bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the use of growth models for forecasting epidemic outbreaks with application to COVID-19 data
Authors: Tovissodé Chénangnon F. , Lokonon Bruno E. , Kakaï Romain Glèlè 
Published: August 2020

AbstractThe initial phase dynamics of an epidemic without containment measures is commonly well modeled using exponential growth models. However, in the presence of containment measures, the exponential model becomes less appropriate. Under the implementation of an isolation measure for detected infectives, we propose to model epidemic dynamics by fitting a flexible growth model curve to reported positive cases and to infer the overall epidemic dynamics by introducing information on the detection/testing effort and recovery and death rates. The resulting modeling approach is close to the SIQR (Susceptible-Infectious-Quarantined-Recovered) model framework. We focused on predicting the peaks (time and size) in positive cases, actives cases and new infections. We applied the approach to data from the COVID-19 outbreak in Italy. Fits on limited data before the observed peaks illustrate the ability of the flexible growth model to approach the estimates from the whole data.
Impacts on Surgery Resident Education at a first wave COVID-19 epicenter
Authors: Ostapenko Alexander , McPeck Samantha , Liechty Shawn , Kleiner Daniel 
Published: August 2020

AbstractBackgroundThis study aims to identify the effects of the COVID-19 pandemic on surgical resident training and education at Danbury Hospital.MethodsWe conducted an observational study at a Western Connecticut hospital heavily affected by the first wave of the COVID-19 pandemic to assess its effects on surgical residents, focusing on surgical education, clinical experience, and operative skills development. Objective data was available through recorded work hours, case logs, and formal didactics. In addition, we created an anonymous survey to assess resident perception of their residency experience during the pandemic.ResultsThere are 22 surgical residents at our institution; all were included in the study. Resident weekly duty hours decreased by 23.9 hours with the majority of clinical time redirected to caring for COVID-19 patients. Independent studying increased by 1.6 hours (26.2%) while weekly didactics decreased by 2.1 hours (35.6%). The operative volume per resident decreased by 65.7% from 35.0 to 12.0 cases for the period of interest, with a disproportionately high effect on junior residents, who experienced a 76.2% decrease. Unsurprisingly, 70% of residents reported a negative effect of the pandemic on their surgical skills.ConclusionsDuring the first wave of the COVID-19 pandemic, surgical residents’ usual workflows changed dramatically, as much of their time was dedicated to the critical care of patients with COVID-19. However, the consequent opportunity cost was to surgery-specific training; there was a significant decrease in operative cases and time spent in surgical didactics, along with elevated concern about overall preparedness for their intended career.
Protection Level and Reusability of a Modified Full-Face Snorkel Mask as Alternative Personal Protective Equipment for Healthcare Workers During the COVID-19 Pandemic
Authors: Schmitt Jean , Jones Lewis S. , Aeby Elise A. , Gloor Christian , Moser Berthold , Wang Jing 
Published: August 2020

AbstractThe worldwide outbreak of the COVID-19 drastically increased pressure on medical resources and highlighted the need for rapidly available, large-scale and low-cost personal protective equipment (PPE). In this work, an alternative full-face mask is adapted from a modified snorkel mask to be used as PPE with two medical grade filters and a 3D-printed adapter. As the mask covers the eyes, mouth and nose, it acts as a full-face shield, providing additional protection to healthcare workers. The filtration efficiency of different medical filters is measured for particles below 300 nm to cover the size of the SARS-CoV-2 and small virus-laden droplets. The filtration performance of the adapted full-face mask is characterized using NaCl particles below 500 nm and different fitting scenarios. The mask is compared to a commercial respirator and characterized according to the EN 149 standard, demonstrating that the protection fulfills the requirements for the FFP2 level (filtering face-piece 2, stopping at least 94% of airborne particles). The device shows a good resistance to several cycles of decontamination (autoclaving and ethanol immersion), is easy to be produced locally at low cost and helps addressing the shortage in FFP2 masks and face shields by providing adequate protection to healthcare workers against particles below 500 nm.
Interobserver Agreement of Lung Ultrasound Findings of COVID-19
Authors: Kumar Andre , Weng Yingjie , Graglia Sally , Chung Sukyung , Duanmu Youyou , Lalani Farhan , Gandhi Kavita , Lobo Viveta , Jensen Trevor , Nahn Jeffrey , Kugler John 
Published: August 2020

AbstractBackgroundLung ultrasound (LUS) may be used in the diagnostic evaluation of patients with COVID-19. An abnormal LUS is associated with increased risk for ICU admission in COVID-19. Previously described LUS manifestations for COVID-19 include B-lines, consolidations, and pleural thickening. The interrater reliability (IRR) of these findings for COVID-19 is unknown.Research QuestionWhat is the interrater reliability of lung ultrasound findings in patients with RT-PCR confirmed COVID-19?Study Design and MethodsThis study was conducted at conducted at two academic medical centers between 03/2020-06/2020. Nine physicians (hospitalists: n=4; emergency medicine: n=5) independently evaluated n=20 LUS scans (n=180 independent observations) collected from RTPCR confirmed COVID-19 patients. These studies were randomly selected from an image database consisting of COVID-19 patients evaluated in the emergency department with portable ultrasound devices. Physicians were blinded to any patient information or previous LUS interpretation. Kappa values (κ) were used to calculate IRR.ResultsThere was substantial IRR on the following items: normal LUS scan (κ=0.79 [95% CI: 0.72-0.87]), presence of B-lines (κ=0.79 [95% CI: 0.72-0.87]), >=3 B-lines observed (κ=0.72 [95% CI: 0.64-0.79]). Moderate IRR was observed for the presence of any consolidation (κ=0.57 [95% CI: 0.50-0.64]), subpleural consolidation (κ=0.49 [95% CI: 0.42-0.56]), and presence of effusion (κ=0.49 [95% CI: 0.41-0.56]). Fair IRR was observed for pleural thickening (κ=0.23 [95% CI: 0.15-0.30]).InterpretationMany LUS manifestations for COVID-19 appear to have moderate to substantial IRR across providers from multiple specialties utilizing differing portable devices. The most reliable LUS findings with COVID-19 may include the presence/count of B-lines or determining if a scan is normal. Clinical protocols for LUS with COVID-19 may require additional observers for the confirmation of less reliable findings such as consolidations.Clinicaltrials.gov Registration:NCT04384055DisclosuresAndre Kumar, MD, MEd is a paid consultant for Vave Health, which manufactures one of the ultrasound devices used in this study. His consultant duties include providing feedback on product development. The other authors do not have any items to disclose.
Reclassification ofBrucella cicerias later heterotypic synonyms ofBrucella intermedia
Authors: Sánchez-Reyes Ayixon 
Published: August 2020

AbstractRecently Hördt et al. 2020 proposed to mergeOchrobactrumandBrucellagenera based on up to date phylogenomic evidence and overall genomic divergence amongBrucella-Ochrobactrumclade. This led to the description of the new combinationsBrucella cicericomb. nov., basonym:Ochrobactrum ciceriImran et al. 2010 andBrucella intermediacomb. nov., basonym:Ochrobactrum intermediumVelasco et al. 1998. However, the type species forBrucella ciceriDSM 22292TandBrucella intermediaLMG 3301Tshow whole-genome coherence at the species level (ANI = 98.21 %, Mash D = 0.0154006, dDDH relatedness >70%), suggesting that may belong to the same genomospecies. Also, both taxa formed a single clade in the phylogenomic tree based on single-copy gene sequences. Previously reported phenotypic data offer a context where both taxa are highly related supporting this synonymy. Therefore,Brucella cicerishould be reclassified as later heterotypic synonyms ofBrucella intermedia, which has priority. The species description is consequently amended.
Experimental parasite community perturbation reveals associations between Sin Nombre virus and gastrointestinal nematodes in a rodent reservoir host
Authors: Sweeny Amy R. , Thomason Courtney A. , Carbajal Edwin A. , Hansen Christina B. , Graham Andrea L. , Pedersen Amy B. 
Published: August 2020

AbstractIndividuals are often co-infected with several parasite species, yet measuring within-host interactions remains difficult in the wild. Consequently, such interactions’ impacts on host fitness and epidemiology are often unknown. We used anthelmintic drugs to experimentally reduce nematode infection and measured the effects on both nematodes and the important zoonosis Sin Nombre virus (SNV) in its primary wild reservoir (Peromyscus spp.). Treatment significantly reduced nematode infection, but increased SNV seroprevalence. Furthermore, mice that were co-infected with both nematodes and SNV were in better condition and survived as much as four times longer than mice infected with either parasite alone. These results highlight the importance of investigating multiple parasites for understanding interindividual variation and epidemiological dynamics in reservoir populations with zoonotic transmission potential.
Quantitative profiling of microbial communities byde novometaproteomics
Authors: Kleikamp Hugo B. C. , Pronk Mario , Tugui Claudia , da Silva Leonor Guedes , Abbas Ben , Lin Yue Mei , van Loosdrecht Mark C.M. , Pabst Martin 
Published: August 2020

ABSTRACTMetaproteomics has emerged as one of the most promising approaches for determining the composition and metabolic functions of complete microbial communities. Conventional metaproteomics approaches however, rely on the construction of protein sequence databases and efficient peptide-spectrum matching algorithms. Thereby, very large sequence databases impact on computational efforts and sensitivity. More recently, advancedde novosequencing strategies—which annotate peptide sequences without the requirement for a database—have become (again) increasingly proposed for proteomics applications. Such approaches would vastly expand many metaproteomics applications by enabling rapid community profiling and by capturing unsequenced community members, which otherwise remain inaccessible for further interpretation. Nevertheless, because of the lack of efficient pipelines and validation procedures, those strategies have only rarely been employed for community proteomics.Here we report on a newly established de novo metaproteomics pipeline which was evaluated for its quantitative performance using synthetic and natural communities. Additionally, we introduce a novel validation strategy and investigate the actual content of community members within community proteomics data.
Dorsal and ventral striatal functional connectivity shift with the medial frontal gyrus in internet gaming disorder: Potential mechanisms underlying addictive engagement
Authors: Dong Guang-Heng , Dong Haohao , Wang Min , Zhang Jialin , Zhou Weiran , Zheng Yanbin , Potenza Marc N. 
Published: August 2020

AbstractBackgroundAnimal models suggest transitions from non-addictive to addictive behavioral engagement are associated with ventral-to-dorsal striatal shifts. However, few studies have examined such features in humans, especially in internet gaming disorder (IGD), a behavioral addiction.MethodsFour-hundred-and-eighteen subjects (174 with IGD; 244 with recreational game use (RGU)) were recruited. Resting-state fMRI data were collected and functional connectivity (FC) analyses were performed based on ventral and dorsal striatal seeds. Correlations and follow-up spectrum dynamic causal model (spDCM) analyses were performed to examine relationships between ventral/dorsal striatum to medial frontal gyrus (MFG) and IGD severity. Longitudinal data from 40 subjects (22 IGD; 18 RGU) were also analysed to investigate further.ResultsInteractions were observed between group (IGD, RGU) and striatal regions (ventral, dorsal). IGD relative to RGU subjects showed lower ventral-striatum-to-MFG (mostly involving supplementary motor area (SMA)) and higher dorsal-striatum-to-MFG functional connectivity. spDCM revealed that left dorsal-striatum-to-MFG connectivity was correlated with IGD severity. Longitudinal data further support for ventral-to-dorsal striatal MFG relationships in IGD.ConclusionsConsistent with animal models of substance addictions, ventral-to-dorsal striatal transitions in involvement coritico-striatal circuitry may underlie IGD and its severity. These findings suggest possible neurobiological mechanisms that may be targeted in treatments for IGD.
Data-Driven Development of a Small-Area COVID-19 Vulnerability Index for the United States
Authors: Amram Ofer , Amiri Solmaz , Thorn Emily L. , Mansfield Jacob J. , Mellacheruvu Pranav , Monsivais Pablo 
Published: August 2020

ABSTRACTAs the COVID-19 pandemic continues to surge in the United States, it has become clear that infection risk is higher in certain populations, particularly socially and economically marginalized groups. Social risk factors, together with other demographic and community characteristics, may reveal local variations and inequities in COVID risk that could be useful for targeting testing and interventions. Yet to date, rates of infection and estimations of COVID risk are typically reported at the county and state level. In this study we develop a small area vulnerability index based on publicly-available sociodemographic data and 668,428 COVID diagnoses reported in 4,803 ZIP codes in the United States (15% of all ZIP codes). The outcome was COVID-19 diagnosis rates per 100,000 people by ZIP code. Explanatory variables included sociodemographic characteristics obtained from the 2018 American Community Survey 5-year estimates. Bayesian multivariable techniques were used to capture complexities of spatial data and spatial autocorrelation and identify individual risk factors and derive their respective weights in the index. COVID-19 diagnosis rates varied from zero to 29,508 per 100,000 people. The final vulnerability index showed that higher population density, higher percentage of noninsured, nonwhite race and Hispanic ethnicity were positively associated with COVID-19 diagnosis rates. Our findings indicate disproportionate risk of COVID-19 infection among some populations and validate and expand understanding of these inequities, integrating several risk factors into a summary index reflecting composite vulnerability to infection. This index can provide local public health and other agencies with evidence-based metrics of COVID risk at a geographical scale that has not been previously available to most US communities.
SARS-CoV-2 antibody responses in children with MIS-C and mild and severe COVID-19
Authors: Anderson Elizabeth M. , Diorio Caroline , Goodwin Eileen C. , McNerney Kevin O. , Weirick Madison E. , Gouma Sigrid , Bolton Marcus J. , Arevalo Claudia P. , Chase Julie , Hicks Philip , Manzoni Tomaz B. , Baxter Amy E. , Andrea Kurt P. , Burudpakdee Chakkapong , Lee Jessica H. , Vella Laura A. , Henrickson Sarah E. , Harris Rebecca M. , John Wherry E. , Bates Paul , Bassiri Hamid , Behrens Edward M. , Teachey David T. , Hensley Scott E. 
Published: August 2020

ABSTRACTSARS-CoV-2 antibody responses in children remain poorly characterized. Here, we show that pediatric patients with multisystem inflammatory syndrome in children (MIS-C) possess higher SARS-CoV-2 spike IgG titers compared to those with severe coronavirus disease 2019 (COVID-19), likely reflecting a longer time since onset of infection in MIS-C patients.
BiG-SLiCE: A Highly Scalable Tool Maps the Diversity of 1.2 Million Biosynthetic Gene Clusters
Authors: Kautsar Satria A. , van der Hooft Justin J. J. , de Ridder Dick , Medema Marnix H. 
Published: August 2020

AbstractBackgroundGenome mining for Biosynthetic Gene Clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. However, current tools suffer from a bottleneck caused by the expensive network-based approach used to group these BGCs into Gene Cluster Families (GCFs).ResultsHere, we introduce BiG-SLiCE, a tool designed to cluster massive numbers of BGCs. By representing them in Euclidean space, BiG-SLiCE can group BGCs into GCFs in a non-pairwise, near-linear fashion. We used BiG-SLiCE to analyze 1,225,071 BGCs collected from 209,206 publicly available microbial genomes and metagenome-assembled genomes (MAGs) within ten days on a typical 36-cores CPU server. We demonstrate the utility of such analyses by reconstructing a global map of secondary metabolic diversity across taxonomy to identify uncharted biosynthetic potential. BiG-SLiCE also provides a "query mode" that can efficiently place newly sequenced BGCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration.ConclusionsBiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global, searchable interconnected network of BGCs. As more genomes get sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available viahttps://github.com/medema-group/bigslice.
Neuroimmune circuits involved in β-lactoglobulin-induced food allergy
Authors: Lemos Luísa , Assis Helder Carvalho , Alves Juliana Lima , Reis Daniela Silva , Canesso Maria Cecilia Campos , Moreira Thais Garcias , Miranda Barbara Kaori Sato , Batista Luara Augusta , de Souza Gomes Lenzi Julia Ariana , Moraes Muiara Aparecida , Pereira Luciana Melo , Aguiar Daniele Cristina , Souza Bruno Rezende , Cara Denise Carmona , Gomes-Santos Ana Cristina , Faria Ana Maria Caetano 
Published: August 2020

ABSTRACTCow’s milk allergy is the most prevalent food allergy that usually begins early in life and β- lactoglobulin (BLG) is the milk component with the highest allergenicity. It has been described that ovalbumin (OVA)-induced food allergy in mice is associated with anxiety and aversive behavior. However, it is yet to be determined whether altered behavior is a general component of food allergy or whether it is specific for some types of allergens. Thus, we investigated behavioral and neuroimmune circuits triggered by allergic sensitization to BLG. We found a neuroimmune conflict between aversion and reward in a model of food allergy induced to BLG. Mice sensitized to BLG did not present aversive behavior when the allergen was used for sensitization and oral challenge. Mice allergic to BLG preferred to drink the allergen-containing solution over water even though they presented high levels of specific IgE, inflammatory cells in the intestinal mucosa and significant weight loss. When sensitized to OVA and orally challenged with the same antigen, mice had display neuron activation in the amygdala suggesting an anxiety-related sensation. On the other hand, OVA-sensitized mice showed preference to consume a mixture of BLG and OVA during oral challenge in spite of their aversion to OVA. Consumption of OVA-BLG solution was associated with neuron activation in the nucleus accumbens, suggesting a reward sensation. Thus, the aversive behavior observed in food allergy to OVA does not apply to all antigens and some allergens may induce preference rather than aversion. Our study provides new insights into the neuroimmune conflicts regarding preference and avoidance to a common antigen associated with food allergy.
Probing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment
Authors: Moses David , Yu Feng , Ginell Garrett M. , Shamoon Nora M. , Koenig Patrick S. , Holehouse Alex S. , Sukenik Shahar 
Published: August 2020

AbstractIntrinsically disordered proteins and protein-regions (IDRs) make up roughly 30% of the human proteome and play vital roles in a wide variety of biological processes. Given a lack of persistent tertiary structure, all of the residues in an IDR are, to some extent, solvent exposed. This extensive surface area, coupled with the absence of strong intramolecular contacts, makes IDRs inherently sensitive to their chemical environment. Despite this sensitivity, our understanding of how IDR structural ensembles are influenced by changes in their chemical environment is limited. This is particularly relevant given a growing body of evidence showing that IDR function is linked to the underlying structural ensemble. We develop and use a combined experimental, computational, and analytical framework for high-throughput characterization of IDR sensitivity we call solution space scanning. Our framework reveals that IDRs show sequence-dependent sensitivity to solution chemistry, with complex behavior that can be interpreted through relatively simple polymer models. Our results imply that solution-responsive IDRs are ubiquitous and can provide an additional layer of biological regulation.
Mapping quantitative trait loci and predicting candidate genes for leaf angle in maize
Authors: Zhang Ning , Huang Xueqing 
Published: August 2020

ABSTRACTLeaf angle of maize is a fundamental determinant of plant architecture and an important trait influencing photosynthetic efficiency and crop yields. To broaden our understanding of the genetic mechanisms of leaf angle formation, we constructed an F3:4recombinant inbred lines (RIL) population derived from a cross between a model inbred line (B73) with expanded leaf architecture and an elite inbred line (Zheng58) with compact leaf architecture to map QTL for leaf angle. A sum of 8 QTL were detected on chromosome 1, 2, 3, 4 and 8. Single QTL explained 4.3 to 14.2% of the leaf angle variance. Additionally, some important QTL were confirmed through a heterogeneous inbred family(HIF) approach. Furthermore, twenty-four candidate genes for leaf angle were predicted through whole-genome resequencing and expression analysis in qLA02-01and qLA08-01 regions. These results will be helpful to elucidate the genetic mechanism of leaf angle formation in maize and benefit to clone the favorable allele for leaf angle or develop the novel maize varieties with ideal plant architecture through marker-assisted selection.