bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic causal modeling of the COVID-19 pandemic in northern Italy predicts possible scenarios for the second wave
Authors: Gandolfi Daniela , Pagnoni Giuseppe , Filippini Tommaso , Goffi Alessia , Vinceti Marco , D’Angelo Egidio , Mapelli Jonathan 
Published: August 2020

AbstractThe COVID-19 pandemic has sparked an intense debate about the factors underlying the dynamics of the outbreak. Mitigating virus spread could benefit from reliable predictive models that inform effective social and healthcare strategies. Crucially, the predictive validity of these models depends upon incorporating behavioral and social responses to infection that underwrite ongoing social and healthcare strategies. Formally, the problem at hand is not unlike the one faced in neuroscience when modelling brain dynamics in terms of the activity of a neural network: the recent COVID-19 pandemic develops in epicenters (e.g. cities or regions) and diffuses through transmission channels (e.g., population fluxes). Indeed, the analytic framework known as “Dynamic Causal Modeling” (DCM) has recently been applied to the COVID-19 pandemic, shedding new light on the mechanisms and latent factors driving its evolution. The DCM approach rests on a time-series generative model that provides — through Bayesian model inversion and inference — estimates of the factors underlying the progression of the pandemic. We have applied DCM to data from northern Italian regions, which were the first areas in Europe to contend with the COVID-19 outbreak. We used official data on the number of daily confirmed cases, recovered cases, deaths and performed tests. The model — parameterized using data from the first months of the pandemic phase — was able to accurately predict its subsequent evolution (including social mobility, as assessed through GPS monitoring, and seroprevalence, as assessed through serologic testing) and revealed the potential factors underlying regional heterogeneity. Importantly, the model predicts that a second wave could arise due to a loss of effective immunity after about 7 months. This second wave was predicted to be substantially worse if outbreaks are not promptly isolated and contained. In short, dynamic causal modelling appears to be a reliable tool to shape and predict the spread of the COVID-19, and to identify the containment and control strategies that could efficiently counteract its second wave, until effective vaccines become available.
Where will they grow from here? Association between height at 24 months and adult attained height in a population with a high prevalence of linear growth restriction
Authors: Schwarz Julia , Yori Pablo Peñataro , Pan William K. , Olortegui Maribel Paredes , Klapheke Robert , Kosek Margaret N. 
Published: August 2020

AbstractThis was a longitudinal observational cohort study to investigate the association of stunting at 24 months of age and attained adult height. A cohort of 104 Peruvian males (n = 47) and females (n = 57) was studied from 24 months to after puberty in a rural community in the Peruvian Amazon located 15 km southeast from the urban center of Iquitos. Anthropometric measures were made at 24 months and after puberty. Height for Age Z (HAZ) Scores were calculated and compared to assess the association of HAZ score at 24 months and adult height. 67.7% of males and 54.1% of females who were stunted at 24 m (HAZ<-2.0) recovered (HAZ>-2.0) after puberty, whereas 6.25% of males and 6.06% of females who were not stunted at 24 m (HAZ>-2.0) became stunted (HAZ<-2.0) after puberty. The first 1000 days are not the only critical window for growth promotion. Global and national initiatives to reduce stunting should not exclusively focus on the first two years of life, but also work to promote the nutritional initiatives to promote optimal nutrition and growth throughout childhood and adolescence.
Poor knowledge of COVID-19 and unfavourable perception of the response to the pandemic by healthcare workers at the Bafoussam Regional Hospital (West Region - Cameroon)
Authors: Fouogue Jovanny Tsuala , Noubom Michel , Kenfack Bruno , Dongmo Norbert Tanke , Tabeu Maxime , Megozeu Linda , Alima Jean Marie , Fogang Yannick Fogoum , Nyam Rim Landry Charles A , Fouelifack Florent Ymele , Fouedjio Jeanne Hortence , Nzogning Manebou Pamela Leonie Fouogue , Bibou Ze Clotaire Damien , Kouam Brice Foubi , Fomete Lauriane Nomene , Tebeu Pierre Marie , Ngowa Kemfang Jean Dupont , Foumane Pascal , Sando Zacharie , Enow Orock George Enownchong 
Published: August 2020

AbstractBackgroundThe World Health Organization has warned against a dramatic impact of COVID-19 in sub-Saharan Africa unless adequate response strategies are implemented. Whatever the strategy, the role of health care workers is pivotal. We undertook this study to assess knowledge of COVID-19 and perception of the response to the pandemic among the staff of a regional hospital in charge of COVID-19 patients in West Cameroon.MethodsWe used a convenience non probabilistic sampling method to carry out a survey with a self-administered questionnaire from April 14, 2020 to April 29, 2020 at the Bafoussam Regional Hospital (BRH). All the staff was invited to participate. Statistical analyses were done using Microsoft Excel 2010 and Epi-lnfo version 7.1.5.2 software.ResultsResponse rate was 76.1% (464/610). Mean age (SD) and average work experience (SD) were 35.0 (8.9) and 8.4 (7.4) years respectively. Sex ratio (M/F) was 101/356. Nursing and midwifery staff (56.8%) and in-patients units (49.94%) were predominant. Knowledge on origin and transmission of SARS-CoV-2 was poor but knowledge of clinical signs and the role of laboratory tests were good. 53.2% of respondents said all therapeutic regimens are only supportive and only a third of them trusted drugs recommended by health authorities. For 36.9% of respondents, herbal remedies can prevent/cure COVID-19. 70% of staffs felt they were not knowledgeable enough to handle COVID-19 cases. 85.6% of respondents thought the BRH had insufficient resources to adequately respond to COVID-19 and 55.6% were dissatisfied with its response to the pandemic (weaknesses: medicines/technologies (74.5%), service delivery (28.1%), human resource (10.9%)). 68% of staff felt insufficiently protected on duty and 76.5% reported that the pandemic significantly reduced non-COVID-19 services. 85.5% said they complied with preventive measures while in the community. For 44% of respondents Cameroonian regulations on COVID-19 corpses should be made more culture-sensitive. 51.2% of respondents were against vaccine trial in their community.ConclusionKnowledge of COVID-19 was poor and perception of the response to the pandemic was unfavorable.
Circulating CD8+ MAIT cells correlate with improved outcomes in anti-PD1 treated melanoma patients
Authors: Vorwald Victoria M. , Davis Dana M. , Van Gulick Robert J. , Torphy Robert J. , Borgers Jessica S.W. , Klarquist Jared , Couts Kasey L. , Amato Carol M. , Cogswell Dasha T. , Fujita Mayumi , Davis Timothy , Lozupone Catherine , Medina Theresa M. , Robinson William A. , Gapin Laurent , McCarter Martin D. , Tobin Richard P. 
Published: August 2020

AbstractWhile much of the research concerning factors associated with responses to immunotherapies focuses on the contributions of conventional peptide-specific T cells, the role of unconventional T cells, such as mucosalassociated invariant T (MAIT) cells, in human melanoma remains largely unknown. MAIT cells are innate-like T cells expressing a semi-invariant T cell receptor restricted to the non-classical MHC class I molecule MR1 presenting vitamin metabolites derived from bacteria. In this prospective clinical study, we sought to characterize MAIT cells in melanoma patients and determine their association with clinical outcomes. We identified tumor-infiltrating MAIT cells in melanomas across metastatic sites and found that the number of circulating MAIT cells is reduced in melanoma patients. However, circulating MAIT cell frequency is restored by anti-PD1 treatment in responding patients, correlating with treatment responses in which patients with high frequencies of MAIT cells exhibited improved overall survival. These data provide evidence for leveraging MAIT cells and their functions as novel targets for future therapies.
Phenotyping Neuropsychiatric Symptoms Profiles of Alzheimer’s Disease Using Cluster Analysis on EEG Power
Authors: Liu Friedrich , Fuh Jong-Ling , Peng Chung-Kang , Yang Albert C. 
Published: August 2020

AbstractThere has been an increasing interest in studying electroencephalogram (EEG) as a biomarker of Alzheimer’s disease but the association between EEG signals and patients’ neuropsychiatric symptoms remains unclear. We studied EEG signals of patients with Alzheimer’s disease to explore the associations between patients’ neuropsychiatric symptoms and clusters of patients based on their EEG powers. A total of 69 patients with mild Alzheimer’s disease (the Clinical Dementia Rating = 1) were enrolled and their EEG signals from 19 channels/electrodes were recorded in three sessions for each patient. The EEG power was calculated by Fourier transform for the four frequency bands (beta: 13–40 Hz, alpha: 8–13 Hz, theta: 4–8 Hz, and delta: < 4 Hz). We performed K-means cluster analysis to classify the 69 patients into two distinct groups by the log-transformed EEG powers (4 frequency bands x 19 channels) for the three EEG sessions. In each session, both clusters were compared with each other to assess the differences in their behavioral/psychological symptoms in terms of the Neuropsychiatric Inventory (NPI) score. While EEG band powers were highly consistent across all three sessions before clustering, EEG band powers were different between the two clusters in each session, especially for the delta waves. The delta band powers differed significantly between the two clusters in most channels across the three sessions. Patients’ demographics and cognitive function were not different between both clusters. However, their behavioral/psychological symptoms were different between the two clusters classified based on EEG powers. A higher NPI score was associated with the clustering of higher EEG powers. The results suggest that EEG delta band power correlates to behavioral and psychological symptoms among patients with mild Alzheimer’s disease. The clustering approach of EEG signals may provide a novel and cost-effective method to differentiate the severity of neuropsychiatric symptoms and/or predict the prognosis for Alzheimer’s patients.
A Noninvasive Approach to Optogenetics Using Focused Ultrasound Blood Brain Barrier Disruption for the Delivery of Radioluminescent Particles
Authors: Rich Megan , Zhang Eric , Dickey Ashley , Jones Haley , Cannon Kelli , Bandera Yuriy , Foulger Stephen , Lubin Farah , Bolding Mark 
Published: August 2020

AbstractOptogenetics, the genetic incorporation of light-sensitive proteins such as Channelrhodopsin-2 (ChR2) into target mammalian neurons, has enabled activation, silencing, and receptor subtype specific neuromodulation with high spatiotemporal resolution. However, the essential components of the ontogenetic system require invasive procedures with very few non-invasive alternatives preventing its use as a translational tool. The implantation of light emitting fibers deep within brain structures is both technically demanding and causes tissue scarring in target brain regions. To overcome these limitations, while maintaining the highly-tuned components of optogenetics we have developed a novel noninvasive alternative. Our approach replaces fibers with light-emitting radioluminescent particles (RLPs) that can be activated non-invasively with X-ray exposure. Here, we report successful noninvasive delivery of RLPs to target brain regions using MRI-guided focused ultrasound (FUS) blood brain barrier opening. In addition, FUS BBBO can be used to deliver viral vectors for light sensitive channel expression. Combined, these components can provide a completely non-invasive optogenetic system.
Path tortuosity changes the transport cost paradigm in terrestrial animals
Authors: Wilson R. P. , Rose K. A. R. , Metcalfe R. S. , Holton M. D. , Redcliffe J. , Gunner R. , Börger L. , Loison A. , Miloš J. , Painter M. S. , Silovský V. , Marks N. , Garel M. , Toigo C. , Marchand P. , Bennett N. C. , McNarry M. A. , Mackintosh K. A. , Brown M. R. , Scantlebury D. M. 
Published: August 2020

AbstractAnimal movement paths are variously tortuous, with high turn rates predicted to be energetically costly, especially at high speeds. Animals travel most efficiently at the speed that gives the lowest cost of transport (COT), a well-defined point for movement in fluid media. However, theoretically, land animals should travel at their maximum speed to minimize COT, which they do not, instead travelling at walking pace. We measured oxygen consumption in humans to demonstrate that the energetic costs of turning increase disproportionately with both speed and angular velocity. This resulted in the minimum COT speed occurring at very low speeds, which reduced with increased path tortuosity. Data on turn rates from six free-ranging terrestrial species underpinned this because all individuals turned faster at the slowest speeds across the full speed range. The optimum movement speed for minimum COT in land animals thus depends on the environment and behavior since both affect track tortuosity.
Re-emergence of BTV serotype 4 in North Macedonia, July 2020
Authors: Flannery John , King Simon , Rajko-Nenow Paulina , Popova Zagorka , Krstevski Kiril , Djadjovski Igor , Batten Carrie 
Published: August 2020

SummaryBluetongue virus serotype 4 (BTV-4) was confirmed in sheep in North Macedonia in July 2020. The full genome of this BTV-4 strain (MKD2020/06) was shown to be most closely related (99.74% nt identity) to the Greek GRE2014/08 and the Hungarian HUN1014 strains, indicating the re-emergence of this BTV serotype in the Balkan region since it was last reported in 2017.
The cytoskeleton adaptor protein Sorbs1 controls the development of lymphatic and venous vessels in zebrafish
Authors: Veloso Alexandra , Bleuart Anouk , Orban Tanguy , Bruyr Jonathan , Cabochette Pauline , Germano Raoul F.V. , Bernard Alice , Vanhollebeke Benoit , Martin Maud , Dequiedt Franck 
Published: August 2020

AbstractLymphangiogenesis, the formation of lymphatic vessels is tightly linked to the development of the venous vasculature, both at the cellular and molecular levels. Here, we identify a novel role for Sorbs1, the founding member of the SoHo family of cytoskeleton adaptor proteins, in vascular and lymphatic development in zebrafish. We show that Sorbs1 is required for secondary sprouting and emergence of several vascular structures specifically derived from the axial vein. Most notably, formation of the precursor parachordal lymphatic structures is affected insorbs1mutant embryos, severely impacting the establishment of a proper trunk lymphatic network and leading to edema development. We show that Sorbs1 is probably not part of the Vegfc signaling, but instead might interacts with the BMP pathways. Mechanistically, we show that Sorbs1 controls FAK/Src signaling to impact on Rac1 and RhoA GTPases-regulated cytoskeleton processes. Inactivation of Sorbs1 altered cell-extracellular matrix (ECM) contact rearrangement and cytoskeleton dynamics, leading to specific defects in endothelial cell migratory and adhesive properties. Our data thus establish Sorbs1 as an important regulator of lymphangiogenesis distinct from the Vegfc signaling axis, increasing our understanding of context-specific vascular and lymphatic development.
Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking
Authors: Wu Anqi , Buchanan E. Kelly , Whiteway Matthew R , Schartner Michael , Meijer Guido , Noel Jean-Paul , Rodriguez Erica , Everett Claire , Norovich Amy , Schaffer Evan , Mishra Neeli , Salzman C. Daniel , Angelaki Dora , Bendesky Andrés ,   The International Brain Laboratory, Cunningham John , Paninski Liam 
Published: August 2020

AbstractNoninvasive behavioral tracking of animals is crucial for many scientific investigations. Recent transfer learning approaches for behavioral tracking have considerably advanced the state of the art. Typically these methods treat each video frame and each object to be tracked independently. In this work, we improve on these methods (particularly in the regime of few training labels) by leveraging the rich spatiotemporal structures pervasive in behavioral video — specifically, the spatial statistics imposed by physical constraints (e.g., paw to elbow distance), and the temporal statistics imposed by smoothness from frame to frame. We propose a probabilistic graphical model built on top of deep neural networks, Deep Graph Pose (DGP), to leverage these useful spatial and temporal constraints, and develop an efficient structured variational approach to perform inference in this model. The resulting semi-supervised model exploits both labeled and unlabeled frames to achieve significantly more accurate and robust tracking while requiring users to label fewer training frames. In turn, these tracking improvements enhance performance on downstream applications, including robust unsupervised segmentation of behavioral “syllables,” and estimation of interpretable “disentangled” low-dimensional representations of the full behavioral video. Open source code is available athttps://github.com/paninski-lab/deepgraphpose.
Aquatic insects are dramatically underrepresented in genomic research
Authors: Hotaling Scott , Kelley Joanna L. , Frandsen Paul B. 
Published: August 2020

AbstractAquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ∼9 terrestrial insect genomes. Instead, ∼24 terrestrial insect genomes have been sequenced for every aquatic insect genome. This discrepancy is even more dramatic if thequalityof genomic resources is considered; for instance, while no aquatic insect genome has been assembled to the chromosome level, 29 terrestrial insect genomes spanning four orders have. We argue that a lack of aquatic insect genomes is not due to any underlying difficulty (e.g., small body sizes or unusually large genomes) yet it is severely hampering aquatic insect research at both fundamental and applied scales. By expanding the availability of aquatic insect genomes, we will gain key insight into insect diversification and empower future research for a globally important taxonomic group.Simple SummaryAquatic insects comprise 10% of all insect diversity, can be found on every continent except Antarctica, and are key components of freshwater ecosystems. Yet aquatic insect genome biology lags dramatically behind that of terrestrial insects. If genomic effort was spread evenly, one aquatic insect genome would be sequenced for every ∼9 terrestrial insect genomes. Instead, ∼24 terrestrial insect genomes have been sequenced for every aquatic insect genome. We argue that the limited availability of aquatic insect genomes is not due to practical limitations—e.g., small body sizes or overly complex genomes—but instead reflects a lack of research interest. We call for targeted efforts to expand the availability of aquatic insect genomic resources to gain key molecular insight into insect diversification and empower future research.
Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens
Authors: Guo Xinyi , Wessels Hans-Hermann , Méndez-Mancilla Alejandro , Haro Daniel , Sanjana Neville E. 
Published: August 2020

AbstractCRISPR-Cas13 mediates robust transcript knockdown in human cells through direct RNA targeting. Compared to DNA-targeting CRISPR enzymes like Cas9, RNA targeting by Cas13 is transcript- and strand-specific: It can distinguish and specifically knock-down processed transcripts, alternatively spliced isoforms and overlapping genes, all of which frequently serve different functions. Previously, we identified optimal design rules forRfxCas13d guide RNAs (gRNAs), and developed a computational model to predict gRNA efficacy for all human protein-coding genes. However, there is a growing interest to target other types of transcripts, such as noncoding RNAs (ncRNAs) or viral RNAs, and to target transcripts in other commonly-used organisms. Here, we predicted relative Cas13-driven knock-down for gRNAs targeting messenger RNAs and ncRNAs in six model organisms (human, mouse, zebrafish, fly, nematode and flowering plants) and four abundant RNA virus families (SARS-CoV-2, HIV-1, H1N1 influenza and MERS). To allow for more flexible gRNA efficacy prediction, we also developed a web-based application to predict optimal gRNAs for any RNA target entered by the user. Given the lack of Cas13 guide design tools, we anticipate this resource will facilitate CRISPR-Cas13 RNA targeting in common model organisms, emerging viral threats to human health, and novel RNA targets.
Characterization of cells susceptible to SARS-COV-2 and methods for detection of neutralizing antibody by focus forming assay
Authors: Stone E. Taylor , Geerling Elizabeth , Steffen Tara L. , Hassert Mariah , Dickson Alexandria , Spencer Jacqueline F. , Toth Karoly , DiPaolo Richard J. , Brien James D. , Pinto Amelia K. 
Published: August 2020

AbstractThe SARS-CoV-2 outbreak and subsequent COVID-19 pandemic have highlighted the urgent need to determine what cells are susceptible to infection and for assays to detect and quantify SARS-CoV-2. Furthermore, the ongoing efforts for vaccine development have necessitated the development of rapid, high-throughput methods of quantifying infectious SARS-CoV-2, as well as the ability to screen human polyclonal sera samples for neutralizing antibodies against SARS-CoV-2. To this end, our lab has adapted focus forming assays for SARS-CoV-2 using Vero CCL-81 cells, referred to in this text as Vero WHO. Using the focus forming assay as the basis for screening cell susceptibility and to develop a focus reduction neutralization test. We have shown that this assay is a sensitive tool for determining SARS-CoV-2 neutralizing antibody titer in human, non-human primate, and mouse polyclonal sera following SARS-CoV-2 exposure. Additionally, we describe the viral growth kinetics of SARS-CoV-2 in a variety of different immortalized cell lines and demonstrate via human ACE2 and viral spike protein expression that these cell lines can support viral entry and replication.
Computationally Guided Design of BCR-ABL Tyrosine Kinase Inhibitors
Authors: Duan Chenghao , Chu Simon K. S. , Siegel Justin B. , Fell Jason S. 
Published: August 2020

ABSTRACTBCR-ABLtyrosine kinase inhibitors (TKI) are used to treat the chronic myeloid leukemia (CML). Many TKI have been developed as the primary treatment to the CML.Imatinib, a first generation TKI, directly targetsBCR-ABLwith effective results. As the disease becomes more advanced, patients start to develop resistance toimatinib. Due to this effect it is necessary to generate novel treatments for advanced stage CML. Computational tools can predict new drug candidates to targetBCR-ABL. We have designed two new drug candidates with different levels of modification, based on the predicted structure activity relationships withBCR-ABL. These new drug candidates are predicted to have better binding affinities withBCR-ABLthanimatinib, which can be more potent treatments of the disease.