bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of air change rate and aerosol behavior during an outbreak of COVID-19 in a geriatric care facility
Authors: Ishigaki Yo , Yokogawa Shinji , Minamoto Yuki , Saito Akira , Kitamura Hiroko , Kawauchi Yuto 
Published: January 2022

AbstractBackgroundVentilation plays an important role in controlling aerosol transmission of coronavirus disease (COVID-19), and mass transmission of COVID- 19 has been reported in poorly ventilated areas.ObjectiveA real-world mass infection outbreak which occurred in an elderly nursing home, in Miyagi Prefecture, Japan, was simulated experimentally and numerically to investigate the controlling factors and quantify the effectiveness of various natural ventilation settings by means of air change rate (ACR).MethodsUsing the CO2 tracer gas method, the ACR values at the time of the outbreak were estimated to be 2.0–6.2 h-1 in rooms in the facility. Furthermore, a low-cost intervention of opening windows improved the ventilation frequency by a factor of 1.48–5.74. This implies that advective fluid flows are the key in the spread of high CO2 concentration zones. A numerical simulation was performed to obtain spatio-temporal evolution on such high CO2 concentration zones under similar conditions to the present experiment.ResultsThe results showed that ventilation was significantly dependent on the window opening conditions in all rooms (p-values ranging from 0.001 to 0.03 for all the rooms). In contrast, there was no significant dependence on the location of the sensor in any of the areas. Development of high CO2 concentration zones occurs in the first few minutes. Furthermore, the leading edge of such zones towards the common room yields a relatively high fluid velocity, suggesting that the large-scale advective flow dictates the spread of such high CO2 concentration zones.ConclusionsThe present results suggest that secondary infections could occur due to the aerosol advection driven by such large-scale flows, even when the building design adheres the ventilation guidelines. In elderly care facilities, open architectural spaces are recommended to realize quality of life and monitor residents. However, management is required to reduce the downwind infection risk from aerosols and ACR.
Acute upper airway disease in children with the omicron (B.1.1.529) variant of SARS-CoV-2: a report from the National COVID Cohort Collaborative (N3C)
Authors: Martin Blake , DeWitt Peter E. , Russell Seth , Sanchez-Pinto L. Nelson , Haendel Melissa A. , Moffitt Richard , Bennett Tellen D. 
Published: January 2022

AbstractBackgroundReports of SARS-CoV-2 causing laryngotracheobronchitis (commonly known as croup) have been limited to small case series. Early reports suggest the Omicron (B.1.1.529) strain of SARS-CoV-2 (the dominant circulating US strain since the week of 12/25/2021) replicates more efficiently in the conducting airways. This may increase the risk of a croup phenotype in children as they have smaller airway calibers.MethodsDescription of the incidence, change over time, and characteristics of children with SARS-CoV-2 and upper airway infection (UAI) diagnoses within the National COVID Cohort Collaborative (N3C) before and during the rise of the Omicron variant. We compare the demographics, comorbidities, and clinical outcomes of hospitalized SARS-CoV-2 positive children with and without UAI.ResultsSARS-CoV-2 positive UAI cases increased to the highest number per month (N = 170) in December 2021 as the Omicron variant became dominant. Of 15,806 hospitalized children with SARS-CoV-2, 1.5% (234/15,806) had an UAI diagnosis. Those with UAI were more likely to be male, younger, white, have asthma and develop severe disease as compared to those without UAI.ConclusionsPediatric acute UAI cases have increased during the Omicron variant surge with many developing severe disease. Improved understanding of this emerging clinical phenotype could aid in therapeutic decision-making and healthcare resource planning.
Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022
Authors: Stefanelli Paola , Trentini Filippo , Petrone Daniele , Mammone Alessia , Ambrosio Luigina , Manica Mattia , Guzzetta Giorgio , d’Andrea Valeria , Marziano Valentina , Zardini Agnese , Grane Carla Molina , Ajelli Marco , Di Martino Angela , Riccardo Flavia , Bella Antonino , Schepisi Monica Sane , Maraglino Francesco , Poletti Piero , Palamara Anna Teresa , Brusaferro Silvio , Rezza Giovanni , Pezzotti Patrizio , Merler Stefano ,   the Genomic SARS-CoV-2 National Surveillance Working Group,   the Italian Integrated Surveillance of COVID-19 Study Group
Published: January 2022

AbstractThe SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7–3.1 days. The mean net reproduction number rose from about 1.15 in absence of Omicron to a peak of 1.83 for symptomatic cases and 1.33 for hospitalized cases, while it remained stable for critical cases.
A Micronized Electrostatic Precipitator Respirator Effectively Removes Ambient SARS-CoV-2 Bioaerosols
Authors: Redmann Rachel K. , Beddingfield Brandon J. , Spencer Skye , Chirichella Nicole R. , Henley Julian L. , Hager Wes , Roy Chad J. 
Published: January 2022

RationaleInhalation of ambient SARS-CoV-2-containing bioaerosols leads to infection and pandemic airborne transmission in susceptible populations. Filter-based respirators effectively reduce exposure but complicate normal respiration through breathing zone pressure differential and are therefore impractical for long-term use.ObjectivesWe tested the comparative effectiveness of a prototyped micronized electrostatic precipitator (mEP) to a filter-based respirator (N95) in the removal of viral bioaerosols from a simulated inspired air stream.MethodsEach respirator was tested within a 16-liter environmental chamber housed within a Class III biological safety cabinet within biosafety level 3 containment. SARS-CoV-2 containing bioaerosols were generated into the chamber, drawn by vacuum through each respirator, and physical particle removal and viral genomic RNA were measured distal to the breathing zone of each device.Measurement and Main ResultsThe mEP respirator removed particles (96.5±0.4%) approximating efficiencies of the N95 (96.9±0.6%). The mEP respirator similarly decreased SARS-CoV-2 viral RNA (99.792%) when compared to N95 removal (99.942%) as a function of particle removal from the airstream distal to the breathing zone of each respirator.ConclusionsThe mEP respirator approximated performance of a filter-based N95 respirator for particle removal and viral RNA as a constituent of the SARS-CoV-2 bioaerosols generated for this evaluation. In practice, the mEP respirator would provide equivalent protection from ambient infectious bioaerosols as the N95 respirator without undue pressure drop to the wearer, thereby facilitating long-term use in an unobstructed breathing configuration.
Liver Echinococcosis Lesion Classification Tool by Deep Learning: development, deployment, and validations
Authors: Huang Liang , Xi Xiaohong , Chen Zhu , Zeng Yilan 
Published: January 2022

AbstractThe endemic of Echinococcosis imposed heavy disease burden in some areas. The sonography for Echinococcosis lesions was essential to disease diagnosis and managements. Especially the biological typing of lesions was key to disease treatments. We used deep-learning tools to help sonographer to classify the lesion types. The model achieved 85%(302/376) accuracy, in contrast to senior sonographer achieved 72%(61/85) accuracy. The accuracy of AI model was higher than senior sonographer (p-value=0.01), could be a feasible method to help sonographer in remote area.
Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types
Authors: Ximerakis Methodios , Holton Kristina M. , Giadone Richard M. , Ozek Ceren , Saxena Monika , Santiago Samara , Adiconis Xian , Dionne Danielle , Nguyen Lan , Shah Kavya M. , Goldstein Jill M. , Gasperini Caterina , Lipnick Scott L. , Simmons Sean K. , Buchanan Sean M. , Wagers Amy J. , Regev Aviv , Levin Joshua Z. , Rubin Lee L. 
Published: January 2022

AbstractAging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors.
Encoding and decoding analysis of music perception using intracranial EEG
Authors: Bellier Ludovic , Llorens Anaïs , Marciano Déborah , Schalk Gerwin , Brunner Peter , Knight Robert T. , Pasley Brian N. 
Published: January 2022

AbstractMusic perception engages multiple brain regions, however the neural dynamics of this core human experience remains elusive. We applied predictive models to intracranial EEG data from 29 patients listening to a Pink Floyd song. We investigated the relationship between the song spectrogram and the elicited high-frequency activity (70-150Hz), a marker of local neural activity. Encoding models characterized the spectrotemporal receptive fields (STRFs) of each electrode and decoding models estimated the population-level song representation. Both methods confirmed a crucial role of the right superior temporal gyri (STG) in music perception. A component analysis on STRF coefficients highlighted overlapping neural populations tuned to specific musical elements (vocals, lead guitar, rhythm). An ablation analysis on decoding models revealed the presence of unique musical information concentrated in the right STG and more spatially distributed in the left hemisphere. Lastly, we provided the first song reconstruction decoded from human neural activity.
N Gene Target Failure (NGTF) for detection of Omicron: a way out for the ‘stealth’ too?
Authors: Harankhedkar Shivangi , Chatterjee Gaurav , Rajpal Sweta , Khan Afreen , Srivastava Tuhina , Mirgh Sumeet , Gokarn Anant , Punatar Sachin , Shetty Nitin , Joshi Amit , Nair Sudhir , Murthy Vedang , Tembhare Prashant , More Ashwini , Kamtalwar Sujeet , Chavan Preeti , Bhat Vivek , Patil Amar , Dhumal Sachin , Bhat Prashant , Subramanian Papagudi , Tripathi Rachana , Munipally Shesheer , Gujral Sumeet , Khattry Navin , Gupta Sudeep , Patkar Nikhil 
Published: January 2022

AbstractS-gene target failure (SGTF) is neither specific nor accurate for identification of Omicron lineage of SARS-CoV-2. We observed N-gene target failure (NGTF) in 402 out of 412 SARS-CoV2 positive cases from December to mid-January 2022 using a commercially available assay. This phenomenon was not observed with more than 15,000 cases tested previously. We sequenced the genome of five samples with NGTF and compared these results with six cases where NGTF was not seen. We confirm that cases with NGTF were the Omicron lineage while cases with preserved N-gene amplification belonged to Delta lineage. We discovered that the ERS31-33 deletion (nucleotide 28362-28370del) overlaps with N gene probe used, explaining NGTF. As the ‘stealth’ Omicron variant also harbors ERS31-33 deletion, this approach will work for the detection of ‘stealth’ Omicron variant as well. We suggest that NGTF can be used as a low cost, rapid screening strategy for detection of Omicron.
Limit of Detection for Rapid Antigen Testing of the SARS-CoV-2 Omicron Variant
Authors: Stanley Sydney , Hamel Donald J. , Wolf Ian D. , Riedel Stefan , Dutta Sanjucta , Cheng Annie , Kirby James E. , Kanki Phyllis J. 
Published: January 2022

AbstractThere has been debate in the literature about the ability of antigen tests to detect the SARS-CoV-2 Omicron variant including indication on the US Food and Drug administration website that antigen tests may have lower sensitivity for the Omicron variant without provision of data or the potential scale of the issue (seehttps://www.fda.gov/medical-devices/coronavirus-covid-19-and-medical-devices/sars-cov-2-viral-mutations-impact-covid-19-tests-omicronvariantimpact, accessed 1/27/2022). Here we determined the limit of detection (LoD) for the Omicron variant compared with the WA1 strain used for LoD studies described in the Instructions for Use for all Emergency Use Authorization (EUA)-approved antigen tests. Using live virus (to avoid artifactual findings potentially obtained with gamma-irradiated or heat-killed virus) quantified by plaque forming units (PFU), we examined the analytical sensitivity of three antigen tests widely used in the United States: the Abbott Binax Now, the AccessBio CareStart, and LumiraDx antigen tests. We found that the 95% detection threshold (LoD) for antigen tests was at least as good for Omicron as for the WA1 strain. Furthermore, the relationship of genome copies to plaque forming units for Omicron and WA1 overlap. Therefore, the LoD equivalency also applies if the quantitative comparator is genome copies determined from live virus preparations. Taken together, our data support the continued ability of the antigen tests examined to detect the Omicron variant.
Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation
Authors: Griffith Gareth J , Owen Gwilym , Manley David , Howe Laura D , Smith George Davey 
Published: January 2022

AbstractBackgroundObservational studies have highlighted that where individuals live is far more important for risk of dying with COVID-19, than for dying of other causes. Deprivation is commonly proposed as explaining such differences. During the period of localised restrictions in late 2020, areas with higher restrictions tended to be more deprived. We explore how this impacted the relationship between deprivation and mortality and see whether local or regional deprivation matters more for inequalities in COVID-19 mortality.MethodsWe use publicly available population data on deaths due to COVID-19 and all-cause mortality between March 2020 and April 2021 to investigate the scale of spatial inequalities. We use a multiscale approach to simultaneously consider three spatial scales through which processes driving inequalities may act. We go on to explore whether deprivation explains such inequalities.ResultsAdjusting for population age structure and number of care homes, we find highest regional inequality in October 2020, with a COVID-19 mortality rate ratio of 5.86 (95% CI 3.31 to 19.00) for the median between-region comparison. We find spatial context is most important, and spatial inequalities higher, during periods of low mortality. Almost all unexplained spatial inequality in October 2020 is removed by adjusting for deprivation. During October 2020, one standard deviation increase in regional deprivation was associated with 2.45 times higher local mortality (95% CI, 1.75 to 3.48).ConclusionsSpatial inequalities are greatest in periods of lowest overall mortality, implying that as mortality declines it does not do so equally. During the prolonged period of low restrictions and low mortality in summer 2020, spatial inequalities strongly increased. Contrary to previous months, we show that the strong spatial patterning during autumn 2020 is almost entirely explained by deprivation. As overall mortality declines, policymakers must be proactive in detecting areas where this is not happening, or risk worsening already strong health inequalities.Key messages-Spatial inequalities in local mortality are highest in periods of lower overall mortality.-Spatial inequality in COVID-19 mortality peaked in October 2020, before decreasing strongly in November and over the winter period.-Deprivation explains almost all inequality during October when inequality was at its highest.-Regional deprivation was far more strongly associated with local mortality than local deprivation during September to November 2020.-This is consistent with an overdispersed distribution of secondary infections governed by transmission heterogeneity structured by deprivation.
Transmission of SARS-CoV-2 Omicron VOC subvariants BA.1 and BA.2: Evidence from Danish Households
Authors: Lyngse Frederik Plesner , Kirkeby Carsten Thure , Denwood Matthew , Christiansen Lasse Engbo , Mølbak Kåre , Møller Camilla Holten , Skov Robert Leo , Krause Tyra Grove , Rasmussen Morten , Sieber Raphael Niklaus , Johannesen Thor Bech , Lillebaek Troels , Fonager Jannik , Fomsgaard Anders , Møller Frederik Trier , Stegger Marc , Overvad Maria , Spiess Katja , Mortensen Laust Hvas 
Published: January 2022

1AbstractThe Omicron SARS-CoV-2 variant of concern (VOC lineage B.1.1.529), which became dominant in many countries during early 2022, includes several subvariants with strikingly different genetic characteristics. Several countries, including Denmark, have observed the two Omicron subvariants: BA.1 and BA.2. In Denmark the latter has rapidly replaced the former as the dominant subvariant.Based on nationwide Danish data, we estimate the transmission dynamics of BA.1 and BA.2 following the spread of Omicron VOC within Danish households in late December 2021 and early January 2022.Among 8,541 primary household cases, of which 2,122 were BA.2, we identified a total of 5,702 secondary infections among 17,945 potential secondary cases during a 1-7 day follow-up period. The secondary attack rate (SAR) was estimated as 29% and 39% in households infected with Omicron BA.1 and BA.2, respectively.We found BA.2 to be associated with an increased susceptibility of infection for unvaccinated individuals (Odds Ratio (OR) 2.19; 95%-CI 1.58-3.04), fully vaccinated individuals (OR 2.45; 95%-CI 1.77-3.40) and booster-vaccinated individuals (OR 2.99; 95%-CI 2.11-4.24), compared to BA.1. We also found an increased transmissibility from unvaccinated primary cases in BA.2 households when compared to BA.1 households, with an OR of 2.62 (95%-CI 1.96-3.52). The pattern of increased transmissibility in BA.2 households was not observed for fully vaccinated and booster-vaccinated primary cases, where the OR of transmission was below 1 for BA.2 compared to BA.1.We conclude that Omicron BA.2 is inherently substantially more transmissible than BA.1, and that it also possesses immune-evasive properties that further reduce the protective effect of vaccination against infection, but do not increase its transmissibility from vaccinated individuals with breakthrough infections.
Single-cell mapping links neurogenesis and angiogenesis in aggressive breast cancer
Authors: Wik Elisabeth , Aziz Sura , Finne Kenneth , Kleftogiannis Dimitrios , Askeland Cecilie , Knutsvik Gøril , Krüger Kristi , Svanøe Amalie A. , Birkeland Even , Kjølle Silje , Davidsen Benedicte , Stefansson Ingunn M. , Vethe Heidrun , Akslen Lars A. 
Published: January 2022

AbstractThe tumor microenvironment (TME) is important for cancer growth and progression. While angiogenesis is an established hallmark of cancer, the role of nerve fibers is less studied. Here, we investigated neurogenesis and angiogenesis in breast cancer and found them to be closely associated. Single-cell based spatial mapping by imaging mass cytometry (IMC) indicated close proximity between neural and vascular structures. Subsequent validation by tissue-based markers of neurogenesis and angiogenesis, supported by proteomics and transcriptomics data of tissues and cell lines, supported a link between these processes. A consolidated neuro-angiogenic signature score was linked to high-grade breast cancer and reduced patient survival, also within the low-grade luminal tumor subgroup. Our findings support that neurogenesis and angiogenesis are related in aggressive breast cancer and might possibly improve tumor stratification and clinical management.
Comparative analysis of machine learning algorithms on the microbial strain-specific AMP prediction
Authors: Vishnepolsky Boris , Grigolava Maya , Managadze Grigol , Gabrielian Andrei , Rosenthal Alex , Hurt Darrell E. , Tartakovsky Michael , Pirtskhalava Malak 
Published: January 2022

ABSTRACTThe evolution of drug-resistant pathogenic microbial species is a major global health concern. Naturally occurring, antimicrobial peptides (AMPs) are considered promising candidates to address antibiotic resistance problems. A variety of computational methods have been developed to accurately predict AMPs. The majority of such methods are not microbial strain-specific (MSS): they can predict whether a given peptide is active against some microbe, but cannot accurately calculate whether such peptide would be active against a particular microbial strain. Due to insufficient data on most microbial strains, only a few MSS predictive models have been developed so far. To overcome this problem, we developed a novel approach that allows to improve MSS predictive models (MSSPM), based on properties, computed for AMP sequences and characteristics of genomes, computed for target microbial strains. New models can perform predictions of AMPs for microbial strains that do not have data on peptides tested on them. We tested various types of feature engineering as well as different machine learning (ML) algorithms to compare the predictive abilities of resulting models. Among the ML algorithms, Random Forest and AdaBoost performed best. By using genome characteristics as additional features, the performance for all models increased significantly—on average by 7%—relative to models relying on AMP sequence-based properties only. Our novel MSS AMP predictor is freely accessible as part of DBAASP database resource at https://dbaasp.org/tools?page=genome-prediction