bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of COVID-19 Pandemic on Cardiology Services
Authors: Fersia Omar , Bryant Sue , Nicholson Rachael , McMeeken Karen , Brown Carolyn , Donaldson Brenda , Jardine Aaron , Grierson Valerie , Whalen Vanessa , Mackay Alistair
Published: June 2020

Objective

COVID-19 pandemic resulted in prioritisation of NHS resources to cope with the surge in infected patients. However, there have been no studies in the UK looking at the effect of COVID-19 work pattern on the provision of cardiology services. We aim to assess the impact of the pandemic on the cardiology services and clinical activity.

Methods

We analysed key performance indicators in cardiology services in a single centre in the UK in the intervals prior and during the lockdown to assess for reduction or changes to service provisions.

Results

There has been more than 50% drop in patients presenting to cardiology and those diagnosed with myocardial infarction. All cardiology service provisions sustained significant reductions which included outpatient clinics, investigations, procedures and cardiology community services such as heart failure and cardiac rehabilitation.

Conclusion

As ischaemic heart disease continues to be the leading cause of death nationally and globally, cardiology services need to prepare for a significant increase in workload in the recovery phase and develop new pathways to urgently help those adversely affected by the changes in service provisions.

Key Questions

What is already known about this subject?

COVID-19 affected the way healthcare is delivered through restructuring and prioritisation of resources. It is therefore expected that COVID-19 work pattern will have an impact on the delivery of medical and surgical services. Quantifying this effect is necessary to plan on how to deal with COVID-19 sequelae in the recovery phase.

What does this study add?

As ischaemic heart disease continues to be the leading cause of death in the world, assessing the direct and indirect effect of COVID-19 on cardiology through COVID-19 related cardiac diseases and through the restriction of cardiology provisions is necessary to plan our services in the post COVID-19 era.

How might this impact on clinical practice?

The impact of COVID-19 will be felt beyond the direct effect of COVID-19 related cardiac diseases. The provisions of cardiac services were severely restricted due to a shift in the focus in dealing with the surge of patients with COVID-19 and patients’ reluctance to seek medical help during the lockdown period. There was therefore a reduction across all cardiology performance indicators from referrals to investigations, diagnoses and management of cardiology patients. It is therefore expected that there will be another surge of patients seeking cardiology care and that services need to plan to treat these patients early and urgently to prevent any long term complications.
Two New Improved Methods for Determination of Cobb’s Angle of Scoliosis
Authors: Hellen Dietrich W. , Teusner Michael
Published: June 2020

Cobb’s traditional method for measuring the angle of scoliosis is complicated and error-prone in application. Angles measured with this method are inaccurate and it therefore stands to reason to search for improved procedures.

We propose Cobb’s angle to be determined by two novel methods: the distance method and the two-angle method. Using mathematical error analysis and experimental test measurings we demonstrate that the two proposed methods offer significant advantages over the current standard. They simplify the measurement process and increase outcome accuracy.

For Cobb’s angles larger than 30 degrees, the two-angle method reduces the error-variation by approx. 25%. For Cobb’s angles below 30 degrees the distance method reduces the error-variation by approx. 50%.
Symptom clusters in Covid19: A potential clinical prediction tool from the COVID Symptom study app
Authors: Sudre Carole H. , Lee Karla A. , Lochlainn Mary Ni , Varsavsky Thomas , Murray Benjamin , Graham Mark S. , Menni Cristina , Modat Marc , Bowyer Ruth C E , Nguyen Long H. , Drew David A. , Joshi Amit D. , Ma Wenjie , Guo Chuan-Guo , Lo Chun-Han , Ganesh Sajaysurya , Buwe Abubakar , Pujol Joan Capdevila , du Cadet Julien Lavigne , Visconti Alessia , Freidin Maxim B , El-Sayed Moustafa Julia S. , Falchi Mario , Davies Richard , Gomez Maria F. , Fall Tove , Cardoso M. Jorge , Wolf Jonathan , Franks Paul W. , Chan Andrew T. , Spector Tim D. , Steves Claire J , Ourselin Sébastien
Published: June 2020

As no one symptom can predict disease severity or the need for dedicated medical support in COVID-19, we asked if documenting symptom time series over the first few days informs outcome. Unsupervised time series clustering over symptom presentation was performed on data collected from a training dataset of completed cases enlisted early from the COVID Symptom Study Smartphone application, yielding six distinct symptom presentations. Clustering was validated on an independent replication dataset between May 1-May 28th, 2020. Using the first 5 days of symptom logging, the ROC-AUC of need for respiratory support was 78.8%, substantially outperforming personal characteristics alone (ROC-AUC 69.5%). Such an approach could be used to monitor at-risk patients and predict medical resource requirements days before they are required.

One sentence summary

Longitudinal clustering of symptoms can predict the need for respiratory support in severe COVID-19.
Increased plasma heparanase activity in COVID-19 patients
Authors: Buijsers Baranca , Yanginlar Cansu , Nooijer Aline de , Grondman Inge , Maciej-Hulme Marissa L. , Jonkman Inge , Janssen Nico A.F. , Rother Nils , de Graaf Mark , Pickkers Peter , Kox Matthijs , Joosten Leo A.B. , Nijenhuis Tom , Netea Mihai G. , Hilbrands Luuk , van de Veerdonk Frank L. , Duivenvoorden Raphaël , de Mast Quirijn , van der Vlag Johan
Published: June 2020

Reports suggest a role of endothelial dysfunction and loss of endothelial barrier function in COVID-19. It is well established that the endothelial glycocalyx-degrading enzyme heparanase contributes to vascular leakage and inflammation. Low molecular weight heparins (LMWH) serve as an inhibitor of heparanase. We hypothesize that heparanase contributes to the pathogenesis of COVID-19, and that heparanase may be inhibited by LMWH. Heparanase activity and heparan sulfate levels were measured in plasma of healthy controls (n=10) and COVID-19 patients (n=48).

Plasma heparanase activity and heparan sulfate levels were significantly elevated in COVID-19 patients. Heparanase activity associated with disease severity including the need for intensive care and mechanical ventilation, lactate dehydrogenase levels and creatinine levels. Use of prophylactic LMWH in non-ICU patients was associated with a reduced heparanase activity. Since there is no other clinically applied heparanase inhibitor currently available, therapeutic treatment of COVID-19 patients with low molecular weight heparins should be explored.
Spreading Analysis of COVID-19 Epidemic in Bangladesh by Dynamical Mathematical Modelling
Authors: Fargana A , Arifutzzaman A , Rakhimov A A
Published: June 2020

The coronavirus disease 2019 (COVID-19), which emerged from Wuhan, China, is now a pandemic, affecting across the globe. Bangladesh also is experiencing the rapid growth of COVID-19 infection and death cases started from 8th March 2020. The purpose of providing a simple yet effective explanatory model for prediction of the future evolution of the contagion and verification of the effectiveness of the containment and lockdown measures in Bangladesh. In this study, using a modified SIR (Susceptible-Infected-Recovered) model a forecast is generated to predict the trends of COVID-19 cases in Bangladesh. The epidemic model was proposed to accommodate the effects of lockdown and individual based precautionary measures. Data has been taken and analyzed for before and after the movement control order (MCO) and during the MCO period. Modified SIR model in this work offers us an idea how the outbreak would progress based on the current data. It also has estimated that, the peak in terms of the number of infected cases will start from last of June 2020. For the total population (100%) the model gets the peaks at 214875 (infected cases) and 7743 (death cases). For the 90% population, the model shows the peaks at 244356 (infected cases) and 9100 (death cases). Analysis revealed that the lockdown and recommended individual hygiene can slow down the outbreak but unable to eradicate the disease from the society. With the current infection and death rate and existing level of personal precautionary the number of infected individuals will be increasing.
Neutrophil nuclear patterns to distinguish between pathological and non-pathological autoantibodies detected on HEp-2 cells
Authors: Won Dong Il , Park Jihea , Kim Beom Soo , Kim Chae Eun , Yoon Heon Sik , Jung Ji Soo
Published: June 2020

Background

Antinuclear antibody (ANA) testing is used to diagnose systemic autoimmune rheumatic disease (SARD). Autoantibodies (Abs) associated with the “homogeneous-like” pattern on ANA HEp-2 cell nuclei can be classified as pathological (e.g., anti-dsDNA, anti-nucleosome, anti-histone, anti-Scl-70 Abs) or non-pathological (e.g., anti-DFS70 Abs).

Methods

Anti-neutrophil cytoplasmic anti-antibody (ANCA) testing was used to classify individuals who presented with a homogeneous-like pattern on ANA testing. Enrolled subjects included (1) young individuals with a dense fine speckled pattern on ANA testing (young non-SARD group, n = 62) and patients with (2) systemic lupus erythematosus (SLE) with anti-dsDNA Abs (SLE group, n = 33), (3) rheumatoid arthritis (RA) with anti-nucleosome, anti-histone Abs, and others (RA group, n = 45), and (4) diffuse systemic sclerosis (SSc) with Scl-70 Abs (diffuse SSc group, n = 11).

Results

Negative rates (95% confidence interval) of neutrophil nuclear patterns on ANCA testing were: 96.8% (88.8%–99.6%) of the young non-SARD group, 3.0% (0.1 %–15.8%) of the SLE group, 4.4% (0.5%–15.2%) of the RA group, and 54.5% (23.4%–83.3%) of the diffuse SSc group. The negative rate of the non-SARD group was significantly higher than those of the SARD group (all P < 0.05).

Conclusions

ANCA testing helps to identify individuals with non-pathological anti-DFS70 Abs who present with homogeneous-like patterns in HEp-2 cell nuclei on ANA testing.
Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia. When late administration is too late
Authors: Hernández-Mora Miguel Górgolas , Úbeda Alfonso Cabello , Pérez Laura Prieto , Álvarez Felipe Villar , Álvarez Beatriz Álvarez , Rodríguez Nieto María Jesús , Acosta Irene Carrillo , Fernández Ormaechea Itziar , Mohammed Al-Hayani Aws Waleed , Carballosa Pilar , Martínez Silvia Calpena , Ezzine Farah , González Marina Castellanos , Naya Alba , de las Heras Marta López , Rodríguez Guzmán Marcel José , Guijarro Ana Cordero , Lavado Antonio Broncano , Valcayo Alicia Macías , García Marta Martín , Martínez Javier Bécares , Roblas Ricardo Fernández , Piris Pinilla Miguel Ángel , Alen José Fortes , Pernaute Olga Sánchez , Bueno Fredeswinda Romero , Frades Sarah Heili , Barba Romero Germán Peces ,   the COVID-FJD-TEAM
Published: June 2020

Introduction

Tocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). However, there is no data about the best moment for its administration along the course of the disease.

Methods

We provided tocilizumab on a compassionate-use basis to patients with SSP hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. Primary endpoint was intubation or death after 24 hours of its administration. Patients received at least one dose of 400 mg intravenous tocilizumab during March 8-2020, through April 20-2020.

Findings

A total of 207 patients were studied and 186 analysed. The mean age was 65 years and 68% were male. A co-existing condition was present in 68 % of cases. At baseline, 114 (61%) required oxygen support with FiO2 >0.5 % and 72 (39%) ≤0.5%. Early administration of tocilizumab, when the need of oxygen support was still below FiO2 ≤0.5%, was significantly more effective than given it in advanced stages (FiO2 >0.5 %), achieving lower rates of intubation or death (13% vs 37% repectively, p<0·001).

Interpretation

The benefit of tocilizumab in severe SARS-Cov-2 pneumonia is only expected when it is administrated before the need of high oxygen support.

Funding

None.
Impact Of Temperature and Sunshine Duration on Daily New Cases and Death due to COVID-19
Authors: Thangariyal Swati , Rastogi Aayushi , Tomar Arvind , Bhadoria Ajeet , Baweja Sukriti
Published: June 2020

Background

The coronavirus pandemic (COVID-19) control has now become a critical issue for public health. Many ecological factors are proven to influence the transmission and survival of the virus. In this study, we aim to determine the association of different climate factors with the spread and mortality due to COVID-19.

Methods

The climate indicators included in the study were duration of sunshine, average minimum temperature and average maximum temperature, with cumulative confirmed cases, deceased and recovered cases. The data was performed for 138 different countries of the world, between January 2020 to May 2020. Both univariate and multivariate was performed for cumulative and month-wise analysis using SPSS software.

Results

The average maximum temperature, and sunshine duration was significantly associated with COVID-19 confirmed cases, deceased and recovered. For every one degree increase in mean average temperature, the confirmed, deceased and recovered cases decreased by 2047(p=0.03), 157(p=0.016), 743 (p=0.005) individuals. The association remained significant even after adjusting for environmental such as sunshine duration as well as non-environmental variables. Average sunshine duration was inveserly correlated with increase in daily new cases (ρ= -2261) and deaths (ρ= -0.2985).

Conclusion

Higher average temperature and longer sunshine duration was strongly associated with COVID-19 cases and deaths in 138 countries. Hence the temperature is an important factor in SARS CoV-2 survival and this study will help in formulating better preventive measures to combat COVID-19 based on their climatic conditions.
Are health indicators able to describe the ability to cope of Health Systems with COVID-19 epidemic?
Authors: Castaldi Silvana , Luconi Ester , Rivieccio Bruno Alessandro , Boracchi Patrizia , Marano Giuseppe , Pariani Elena , Romanò Luisa , Auxilia Francesco , Nicolussi Federica , Micheletti Alessandra , Manzi Giancarlo , Salini Silvia , Galli Massimo , Biganzoli Elia
Published: June 2020

The Coronavirus Disease 19 epidemic is an infectious disease which was declared as a pandemic and hit all the Countries, all over the world, from the beginning of the year 2020.

Despite the emergency vigilance plans, in all the Countries, Health Systems experienced a different ratio of lethality, admissions to intensive care units and managing quarantine of positive patients.

The aim of this study is to investigate if some health indicators might have been useful to understand the capacity of Italian National Health Service to manage the COVID 19 epidemic.

We will compare data in two different Italian regions in the Northern part of Italy (Lombardy and Veneto) with the national data to understand if different health strategies might be significant to explain different patterns of COVID 19 epidemic in Italy.

The two regions have two different health policies to face CoViD-2019 epidemic.

To face epidemic like this one the answer should be outside hospitals but this means to have general practitioners well-trained and enough healthcare personnel working outside hospitals.
Simulation of Non-Pharmaceutical Interventions on COVID-19 with an Agent-based Model of Zonal Restraint
Authors: Álvarez Lindsay , Rojas-Galeano Sergio
Published: June 2020

Non-Pharmaceutical Interventions (NPI) are currently the only mechanism governments can use to mitigate the impact of the COVID-19 epidemic. Similarly to the actual spread of the disease, the dynamics of the contention patterns emerging from the application of NPIs are complex and depend on interactions between people within a specific region as well as other stochastic factors associated to demographic, geographic, political and economical conditions. Agent-based models simulate microscopic rules of simultaneous spatial interactions between multiple agents within a population, in an attempt to reproduce the complex dynamics of the effect of the contention measures. In this way, it is possible to design individual behaviours along with NPI scenarios, measuring how the simulation dynamics is affected and therefore, yielding rapid insights to perform a broad assessment of the potential of composite interventions at different stages of the epidemic. In this paper we describe a model and a tool to experiment with such kind of analysis applied to a conceptual city, considering a number of widely-applied NPIs such as social distancing, case isolation, home quarantine, total lockdown, sentinel testing, mask wearing and a distinctive “zonal” enforcement measure, requiring these interventions to be applied gradually to separated enclosed districts (zones). We find that the model is able to capture emerging dynamics associated to these NPIs; besides, the zonal contention strategy yields an improvement on the mitigation impact across all scenarios of combination with individual NPIs. The model and tool are open to extensions to account for omitted or newer factors affecting the planning and design of NPIs intended to counter the late stages or forthcoming waves of the COVID-19 crisis.
Is tracking and modeling Covid-19 infection dynamics for Bangladesh using daily data feasible?
Authors: Ahsan Karar Zunaid , Ijdi Rashida E , Streatfield Peter Kim
Published: June 2020

Given the low Covid-19 testing coverage in the country, this study tested whether the daily change in the number of new Covid-19 cases is due to increase (or decrease) in the number of tests done daily. We performed Granger causality test based on vector autoregressive models on Bangladesh’s case and test numbers between 8 March and 5 June 2020, using publicly available data. The test results show that the daily number of tests Granger-cause the number of new cases (p <0.001), meaning the daily number of new cases is perhaps due to an increase in test capacity rather than a change in the infection rates. From the results of this test we can infer that if the number of daily tests does not increase substantially, data on new infections will not give much information for understanding covid-19 infection dynamics in Bangladesh.
Classifications of Breast Cancer Images by Deep Learning
Authors: Liu Wenzhong , Li Hualan , Hua Caijian , Zhao Liangjun
Published: June 2020

Background

Breast cancer is a leading cause of cancer-related death in women. Classifications of pathological images are important for its diagnosis and prognosis. However, the existing computational methods can sometimes hardly meet the accuracy requirement of clinical applications, due to uneven color distribution and subtle difference in features.

Methods

In this study, a novel classification method DeepBC was proposed for classifying the pathological images of breast cancer, based on the deep convolution neural networks. DeepBC integrated Inception, ResNet, and AlexNet, extracted features from images, and classified images of benign and malignant tissues.

Results

Additionally, complex tests were performed on the existing benchmark dataset to evaluate the performance of DeepBC. The evaluation results showed that, DeepBC achieved 92% and 96.43% accuracy rates in classifying patients and images, respectively, with the F1-score of 97.38%, which better than the state-of-the-art methods.

Conclusions

These findings indicated that, the model had favorable robustness and generalization, and was advantageous in the clinical classifications of breast cancer.
Differential cellular responses to adhesive interactions with galectin-8 and fibronectin coated substrates
Authors: Li Wenhong , Sancho Ana , Groll Jürgen , Zick Yehiel , Bershadsky Alexander , Geiger Benjamin
Published: June 2020

The mechanisms underlying the cellular response to extracellular matrices (ECM), consisting of multiple adhesive ligands, each with distinct properties, are still poorly understood. Here we address this topic by monitoring the cellular responses to two very different extracellular adhesion molecules – fibronectin and galectin-8 – and to mixtures of the two. Fibronectin is one of the major integrin ligands, inducing cell spreading and development of focal adhesions associated with contractile stress fibers. Galectin-8 is a mammalian lectin, which specifically binds to β-galactoside residues present on some integrins, as well as to other cell surface receptors. We found marked differences in HeLa-JW cell spreading, assembly of focal adhesions and actomyosin stress fibers, and formation of adherent filopodia, on rigid flat substrates functionalized by fibronectin or galectin-8 alone, or by mixtures of these two proteins. Spreading on galectin-8 resulted in a larger projected cell area compared to that on fibronectin, by more extensive formation of filopodia, coupled with an inability to activate focal adhesion and stress fiber assembly. These differences could be partially reversed by experimental manipulations of small G-proteins of the Rho family and their downstream targets, such as formins, the Arp2/3 complex, and Rho kinase. Another factor affecting the spreading process was shown to be the enhanced physical adhesion of the cells to galectin-8, as compared to fibronectin. Notably, at least one process, the formation of adherent filopodia, was synergistically upregulated by both ligands, so filopodia development on the substrate coated with a mixture of fibronectin and galectin-8 was far more prominent than on each ligand alone.
Galaxy-SynBioCAD: Synthetic Biology Design Automation tools in Galaxy workflows
Authors: du Lac Melchior , Duigou Thomas , Hérisson Joan , Carbonell Pablo , Swainston Neil , Zulkower Valentin , Shah Forum , Faure Léon , Mahdy Mostafa , Soudier Paul , Faulon Jean-Loup
Published: June 2020

Many computer-aided design tools are available for synthetic biology and metabolic engineering. Yet, these tools can be difficult to apprehend, sometimes requiring a level of expertise that limits their use by a wider community. Furthermore, some of the tools, although complementary, rely on different input and output formats and cannot communicate with one another. Scientific workflows address these shortcomings while offering a novel design strategy. Among the workflow systems available, Galaxy is a web-based platform for performing findable and accessible data analyses for all scientists regardless of their informatics expertise, along with interoperable and reproducible computations regardless of the particular platform that is being used.

Here, we introduce the Galaxy-SynBioCADaportal, the first Galaxy toolshed for synthetic biology and metabolic engineering. It allows one to easily create workflows or use those already developed by the community. The portal is a growing community effort where developers can add new tools and users can evaluate the tools performing design for their specific projects. The tools and workflows currently shared on the Galaxy-SynBioCAD portal cover an end-to-end metabolic pathway design process from the selection of strain and target to the calculation of DNA parts to be assembled to build libraries of strains to be engineered to produce the target.

Standard formats are used throughout to enforce the compatibility of the tools. These include SBML for strain and pathway and SBOL for genetic layouts. The portal has been benchmarked on 81 literature pathways, overall, we find we have a 65% (and 88%) success rate in retrieving the literature pathways among the top 10 (50) pathways predicted and generated by the workflows.
Stiffening of prostate cancer cells driven by actin filaments – microtubules crosstalk confers resistance to microtubule-targeting drugs
Authors: Kubiak Andrzej , Chighizola Matteo , Schulte Carsten , Bryniarska Natalia , Wesołowska Julita , Pudełek Maciej , Ryszawy Damian , Basta-Kaim Agnieszka , Laidler Piotr , Podesta Alessandro , Lekka Malgorzata
Published: June 2020

The crucial role of microtubules in the mitotic-related segregation of chromosomes makes them an excellent target for anticancer microtubule targeting drugs (MTDs) such as vinflunine, colchicine, and docetaxel. MTDs affect mitosis by directly perturbing the structural organization of microtubules. By a direct assessment of the biomechanical properties of prostate cancer cells exposed to different MTDs using atomic force microscopy, we show that cell stiffening is a candidate mechanism through which cancer cells preserve the original phenotype in response to the application of MTDs. While changes in cellular rigidity are typically mainly attributed to remodeling of the actin filaments in the cytoskeleton, here we provide evidence that cell stiffening can be driven by a crosstalk between actin filaments and microtubules in drug-treated cells. Our findings improve the interpretation of biomechanical data obtained for living cells in studies of various physiological and pathological processes.
Hybridization history and repetitive element content in the genome of a homoploid hybrid,Yucca gloriosa(Asparagaceae)
Authors: Heyduk Karolina , McAssey Edward V. , Grimwood Jane , Shu Shengqiang , Schmutz Jeremy , McKain Michael R. , Leebens-Mack Jim
Published: June 2020

Hybridization in plants results in phenotypic and genotypic perturbations that can have dramatic effects on hybrid physiology, ecology, and overall fitness. Hybridization can also perturb epigenetic control of transposable elements, resulting in their proliferation. Understanding the mechanisms that maintain genomic integrity after hybridization is often confounded by changes in ploidy that occur in hybrid plant species. Homoploid hybrid species, which have no change in chromosome number relative to their parents, offer an opportunity to study the genomic consequences of hybridization in the absence of change in ploidy.Yucca gloriosa(Asparagaceae) is a young homoploid hybrid species, resulting from a cross betweenYucca aloifoliaandYucca filamentosa. Previous analyses of ~11kb of the chloroplast genome and nuclear-encoded microsatellites implicated a singleY. aloifoliagenotype as the maternal parent ofY. gloriosa.Using whole genome resequencing, we assembled chloroplast genomes from multiple accessions of all three species to re-assess the hybrid origins ofY. gloriosa.We further used re-sequencing data to annotate transposon abundance in the three species and mRNA-seq to analyze transcription of transposons. The chloroplast phylogeny and haplotype analysis suggest multiple hybridization events contributing to the origin ofY. gloriosa,with both parental species acting as the maternal donor. Transposon abundance at the superfamily level was significantly different between the three species; the hybrid was frequently intermediate to the parental species in TE superfamily abundance or appeared more similar to one or the other parent. In only one case –CopiaLTR transposons – didY. gloriosahave a significantly higher abundance relative to either parent. Expression patterns across the three species showed little increased transcriptional activity of transposons, suggesting that either no transposon release occurred inY. gloriosaupon hybridization, or that any transposons that were activated via hybridization were rapidly silenced. Further work will assess the degree to which transposon abundance and location has affected the epigenomic landscape, gene expression, and ecophysiology inY. gloriosa.
Human prefoldin modulates co-transcriptional pre-mRNA splicing
Authors: Payán-Bravo Laura , Fontalva Sara , Peñate Xenia , Cases Ildefonso , Guerrero-Martínez José Antonio , Pareja-Sánchez Yerma , Odriozola-Gil Yosu , Lara Esther , Jimeno-González Silvia , Suñé Carles , Muñoz-Centeno Mari Cruz , Reyes José C. , Chávez Sebastián
Published: June 2020

Prefoldin is a heterohexameric complex conserved from archaea to humans that plays a cochaperone role during the co-translational folding of actin and tubulin monomers. Additional functions of prefoldin have been described, including a positive contribution to transcription elongation and chromatin dynamics in yeast. Here we show that prefoldin perturbations provoked transcriptional alterations across the human genome. Severe pre-mRNA splicing defects were also detected, particularly after serum stimulation. We found impairment of co-transcriptional splicing during transcription elongation, which explains why the induction of long genes with a high number of introns was affected the most. We detected genome-wide prefoldin binding to transcribed genes and found that it correlated with the negative impact of prefoldin depletion on gene expression. Lack of prefoldin caused global decrease in Ser2 and Ser5 phosphorylation of the RNA polymerase II carboxy-terminal domain. It also reduced the recruitment of the CTD kinase CDK9 to transcribed genes, and the association of splicing factors PRP19 and U2AF65 to chromatin, which is known to depend on CTD phosphorylation. Altogether the reported results indicate that human prefoldin is able to act locally on the genome to modulate gene expression by influencing phosphorylation of elongating RNA polymerase II, and thereby regulating co-transcriptional splicing.
Interdependence of CTL and NK cell cytotoxicity against melanoma cells
Authors: Friedmann Kim S. , Knörck Arne , Cappello Sabrina , Hoxha Cora , Schwär Gertrud , Iden Sandra , Bogeski Ivan , Kummerow Carsten , Schwarz Eva C. , Hoth Markus
Published: June 2020

CTL and NK cells recognize and eliminate cancer cells. However, immune evasion, down regulation of immune function by the tumor microenvironment, or resistance of cancer cells are a major problem. While CTL and NK cells are both important to eliminate cancer, most studies address them individually. In a new experimental human model, we analysed combined primary human CTL and NK cell cytotoxicity against the melanoma cell line SK-Mel-5. At high effector-to-target ratios, MART-1-specific CTL or NK cells eliminated SK-Mel-5 cells within 24 hours indicating that SK-Mel-5 cells are initially not resistant. However, at lower effector-to-target ratios, which resemble conditions of the immune contexture in human cancer, a significant number of SK-Mel-5 cells survived. Whereas CTL pre-exposure induced resistance in surviving SK-Mel-5 cells to subsequent CTL or NK cell cytotoxicity, NK cell pre-exposure induced resistance in surviving SK-Mel-5 cells to NK cells but not to MART-1 specific CTL. In contrast, there was even a slight enhancement of CTL cytotoxicity against SK-Mel-5 cells following NK cell pre-exposure. In all other combinations, resistance to subsequent cytotoxicity was higher, if melanoma cells were pre-exposed to larger numbers of CTL or NK cells. Increases in human leukocyte antigen class I expression correlated with resistance to NK cells, while reduction in MART-1 antigen expression correlated with reduced CTL cytotoxicity. CTL cytotoxicity was rescued beyond control levels by exogenous MART-1 antigen. This study quantifies the interdependence of CTL and NK cell cytotoxicity and may guide strategies for efficient CTL-NK cell anti-melanoma therapies.

Key points summary

Cytotoxic T lymphocytes (CTL) and natural killer (NK) cells eliminate cancer cells. CTL and NK work in parallel, but most studies address them individually.

In a new human experimental model, antigen-specific CTL and NK cell cytotoxicity interdependence against melanoma is shown.

Whereas high numbers of antigen-specific CTL and NK cells eliminate all melanoma cells, lower, more physiological numbers induce resistance, in case secondary CTL or NK cell exposure follow initial CTL cell exposure or if secondary NK cell exposure follows initial NK cell exposure; only if secondary CTL exposure follows initial NK cell exposure no resistance of melanoma but even a slight enhancement of cytotoxicity was observed.

Alterations in HLA-I expression correlated with resistance to NK cells, while reduction in antigen expression correlated with reduced CTL cytotoxicity. CTL cytotoxicity was rescued beyond control levels by exogenous antigen.

The results should help to better understand and optimize immune therapies against cancer.

Graphical abstract
Human library of cardiac promoters and enhancers
Authors: Deviatiiarov Ruslan M. , Gams Anna , Syunyaev Roman , Tatarinova Tatiana V. , Gusev Oleg , Efimov Igor R.
Published: June 2020

Genome regulatory elements play a critical role during cardiac development and maintenance of normal physiological homeostasis, and genome-wide association studies identified a large number of SNPs associated with cardiovascular diseases localized in intergenic zones. We used cap analysis of gene expression (CAGE) to identify transcription start sites (TSS) with one nucleotide resolution that effectively maps genome regulatory elements in a representative collection of human heart tissues. Here we present a comprehensive and fully annotated CAGE atlas of human promoters and enhancers from four chambers of the non-diseased human donor hearts, including both atria and ventricles. We have identified 10,528 novel regulatory elements, where 2,750 are classified as TSS and 4,258 novel enhancers, which were validated with ChIP-seq libraries and motif enrichment analysis. We found that heart-region specific expression patterns are primarily based on the alternative promoter and specific enhancer activity. Our study significantly increased evidence of the association of regulatory elements-located variants with heart morphology and pathologies. The precise location of cardiac disease-related SNPs within the regulatory regions and their correlation with a specific cell type offers a new understanding of genetic heart diseases.
Calcium ion chelation preserves platelet function during cold storage
Authors: Xiang Binggang , Zhang Guoying , Zhang Yan , Wu Congqing , Joshi Smita , Morris Andrew J. , Ware Jerry , Smyth Susan S. , Whiteheart Sidney W. , Li Zhenyu
Published: June 2020

Objective

Platelet transfusion is a life-saving therapy to prevent or treat bleeding in patients with thrombocytopenia or platelet dysfunction. However, for more than six decades, safe and effective strategies for platelet storage have been an impediment to widespread use of platelet transfusion. Refrigerated platelets are cleared rapidly from circulation, precluding cold storage of platelets for transfusion. Consequently, platelets are stored at room temperature (RT) with an upper limit of 5 days due to risks of bacterial contamination and loss of platelet function. This practice severely limits platelet availability for transfusion. This study is to identify the mechanism of platelet clearance after cold storage and develop a method for platelet cold storage.

Approach and Results

We found that rapid clearance of cold-stored platelets was largely due to integrin activation and apoptosis. Deficiency of integrin β3 or caspase-3 prolonged cold-stored platelets in circulation. Pre-treatment of platelets with EGTA, a cell impermeable calcium ion chelator, reversely inhibited cold storage-induced platelet activation and consequently prolonged circulation of cold-stored platelets. Moreover, transfusion of EGTA-treated, cold-stored platelets, but not RT-stored platelets, into the mice deficient in glycoprotein Ibα significantly shortened tail-bleeding times and diminished blood loss.

Conclusion

Integrin activation and apoptosis is the underlying mechanism of rapid clearance of platelets after cold storage. Addition of a cell impermeable calcium ion chelator to platelet products is potentially a simple and effective method to enable cold storage of platelets for transfusion.
De novogenome assembly and transcriptome analysis for the drought and salt resistantSolanum sitiens
Authors: Molitor C. , Kurowski T.J. , Fidalgo de Almeida P.M. , Eerolla P. , Spindlow D.J. , Kashyap S.P. , Singh B. , Prasanna H.C. , Thompson A.J. , Mohareb F.R.
Published: June 2020

Solanum sitiensis a self-incompatible wild relative of tomato, characterised by salt and drought resistance traits, with the potential to contribute to crop improvement in cultivated tomato. This species has a distinct morphology, classification and ecotype compared to other stress resistant wild tomato relatives such asS. pennelliiandS. chilense. Therefore, the availability of a high-quality reference genome forS. sitienswill facilitate the genetic and molecular understanding of salt and drought resistance. Here, we present ade novogenome and transcriptome assembly forS. sitiens(Accession LA1974). A hybrid assembly strategy was followed using Illumina short reads (∼159X coverage) and PacBio long reads (∼44X coverage), generating a total of ∼262 Gbp of DNA sequence; in addition, ∼2,670 Gbp of BioNano data was obtained. A reference genome of 1,245 Mbp, arranged in 1,481 scaffolds with a N50 of 1,826 Mbp was generated. Genome completeness was estimated at 95% using the Benchmarking Universal Single-Copy Orthologs (BUSCO) and the K-mer Analysis Tool (KAT); this is within the range of current high-quality reference genomes for other tomato wild relatives. Additionally, we identified three large inversions compared toS. lycopersicum, containing several drought resistance related genes, such asbeta-amylase 1andYUCCA7.

In addition, ∼63 Gbp of RNA-Seq were generated to support the prediction of 31,164 genes from the assembly, and perform ade novotranscriptome. Some of the protein clusters unique toS. sitienswere associated with genes involved in drought and salt resistance, includingGLO1andFQR1.

This first reference genome forS. sitienswill provide a valuable resource to progress QTL studies to the gene level, and will assist molecular breeding to improve crop production in water-limited environments.
Synthetic data generation with probabilistic Bayesian Networks
Authors: Gogoshin Grigoriy , Branciamore Sergio , Rodin Andrei S.
Published: June 2020

Bayesian Network (BN) modeling is a prominent and increasingly popular computational systems biology method. It aims to construct probabilistic networks from the large heterogeneous biological datasets that reflect the underlying networks of biological relationships. Currently, a variety of strategies exist for evaluating BN methodology performance, ranging from utilizing artificial benchmark datasets and models, to specialized biological benchmark datasets, to simulation studies that generate synthetic data from predefined network models. The latter is arguably the most comprehensive approach; however, existing implementations are typically limited by their reliance on the SEM (structural equation modeling) framework, which includes many explicit and implicit assumptions that may be unrealistic in a typical biological data analysis scenario. In this study, we develop an alternative, purely probabilistic, simulation framework that more appropriately fits with real biological data and biological network models. In conjunction, we also expand on our current understanding of the theoretical notions of causality and dependence / conditional independence in BNs and the Markov Blankets within.
Dose-dependent enhancement of motion direction discrimination with transcranial magnetic stimulation of visual cortex
Authors: Gamboa Arana Olga Lucia , Palmer Hannah , Dannhauer Moritz , Hile Connor , Liu Sicong , Hamdan Rena , Brito Alexandra , Cabeza Roberto , Davis Simon W. , Peterchev Angel V. , Sommer Marc A. , Appelbaum Lawrence G.
Published: June 2020

Despite the widespread use of transcranial magnetic stimulation (TMS) in research and clinical care, the underlying mechanisms-of-actions that mediate modulatory effects remain poorly understood. To fill this gap, we studied dose–response functions of TMS for modulation of visual processing. Our approach combined electroencephalography (EEG) with application of single pulse TMS to visual cortex as participants performed a motion perception task. During participants’ first visit, motion coherence thresholds, 64-channel visual evoked potentials (VEPs), and TMS resting motor thresholds (RMT) were measured. In second and third visits, single pulse TMS was delivered 30 ms before the onset of motion or at the onset latency of the N2 VEP component derived from the first session. TMS was delivered at 0%, 80%, 100%, or 120% of RMT over the site of N2 peak activity, or at 120% over vertex. Behavioral results demonstrated a significant main effect of TMS timing on accuracy, with better performance when TMS was applied at N2-Onset timing versus Pre-Onset, as well as a significant interaction, indicating that 80% intensity produced higher accuracy than other conditions. TMS effects on VEPs showed reduced amplitudes in the 80% Pre-Onset condition, an increase for the 120% N2-Onset condition, and monotonic amplitude scaling with stimulation intensity. The N2 component was not affected by TMS. These findings reveal dose–response relationships between intensity and timing of TMS on visual perception and electrophysiological brain activity, generally indicating greater facilitation at stimulation intensities below RMT.
Ab initio Spillover Compensation in CyTOF Data
Authors: Miao Qi , Wang Fang , Dou Jinzhuang , Iqbal Ramiz , Muftuoglu Muharrem , Basar Rafet , Li Li , Rezvani Katy , Chen Ken
Published: June 2020

Signal intensity measured in a mass cytometry (CyTOF) channel can often be affected by the neighboring channels due to technological limitations. Such signal artifacts are known as spillover effects and can substantially limit the accuracy of cell population clustering. Current approaches reduce these effects by using additional beads for normalization purposes known as single-stained controls. While effective in compensating for spillover effects, incorporating single-stained controls can be costly and require customized panel design. This is especially evident when executing large-scale immune profiling studies. We present a novel statistical method, named CytoSpill that independently quantifies and compensates the spillover effects in CyTOF data without requiring the use of single-stained controls. Our method utilizes knowledge-guided modeling and statistical techniques, such as finite mixture modeling and sequential quadratic programming, to achieve optimal error correction. We evaluated our method using five publicly available CyTOF datasets obtained from human peripheral blood mononuclear cells (PBMCs), C57BL/6J mouse bone marrow, healthy human bone marrow, chronic lymphocytic leukemia patient, and healthy human cord blood samples. In the PBMCs with known ground truth, our method achieved comparable results to experiments that incorporated single-stained controls. In datasets without ground-truth, our method not only reduced spillover on likely affected markers, but also led to the discovery of potentially novel subpopulations expressing functionally meaningful, cluster-specific markers. CytoSpill (developed in R) will greatly enhance the execution of large-scale cellular profiling of tumor immune microenvironment, development of novel immunotherapy, and the discovery of immune-specific biomarkers. The implementation of our method can be found athttps://github.com/KChen-lab/CytoSpill.git.
Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein
Authors: Faulkner Matthew , Szabó István , Weetman Samantha L. , Sicard Francois , Huber Roland G. , Bond Peter J. , Rosta Edina , Liu Lu-Ning
Published: June 2020

Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of molecules in an effective manner has remained elusive. Here we use molecular dynamics and umbrella sampling calculations to determine the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate associated with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating molecular transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated experimentally by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates molecular transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intend of engineering BMC-based metabolic modules for new functions in synthetic biology.
Function and regulation of an aldehyde dehydrogenase essential for ethanol and methanol metabolism of the yeast,Komagataella phaffii
Authors: Rao Kamisetty Krishna , Sahu Umakant , Rangarajan Pundi N
Published: June 2020

The genome of the methylotrophic yeast,Komagataella phaffiiharbours multiple genes encoding putative alcohol dehydrogenases and aldehyde dehydrogenases (ALDs). Here, we demonstrate that one of the ALDs denoted as ALD-A is essential for ethanol metabolism. A zinc finger transcription factor known as Mxr1p regulatesALD-Atranscription by binding to Mxr1p response elements (MXREs) in theALD-Apromoter. Mutations which abrogate Mxr1p binding toALD-AMXREsin vitroabolish transcriptional activation fromALD-Apromoterin vivo. Mxr1p regulatesALD-Aexpression during ethanol as well as methanol metabolism. ALD-A is essential for the utilization of methanol andΔald-ais deficient in alcohol oxidase (AOX), a key enzyme of methanol metabolism. AOX protein but not mRNA levels are down regulated inΔald-a.ALD-A and AOX localize to cytosol and peroxisomes respectively during methanol metabolism suggesting that they are unlikely interact with each otherin vivo. This study has led to the identification of Mxr1p as a key regulator ofALD-Atranscription during ethanol and methanol metabolism ofK. phaffii. Post-transcriptional regulation of AOX protein levels by ALD-A during methanol metabolism is another unique feature of this study.
Rubisco activase remodels plant Rubisco via the large subunit N-terminus
Authors: Ng Jediael , Mueller-Cajar Oliver
Published: June 2020

The photosynthetic CO2fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) forms inhibited complexes with multiple sugar phosphates, including its substrate ribulose 1,5-bisphosphate. At least three classes of ATPases associated with diverse cellular activities (AAA+ proteins) termed Rubisco activases (Rcas) have evolved to remodel inhibited Rubisco complexes. The mechanism of green-type Rca found in higher plants has proved elusive, because until recently higher plant Rubiscos could not be expressed recombinantly. Towards identifying interaction sites between Rubisco and Rca, here we produce and characterize a suite of 33 Arabidopsis Rubisco mutants for their ability to be activated by Rca. We find that Rca activity is highly sensitive to truncations and mutations in the conserved N-terminus of the Rubisco large subunit. Both T5A and T7A substitutions cannot be activated by Rca, but present with increased carboxylation velocities. Our results are consistent with a model where Rca functions by transiently threading the Rubisco large subunit N-terminus through the axial pore of the AAA+ hexamer.