bluuebunny/crossref_metadata_2025 huggingface dataset:
Arrhythmia variant associations and reclassifications in the eMERGE-III sequencing study
Authors: Glazer Andrew M. , Davogustto Giovanni , Shaffer Christian M. , Vanoye Carlos G. , Desai Reshma R. , Farber-Eger Eric H. , Dikilitas Ozan , Shang Ning , Pacheco Jennifer A. , Yang Tao , Muhammad Ayesha , Mosley Jonathan D. , Driest Sara L. Van , Wells Quinn S. , Rinke Lauren Lee , Kalash Olivia R. , Wada Yuko , Bland Sarah , Yoneda Zachary T. , Mitchell Devyn W. , Kroncke Brett M. , Kullo Iftikhar J. , Jarvik Gail P. , Gordon Adam S. , Larson Eric B. , Manolio Teri A. , Mirshahi Tooraj , Luo Jonathan Z. , Schaid Daniel , Namjou Bahram , Alsaied Tarek , Singh Rajbir , Singhal Ashutosh , Liu Cong , Weng Chunhua , Hripcsak George , Ralston James D. , McNally Elizabeth M. , Chung Wendy K. , Carrell David S. , Leppig Kathleen A. , Hakonarson Hakon , Sleiman Patrick , Sohn Sunghwan , Glessner Joseph ,   the eMERGE Network, Denny Joshua , Wei Wei-Qi , George Alfred L. , Shoemaker M. Benjamin , Roden Dan M.
Published: April 2021

In 21,846 eMERGE-III participants, sequencing 10 arrhythmia syndrome disease genes identified 123 individuals with pathogenic or likely pathogenic (P/LP) variants. Compared to non-carriers, P/LP carriers had a significantly higher burden of arrhythmia phenotypes in their electronic health records (EHRs). Fifty one participants had variant results returned. Eighteen of these 51 participants had inherited arrhythmia syndrome diagnoses (primarily long QT syndrome), and 11/18 of these diagnoses were made only after variant results were returned. Afterin vitrofunctional evaluation of 50 variants of uncertain significance (VUS), we reclassified 11 variants: 3 to likely benign and 8 to P/LP. As large numbers of people are sequenced, the disease risk from rare variants in arrhythmia genes can be assessed by integrating genomic screening, EHR phenotypes, andin vitrofunctional studies.
Cost-effectiveness of Stockholm3 test and magnetic resonance imaging in prostate cancer screening: a microsimulation study
Authors: Hao Shuang , Heintz Emelie , Östensson Ellinor , Discacciati Andrea , Jäderling Fredrik , Grönberg Henrik , Eklund Martin , Nordström Tobias , Clements Mark
Published: April 2021

Objective

Assess the cost-effectiveness of no screening and quadrennial magnetic resonance imaging (MRI)-based screening for prostate cancer using either Stockholm3 or prostate-specific antigen (PSA) test as a reflex test.

Methods

Test characteristics were estimated from the STHLM3-MR study (NCT03377881). A cost-utility analysis was conducted from a lifetime societal perspective using a microsimulation model for men aged 55-69 in Sweden for no screening and three quadrennial screening strategies, including: PSA≥3ng/mL; and Stockholm3 with reflex test thresholds of PSA≥1.5 and 2ng/mL. Men with a positive test had an MRI, and those MRI positive had combined targeted and systematic biopsies. Predictions included the number of tests, cancer incidence and mortality, costs, quality-adjusted life-years (QALYs) and incremental cost-effectiveness ratios (ICERs). Uncertainties in key parameters were assessed using sensitivity analyses.

Results

Compared with no screening, the screening strategies were predicted to reduce prostate cancer deaths by 7-9% across a lifetime and were considered to be moderate costs per QALY gained in Sweden. Using Stockholm3 with a reflex threshold of PSA≥2ng/mL resulted in a 60% reduction in MRI compared with screening using PSA. This Stockholm3 strategy was cost-effective with a probability of 70% at a cost-effectiveness threshold of €47,218 (500,000 SEK).

Conclusions

All screening strategies were considered to be moderate costs per QALY gained compared with no screening. Screening with Stockholm3 test at a reflex threshold of PSA≥2ng/mL and MRI was predicted to be cost-effective in Sweden. Use of the Stockholm3 test may reduce screening-related harms and costs while maintaining the health benefits from early detection.
First-in-Human Trial of a Recombinant Stabilized Prefusion SARS-CoV-2 Spike Protein Vaccine with Adjuvant of Aluminum Hydroxide and CpG 1018
Authors: Hsieh Szu-Min , Liu Wang-Da , Huang Yu-Shan , Lin Yi-Jiun , Hsieh Erh-Fang , Lian Wei-Cheng , Chen Charles , Tai I-Chen , Chang Shan-Chwen
Published: April 2021

Design

This is a phase 1, dose-escalation open-label trial to evaluate the safety and immunogenicity of MVC-COV1901, a recombinant stabilized prefusion SARS-CoV-2 spike (S-2P) protein vaccine with adjuvant of aluminum hydroxide and CpG 1018.

Methods

We enrolled 45 healthy adults from 20 to 49 years of age to be administered with two vaccinations of MVC-COV1901 in a low dose (LD), middle dose (MD), and high dose (HD) of spike protein at 28 days apart. There were 15 participants in each dose group, and all of them were followed up for 28 days after the second vaccination at the time of interim analysis. Adverse events (AEs) and laboratory data were recorded for safety evaluation. Blood samples were collected for wild-type SARS-CoV-2 and pseudovirus neutralization assays as well as SARS-CoV-2 spike-specific immunoglobulin G (IgG) at various times. Overall, the study duration will be 7 months.

Results

Solicited events were mostly mild and similar in the participants of all three dose groups. No subject experienced fever. There were no serious nor adverse events of special interest at the time point of this interim report. After the second vaccination, the SARS-CoV-2 spike specific IgG titers increased with peak geometric mean titers at 7178.245 (LD), 7746.086 (MD), and 11220.58 (HD), respectively. Serum neutralizing activity was detected by two methods in all participants of MD and HD groups, with geometric mean values generally comparable to those of a panel of control convalescent serum specimens. All of the participants in the MD and HD groups were seroconverted after the second vaccination.

Conclusions

The MVC-COV1901 vaccine is safe and elicits remarkable immune responses especially in the MD and HD groups.

Trial Registration

ClinicalTrials.gov NCT 04487210
The prevalence and density of asymptomatic Plasmodium falciparum infections among children and adults in three communities of western Kenya
Authors: Salgado Christina , Ayodo George , Macklin Michael D. , Gould Meetha P. , Nallandhighal Srinivas , Odhiambo Eliud O. , Obala Andrew , O’Meara Prudhomme Wendy , John Chandy C. , Tran Tuan M.
Published: April 2021

Background

Further reductions in malaria incidence as more countries approach malaria elimination require the identification and treatment of asymptomatic individuals who carry mosquito-infective Plasmodium gametocytes that are responsible for furthering malaria transmission. Assessing the relationship between total parasitemia and gametocytemia in field surveys can provide insight as to whether detection of low-density, asymptomatic Plasmodium falciparum infections using sensitive molecular methods can sufficiently detect the majority of infected individuals who are potentially capable of onward transmission.

Methods

In a cross-sectional survey of 1,354 healthy children and adults in three communities in western Kenya across a gradient of malaria transmission (Ajigo, Webuye, and Kapsisywa-Kipsamoite), we screened for asymptomatic P. falciparum infections by rapid diagnostic tests, blood smear, and quantitative PCR of dried blood spots targeting the varATS gene in genomic DNA. A multiplex quantitative reverse-transcriptase PCR assay targeting female and male gametocyte genes (pfs25, pfs230p), a gene with a transcriptional pattern restricted to asexual blood-stages (piesp2), and human GAPDH was also developed to determine total parasite and gametocyte densities among parasitemic individuals.

Results

The prevalence of varATS-detectable asymptomatic infections was greatest in Ajigo (42%), followed by Webuye (10%). Only two infections were detected in Kapsisywa. No infections were detected in Kipsamoite. Across all communities, children aged 11-15 years account for the greatest proportion total and sub-microscopic asymptomatic infections. In younger age groups, the majority of infections were detectable by microscopy, while 68% of asymptomatically infected adults (>21 years old) had sub-microscopic parasitemia. Piesp2-derived parasite densities correlated poorly with microscopy-determined parasite densities in patent infections relative to varATS-based detection. In general, both male and female gametocytemia increased with increasing varATS-derived total parasitemia. A substantial proportion (41.7%) of individuals with potential for onward transmission had qPCR-estimated parasite densities below the limit of microscopic detection but above the detectable limit of varATS qPCR.

Conclusions

This assessment of parasitemia and gametocytemia in three communities with different transmission intensities revealed evidence of a substantial sub-patent infectious reservoir among asymptomatic carriers of P. falciparum. Experimental studies are needed to definitively determine whether the low-density infections in communities such as Ajigo and Webuye contribute significantly to malaria transmission.
Development of Childhood Asthma Prediction Models using Machine Learning Approaches
Authors: Kothalawala Dilini M. , Murray Clare S. , Simpson Angela , Custovic Adnan , Tapper William J. , Arshad S. Hasan , Holloway John W. , Rezwan Faisal I.
Published: April 2021

Background

Wheeze is common in early life and often transient. It is difficult to identify which children will experience persistent symptoms and subsequently develop asthma. Machine learning approaches have the potential for better predictive performance and generalisability over existing childhood asthma prediction models.

Objective

To apply machine learning approaches for predicting school-age asthma (age 10) in early life (Childhood Asthma Prediction in Early life, CAPE model) and at preschool age (Childhood Asthma Prediction at Preschool age, CAPP model).

Methods

Data on clinical symptoms and environmental exposures were collected from children enrolled in the Isle of Wight Birth Cohort (N=1368, ∼15% asthma prevalence). Recursive Feature Elimination (RFE) identified the optimal subset of features predictive of school-age asthma for each model. Seven state-of-the-art machine learning classification algorithms were used to develop the models and the results were compared. To optimize the models, training was performed by applying 5-fold cross-validation, imputation and resampling. Predictive performances were evaluated on the test set and externally validated in the Manchester Asthma and Allergy Study (MAAS) cohort.

Results

RFE identified eight and 12 predictors for the CAPE and CAPP models, respectively. The best predictive performance was demonstrated by a Support Vector Machine (SVM) algorithm for both the CAPE model (area under the receiver operating curve, AUC=0.71) and CAPP model (AUC=0.82). Both models demonstrated good generalisability in MAAS (CAPE 8YR=0.71, 11YR=0.71, CAPP 8YR=0.83, 11YR=0.79).

Conclusion

Using machine learning approaches improved upon the predictive performance of existing regression-based models, with good generalisability and ability to rule in asthma.
Covid-19, non-Covid-19 and excess mortality rates not comparable across countries
Authors: Kelly Gabrielle , Petti Stefano , Noah Norman
Published: April 2021

Evidence that more people in some countries and fewer in others are dying because of the pandemic, than is reflected by reported Covid-19 mortality rates, is derived from mortality data. Using publicly available databases, deaths attributed to Covid-19 in 2020 and all deaths for the years 2015-2020 were tabulated for 35 countries together with economic, health, demographic, and government response stringency index variables. Residual mortality rates (RMR) in 2020 were calculated as excess mortality minus reported mortality rates due to Covid-19 where excess deaths were observed deaths in 2020 minus the average for 2015-2019. Differences in RMR are differences not attributed to reported Covid-19. For about half the countries, RMR’s were negative and for half, positive. The absolute rates in some countries were double those in others. In a regression analysis, population density and proportion of female smokers were positively associated with both Covid-19 and excess mortality while the human development index and proportion of male smokers were negatively associated with both. RMR was not associated with any of the investigated variables. The results show that published data on mortality from Covid-19 cannot be directly comparable across countries. This may be due to differences in Covid-19 death reporting and in addition, the unprecedented public health measures implemented to control the pandemic may have produced either increased or reduced excess deaths due to other diseases. Further data on cause-specific mortality is required to determine the extent to which residual mortality represents non-Covid-19 deaths and to explain differences between countries.
A BIBLIOMETRIC ANALYSIS OF RHEUMATOLOGY AND COVID-19 RESEARCHES
Authors: Pasin Ozge , Pasin Tugce
Published: April 2021

Objectives

COVID-19 has had a substantial impact on rheumatology. This study provides a general overview of studies on rheumatology and COVID-19.

Methods

Data were taken from the Web of Science (WoS) website. Analysis and network visualization mapping processes were carried out using VOSviewer. A total of 234 publications were analyzed, and the correlations between citation numbers and reference counts, usage counts and page numbers were analyzed with Spearman correlation coefficients.

Results

The average number of citations per item was 6.03. The studies were cited 1,411 times in total, and 1,121 times without self-citations. The countries with the highest number of publications on rheumatology and COVID-19 were the USA and England; the countries with the highest number of citations were Italy and the USA, and Jinoos Yazdany was the most cited author. The Annals of the Rheumatic Diseases was the most cited journal, whereas the highest number of articles on rheumatology and COVID-19 were published in Arthritis and Rheumatology.

Conclusions

Bibliometric analysis of rheumatology and COVID-19 can be useful to future studies because it provides a general perspective on the studies. This study provides an insight into the development of publications on rheumatology during the COVID-19 pandemic.
Using deep learning algorithms to simultaneously identify right and left ventricular dysfunction from the electrocardiogram
Authors: Vaid Akhil , Johnson Kipp W , Badgeley Marcus A , Somani Sulaiman S , Bicak Mesude , Landi Isotta , Russak Adam , Zhao Shan , Levin Matthew , Freeman Robert S , Charney Alexander W , Kukar Atul , Kim Bette , Danilov Tatyana , Lerakis Stamatios , Argulian Edgar , Narula Jagat , Nadkarni Girish N , Glicksberg Benjamin S
Published: April 2021

Background

Rapid evaluation of left and right ventricular function using deep learning (DL) on electrocardiograms (ECG) can assist diagnostic workflow. However, DL tools to estimate right ventricular (RV) function do not exist, while ones to estimate left ventricular (LV) function are restricted to quantification of very low LV function only.

Objectives

This study sought to develop deep learning models capable of comprehensively quantifying left and right ventricular dysfunction from ECG data in a large, diverse population.

Methods

A multi-center study was conducted with data from five New York City hospitals; four for internal testing and one serving as external validation. We created novel DL models to classify Left Ventricular Ejection Fraction (LVEF) into categories derived from the latest universal definition of heart failure, estimate LVEF through regression, and predict a composite outcome of either RV systolic dysfunction or RV dilation.

Results

We obtained echocardiogram LVEF estimates for 147,636 patients paired to 715,890 ECGs. We used Natural Language Processing (NLP) to extract RV size and systolic function information from 404,502 echocardiogram reports paired to 761,510 ECGs for 148,227 patients.

For LVEF classification in internal testing, Area Under Curve (AUC) at detection of LVEF<=40%, 40%<LVEF<=50%, and LVEF>50% was 0.94 (95% CI:0.94-0.94), 0.82 (0.81-0.83), and 0.89 (0.89-0.89) respectively. For external validation, these results were 0.94 (0.94-0.95), 0.73 (0.72-0.74) and 0.87 (0.87-0.88). For regression, the mean absolute error was 5.84% (5.82-5.85) for internal testing, and 6.14% (6.13-6.16) in external validation. For prediction of the composite RV outcome, AUC was 0.84 (0.84-0.84) in both internal testing and external validation.

Conclusions

DL on ECG data can be utilized to create inexpensive screening, diagnostic, and predictive tools for both LV/RV dysfunction. Such tools may bridge the applicability of ECGs and echocardiography, and enable prioritization of patients for further interventions for either sided failure progressing to biventricular disease.
Using 2D Video-based Pose Estimation for Automated Prediction of Autism Spectrum Disorders in Preschoolers
Authors: Kojovic Nada , Natraj Shreyasvi , Mohanty Sharada Prasanna , Maillart Thomas , Schaer Marie
Published: April 2021

Clinical research in autism has recently witnessed promising digital phenotyping results, mainly focused on single feature extraction, such as gaze, head turn on name-calling or visual tracking of the moving object. The main drawback of these studies is the focus on relatively isolated behaviors elicited by largely controlled prompts. We recognize that while the diagnosis process understands the indexing of the specific behaviors, ASD also comes with broad impairments that often transcend single behavioral acts. For instance, the atypical nonverbal behaviors manifest through global patterns of atypical postures and movements, fewer gestures used and often decoupled from visual contact, facial affect, speech. Here, we tested the hypothesis that a deep neural network trained on the non-verbal aspects of social interaction can effectively differentiate between children with ASD and their typically developing peers. Our model achieves an accuracy of 80.9% (F1 score: 0.818; precision: 0.784; recall: 0.854) with the prediction probability positively correlated to the overall level of symptoms of autism in social affect and repetitive and restricted behaviors domain. Provided the non-invasive and affordable nature of computer vision, our approach carries reasonable promises that a reliable machine-learning-based ASD screening may become a reality not too far in the future.
Suppression of endothelial miR-22-3p mediates non-small cell lung cancer cell-induced angiogenesis
Authors: Gu Yuan , Pais Gianni , Becker Vivien , Körbel Christina , Ampofo Emmanuel , Ebert Elke , Hohneck Johannes , Ludwig Nicole , Meese Eckart , Bohle Rainer M. , Zhao Yingjun , Menger Michael D. , Laschke Matthias W.
Published: April 2021

MicroRNAs (miRNAs) expressed in endothelial cells (ECs) are powerful regulators of angiogenesis, which is essential for tumor growth and metastasis. Here, we demonstrated that miR-22-3p (miR-22) is preferentially and highly expressed in ECs, while its endothelial level is significantly down-regulated in human non-small cell lung cancer (NSCLC) tissues when compared to matched non-tumor lung tissues. This reduction of endothelial miR-22 is induced by NSCLC cell-secreted tumor necrosis factor (TNF)-α and interleukin (IL)-1β. Endothelial miR-22 functions as a potent angiogenesis inhibitor that inhibits all the key angiogenic activities of ECs and consequently NSCLC growth through directly targeting sirtuin (SIRT)1and fibroblast growth factor receptor (FGFR)1in ECs, leading to inactivation of AKT/mammalian target of rapamycin (mTOR) signaling. These novel findings provide insight into the molecular mechanisms of NSCLC angiogenesis and indicate that endothelial miR-22 represents a potential target for the future anti-angiogenic treatment of NSCLC.
MSABrowser: dynamic and fast visualization of sequence alignments, variations, and annotations
Authors: Torun Furkan M. , Bilgin Halil I. , Kaplan Oktay I.
Published: April 2021

Sequence alignment is an excellent way to visualize the similarities and differences between DNA, RNA, or protein sequences, yet it is currently difficult to jointly view sequence alignment data with genetic variations, modifications such as post-translational modifications, and annotations (i.e. protein domains). Here, we develop the MSABrowser tool that makes it easy to co-visualize genetic variations, modifications, and annotations on the respective positions of amino acids or nucleotides in pairwise or multiple sequence alignments. MSABrowser is developed entirely in JavaScript and works on any modern web browser at any platform, including Linux, Mac OS X, and Windows systems without any installation. MSABrowser is also freely available for the benefit of the scientific community.

Availability and implementation

MSABrowser is released as open-source and web-based software under GNU General Public License, version 3.0 (GPLv3). The visualizer, documentation, all source codes, and examples are available athttp://thekaplanlab.github.io/and GitHub repositoryhttps://github.com/thekaplanlab/msabrowser.

Supplementary information

Supplementary data are available online.
Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vectorAnopheles stephensi
Authors: Mishra Shobhna , Sharma Gunjan , Das Manoj K. , Pande Veena , Singh Om P.
Published: April 2021

Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 ofAnopheles stephensihave been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA ofAn. stephensiand hypothesizes that observed intra-specific differences in this species may have resulted due to ambiguous DNA sequence-chromatogram resulting from intragenomic heterogeneity.Anopheles stephensicollected from different parts of India were sequenced for complete ITS2 and the variable region of 28S-rDNA (d1-d3 domains). Intragenomic variations were found in ITS2 region of allAn. stephensisequenced, but no such variation was observed in d1 to d3 domains of 28S-rDNA. Cloning and sequencing of ITS2 through the d3 domain of the 28S region of rDNA from representative samples from northern, central, and southern India confirmed the presence of intragenomic variation in ITS2 due to transitions at three loci and two bp indel in a di-nucleotide microsatellite locus. Multiple haplotypes were observed in ITS2 raised from such variations. Due to the absence of detectable intragenomic sequence variation in the d1 to d3 domain of 28S rDNA ofAn. stephensi, this region can serve as an ideal reference sequence for taxonomic and phylogenetic studies. The presence of intragenomic variation in rDNA should be carefully examined before using this as a molecular marker for species delimitation or phylogenetic analyses.
Heatrich-BS enables efficient CpG enrichment and highly scalable cell-free DNA methylation profiling
Authors: Cheruba Elsie , Viswanathan Ramya , Wong Pui-Mun , Womersley Howard John , Lau Yiting , Gan Anna , Poon Polly S.Y. , Ng Sarah B. , Chong Dawn Qingqing , Tan Iain Beehuat , Cheow Lih Feng
Published: April 2021

Genome wide analysis of cell-free DNA (cfDNA) methylation profile has been shown to be a promising approach for sensitive and specific multi-cancer detection. However, scaling these assays for clinical translation is impractical due to the high cost of whole genome bisulfite sequencing. We showed that the small fraction of GC-rich genome is highly enriched in CpG sites and disproportionately harbored the majority of cancer-specific methylation signature. Here, we report on the simple but effective Heat enrichment of CpG-rich regions for Bisulfite Sequencing (Heatrich-BS) platform that enables focused methylation profiling in these highly informative regions. Our novel method and bioinformatics algorithm enable high accuracy and sensitivity in tumor burden estimation and quantitative monitoring of colorectal patient response to treatment, at much reduced sequencing requirement. Heatrich-BS holds great potential for highly scalable screening and regular monitoring of cancer using liquid biopsy.
Cerebello-Basal Ganglia Networks and Cortical Network Global Efficiency
Authors: Jackson T. Bryan , Bernard Jessica A.
Published: April 2021

The cerebellum (CB) and basal ganglia (BG) each have topographically distinct functional subregions that are functionally and anatomically interconnected with cortical regions through discrete thalamic loops and with each other via disynaptic connections, with previous work detailing high levels of functional connectivity between these phylogenetically ancient regions. It was posited that this CB-BG network provides support for cortical systems processing, spanning cognitive, emotional, and motor domains, implying subcortical network measures are strongly related to cortical network measures (Bostan & Strick, 2018); however, it is currently unknown how network measures within distinct CB-BG networks relate to cortical network measures. Here, 122 regions of interest comprising cognitive and motor CB-BG networks and 7 canonical cortical resting-state were used to investigate whether the integration (quantified using global efficiency, GE) of cognitive CB-BG network (CCBN) nodes and their segregation from motor CB-BG network (MCBN) nodes is related to cortical network GE and segregation in 233 non-related, right- handed participants (Human Connectome Project-1200). CCBN GE positively correlated with GE in the default mode, motor, and auditory networks and MCBN GE positively correlated with GE in all networks except the default mode and emotional. MCBN segregation was related to MN segregation. These findings highlight the CB-BG network’s role in executive function, task switching, and verbal working memory. This work has implications for understanding cortical network organization and cortical-subcortical interactions in healthy adults and may help in deciphering subcortical differences seen in disease states.
Optimizing touchscreen measures of rodent cognition by eliminating image bias
Authors: Belarde James A. , Chen Claire W. , Rafikian Elizabeth , Yang Mu , Troy Carol M.
Published: April 2021

For the last twenty years, the Bussey-Saksida touchscreen-based operant conditioning platform has evolved in close parallel alongside the Cambridge Neuropsychological Test Automated Battery (CANTAB) to produce batteries of tests for studying complex cognitive functions in rodents that are increasingly analogous to human diagnostic tests and greatly narrow the translational gap in cognition research. Naturally, with this increasing usefulness comes increasing use, particularly by non-experts. This necessitates a greater understanding of, and a better controlling for, confounding factors that may limit the system’s ability to optimally detect cognitive deficits when used as a widely accessible and commercially available standardized task. In the present study, we show a strong image preference bias in a standard pairwise discrimination task with a widely used spider-plane image pairing in a putative animal model for intellectual disability. This bias greatly influenced the performance of our experimental mice, significantly affecting the length of time it took mice to complete the task, their progress over time, and several accessory measures usefully recorded by the Bussey-Saksida touchscreen system. We further show that this bias can be corrected by using more similar image pairings without sacrificing the animal’s ability to learn to distinguish the stimuli. This approach eliminated all significant stimuli specific differences seen with the spider-plane pairing. We then analyzed the pixel composition of the various stimuli to suggest that the bias is due to a difference in image brightness. These findings highlight the importance of carefully modulating paired touchscreen stimuli to ensure equivalence prior to learning and the need for more studies of visual perception in mice, particularly as it relates to their performance in cognitive assays.
Modeling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies
Authors: Machado Gustavo , Farthing Trevor , Andraud Mathieu , Lopes Francisco Paulo Nunes , Lanzas Cristina
Published: April 2021

African swine fever (ASF) is considered the most impactful transboundary swine disease. In the absence of effective vaccines, control strategies are heavily dependent on mass depopulation and movement restrictions. Here we developed a nested multiscale model for the transmission of ASF, combining spatially explicit network model of animal movements with a deterministic compartmental model for the dynamics of two ASF strains within-pixels of 3 km x 3 km, amongst the pig population in one Brazilian state. The model outcomes are epidemic duration, number of secondary infected farms and pigs, and distance of ASF spread. The model also shows the spatial distribution of ASF epidemics. We analyzed quarantine-based control interventions in the context of mortality trigger thresholds for the deployment of control strategies.

The mean epidemic duration of a moderately virulent strain was 11.2 days assuming the first infection is detected (best-case scenario) and 15.9 days when detection is triggered at 10 % mortality. For a highly virulent strain, the epidemic duration was 6.5 days and 13.1 days, respectively. The distance from the source to infected locations and the spatial distribution was not dependent on strain virulence. Under the best-case scenario, we projected an average number of infected farms of 23.77 farms and 18.8 farms for the moderate and highly virulent strains, respectively. At 10% mortality-trigger, the predicted number of infected farms was on average 46.27 farms and 42.96 farms, respectively. We also demonstrated that the establishment of ring quarantine zones regardless of size (i.e., 5 km, 15 km) was outperformed by backward animal movement tracking. The proposed modeling framework provides an evaluation of ASF epidemic potential, providing a ranking of quarantine-based control strategies that could assist animal health authorities in planning the national preparedness and response plan.
Synapse development is regulated by microglial THIK-1 K+channels
Authors: Izquierdo Pablo , Shiina Hiroko , Hirunpattarasilp Chanawee , Sethi Huma , Attwell David
Published: April 2021

Microglia are the resident immune cells of the central nervous system. They constantly survey the brain parenchyma for redundant synapses, debris or dying cells, which they remove through phagocytosis. Microglial ramification, motility and cytokine release are regulated by tonically active THIK-1 K+channels on the microglial plasma membrane. Here, we examined whether these channels play a role in phagocytosis. Using pharmacological blockers and THIK-1 knockout (KO) mice, we found that lack of THIK-1 activity reduced microglial phagocytosis, which may result in impaired pruning of synapses. In hippocampus, mice lacking THIK-1 expression had an increased number of glutamatergic synapses during development. This resulted from an increased number of presynaptic terminals, due to impaired removal by THIK-1 KO microglia. In microglia in brain slices from fresh human biopsies, modulating THIK-1 function had effects similar to those in rodents: blocking THIK-1 rapidly reduced microglial process ramification and increased synaptic density. The dependence of synapse number on THIK-1 K+channels, which control microglial surveillance and phagocytic ability, implies that changes in THIK-1 expression level over the lifespan or in disease states may contribute to altering neural circuit function.

Significance

Microglia are the brain’s resident immune cells, surveying it with motile processes, which can remove pathogens but also prune unnecessary junctions between the neurons (synapses). A potassium channel, THIK-1, in the microglial membrane allows efflux of potassium from these cells, and thereby regulates their membrane voltage as well as their process motility and release of inflammatory mediators. Here, using THIK-1-blocking drugs and THIK-1-deficient mice, we demonstrate that THIK-1 controls removal of synaptic material by microglia, which reduces the number of functional synapses. We also show that blocking THIK-1, as some anaesthetics do, affects microglial structure and increases the number of synapses in living brain slices from both rodents and humans, and could thus alter network function in the brain.
Large-scale voltage imaging in the brain using targeted illumination
Authors: Xiao Sheng , Lowet Eric , Gritton Howard J. , Fabris Pierre , Wang Yangyang , Sherman Jack , Mount Rebecca , Tseng Hua-an , Man Heng-Ye , Mertz Jerome , Han Xue
Published: April 2021

Recent improvements in genetically encoded voltage indicators enabled optical imaging of action potentials and subthreshold membrane voltage dynamics from single neurons in the mammalian brain. To perform high speed voltage imaging, widefield microscopy remains an essential tool for recording activity from many neurons simultaneously over a large anatomical area. However, the lack of optical sectioning makes widefield microscopy more prone to background signal contamination, and thus far voltage imaging using fully genetically encoded voltage indicators remains limited to simultaneous sampling of a few cells over a restricted field-of-view. We here demonstrate a strategy for large scale voltage imaging using the fully genetically encoded voltage indicator SomArchon and targeted illumination. We implemented a simple, low-cost digital micromirror device based targeted illumination strategy to restrict illumination to the cells of interest, and systematically quantified the improvement of this microscopy design theoretically and experimentally with SomArchon expressing neurons in single layer cell cultures and in the brains of awake mice. We found that targeted illumination, in comparison to widefield illumination, increased SomArchon signal contrast and reduced background cross-contamination in the brain. Such improvement permitted the reduction of illumination intensity, and thus reduced fluorescence photobleaching and prolonged imaging duration. When coupled with a high-speed, large area sCMOS camera, we routinely imaged tens of spiking neurons simultaneously over minutes in the brain. Thus, the widefield microscopy design with an integrated targeted illumination system described here offers a simple solution for voltage imaging analysis of large neuron populations in behaving animals.
ECNano: A Cost-Effective Workflow for Target Enrichment Sequencing and Accurate Variant Calling on 4,800 Clinically Significant Genes Using a Single MinION Flowcell
Authors: Leung Amy Wing-Sze , Leung Henry Chi-Ming , Wong Chak-Lim , Zheng Zhen-Xian , Lui Wui-Wang , Luk Ho-Ming , Lo Ivan Fai-Man , Luo Ruibang , Lam Tak-Wah
Published: April 2021

Background

The application of long-read sequencing using the Oxford Nanopore Technologies (ONT) MinION sequencer is getting more diverse in the medical field. Having a high sequencing error of ONT and limited throughput from a single MinION flowcell, however, limits its applicability for accurate variant detection. Medical exome sequencing (MES) targets clinically significant exon regions, allowing rapid and comprehensive screening of pathogenic variants. By applying MES with MinION sequencing, the technology can achieve a more uniform capture of the target regions, shorter turnaround time, and lower sequencing cost per sample.

Method

We introduced a cost-effective optimized workflow, ECNano, comprising a wet-lab protocol and bioinformatics analysis, for accurate variant detection at 4,800 clinically important genes and regions using a single MinION flowcell. The ECNano wet-lab protocol was optimized to perform long-read target enrichment and ONT library preparation to stably generate high-quality MES data with adequate coverage. The subsequent variant-calling workflow, Clair-ensemble, adopted a fast RNN-based variant caller, Clair, and was optimized for target enrichment data. To evaluate its performance and practicality, ECNano was tested on both reference DNA samples and patient samples.

Results

ECNano achieved deep on-target depth of coverage (DoC) at average >100x and >98% uniformity using one MinION flowcell. For accurate ONT variant calling, the generated reads sufficiently covered 98.9% of pathogenic positions listed in ClinVar, with 98.96% having at least 30x DoC. ECNano obtained an average read length of 1,000 bp. The long reads of ECNano also covered the adjacent splice sites well, with 98.5% of positions having ≥ 30x DoC. Clair-ensemble achieved >99% recall and accuracy for SNV calling. The whole workflow from wet-lab protocol to variant detection was completed within three days.

Conclusion

We presented ECNano, an out-of-the-box workflow comprising (1) a wet-lab protocol for ONT target enrichment sequencing and (2) a downstream variant detection workflow, Clair-ensemble. The workflow is cost-effective, with a short turnaround time for high accuracy variant calling in 4,800 clinically significant genes and regions using a single MinION flowcell. The long-read exon captured data has potential for further development, promoting the application of long-read sequencing in personalized disease treatment and risk prediction.
Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters
Authors: Saleh Moustafa M. , Jeronimo Célia , Robert François , Zentner Gabriel E.
Published: April 2021

The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We suggest that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.
Linking null models to hypotheses to improve nestedness analysis
Authors: Pereira Pinheiro Rafael Barros , Dormann Carsten F. , Félix Ferreira Gabriel Moreira , Ribeiro Mello Marco Aurelio
Published: April 2021

Nestedness is a common pattern in metacommunities and interaction networks, whose causes are still subject to investigation. Nestedness inference is challenging because, beyond calculating an index, we need to compare observed and expected values using null models. There are many different null models and the choice between them strongly affects test outcomes. Furthermore, there is no theoretical basis to guide this choice.

Here, we propose a different look at the meaning of nestedness that improves our understanding of its causes and directly links null models to hypotheses. The nestedness of a matrix is the combination of marginal sum inequality and high overlap. The higher the overlap, the more predictable the cell values by marginal sums. Therefore, the only way a process can increase nestedness is by promoting marginal sum inequalities, without concomitantly introducing preferences. We propose a combination of null models to test for different topological hypotheses. In these null models, interactions are randomized following a probability matrix. The probability matrix of the equiprobable model excludes marginal sum inequalities and consequently all nestedness-generating mechanisms, providing a distribution of expected values for nestedness significance tests. The probability matrix of the proportional model, by conserving marginal sums and maximizing overlap, conserves nestedness-generating mechanisms and excludes nestedness-disrupting mechanisms, thereby yielding the expected nestedness values for fully nested matrices.

We advance a new protocol to test for nestedness in binary and weighted matrices, in which those two null models represent different topological hypotheses. Our protocol helps to tell apart cases in which nestedness is different from expected by chance and cases in which nestedness represents the best topological archetype. We also evaluate the efficiency of applying this protocol using some common nestedness indices. Analyses based on weighted data proved to be highly efficient and informative, while binary analyses induced severe distortions. Finally, we empirically illustrate our approach using a plant-pollinator network.

Through a shift of perspective, our approach reconciliates contradictions in null model analysis and provides a guideline for nestedness interpretation.
Novel antiviral interferon sensitive genes unveiled by correlation-driven gene selection and integrated systems biology approaches
Authors: Cheroni Cristina , Manganaro Lara , Donnici Lorena , Bevilacqua Valeria , Bonnal Raoul J.P. , Rossi Riccardo L. , De Francesco Raffaele
Published: April 2021

Interferons (IFNs) are key cytokines involved in alerting the immune system to viral infection. After IFN stimulation, cellular transcriptional profile critically changes, leading to the expression of several IFN stimulated genes (ISGs) that exert a wide variety of antiviral activities. Despite many ISGs have been already identified, a comprehensive network of coding and non-coding genes with a central role in IFN-response still needs to be elucidated. We performed a global RNA-Seq transcriptome profile of the HCV permissive human hepatoma cell line Huh7.5 and its parental cell line Huh7, upon IFN treatment, to define a network of genes whose coordinated modulation plays a central role in IFN-response. Our study adds molecular actors, coding and non-coding genes, to the complex molecular network underlying IFN-response and shows how systems biology approaches, such as correlation networks, network’s topology and gene ontology analyses can be leveraged to this aim.
R-SPONDIN2+Mesenchymal Cells Form the Bud Tip Progenitor Niche During Human Lung Development
Authors: Hein Renee F.C. , Wu Joshua H. , Tsai Yu-Hwai , Wu Angeline , Miller Alyssa J. , Holloway Emily M. , Frum Tristan , Conchola Ansley S. , Szenker-Ravi Emmanuelle , Reversade Bruno , Yan Kelley S. , Kuo Calvin J. , Spence Jason R.
Published: April 2021

Mammalian respiratory system development is regulated by complex reciprocal signaling events that take place between epithelial cells and the surrounding mesenchymal cells; however, mesenchymal heterogeneity and function in the developing human lung is poorly understood. We interrogated single cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonistR-SPONDIN2(RSPO2), and we found that adjacent epithelial bud tip progenitors are enriched for the RSPO2 receptorLGR5. By carrying out functional experiments using organoid models, lung explant cultures, and FACS-isolatedRSPO2+mesenchyme, we show that RSPO2 is a critical niche cue that potentiates WNT signaling in human lung progenitors to maintain their multipotency.
Species-specific gene duplication inArabidopsis thalianaevolved novel phenotypic effects on morphological traits under strong positive selection
Authors: Huang Yuan , Chen Jiahui , Dong Chuan , Sosa Dylan , Xia Shengqian , Ouyang Yidan , Fan Chuanzhu , Li Dezhu , Mortola Emily , Long Manyuan , Bergelson Joy
Published: April 2021

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, the ways in which new duplicate genes contribute to phenotypic evolution remain largely unknown, especially in plants, owing to a lack of experimental and phenotypic data. In this study, we identified the new geneExov,derived from a partial gene region duplication of its parental geneExov-L, which is a member of an exonuclease family, into a different chromosome inArabidopsis thaliana. We experimentally investigated the phenotypic effects ofExovandExov-Lin an attempt to understand how the new gene diverged from the parental copy and contributes to phenotypic evolution. Evolutionary analysis demonstrated thatExovis a species-specific gene that originated within the last 3.5 million years and shows strong signals of positive selection. Unexpectedly, RNAseq analyses reveal that the new gene, despite its young age, has acquired a large number of novel direct and indirect interactions in which the parental gene does not engage. This is consistent with a high, selection-driven substitution rate in the protein sequence encoded byExovin contrast to the slowly evolvingExov-L, suggesting an important role forExovin phenotypic evolution. We analyzed phenotypic effects ofexovandexov-lsingle T-DNA-insertion mutants;doubleexov, exov-lT-DNA insertion mutants; and CRISPR/Cas9-mediatedexovcrpandexov-lcrpknockouts on seven morphological traits in both the new and parental genes. We detected significant segregation of morphological changes for all seven traits when assessed in terms of single mutants, as well as morphological changes for seven traits associated with segregation of doubleexov, exov-lmutants. Substantial divergence of phenotypic effects between new and parental genes was revealed by principal component analyses, suggesting neofunctionalization in the new gene. These results reveal a young gene that plays critical roles in biological processes that underlie morphological and developmental evolution inArabidopsis thaliana.
Optimized tight binding between the S1 segment and KCNE3 is required for the constitutively open nature of the KCNQ1-KCNE3 channel complex
Authors: Kasuya Go , Nakajo Koichi
Published: April 2021

Tetrameric voltage-gated K+channels have four identical voltage sensor domains, and they regulate channel gating. KCNQ1 (Kv7.1) is a voltage-gated K+channel, and its auxiliary subunit KCNE proteins dramatically regulate its gating. For example, KCNE3 makes KCNQ1 a constitutively open channel at physiological voltages by affecting the voltage sensor movement. However, how KCNE proteins regulate the voltage sensor domain is largely unknown. In this study, by utilizing the KCNQ1-KCNE3-calmodulin complex structure, we thoroughly surveyed amino acid residues on KCNE3 and the S1 segment of the KCNQ1 voltage sensor facing each other. By changing the side-chain bulkiness of these interacting amino acid residues, we found that the distance between the S1 segment and KCNE3 is elaborately optimized to achieve the constitutive activity. In addition, we identified two pairs of KCNQ1 and KCNE3 mutants that partially restored constitutive activity by co-expression. Our work suggests that tight binding of the S1 segment and KCNE3 is crucial for controlling the voltage sensor domains.