bluuebunny/crossref_metadata_2025_split huggingface dataset:
Starvation induces shrinkage of the bacterial cytoplasm
Authors: Shi Handuo , Westfall Corey S. , Kao Jesse , Odermatt Pascal D. , Cesar Spencer , Anderson Sarah , Sievert Montana , Moore Jeremy , Gonzalez Carlos G. , Zhang Lichao , Elias Joshua E. , Chang Fred , Huang Kerwyn Casey , Levin Petra Anne 
Published: December 2020

AbstractEnvironmental fluctuations are a common challenge for single-celled organisms; enteric bacteria such asEscherichia coliexperience dramatic changes in nutrient availability, pH, and temperature during their journey into and out of the host. While the effects of altered nutrient availability on gene expression and protein synthesis are well known, their impacts on cytoplasmic dynamics and cell morphology have been largely overlooked. Here, we discover that depletion of utilizable nutrients results in shrinkage ofE. coli’sinner membrane from the cell wall. Shrinkage was accompanied by a ∼17% reduction in cytoplasmic volume and a concurrent increase in periplasmic volume. Inner membrane retraction occurred almost exclusively at the new cell pole. This phenomenon was distinct from turgor-mediated plasmolysis and independent of new transcription, translation, or canonical starvation-sensing pathways. Cytoplasmic dry-mass density increased during shrinkage, suggesting that it is driven primarily by loss of water. Shrinkage was reversible: upon a shift to nutrient-rich medium, expansion started almost immediately at a rate dependent on carbon-source quality. Robust recovery from starvation required the Tol-Pal system, highlighting the importance of envelope coupling during recovery.Klebsiella pneumoniaealso exhibited shrinkage when shifted to carbon-free conditions, suggesting a conserved phenomenon. These findings demonstrate that even when Gram-negative bacterial growth is arrested, cell morphology and physiology are still dynamic.Significance statementBacterial cells constantly face nutrient fluctuations in their natural environments. While previous studies have identified gene expression changes upon nutrient depletion, it is much less well known how cellular morphology and cytoplasmic properties respond to shifts in nutrient availability. Here, we discovered that switching fast-growingEscherichia colicells to nutrient-free conditions results in substantial shrinkage of the inner membrane away from the cell wall, especially at the new pole. Shrinkage was primarily driven by loss of cytoplasmic water contents. Shrinkage was also exhibited by cells naturally entering stationary phase, highlighting its biological relevance across starvation conditions. The membrane-spanning Tol-Pal system was critical for robust entry into and recovery from shrinkage, indicating the importance of cell-envelope homeostasis in surviving nutrient starvation.
Mathematical model of tumour spheroid experiments with real-time cell cycle imaging
Authors: Jin Wang , Spoerri Loredana , Haass Nikolas K. , Simpson Matthew J. 
Published: December 2020

AbstractThree-dimensional (3D)in vitrotumour spheroid experiments are an important tool for studying cancer progression and potential drug therapies. Standard experiments involve growing and imaging spheroids to explore how different experimental conditions lead to different rates of spheroid growth. These kinds of experiments, however, do not reveal any information about the spatial distribution of the cell cycle within the expanding spheroid. Since 2008, a new experimental technology called fluorescent ubiquitination-based cell cycle indicator (FUCCI), has enabled real timein situvisualisation of the cell cycle progression. FUCCI labelling involves cells in G1 phase of the cell cycle fluorescing red, and cells in the S/G2/M phase of the cell cycle fluorescing green. Experimental observations of 3D tumour spheroids with FUCCI labelling reveal significant intratumoural structure, as the cell cycle status can vary with location. Although many mathematical models of tumour spheroid growth have been developed, none of the existing mathematical models are designed to interpret experimental observations with FUCCI labelling. In this work we extend the mathematical framework originally proposed by Ward and King (1997) to develop a new mathematical model of FUCCI-labelled tumour spheroid growth. The mathematical model treats the spheroid as being composed of three subpopulations: (i) living cells in G1 phase that fluoresce red; (ii) living cells in S/G2/M phase that fluoresce green; and, (iii) dead cells that do not fluoresce. We assume that the rates at which cells pass through different phases of the cell cycle, and the rate of cell death, depend upon the local oxygen concentration in the spheroid. Parameterising the new mathematical model using experimental measurements of cell cycle transition times, we show that the model can capture important experimental observations that cannot be addressed using previous mathematical models. Further, we show that the mathematical model can be used to quantitatively mimic the action of anti-mitotic drugs applied to the spheroid. All software required to solve the nonlinear moving boundary problem associated with the new mathematical model are available onGitHub.
A minimal model of T cell avidity may identify subtherapeutic vaccine schedules
Authors: Kumbhari Adarsh , Rose Danya , Lee Peter P. , Kim Peter S. 
Published: December 2020

AbstractT cells protect the body from cancer by recognising tumour-associated antigens. Recognising these antigens depends on multiple factors, one of which is T cell avidity, i.e., the total interaction strength between a T cell and a cancer cell. While both high- and low-avidity T cells can kill cancer cells, durable anti-cancer immune responses require the selection of high-avidity T cells. Previous experimentation with anti-cancer vaccines, however, has shown that most vaccines elicit low-avidity T cells. Optimising vaccine schedules may remedy this by preferentially selecting high-avidity T cells. Here, we use mathematical modelling to develop a simple, phenomenological model of avidity selection that may identify vaccine schedules that disproportionately favour low-avidity T cells. We calibrate our model to our prior, more complex model, and then validate it against several experimental data sets. We find that the sensitivity of the model’s parameters change with vaccine dosage, which allows us to use a patient’s data and clinical history to screen for suitable vaccine strategies.
Single-cell multi-omics reveals elevated plasticity and stem-cell-like blasts relevant to the poor prognosis ofKMT2A-rearranged leukemia
Authors: Chen Changya , Yu Wenbao , Alikarami Fatemeh , Qiu Qi , Chen Chia-hui , Flournoy Jennifer , Gao Peng , Uzun Yasin , Fang Li , Hu Yuxuan , Zhu Qin , Wang Kai , Libbrecht Clara , Felmeister Alex , Rozich Isaiah , Ding Yang-yang , Hunger Stephen P. , Wu Hao , Brown Patrick A. , Guest Erin M. , Barrett David M. , Bernt Kathrin M. , Tan Kai 
Published: December 2020

SummaryInfant ALL is a devastating malignancy caused by rearrangements of theKMT2Agene (KMT2A-r) in approximately 70% of patients. The outcome is dismal and younger age at diagnosis is associated with increased risk of relapse. To discover age-specific differences and critical drivers that mediate the poor outcome inKMT2A-rALL, we subjectedKMT2A-rleukemias and normal hematopoietic cells from patients of different ages to multi-omic single cell analysis using scRNA-Seq, scATAC-Seq and snmC-Seq2. We uncovered the following critical new insights: Leukemia cells from infants younger than 6 months have a greatly increased lineage plasticity and contain a hematopoietic stem and progenitor-like (HSPC-like) population compared to older infants. We identified an immunosuppressive signaling circuit between the HSPC-like blasts and cytotoxic lymphocytes in younger patients. Both observations offer a compelling explanation for the ability of leukemias in young infants to evade chemotherapy and immune mediated control. Our analysis also revealed pre-existing lymphomyeloid primed progenitor and myeloid blasts at initial diagnosis of B-ALL. Tracking of leukemic clones in two patients whose leukemia underwent a lineage switch documented the evolution of such clones into frank AML. These findings provide critical insights intoKMT2A-rALL and have potential clinical implications for targeted inhibitors or multi-target immunotherapy approaches. Beyond infant ALL, our study demonstrates the power of single cell multi-omics to detect tumor intrinsic and extrinsic factors affecting rare but critical subpopulations within a malignant population that ultimately determines patient outcome.
Detection ofDeformed wing virus(DWV) in the Vietnamese Walking StickMedauroidea extradentata(Phasmatodea)
Authors: Shelomi Matan , Lin Wei , Johnson Brian R , Furlong Michael J. , Etebari Kayvan 
Published: December 2020

AbstractDeformed wing virus(DWV) is a single-stranded positive sense RNA virus which mainly infects honey bees (Apis mellifera) and can have devastating impacts on the colony. Recent studies have shown the presence of this virus in several species ofApisspp. and some other Hymenoptera, but our knowledge of their host range is very limited. We screened previously sequenced RNAseq libraries from different tissues of Vietnamese Walking Stick,Medauroidea extradentata(Phasmatodea) for DWV. We only found this virus in six libraries from anterior and posterior midgut tissue. From the midgut libraries we were able to construct the complete genome sequence of DWV, which consisted of 10,140 nucleotides and included one open reading frame. Pairwise genome comparison confirmed strong similarity (98.89%) of these assembled sequences with only 113 SNPs to the original DWV genome. PerhapsM. extradentataacquired this virus via a foodborne transmission by consuming DWV-infected material such as pollen or leaves contaminated with virus infected bee faeces.
REGALS: a general method to deconvolve X-ray scattering data from evolving mixtures
Authors: Meisburger Steve P. , Xu Da , Ando Nozomi 
Published: December 2020

AbstractMixtures of biological macromolecules are inherently difficult to study using structural methods, as increasing complexity presents new challenges for data analysis. Recently, there has been growing interest in studying evolving mixtures using small-angle X-ray scattering (SAXS) in conjunction with time-resolved, high-throughput, or chromatography-coupled setups. Deconvolution and interpretation of the resulting datasets, however, are nontrivial when neither the scattering components nor the way in which they evolve are known a priori. To address this issue, we introduce the REGALS method (REGularized Alternating Least Squares), which incorporates simple expectations about the data as prior knowledge and utilizes parameterization and regularization to provide robust deconvolution solutions. The restraints used by REGALS are general properties such as smoothness of profiles and maximum dimensions of species, which makes it well-suited for exploring datasets with unknown species. Here we apply REGALS to analyze experimental data from four types of SAXS experiment: anion-exchange (AEX) coupled SAXS, ligand titration, time-resolved mixing, and time-resolved temperature jump. Based on its performance with these challenging datasets, we anticipate that REGALS will be a valuable addition to the SAXS analysis toolkit and enable new experiments. The software is implemented in both MATLAB and python and is available freely as an open-source software package.
A 6-mRNA host response whole-blood classifier trained on pre-pandemic data accurately predicts severity in COVID-19 and other acute viral infections
Authors: Buturovic Ljubomir , Zheng Hong , Tang Benjamin , Lai Kevin , Kuan Win Sen , Gillett Mark , Santram Rahul , Shojaei Maryam , Almansa Raquel , Ángel Nieto Jose , Muñoz Sonsoles , Herrero Carmen , Antonakos Nikolaos , Koufargyris Panayiotis , Kontogiorgi Marina , Damoraki Georgia , Liesenfeld Oliver , Wacker James , Midic Uros , Luethy Roland , Rawling David , Remmel Melissa , Coyle Sabrina , Liu Yiran E. , Rao Aditya M , Dermadi Denis , Toh Jiaying , Jones Lara Murphy , Donato Michele , Khatri Purvesh , Giamarellos-Bourboulis Evangelos J. , Sweeney Timothy E 
Published: December 2020

AbstractBackgroundDetermining the severity of COVID-19 remains an unmet medical need. Our objective was to develop a blood-based host-gene-expression classifier for the severity of viral infections and validate it in independent data, including COVID-19.MethodsWe developed the classifier for the severity of viral infections and validated it in multiple viral infection settings including COVID-19. We used training data (N=705) from 21 retrospective transcriptomic clinical studies of influenza and other viral illnesses looking at a preselected panel of host immune response messenger RNAs.ResultsWe selected 6 host RNAs and trained logistic regression classifier with a cross-validation area under curve of 0.90 for predicting 30-day mortality in viral illnesses. Next, in 1,417 samples across 21 independent retrospective cohorts the locked 6-RNA classifier had an area under curve of 0.91 for discriminating patients with severe vs. non-severe infection. Next, in independent cohorts of prospectively (N=97) and retrospectively (N=100) enrolled patients with confirmed COVID-19, the classifier had an area under curve of 0.89 and 0.87, respectively, for identifying patients with severe respiratory failure or 30-day mortality. Finally, we developed a loop-mediated isothermal gene expression assay for the 6-messenger-RNA panel to facilitate implementation as a rapid assay.ConclusionsWith further study, the classifier could assist in the risk assessment of COVID-19 and other acute viral infections patients to determine severity and level of care, thereby improving patient management and reducing healthcare burden.
Integrated phenotypic and mutational approach defines EBF3-related HADD syndrome genotype-phenotype relationships
Authors: Deisseroth Cole A. , Nayak Aarushi , Bliss Nathan D. , Lerma Vanesa , LeMaire Ashley W. , Narayanan Vinodh , Balak Christopher , Zanni Ginevra , Valente Enza Maria , Bertini Enrico , Benke Paul J. , Wangler Michael F. , Chao Hsiao-Tuan 
Published: December 2020

AbstractHypotonia, Ataxia, and Delayed Development syndrome is a neurodevelopmental disorder caused by heterozygousEarly B-Cell Factor 3(EBF3) loss-of-function variants. Identified in 2016, the full spectrum of clinical findings and the relationship between theEBF3genotype and clinical outcomes has not been determined beyond its namesake features. We combined a phenotypic assessment of 33 individuals molecularly diagnosed withEBF3pathogenic variants with a meta-analysis of 34 previously reported individuals. The combined 62 unique individuals enabled comparative cross-sectional phenotype and genotype analysis in the largest cohort to date of affected individuals. Cardinal distinguishing features were identified that facilitate phenotypic stratification for clinical diagnosis. We developed assessment scales to ascertain individuals at risk for pathogenicEBF3variants, stratify the clinical severity, and connect variant-specific molecular phenotypes to clinical outcomes. Our findings show that a specific class ofEBF3variants affecting the evolutionarily conserved Zinc Finger (ZNF) motif, which is critical for stabilizing the protein interaction with the DNA target sequence, is associated with an increased risk of persistent motor and language impairments. These findings highlight the impact of combining variant-specific molecular phenotypes with comprehensive clinical data to predict neurodevelopmental outcomes and potentially guide personalized decisions for therapeutic interventions.
Is the glass half full? Extraction-free RT-LAMP to detect SARS-CoV-2 is less sensitive but highly specific compared to standard RT-PCR in 101 samples
Authors: Schellenberg John J. , Ormond Margaret , Keynan Yoav 
Published: December 2020

AbstractThe current scale of public and private testing cannot be expected to meet the emerging need for higher levels of community-level and repeated screening of asymptomatic Canadians for SARS-CoV-2. Rapid point-of-care techniques are increasingly being deployed to fill the gap in screening levels required to identify undiagnosed individuals with high viral loads. However, rapid, point-of-care tests often have lower sensitivity in practice. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) for SARS-CoV-2 has proven sensitive and specific and provides visual results in minutes. Using a commercially available kit for RT-LAMP and primer set targetting nucleocapsid (N) gene, we tested a blinded set of 101 archived nasopharyngeal (NP) swab samples with known RT-PCR results. RT-LAMP reactions were incubated at 65°C for 30 minutes, using heat-inactivated nasopharyngeal swab sample in viral transport medium, diluted tenfold in water, as input. RT-LAMP agreed with all RT-PCR defined negatives (N=51), and all positives with Ct less than 20 (N=24), 65% of positives with Ct between 20-30 (N=17), and no positives with Ct greater than 30 (N=9). RT-LAMP requires fewer and different core components, so may not compete directly with the mainline testing workflow, preserving precious central laboratory resources and gold standard tests for those with the greatest need. Careful messaging must be provided when using less-sensitive tests, so that people are not falsely reassured by negative results – “glass half empty” – in exchange for reliable detection of those with high levels of virus within an hour, using <$10 worth of chemicals – “glass half full”.
Inadequate intention to receive Covid-19 vaccination: indicators for public health messaging needed to improve uptake in UK
Authors: Bachtiger Patrik , Adamson Alexander , Maclean William A , Quint Jennifer K , Peters Nicholas S 
Published: December 2020

AbstractData promising effective Covid-19 vaccines have accelerated the UK’s mass vaccination programme. The UK public’s attitudes to the government’s prioritisation list are unknown, and achieving critical population immunity will require the remaining majority to accept both vaccination and the delay in access of up to a year or more. This cross-sectional observational study sent an online questionnaire to registrants of the UK National Health Service’s largest personal health record. Question items covered willingness for Covid-19 vaccine uptake and attitudes to prioritisation. Among 9,122 responses, 71.5% indicated wanting a vaccine, below what previous modelling indicated as critical levels for progressing towards herd immunity. 22.7% disagreed with the prioritisation list, though 70.3% were against being able to expedite vaccination through payment. Age and female gender were, respectively, strongly positively and negatively associated with wanting a vaccine. Teachers and Black, Asian and Minority Ethnic (BAME) groups were most cited by respondents for prioritisation. This study identifies factors to inform the public health messaging critical to improving uptake.
Diagnostic and monitoring utilities of saliva for SARS-CoV-2
Authors: AbdulRahman AbdulKarim , AlBastaki Ahmed , AlAwadhi Abdulla , Alwazaan Asmaa , AlQahtani Manaf 
Published: December 2020

AbstractIntroductionNasopharyngeal (NP) swab is an invasive procedure that is difficult to perform in pediatric cases and those with special needs. On the other hand, saliva has been a proposed sample given the ease of collection, comfort and the ability to self-collect. The research project aims to study the presence of SARS-CoV-2 in the saliva of suspected COVID-19 patients in comparison to its presence in NP swabs.MethodologyA cross-sectional study was conducted in October 2020 in COVID19 clinic in the Bahrain Defense Force Hospital. The study compared the presence of SARS-CoV2 by PCR in saliva samples to nasopharyngeal samples. COVID-19 Clinic tests symptomatic, staff, close contacts and pre-operation patients.ResultsThe saliva PCR has shown a sensitivity of 72.9% (95% CI: 58.2% - 84.7%) and a specificity of 98.8% (95% CI: 97.8% - 99.4%). The PPV was 74.5% (95% CI 59.7% to 86.1%) and the NPV was 98.6% (95% CI 97.7% to 99.3%). Kappa coefficient of agreement between saliva and NP was 0.723 (95% CI 0.62 to 0.82, p<0.001). Moreover, when restricting cases to symptomatic only, the sensitivity of saliva increased to 86.7% (95% CI 59.5% to 98.3%) while specificity remained high at 97.2%.ConclusionThe findings of the study suggest that saliva samples have the potential to be used as a screening tool for SARS-CoV-2, especially in symptomatic individuals. This is especially important when it is difficult to collect NP samples. Saliva samples are however at risk of producing more false negative tests.
Indicators of past COVID-19 infection status: Findings from a large occupational cohort of staff and postgraduate research students from a UK university
Authors: Davis Katrina A. S. , Carr Ewan , Leightley Daniel , Vitiello Valentina , Bergin-Cartwright Gabriella , Lavelle Grace , Wickersham Alice , Malim Michael H. , Oetzmann Carolin , Polling Catherine , Stevelink Sharon A.M , Razavi Reza , Hotopf Matthew 
Published: December 2020

ABSTRACTBackgroundDefinitive diagnosis of COVID-19 requires resources frequently restricted to the severely ill. Cohort studies must rely on surrogate indicators to define cases of COVID-19 in the community. We describe the prevalence and overlap of potential indicators including self-reported symptoms, suspicion, and routine test results, plus home antibody testing.MethodsAn occupational cohort of 2807 staff and postgraduate students at a large London university. Repeated surveys covering March to June 2020. Antibody test results from ‘lateral flow’ IgG/IgM cassettes in June 2020.Results1882 participants had valid antibody test results, and 124 (7%) were positive. Core symptoms of COVID-19 were common (770 participants positive, 41%), although fewer met criteria on a symptom algorithm (n=297, 16%). Suspicion of COVID-19 (n=509, 27%) was much higher than positive external tests (n=39, 2%). Positive antibody tests were rare in people who had no suspicion (n=4, 1%) or no core symptoms (n=10, 2%). In those who reported external antibody tests, 15% were positive on the study antibody test, compared with 24% on earlier external antibody tests.DiscussionOur results demonstrate the agreement between different COVID indicators. Antibody testing using lateral flow devices at home can detect asymptomatic cases and provide greater certainty to self-report; but due to weak and waning antibody responses to mild infection, may under-ascertain. Multiple indicators used in combination can provide a more complete story than one used alone. Cohort studies need to consider how they deal with different, sometimes conflicting, indicators of COVID-19 illness to understand its long-term outcomes.THUMBNAILWhat is already known on this subject?Research into the effects of COVID-19 in the community is needed to respond to the pandemic, and guidance is needed as to how cohort studies measure COVID-19 infection status retrospectively, particularly given that objective testing for infection was not widely available in the first wave of COVID-19 in many countries. Retrospective testing might be possible using antibodies as a proxy for previous COVID-19 infection.What this study adds?Antibody testing is feasible in community cohorts but sensitivity may be poor. Self-report of suspected infection, recall of symptoms and results of tests received elsewhere add different aspects to the ascertainment of COVID-19 exposure. Combining self-report and objectively measured indicators may enable tailored algorithms for COVID-19 case definition that suits the aims of different research studies.