food or packages contaminated with SARS-CoV-2, revealing the lack of effective disinfection measures in the frozen food chain.

Objective

To evaluate the disinfection efficacy at −20°C of a recently marketed thermal fogging disinfection product, with disinfectant-antifreeze combination being didecyl dimethyl ammonium bromide (DDAB) - propylene glycol (PPG).

Method

Carriers with porcine epidemic diarrhea virus (PEDV) YN1, a coronavirus, and a swine influenza virus H1N1 (SIV-H1N1), and three indicator bacteria,E. coli, S. aureus,andB. subtilisendospores, were respectively placed in a −20°C freezer warehouse with or without DDAB-PPG fogging and activities of the microorganisms were tested.

Results

At −20°C, DDAB-PPG fogging, which fully settles in 3.5−4.5 hours, fully inactivated PEDV of 10−3.5TCID50/0.1ml and SIV-H1N1 of 26hemagglutination titer within 15-30 min, and inactivatedS. aureusandE. colivegetative cells (106/ml) within 15 or 60 min, respectively, but had little effect onB. subtilisspores. The bactericidal effect lasted at least 3 hours for bacteria on carrier plates and for 6 hours for airborne bacteria.

Conclusions

A practical subzero temperature disinfection technology was confirmed its efficacy in killing enveloped viruses and vegetative bacteria. It would help to meet the urgent public health need of environmental disinfection in frozen food logistics against pandemic and other potential pathogens and to enhance national and international biosecurity.

Highlights

First report of efficacy of disinfectant didecyl dimethyl ammonium bromide (DDAB) at subzero temperatures

The customized thermal fogging machine makes fine droplets of DDAB-propylene glycol (PPG) fog which can suspend for ~4 hours at −20°C

DDAB-PPG thermal fogging at −20°C effectively inactivated a coronavirus and an influenza virus

DDAB-PPG thermal fogging at −20°C for effectively killedS. aureusandE. coli

DDAB-PPG thermal fogging at −20°C inactivated airborne microorganism for up to 6 h
Genomic Alterations and Possible Druggable Mutations in Carcinoma of Unknown Primary (CUP)
Authors: Aboulkheyr Es Hamidreza , Mahdizadeh Hamid , Hedayati Asl Amir Abbas , Totonchi Mehdi
Published: March 2021

Carcinoma of Unknown Primary (CUP) is a heterogeneous and metastatic disease where the primary site of origin is undetectable. Currently, chemotherapy is an only state-of-art treatment option for the CUP patient. Employing molecular profiling of the tumour, particularly mutation detection, offers a new treatment for CUP in a personalized fashion. Here, we analyzed mutation and copy number alterations profile of 1,709 CUP samples deposited in GENIE cohort and explored potential druggable mutations. We identified 52 significant mutated genes (SMG) among CUP samples, of which 13 (25%) of SMG were potentially targetable with drugs reproved for the know primary tumour or undergoing clinical trials. The most variants detected wereTP53(43%),KRAS(19.90%),KMT2D(12.60%), andCDKN2A(10.30%). Additionally, the presence of similar variants ofTERTpromoter in CUP compared to NSCLC samples suggests these mutations may serve as a diagnostic marker for identifying the primary tumour in CUP. Taken together, analyzing mutation profiling of the CUP tumours may open a new way of identifying druggable targets and consequently administrating appropriate treatment in a personalized manner.
Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany
Authors: Eze Michael O. , Hose Grant C. , George Simon C. , Daniel Rolf
Published: March 2021

The pollution of terrestrial and aquatic environments by petroleum contaminants, especially diesel fuel, is a persistent environmental threat requiring cost-effective and environmentally sensitive remediation approaches. Bioremediation is one such approach, but is dependent on the availability of microorganisms with the necessary metabolic abilities and environmental adaptability. The aim of this study was to examine the microbial community in a petroleum contaminated site, and isolate organisms potentially able to degrade hydrocarbons. Through successive enrichment of soil microorganisms from samples of an historic petroleum contaminated site in Wietze, Germany, we isolated a bacterial consortium using diesel fuel hydrocarbons as sole carbon and energy source. The 16S rRNA gene analysis revealed the dominance ofAlphaproteobacteria. We further reconstructed a total of 18 genomes from both the original soil sample and the isolated consortium. The analysis of both the metagenome of the consortium and the reconstructed metagenome-assembled genomes show that the most abundant bacterial genus in the consortium,Acidocella, possess many of the genes required for the degradation of diesel fuel aromatic hydrocarbons, which are often the most toxic component. This can explain why this genus proliferated in all the enrichment cultures. Therefore, this study reveals that the microbial consortium isolated in this study and its dominant genus,Acidocella, could potentially serve as an effective inoculum for the bioremediation of sites polluted with diesel fuel or other organic contaminants.
A robust, semi-automated approach for counting cementum increments imaged with X-ray computed tomography
Authors: Newham Elis , Gill Pamela G. , Brown Kate Robson , Gostling Neil J. , Corfe Ian J. , Schneider Philipp
Published: March 2021

Cementum, the tissue attaching mammal tooth roots to the periodontal ligament, grows appositionally throughout life, displaying a series of circum-annual incremental features. These have been studied for decades as a direct record of chronological lifespan. The majority of previous studies on cementum have used traditional thin-section histological methods to image and analyse increments. However, several caveats have been raised in terms of studying cementum increments in thin-sections. Firstly, the limited number of thin-sections and the two-dimensional perspective they impart provide an incomplete interpretation of cementum structure, and studies often struggle or fail to overcome complications in increment patterns that complicate or inhibit increment counting. Increments have been repeatedly shown to both split and coalesce, creating accessory increments that can bias increment counts. Secondly, identification and counting of cementum increments using human vision is subjective, and it has led to inaccurate readings in several experiments studying individuals of known age. Here, we have attempted to optimise a recently introduced imaging modality for cementum imaging; X-ray propagation-based phase-contrast imaging (PPCI). X-ray PPCI was performed for a sample of rhesus macaque (Macaca mulatta) lower first molars (n=10) from a laboratory population of known age. A new method for semi-automatic incrementcounting was then integrated into a purpose-built software package for studying cementum increments. Comparison with data from conventional cementochronology, based on histological examination of tissue sections, confirmed that X-ray PPCI reliably records cementum increments. Validation of the increment counting algorithm suggests that it is robust and provides accurate estimates of increment counts. In summary, we show that our new increment counting method has the potential to overcome caveats of conventional cementochronology approaches, when used to analyse 3D images provided by X-ray PPCI.
Systematics and phylogeography of the Brazilian Atlantic Forest endemic harvestmenNeosadocusMello-Leitão, 1926 (Arachnida: Opiliones: Gonyleptidae)
Authors: Castro-Pereira Daniel , Peres Elen A. , Pinto-da-Rocha Ricardo
Published: March 2021

Neosadocusharvestmen are endemic to the Southern Brazilian Atlantic Forest. Although they are conspicuous and display great morphological variation, their evolutionary history and the biogeographical events underlying their diversification and distribution are still unknown. This contribution aboutNeosadocusincludes the following: a taxonomic revision; a molecular phylogenetic analysis using mitochondrial and nuclear markers; an investigation of the genetic structure and species’ diversity in a phylogeographical framework. Our results show thatNeosadocusis a monophyletic group and comprises four species:N. bufo,N. maximus,N. robustusandN. misandrus(which we did not find on fieldwork and only studied the female holotype). There is astonishing male polymorphism inN. robustus, mostly related to reproductive strategies. The following synonymies have resulted from this work:Bunoweyhia variabilisMello-Leitão, 1935 =Neosadocus bufo(Mello-Leitão, 1926); andBunoweyhia minorMello-Leitão, 1935 =Neosadocus maximus(Giltay, 1928). Most divergences occurred during the Miocene, a geological epoch marked by intense orogenic and climatic events in the Brazilian Atlantic Forest. Intraspecific analyses indicate strong population structure, a pattern congruent with the general behavior and physiological constraints of Neotropical harvestmen.
FPM app: an open-source application for simple and intuitive Fourier ptychographic reconstruction
Authors: Rogalski Mikołaj , Zdańkowski Piotr , Trusiak Maciej
Published: March 2021

Fourier ptychographic microscopy (FPM) is a computational microscopy technique that enables large field of view and high-resolution microscopic imaging of biological samples. However, the FPM does not yet have an adequately capable open-source software. In order to fill this gap we are presenting novel, simple, universal, semi-automatic and highly intuitive graphical user interface (GUI) open-source application called theFPM appenabling wide-scale robust FPM reconstruction. Apart from implementing the FPM in accessible GUI app, we also made several improvements in the FPM image reconstruction process itself, making the FPM more automatic, noise-robust and faster.

Availability and Implementation

FPM appwas implemented in MATLAB and all MATLAB codes along with standalone executable version of theFPM appand the online documentation are freely accessible athttps://github.com/MRogalski96/FPM-app. Our exemplary FPM datasets may be downloaded athttps://bit.ly/2MxNpGb.
Tissue flow through pores: a computational study
Authors: Kempf Felix , Goychuk Andriy , Frey Erwin
Published: March 2021

Abstract

Cell migration is of major importance for the understanding of phenomena such as morphogenesis, cancer metastasis, or wound healing. In many of these situations cells are under external confinement. In this work we show by means of computer simulations with a Cellular Potts Model (CPM) that the presence of a bottleneck in an otherwise straight channel has a major influence on the internal organisation of an invading cellular monolayer and the motion of individual cells therein. Comparable to a glass or viscoelastic material, the cell sheet is found to exhibit features of both classical solids and classical fluids. The local ordering on average corresponds to a regular hexagonal lattice, while the relative motion of cells is unbounded. Compared to an unconstricted channel, we observe that a bottleneck perturbs the formation of regular hexagonal arrangements in the epithelial sheet and leads to pile-ups and backflow of cells near the entrance to the constriction, which also affects the overall invasion speed. The scale of these various phenomena depends on the dimensions of the different channel parts, as well as the shape of the funnel domain that connects wider to narrower regions.
CG2AT2: An Enhanced Fragment-based approach for Serial Multi-scale Molecular Dynamics simulations
Authors: Vickery Owen N. , Stansfeld Phillip J.
Published: March 2021

Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for e.g. membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of eleven system configurations of vary size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.
Lipid membranes modulate the activity of RNA through sequence-dependent interactions
Authors: Czerniak Tomasz , Saenz James P
Published: March 2021

RNA is a ubiquitous biomolecule that can serve as both catalyst and information carrier. Understanding how RNA bioactivity is controlled is crucial for elucidating its physiological roles and potential applications in synthetic biology. Here we show that lipid membranes can act as RNA organization platforms, introducing a novel mechanism for ribo-regulation. The activity of R3C ribozyme can be modified by the presence of lipid membranes, with direct RNA-lipid interactions dependent on RNA nucleotide content, base pairing and length. In particular, the presence of guanine in short RNAs is crucial for RNA-lipid interactions, and G-quadruplex formation further promotes lipid binding. Lastly, by artificially modifying the R3C substrate sequence to enhance membrane binding we generated a lipid-sensitive ribozyme reaction with riboswitch-like behavior. These findings introduce RNA-lipid interactions as a tool for developing synthetic riboswitches and novel RNA-based lipid biosensors, and bear significant implications for RNA World scenarios for the origin of life.
Pseudomonas aeruginosaisolates defective in function of the LasR quorum sensing regulator are frequent in diverse environmental niches
Authors: Groleau Marie-Christine , Taillefer Hélène , Vincent Antony T. , Constant Philippe , Déziel Eric
Published: March 2021

The saprophytePseudomonas aeruginosais a versatile opportunistic pathogen causing infections in immunocompromised individuals. To facilitate its adaptation to a large variety of niches, this bacterium exploits population density-dependant gene regulation systems called quorum sensing. InP. aeruginosa, three distinct but interrelated quorum sensing systems (las,rhlandpqs) regulate the production of many survival and virulence functions. In prototypical strains, thelassystem, through its transcriptional regulator LasR, is important for the full activation of therhlandpqssystems. Still, LasR-deficient isolates have been reported, mostly sampled from the lungs of people with cystic fibrosis, where they are considered selected by the chronic infection environment. In this study, we show that a defect in LasR activity appears to be an actually widespread mechanism of adaptation in this bacterium. Indeed, we found abundant LasR-defective isolates sampled from hydrocarbon-contaminated soils, hospital sink drains, and meat/fish market environments, using an approach based on phenotypic profiling, supported by gene sequencing. Interestingly, several LasR-defective isolates maintain an activerhlsystem or are deficient inpqssystem signaling. The high prevalence of a LasR-defective phenotype among environmentalP. aeruginosaisolates questions the role of quorum sensing in niche adaptation.
scAmpi - A versatile pipeline for single-cell RNA-seq analysis from basics to clinics
Authors: Bertolini Anne , Prummer Michael , Tuncel Mustafa Anil , Menzel Ulrike , Rosano-González María Lourdes , Kuipers Jack , Stekhoven Daniel Johannes ,   Tumor Profiler consortium, Beerenwinkel Niko , Singer Franziska
Published: March 2021

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful technique to decipher tissue composition at the single-cell level and to inform on disease mechanisms, tumor heterogeneity, and the state of the immune microenvironment. Although multiple methods for the computational analysis of scRNA-seq data exist, their application in a clinical setting demands standardized and reproducible workflows, targeted to extract, condense, and display the clinically relevant information. To this end, we designed scAmpi (SingleCellAnalysismRNApipeline), a workflow that facilitates scRNA-seq analysis from raw read processing to informing on sample composition, clinically relevant gene and pathway alterations, andin silicoidentification of personalized candidate drug treatments. We demonstrate the value of this workflow for clinical decision making in a molecular tumor board as part of a clinical study.
Combining IP3affinity chromatography and bioinformatics reveals a novel protein-IP3binding site onPlasmodium falciparumMDR1 transporter
Authors: Alves Eduardo , Nakaya Helder , Guimarães Euzébio , Garcia Célia R. S.
Published: March 2021

Intracellular Ca2+mobilization induced by second messenger IP3controls many cellular events in most of the eukaryotic groups. Despite the increasing evidence of IP3-induced Ca2+in apicomplexan parasites likePlasmodium, responsible for malaria infection, no protein with potential function as an IP3-receptor has been identified. The use of bioinformatic analyses based on previously known sequences of IP3-receptor failed to identify potential IP3-receptor candidates in anyApicomplexa. In this work, we combine the biochemical approach of an IP3affinity chromatography column with bioinformatic meta-analyses to identified potential vital membrane proteins that present binding with IP3inPlasmodium falciparum. Our analyses reveal that PF3D7_0523000, a gene that codes a transport protein associated with multidrug resistance, as a potential target for IP3. This work provides a new insight for probing potential candidates for IP3-receptor inApicomplexa.