bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transmission of B.1.617.2 Delta Variant between vaccinated healthcare workers
Authors: Kemp Steven A. , Cheng Mark TK , Hamilton Will , Kamelian Kimia ,   INSACOG Consortium, Singh Sujit , Rakshit Partha , Aggrawal Anurag , Illingworth Chris , Gupta Ravindra K. 
Published: November 2021

AbstractBreakthrough infections with SARS-CoV-2 Delta variant have been reported in vaccine recipients and in individuals infected with previous variants. However the potential for fully vaccinated individuals (two doses) to transmit SARS-CoV-2 is unclear. We here analyse data from health care workers in two hospitals in India, constructing probable transmission networks from epidemiological and virus genome sequence data using a suite of computational approaches. Among known cases we identify a high probability that doubly vaccinated individuals transmitted SARS-CoV-2, and potential cases of virus transmission between individuals who had received two doses of vaccine. Our findings highlight the need for ongoing infection control measures even in highly vaccinated populations.
Epidemiological and microbiological investigation of the large increase of vibriosis in northern Europe in 2018
Authors: Amato Ettore , Riess Maximilian , Thomas-Lopez Daniel , Linkevicius Marius , Pitkänen Tarja , Wołkowicz Tomasz , Rjabinina Jelena , Jernberg Cecilia , Hjertqvist Marika , MacDonald Emily , Antony-Samy Jeevan Karloss , Bjerre Karsten Dalsgaard , Salmenlinna Saara , Fuursted Kurt , Hansen Anette , Naseer Umaer 
Published: November 2021

AbstractNorthern European countries and countries bordering the Baltic Sea have witnessed an increase of vibriosis cases during recent heatwaves. Here, we described the epidemiology of vibriosis cases and the genetic diversity of Vibrio isolates from Norway, Sweden, Denmark, Finland, Poland, Estonia, and Latvia in 2018, a year with an exceptionally warm summer. We conducted a retrospective study and analysed demographics, geographic distribution, seasonality, causative species, and severity of non-travel related vibriosis cases in 2018. Data sources included surveillance systems, national laboratory notification databases and/or nationwide surveys to public health microbiology laboratories. Moreover, we performed whole genome sequencing and multilocus sequence typing of available isolates from 2014-2018 to map their genetic diversity.In 2018, we identified 445 non-travel related vibriosis cases in the study countries, which was considerably higher than the median of 126 cases between 2014-2017 (range: 87-272). The main reported mode of transmission was exposure to seawater. We observed a species-specific geographic disparity of vibriosis cases across the Nordic-Baltic region. Developing severe vibriosis was associated with infections of Vibrio vulnificus (adjOR: 17.2; 95% CI: 3.3-90.5) or Vibrio parahaemolyticus (adjOR: 2.1; 95% CI: 1.0-4.5), being ≥65 years of age (65-79 years, adjOR: 3.9; 95% CI: 1.7-8.7; 80+ years, adjOR: 15.5; 95% CI: 4.4-54.3) or acquiring infections during summer (adjOR: 5.1; 95% CI: 2.4-10.9). Although phylogenetic analysis revealed diversity between Vibrio isolates, two V. vulnificus clusters (<10 SNPs) were identified. A share sentinel surveillance system for vibriosis during summer months might be highly valuable to monitor this emerging public health issue.
Protective characteristics of COVID-19 convalescent and post-vaccination IgG antibodies
Authors: Klegerman Melvin E. , Peng Tao , Seferovich Ira , Rahbar Mohammad H. , Hessabi Manouchehr , Tahanan Amirali , Wanger Audrey , Grimes Carolyn Z. , Ostrosky-Zeichner Luis Z. , Koster Kent , Cirillo Jeffrey D. , Abeydeera Dinuka , De Lira Steve , McPherson David D. 
Published: November 2021

AbstractSoon after commencement of the SARS-CoV-2 disease outbreak of 2019 (COVID-19), it became evident that the receptor-binding domain of the viral spike protein is the target of neutralizing antibodies that comprise a critical element of protective immunity to the virus. This study addresses the relative lack of information regarding actual antibody concentrations in convalescent plasma samples from COVID-19 patients and extends these analyses to post-vaccination samples to estimate protective IgG antibody (Ab) levels. Both sample populations were similar and a protective Ab level of 7.5 µg/ml was determined, based on 95% of the normal distribution of the post-vaccination population. The results of this study have implications for future vaccine development, projection of protective efficacy duration, and understanding of the immune response to SARS-CoV-2 infection.One-Sentence SummaryUsing two quantitative immunoassays, we have found similar IgG antibody responses to the SARS-CoV-2 spike protein in populations of COVID-19 survivors and vaccine recipients that indicate a protective antibody concentration.
A game theory based analysis of network connectivity reveals that state transition is crucial for epilepsy surgery outcome prediction
Authors: Ivankovic Karla , Principe Alessandro , Montoya Justo , Manubens-Gil Linus , Dierssen Mara , Rocamora Rodrigo 
Published: November 2021

AbstractSeizures recur in half of patients who undergo epilepsy surgery. Presurgical workup mainly focuses on seizures, but only partially helps predicting outcomes, even after invasive electroencephalography. We conceived a generalizable model to detect epileptogenic networks through connectivity changes and identified the crucial role of the transition from pre-seizure to seizure, achieving the highest outcome prediction (93%) to date in a chronological cohort of 21 patients with 3-year follow-up or more.
Baseline hypocapnia is associated with intubation in COVID-19 diagnosed patients
Authors: Gounidis Athanasios , Evangeliou Alexandros P. , Kloura Christina , Manganari Evangelia , Parisi Christiana , Kourtidis Michalis , Kotronis Georgios , Apostolopoulou Martha , Apostolidou-Kiouti Fani 
Published: November 2021

ABSTRACTIntroductionHypocapnia may be one of the several factors predefining the need for intubation of patients needing hospitalization for COVID-19 pneumonia.MethodsA retrospective evaluation of patient files hospitalized for COVID-19 pneumonia from October 2020 until January 2021. Univariate and multivariate regression was used, as well as a multinomial regression to account for multiple endpoints (discharge, intubation, death).ResultsHypocapnia was strongly associated with intubation (OR: 0.86, 95% CI: 0.76, 0.97). Additionally, last pCO2 (OR: 1.08, 95% CI: 1.01, 1.16), baseline FiO2 (OR: 1.05, 95% CI: 1.03, 1.07) as well as last FiO2 (OR: 1.21, 95% CI: 1.11, 1.46), total severity score on admission (OR: 1.18, 95% CI: 1.03, 1.37) and last pO2 (OR: 0.89, 95% CI: 0.85, 0.92) were found to have a significant impact on intubation. Incorporation of deceased patients withheld the negative association with pCO2 levels (OR: 0.88, 95% CI: 0.78, 0.98).ConclusionThe dissociation between respiratory failure and a clinically comfortable patient is partly due to decreased carbon dioxide levels and clinicians should bare it in mind when handling patients with COVID-19 pneumonia. Hypocapnia seems to be a determinant factor of intubation in patients with COVID-19 pneumonia in this study.
Modelling optimal vaccination strategies against Covid-19 in a context of Gamma variant predominance in Brazil
Authors: Ferreira Leonardo Souto , de Almeida Gabriel Berg , Borges Marcelo Eduardo , Simon Lorena Mendes , Poloni Silas , Bagattini Ângela Maria , da Rosa Michelle Quarti Machado , Filho José Alexandre Felizola Diniz , de Souza Kuchenbecker Ricardo , Camey Suzi Alves , Kraenkel Roberto André , Coutinho Renato Mendes , Toscano Cristiana Maria 
Published: November 2021

SummaryBrazil experienced moments of collapse in its health system throughout 2021, driven by a timid initial vaccination strategy against Covid-19, combined with the emergence of variants of interest (VOC). Mathematical modelling has been used to subsidize decision-makers in public health planning. Considering the vaccine products available, effectiveness estimates, the emergence of Gamma as the predominant VOC circulating in 2021, and national estimated doses available for the next several months, we developed a Markov-chain mathematical modelling approach to evaluate optimal strategies for Covid-19 vaccination in Brazil in terms of Covid deaths averted. Our main findings are that in order to reach higher vaccination impact in Brazil, Covid-19 immunization strategies should include recovering vaccination coverage rates in high-risk groups reaching higher coverage; expanding vaccination to younger age groups should be considered only after ensuring at least 80% coverage in older age groups; reducing the interval between doses of AZD1222 from 12 to 8 weeks. We also demonstrate that the latter is only feasible if accompanied by an increase in vaccine supply of at least 50% in the next six month period.
Deep Learning based Intraretinal Layer Segmentation using Cascaded Compressed U-Net
Authors: Yadav Sunil K. , Kafieh Rahele , Zimmermann Hanna G. , Kauer-Bonin Josef , Nouri-Mahdavi Kouros , Mohammadzadeh Vahid , Shi Lynn , Kadas Ella M. , Paul Friedemann , Motamedi Seyedamirhosein , Brandt Alexander U. 
Published: November 2021

AbstractIntraretinal layer segmentation on macular optical coherence tomography (OCT) images generates non invasive biomarkers querying neuronal structures with near cellular resolution. While first deep learning methods have delivered promising results with high computing power demands, a reliable, power efficient and reproducible intraretinal layer segmentation is still an unmet need. We propose a cascaded two-stage network for intraretinal layer segmentation, with both networks being compressed versions of U-Net (CCU-INSEG). The first network is responsible for retinal tissue segmentation from OCT B-scans. The second network segments 8 intraretinal layers with high fidelity. By compressing U-Net, we achieve 392- and 26-time reductions in model size and parameters in the first and second network, respectively. Still, our method delivers almost similar accuracy compared to U-Net without additional constraints of computation and memory resources. At the post-processing stage, we introduce Laplacian-based outlier detection with layer surface hole filling by adaptive non-linear interpolation. We trained our method using 17,458 B-scans from patients with autoimmune optic neuropathies, i.e. multiple sclerosis, and healthy controls. Voxel-wise comparison against manual segmentation produces a mean absolute error of 2.3μm, which is 2.5x better than the device’s own segmentation. Voxel-wise comparison against external multicenter data leads to a mean absolute error of 2.6μm for glaucoma data using the same gold standard segmentation approach, and 3.7μm mean absolute error compared against an externally segmented reference data set. In 20 macular volume scans from patients with severe disease, 3.5% of B-scan segmentation results were rejected by an experienced grader, whereas this was the case in 41.4% of B-scans segmented with a graph-based reference method.
Emergence and widespread circulation of a recombinant SARS-CoV-2 lineage in North America
Authors: Gutierrez Bernardo , Castelán Sánchez Hugo G. , da Silva Candido Darlan , Jackson Ben , Fleishon Shay , Ruis Christopher , Delaye Luis , Rambaut Andrew , Pybus Oliver G. , Escalera-Zamudio Marina 
Published: November 2021

AbstractGenetic recombination is an important driving force of coronavirus evolution. While some degree of virus recombination has been reported during the COVID-19 pandemic, previously detected recombinant lineages of SARS-CoV-2 have shown limited circulation and been observed only in restricted areas. Prompted by reports of unusual genetic similarities among several Pango lineages detected mainly in North and Central America, we present a detailed phylogenetic analysis of four SARS-CoV-2 lineages (B.1.627, B.1.628, B.1.631 and B.1.634) in order to investigate the possibility of virus recombination among them. Two of these lineages, B.1.628 and B.1.631, are split into two distinct clusters (here named major and minor). Our phylogenetic and recombination analyses of these lineages find well-supported phylogenetic differences between the Orf1ab region and the rest of the genome (S protein and remaining reading frames). The lineages also contain several deletions in the NSP6, Orf3a and S proteins that can augment reconstruction of reliable evolutionary histories. By reconciling the deletions and phylogenetic data, we conclude that the B.1.628 major cluster originated from a recombination event between a B.1.631 major virus and a lineage B.1.634 virus. This scenario inferred from genetic data is supported by the spatial and temporal distribution of the three lineages, which all co-circulated in the USA and Mexico during 2021, suggesting this region is where the recombination event took place. We therefore support the designation of the B.1.628 major cluster as recombinant lineage XB in the Pango nomenclature. The widespread circulation of lineage XB across multiple countries over a longer timespan than the previously designated recombinant XA lineage raises important questions regarding the role and potential effects of recombination on the evolution of SARS-CoV-2 during the ongoing COVID-19 pandemic.
SARS-CoV2 serology assays: utility and limits of different antigen based tests through the evaluation and the comparison of four commercial tests
Authors: Gdoura Mariem , Halouani Habib , Mrad Mehdi , Donia Sahli , Chamsa Wafa , Mabrouk Manel , Salem Kamel Ben , Hogga Nahed , Triki Henda 
Published: November 2021

AbstractIntroductionSARS-CoV2 serology testing is multipurpose provided to choose an efficient test. We evaluated and compared 4 different commercial serology tests, three of them had the Food and Drug Administration (FDA) approval. Our goal was to provide new data to help to guide the interpretation and the choice of the serological tests.MethodsFour commercial tests were evaluated: Cobas®Roche®(total anti-N antibodies), VIDAS®Biomerieux®(IgM and IgG anti-RBD antibodies), Mindray®(IgM and IgG anti-N and anti-RBD antibodies) and Access®Beckman Coulter®(IgG anti-RBD antibodies). Were tested: a positive panel (n=72 sera) obtained from COVID-19 confirmed patients and a negative panel (n=119) of pre-pandemic sera. Were determined the analytical performances and was drawn the ROC curve to assess the manufacturer’s threshold.ResultsA large range of variability between the tests was found. Mindray®IgG and Cobas® tests showed the best overall sensitivity 79,2%CI95%[67,9-87,8]. Cobas® showed the best sensitivity after D14; 85,4%CI95%[72,2-93,9]. The best specificity was noted for Cobas®, VIDAS®IgG and Access® IgG(100%CI95%[96,9-100]). Access® had the lower sensitivity even after D14 (55,5% CI95%[43,4-67,3]). VIDAS®IgM and Mindray®IgM tests showed the lowest specificity and sensitivity rates. Overall, only 43 out of 72 sera gave concordant results (59,7%). Retained cut-offs for a significantly better sensitivity and accuracy, without altering significantly the specificity, were: 0,87 for Vidas®IgM(p=0,01), 0,55 for Vidas®IgG(p=0,05) and 0,14 for Access®(p<10−4).ConclusionAlthough FDA approved, each laboratory should realize its own evaluation for commercial tests. Tests variability may raise some concerns that seroprevalence studies may vary significantly based on the used serology test.
Doppler Slicing for Ultrasound Super-Resolution Without Contrast Agents
Authors: Bar-Zion Avinoam , Solomon Oren , Rabut Claire , Maresca David , Eldar Yonina C. , Shapiro Mikhail G. 
Published: November 2021

AbstractMuch of the information needed for diagnosis and treatment monitoring of diseases like cancer and cardiovascular disease is found at scales below the resolution limit of classic ultrasound imaging. Recently introduced vascular super-localization methods provide more than a ten-fold improvement in spatial resolution by precisely estimating the positions of microbubble contrast agents. However, most vascular ultrasound scans are currently performed without contrast agents due to the associated cost, training, and post-scan monitoring. Here we show that super-resolution ultrasound imaging of dense vascular structures can be achieved using the natural contrast of flowing blood cells. Instead of relying on separable targets, we used Fourier-based decomposition to separate signals arising from the different scales of vascular structures while removing speckle noise using multi-ensemble processing. This approach enabled the use of compressed sensing for super-resolution imaging of the underlying vascular structures, improving resolution by a factor of four. Reconstruction of ultrafast mouse brain scans revealed details that could not be resolved in regular Doppler images, agreeing closely with bubble-based super-localization microscopy of the same fields of view. By combining multi-ensemble Doppler acquisitions with narrowband Fourier decomposition and computational super-resolution imaging, this approach opens new opportunities for affordable and scalable super-resolution ultrasound imaging.
The rat frontal cortex encodes a value map for economic decisions under risk
Authors: Zhu Xiaoyue , Bao Chaofei , Moller-Mara Joshua , Li Jingjie , Dubroqua Sylvain , Erlich Jeffrey C. 
Published: November 2021

AbstractNeurons in frontal and parietal cortex encode task variables during decision-making, but causal manipulations of the two regions produce strikingly different results. For example, silencing the posterior parietal cortex (PPC) in rats and monkeys produces minimal effects in perceptual decisions requiring integration of sensory evidence, but silencing frontal cortex profoundly impairs the same decisions. Here, we tested the causal roles of the rat frontal orienting field (FOF) and PPC in economic choice under risk. On each trial, rats chose between a lottery and a small but guaranteed surebet. The magnitude of the lottery was independently varied across trials and was indicated to the rat by the pitch of an auditory cue. As in perceptual decisions, both unilateral and bilateral PPC muscimol inactivations produced minimal effects. FOF inactivations produced substantial changes in behavior even though our task had no working memory component. We quantified control and bilateral inactivation behavior with a multi-agent model consisting of a mixture of a ‘rational’ utility-maximizing agent (U=Vρ) with two ‘habitual’ agents that either choose surebet or lottery. Effects of FOF silencing were best accounted for by a decrease inρ, the exponent of the utility function. The decrease inρcould be parsimoniously explained by a dynamical model where the FOF is part of a network that represents the value of the lottery to compare against a remembered boundary representing the value of the surebet. This dynamical model predicted that neurons in the FOF should increase their activity with increasing lottery values. In line with our predictions, single neurons recorded in the FOF encoded the value of the lottery even when controlling for choice. These results together demonstrate that FOF is a critical node in the neural circuit for decision under risk.
Neural population dynamics reveals disruption of spinal sensorimotor computations during electrical stimulation of sensory afferents
Authors: Secerovic Natalija Katic , Balaguer Josep-Maria , Gorskii Oleg , Pavlova Natalia , Liang Lucy , Ho Jonathan , Grigsby Erinn , Gerszten Peter C. , Karal-ogly Dzhina , Bulgin Dmitry , Orlov Sergei , Pirondini Elvira , Musienko Pavel , Raspopovic Stanisa , Capogrosso Marco 
Published: November 2021

AbstractWhile neurostimulation technologies are rapidly approaching clinical applications for sensorimotor disorders, the impact of electrical stimulation on network dynamics is still unknown. Given the high degree of shared processing in neural structures, it is critical to understand if neurostimulation affects functions that are related to, but not targeted by the intervention. Here we approached this question by studying the effects of electrical stimulation of cutaneous afferents on unrelated processing of proprioceptive inputs. We recorded intra-spinal neural activity in four monkeys while generating proprioceptive inputs from the radial nerve. We then applied continuous stimulation to the radial nerve cutaneous branch and quantified the impact of the stimulation on spinal processing of proprioceptive inputs via neural population dynamics. Proprioceptive pulses consistently produced neural trajectories that were disrupted by concurrent cutaneous stimulation. This disruption propagated to the somatosensory cortex, suggesting that electrical stimulation can perturb natural information processing across the neural axis.
Oxygenated hemoglobin signal provides greater predictive performance of experimental condition than de-oxygenated
Authors: Luke Robert , Shader Maureen J , Gramfort Alexandre , Larson Eric , Lee Adrian KC , McAlpine David 
Published: November 2021

AbstractContinuous-wave functional near-infrared spectroscopy (fNIRS) neuroimaging provides an estimate of relative changes in oxygenated and de-oxygenated hemoglobin content, from which regional neural activity is inferred. The relation between both signals is governed by neurovascular coupling mechanisms. However, the magnitude of concentration changes and the contribution of noise sources to each chromophore is unique. Subsequently, it is not apparent if either chromophore signal practically provides greater information about the underlying neural state and relation to an experimental condition. To assess this question objectively, we applied a machine-learning approach to four datasets and evaluated which hemoglobin signal best differentiated between experimental conditions. To further ensure the objective nature of the analysis, the algorithm utilized all samples from the epoched data rather than pre-selected features. Regardless of experimental task, brain region, or stimulus, the oxygenated hemoglobin signal was better able to differentiate between conditions than the de-oxygenated signal. Incorporating both signals into the analysis provided no additional improvement over oxygenated hemoglobin alone. These results indicate that oxyhemoglobin is the most informative fNIRS signal in relation to experimental condition.