bluuebunny/crossref_metadata_2025 huggingface dataset:
Proof of concept study to develop a novel connectivity-based electric-field modelling approach for individualized targeting of transcranial magnetic stimulation treatment
Authors: Balderston Nicholas L , Beer Joanne C , Seok Darsol , Makhoul Walid , Deng Zhi-De , Girelli Tommaso , Teferi Marta , Smyk Nathan , Jaskir Marc , Oathes Desmond J , Sheline Yvette I
Published: December 2020

Background

Resting state functional connectivity (rsFC) offers promise for individualizing stimulation targets for transcranial magnetic stimulation (TMS) treatments. However current targeting approaches do not account for non-focal TMS effects or large-scale connectivity patterns. To overcome these limitations, we propose a novel targeting optimization approach that combines whole-brain rsFC and electric-field (e-field) modelling to identify single-subject, symptom-specific TMS targets.

Methods

In this proof of concept study, we recruited 91 anxious misery (AM) patients and 25 controls. We measured depression symptoms (MADRS/HAMD) and recorded rsFC. We used a PCA regression to predict symptoms from rsFC and estimate the parameter vector, for input into our e-field augmented model. We modeled 17 left dlPFC and 7 M1 sites using 24 equally spaced coil orientations. We computed single-subject predicted ΔMADRS/HAMD scores for each site/orientation using the e-field augmented model, which comprises a linear combination of the following elementwise products 1) the estimated connectivity/symptom coefficients, 2) a vectorized e-field model for site/orientation, 3) the pre-treatment rsFC matrix, scaled by a proportionality constant.

Results

In AM patients, our pre-stimulation connectivity-based model predicted a significant decrease depression for sites near BA46, but not M1 for coil orientations perpendicular to the cortical gyrus. In control subjects, no site/orientation combination showed a significant predicted change.

Discussion

These results corroborate previous work suggesting the efficacy of left dlPFC stimulation for depression treatment, and predict better outcomes with individualized targeting. They also suggest that our novel connectivity-based e-field modelling approach may effectively identify potential TMS treatment responders and individualize TMS targeting to maximize the therapeutic impact.
Post release immune responses of Tasmanian devils vaccinated with an experimental devil facial tumour disease vaccine
Authors: Pye Ruth , Darby Jocelyn , Flies Andrew , Fox Samantha , Carver Scott , Elmer Jodie , Swift Kate , Hogg Carolyn , Pemberton David , Woods Gregory , Lyons A. Bruce
Published: December 2020

Disease is increasingly becoming a driver of wildlife population declines and extinction risk. Vaccines have been one of the most successful health interventions in human history, but few have been tested for mitigating wildlife disease. The transmissible cancer, devil facial tumour disease (DFTD), triggered the Tasmanian devil’s (Sarcophilus harrisii) inclusion on the international endangered species list. Development of a protective DFTD vaccine would provide a valuable management approach for conservation of the species. In 2016, 33 devils from a DFTD-free insurance population were given an experimental DFTD vaccination prior to their release on the north coast of Tasmania. The release site was already home to an incumbent population of devils, including some individuals with DFTD. To determine the efficacy of the vaccination protocol and the longevity of the response it induced, six trapping trips took place at the site over the 2.5 years following release. Eight of the 33 vaccinated devils were re-trapped, and six of those developed DFTD within the monitoring period. Despite the apparent lack of protection provided by the vaccine for the re-trapped devils, we observed several signs of immune activation not usually found in unvaccinated devils. Firstly, sera collected from the eight devils showed that anti-DFTD antibodies persisted for up to two years post vaccination. Secondly, tumour infiltrating lymphocytes were found in three out of four biopsies collected from vaccinated devils which contrasts with the “immune deserts” typical of DFT’s; only one out of twenty incumbent devils with DFTD trapped during the same period had a tumour biopsy exhibiting immune cell infiltrate. Thirdly, immunohistochemical analysis of tumour biopsies from the vaccinated devils identified the functional immune molecules associated with antigen presenting cells (MHC-II) and T cells (CD3), and the immune checkpoint molecule PD-1, all associated with anti-tumour immunity in other species. These results correlate with our previous study on captive devils in which a prophylactic vaccine primed the devil immune system and, following DFTD challenge and tumour growth, immunotherapy induced complete tumour regressions. The field trial results presented here provide further evidence that the devil immune system can be primed to recognise DFTD cells, but additional immune manipulation could be needed for complete protection or induction of tumour regressions.
The new generation hDHODH inhibitor MEDS433 hinders thein vitroreplication of SARS-CoV-2
Authors: Calistri Arianna , Luganini Anna , Conciatori Valeria , Vecchio Claudia Del , Sainas Stefano , Boschi Donatella , Lolli Marco Lucio , Gribaudo Giorgio , Parolin Cristina
Published: December 2020

Identification and development of effective drugs active against SARS-CoV-2 are urgently needed. Here, we report on the anti-SARS-CoV-2 activity of MEDS433, a novel inhibitor of human dihydroorotate dehydrogenase (hDHODH), a key cellular enzyme of thede novopyrimidines biosynthesis. MEDS433 inhibitsin vitrovirus replication in the low nanomolar range, and through a mechanism that stems from its ability to block hDHODH activity. MEDS433 thus represents an attractive candidate to develop novel anti-SARS-CoV-2 agents.
Global transcriptomics reveals specialized roles for splicing regulatory proteins in the macrophage innate immune response
Authors: West KO , Wagner AR , Scott HM , Vail KJ , Carter KE , Watson RO , Patrick KL
Published: December 2020

Pathogen sensing via pattern recognition receptors triggers massive reprogramming of macro-phage gene expression. While the signaling cascades and transcription factors that activate these responses are well-known, the role of post-transcriptional RNA processing in modulating innate immune gene expression remains understudied. Recent phosphoproteomics analyses revealed that members of the SR and hnRNP families of splicing regulatory proteins are dynamically post-translationally modified in infected macrophages. To begin to test if these splicing factors play a privileged role in controlling the innate immune transcriptome, we analyzed steady state gene expression and alternatively spliced isoform production in ten SR/hnRNP knockdown RAW 264.7 macrophage cell lines following infection with the bacterial pathogenSalmonella entericaserovar Typhimurium (Salmonella). We identified thousands of transcripts whose abundance was increased or decreased by SR/hnRNP knockdown in macrophages. We observed that different SR/hnRNPs control the expression of distinct gene regulons in uninfected andSalmonella-infected macrophages, with several key innate immune genes (Nos2, Mx1, Il1a) relying on multiple SR/hnRNPs to maintain proper induction and/or repression. Knockdown of SR/hnRNPs promoted differential isoform usage (DIU) for a number of key immune sensors and signaling molecules and many of these splicing changes were again, distinct in uninfected andSalmonella-infected macrophages. Finally, after observing a surprising degree of similarity between the DEGs and DIUs in hnRNP K and U knockdown macrophages, we found that these cells are better able to restrict vesicular stomatitis virus replication than control cells, supporting a role for these hnRNPs in controlling infection outcomes in macrophagesex vivo. Based on these findings, we conclude that many innate immune genes have evolved to rely on one or more splicing regulatory factors to ensure the proper timing and magnitude of their induction, bolstering a model wherein pre-mRNA splicing is a critical regulatory node in the innate immune response.
Variation in insect herbivore communities on individual plants reveals phylogenetic signal in uncertainty of attack in Brassicaceae
Authors: Mertens Daan , Bouwmeester Klaas , Poelman Erik H.
Published: December 2020

As a result of co-evolution between plants and herbivores, related plants often interact with similar communities of herbivores. On individual plants, typically only a subset of interactions is realized. The stochasticity of realized interactions leads to uncertainty of attack on individual plants and is likely to determine adaptiveness of plant defence strategies. Here, we show that across 12 plant species in two phylogenetic lineages of the Brassicaceae, variation in realized herbivore communities reveals a phylogenetic signal in the uncertainty of attack on individual plants. Individual plants of Brassicaceae Lineage II were attacked by a larger number of herbivore species from a larger species pool, resulting in a higher uncertainty of realized antagonistic interactions compared to plants in Lineage I. We argue that uncertainty of attack in terms of realized interactions on individual plants is ecologically relevant and must therefore be considered in the evolution of plant defences.
A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry
Authors: Radakovic Aleksandar , Wright Tom H. , Lelyveld Victor S. , Szostak Jack W.
Published: December 2020

Aminoacylated tRNAs are the substrates for ribosomal protein synthesis in all branches of life, implying an ancient origin for aminoacylation chemistry. In the 1970s, Orgel and colleagues reported potentially prebiotic routes to aminoacylated nucleotides and their RNA templated condensation to form amino acid bridged dinucleotides. However, it is unclear whether such reactions would have aided or impeded nonenzymatic RNA replication. Determining whether aminoacylated RNAs could have been advantageous in evolution prior to the emergence of protein synthesis remains a key challenge. We therefore tested the ability of aminoacylated RNA to participate in both templated primer extension and ligation reactions. We find that at low magnesium concentrations that favor fatty acid-based protocells, these reactions proceed orders of magnitude more rapidly than when initiated from the cis-diol of unmodified RNA. We further demonstrate that amino acid bridged RNAs can act as templates in a subsequent round of copying. Our results suggest that aminoacylation facilitated nonenzymatic RNA replication, thus outlining a potentially primordial functional link between aminoacylation chemistry and RNA replication.

Abstract Figure
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

Environmental 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 statement

Bacterial 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

Three-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

T 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

Infant 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

Deformed 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

Mixtures 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

Background

Determining 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.

Methods

We 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.

Results

We 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.

Conclusions

With 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

Hypotonia, 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

The 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

Data 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.
Effects of Electrical Pulse Polarity Shape on Intra Cochlear Neural Responses in Humans: Triphasic Pulses with Anodic and Cathodic Second Phase
Authors: Kretzer Katharina , Herrmann David P. , Pieper Sabrina H. , Bahmer Andreas
Published: December 2020

Modern cochlear implants employ charge-balanced biphasic and triphasic pulses. However, the effectiveness of electrical pulse shape and polarity is still a matter of debate. For this purpose, in a previous study (Bahmer & Baumann, 2013) electrophysiological and psychophysical measurement after triphasic pulse stimulation with cathodic second phase was determined. Depending on the pulse shape configuration, the stimulation effectiveness differed similarly for electrophysiological and psychophysical measurements. However, the experiments were limited to stimulation pulses with cathodic second phase.
In this study, cathodic and anodic second phase stimulation was applied. Evoked compound action potentials (ECAPs) and psychophysical responses were recorded in eleven cochlear implant recipients (SYNCHRONY/SONATAti100/PULSARci100 devices, MED-EL Innsbruck). We compared the strength of the ECAP responses with individual psychophysical threshold levels depending on the pulse shape.
Results for pulses with cathodic second phase showed the weakest ECAP response and highest psychophysical thresholds for symmetric triphasic pulse shapes, and the strongest ECAP response and lowest psychophysical thresholds for biphasic pulses. The ECAP responses for anodic second phase differed from the results of triphasic stimulation with cathodic second phase. The U-shape of the ECAP response with increasing phase amplitude ratio (PAR) for cathodic second phase could not be observed for the anodic second phase. Instead, a flat curve was observed. In contrast, psychophysical threshold curves with increasing PAR were similar between cathodic and anodic second phase stimulation.
Diagnostic and monitoring utilities of saliva for SARS-CoV-2
Authors: AbdulRahman AbdulKarim , AlBastaki Ahmed , AlAwadhi Abdulla , Alwazaan Asmaa , AlQahtani Manaf
Published: December 2020

Introduction

Nasopharyngeal (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.

Methodology

A 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.

Results

The 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%.

Conclusion

The 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

Background

Definitive 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.

Methods

An 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.

Results

1882 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.

Discussion

Our 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.

THUMBNAIL

What 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.
Genome-wide meta-analysis of insomnia in over 2.3 million individuals implicates involvement of specific biological pathways through gene-prioritization
Authors: Watanabe Kyoko , Jansen Philip R. , Savage Jeanne E. , Nandakumar Priyanka , Wang Xin ,   23andMe Research Team, Hinds David A. , Gelernter Joel , Levey Daniel F. , Polimanti Renato , Stein Murray B. , Van Someren Eus J.W. , Smit August B. , Posthuma Danielle
Published: December 2020

Insomnia is a heritable, highly prevalent sleep disorder, for which no sufficient treatment currently exists. Previous genome-wide association studies (GWASs) with up to 1.3 million subjects identified over 200 associated loci. This extreme polygenicity suggested many more loci to be discovered. The current study almost doubled the sample size to over 2.3 million individuals thereby increasing statistical power. We identified 554 risk loci (confirming 190 previously associated loci and detecting 364 novel), and capitalizing on this large number of loci, we propose a novel strategy to prioritize genes using external biological resources and information on functional interactions between genes across risk loci. Of all 3,898 genes naively implicated from the risk loci, we prioritize 289. For these, we find brain-tissue expression specificity and enrichment in specific gene-sets of synaptic signaling functions and neuronal differentiation. We show that the novel gene prioritization strategy yields specific hypotheses on causal mechanisms underlying insomnia, which would not fully have been detected using traditional approaches.
Single-cell RNA sequencing revealsin vivosignatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’
Authors: Fischer David S. , Ansari Meshal , Wagner Karolin I. , Jarosch Sebastian , Huang Yiqi , Mayr Christoph H. , Strunz Maximilian , Lang Niklas J. , D’Ippolito Elvira , Hammel Monika , Mateyka Laura , Weber Simone , Wolff Lisa S. , Witter Klaus , Fernandez Isis E. , Leuschner Gabriela , Milger Kathrin , Frankenberger Marion , Nowak Lorenz , Heinig-Menhard Katharina , Koch Ina , Stoleriu Mircea G. , Hilgendorff Anne , Behr Jürgen , Pichlmair Andreas , Schubert Benjamin , Theis Fabian J. , Busch Dirk H. , Schiller Herbert B. , Schober Kilian
Published: December 2020

Thein vivophenotypic profile of T cells reactive to severe acute respiratory syndrome (SARS)-CoV-2 antigens remains poorly understood. Conventional methods to detect antigen-reactive T cells requirein vitroantigenic re-stimulation or highly individualized peptide-human leukocyte antigen (pHLA) multimers. Here, we used single-cell RNA sequencing to identify and profile SARS-CoV-2-reactive T cells from Coronavirus Disease 2019 (COVID-19) patients. To do so, we induced transcriptional shifts by antigenic stimulationin vitroand took advantage of natural T cell receptor (TCR) sequences of clonally expanded T cells as barcodes for ‘reverse phenotyping’. This allowed identification of SARS-CoV-2-reactive TCRs and revealed phenotypic effects introduced by antigen-specific stimulation. We characterized transcriptional signatures of currently and previously activated SARS-CoV-2-reactive T cells, and showed correspondence with phenotypes of T cells from the respiratory tract of patients with severe disease in the presence or absence of virus in independent cohorts. Reverse phenotyping is a powerful tool to provide an integrated insight into cellular states of SARS-CoV-2-reactive T cells across tissues and activation states.
Evaluation of SARS-CoV-2 neutralization assays for antibody monitoring in natural infection and vaccine trials
Authors: Sholukh Anton M , Fiore-Gartland Andrew , Ford Emily S , Hou Yixuan , Tse Longping Victor , Lempp Florian A , Kaiser Hanna , Saint Germain Russell , Bossard Emily , Kee Jia Jin , Diem Kurt , Stuart Andrew B , Rupert Peter B , Brock Chance , Buerger Matthew , Doll Margaret K , Randhawa April Kaur , Stamatatos Leonidas , Strong Roland K , McLaughlin Colleen , Jerome Keith R. , Baric Ralph S. , Montefiori David , Corey Lawrence
Published: December 2020

Determinants of protective immunity against SARS-CoV-2 infection require the development of well-standardized, reproducible antibody assays to be utilized in concert with clinical trials to establish correlates of risk and protection. This need has led to the appearance of a variety of neutralization assays used by different laboratories and companies. Using plasma samples from COVID-19 convalescent individuals with mild-to-moderate disease from a localized outbreak in a single region of the western US, we compared three platforms for SARS-CoV-2 neutralization: assay with live SARS-CoV-2, pseudovirus assay utilizing lentiviral (LV) and vesicular stomatitis virus (VSV) packaging, and a surrogate ELISA test. Vero, Vero E6, HEK293T cells expressing human angiotensin converting enzyme 2 (hACE2), and TZM-bl cells expressing hACE2 and transmembrane serine protease 2 (TMPRSS2) were evaluated. Live-virus and LV-pseudovirus assay with HEK293T cells showed similar geometric mean titers (GMTs) ranging 141–178, but VSV-pseudovirus assay yielded significantly higher GMT (310 95%CI 211-454; p < 0.001). Fifty percent neutralizing dilution (ND50) titers from live-virus and all pseudovirus assay readouts were highly correlated (Pearson r = 0.81–0.89). ND50 titers positively correlated with plasma concentration of IgG against SARS-CoV-2 spike and receptor binding domain (RBD) (r = 0.63–0.89), but moderately correlated with nucleoprotein IgG (r = 0.46-0.73). There was a moderate positive correlation between age and spike (Spearman's rho=0.37, p=0.02), RBD (rho=0.39, p=0.013) and nucleoprotein IgG (rho=0.45, p=0.003). ND80 showed stronger correlation with age than ND50 (ND80 rho=0.51 (p=0.001), ND50 rho=0.28 (p=0.075)). Our data demonstrate high concordance between cell-based assays with live and pseudotyped virions.
Model-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic
Authors: Rozhnova Ganna , van Dorp Christiaan H , Bruijning-Verhagen Patricia , Bootsma Martin C J , van de Wijgert Janneke H H M , Bonten Marc J M , Kretzschmar Mirjam E
Published: December 2020

Background:
In autumn 2020, many countries, including the Netherlands, are experiencing a second wave of the COVID-19 pandemic. Health policymakers are struggling with choosing the right mix of measures to keep the COVID-19 case numbers under control, but still allow a minimum of social and economic activity. The priority to keep schools open is high, but the role of school-based contacts in the epidemiology of SARS-CoV-2 is incompletely understood. We used a transmission model to estimate the impact of school contacts on the transmission of SARS-CoV-2 and to assess the effects of school-based measures, including school closure, on controlling the pandemic at different time points during the pandemic.
Methods and Findings: The age-structured model was fitted to age-specific seroprevalence and hospital admission data from the Netherlands during spring 2020. Compared to adults older than 60 years, the estimated susceptibility was 23% (95%CrI 20-28%) for children aged 0 to 20 years and
61% (95%CrI 50%-72%) for the age group of 20 to 60 years. The time points considered in the analyses were (i) August 2020 when the effective reproduction number (R_e) was estimated to be 1.31 (95%CrI 1.15-2.07), schools just opened after the summer holidays and measures were reinforced with the aim to reduce R_e to a value below 1, and (ii) November 2020 when measures had reduced R_e to 1.00 (95%CrI 0.94-1.33). In this period schools remained open. Our model predicts that keeping schools closed after the summer holidays, in the absence of other measures, would have reduced R_e by 10% (from 1.31 to 1.18 (95%CrI 1.04-1.83)) and thus would not have prevented the second wave in autumn 2020. Reducing non-school-based contacts in August 2020 to the level observed during the first wave of the pandemic would have reduced R_e to 0.83 (95%CrI 0.75-1.10). Yet, this reduction was not achieved and the observed R_e in November was 1.00. Our model predicts that closing schools in November 2020 could reduce R_e from the observed value of 1.00 to 0.84 (95%CrI 0.81-0.90), with unchanged non-school based contacts. Reductions in R_e due to closing schools in November 2020 were 8% for 10 to 20 years old children, 5% for 5 to 10 years old children and negligible for 0 to 5 years old children.
Conclusions: The impact of measures reducing school-based contacts, including school closure, depends on the remaining opportunities to reduce non-school-based contacts. If opportunities to reduce R_e with non-school-based measures are exhausted or undesired and R_e is still close to 1, the additional benefit of school-based measures may be considerable, particularly among the older school children.
Characterization and safety profile of Imuno TF®, a nutritional supplement for immune system regulation containing transfer factors
Authors: Polonini Hudson , de Souza Schmidt Gonçalves Any Elisa , Dijkers Eli , de Oliveira Ferreira Anderson
Published: December 2020

Imuno TF®is a nutritional supplement composed of isolated transfer factors (TF) from porcine spleen. It is composed of a specific mixture of molecules that impact functions of the biological systems, and historically is linked to the immune system regulation. In this study, we demonstrate for the first time its proteomic analysis, nutritional composition, and safety profile in terms of mutagenic potential and acute oral dose (LD50). The obtained analysis indicated the product is a complex set of oligo- and polypeptides constituted of 163 different peptides which can potentially act on multiple mechanisms on the immune system pathways. The chemical composition showed low fat and low sugar content, saturated fatty acids-free and the presence of 10 vitamins and 11 minerals. No mutagenic effect was observed, and the LD50was 5,000 mg kg-1body weight. This accounts for a safe product to be used by oral route, with potential benefits for the immune system.
Systematic comparison of incomplete-supervision approaches for biomedical imaging classification
Authors: Boushehri Sayedali Shetab , Qasim Ahmad Bin , Waibel Dominik , Schmich Fabian , Marr Carsten
Published: December 2020

Deep learning based classification of biomedical images requires manual annotation by experts, which is time-consuming and expensive. Incomplete-supervision approaches including active learning, pre-training and semi-supervised learning address this issue and aim to increase classification performance with a limited number of annotated images. Up to now, these approaches have been mostly benchmarked on natural image datasets, where image complexity and class balance typically differ considerably from biomedical classification tasks. In addition, it is not clear how to combine them to improve classification performance on biomedical image data.

We thus performed an extensive grid search combining seven active learning algorithms, three pre-training methods and two training strategies as well as respective baselines (random sampling, random initialization, and supervised learning). For four biomedical datasets, we started training with 1% of labeled data and increased it by 5% iteratively, using 4-fold cross-validation in each cycle. We found that the contribution of pre-training and semi-supervised learning can reach up to 25% macro F1-score in each cycle. In contrast, the state-of-the-art active learning algorithms contribute less than 5% to macro F1-score in each cycle. Based on performance, implementation ease and computation requirements, we recommend the combination of BADGE active learning, ImageNet-weights pre-training, and pseudo-labeling as training strategy, which reached over 90% of fully supervised results with only 25% of annotated data for three out of four datasets.

We believe that our study is an important step towards annotation and resource efficient model training for biomedical classification challenges.