bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions
Authors: Squire Marietta M. , Munsamy Megashnee , Lin Gary , Telukdarie Arnesh , Igusa Takeru 
Published: August 2020

AbstractThe objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. The intervention control measures evaluated include use of negative pressure (NP) treatment rooms and xenon pulsed ultraviolet (XP-UV) infection control equipment. After projecting COVID-19 hospitalizations, a Hospital Energy Model and Infection De-escalation Models are applied to quantify increases in energy demand and reductions in secondary infections. The scope of the interventions consisted of implementing NP in 11, 22, and 44 rooms (at small, medium, and large hospitals) while the XP-UV equipment was used eight, nine, and ten hours a day, respectively. The annum kilowatt-hours (kWh) for NP (and costs were at $0.1015 per kWh) were 116,700 ($11,845), 332,530 ($33,752), 795,675 ($80,761) for small, medium, and large hospitals ($1,077, $1,534 $1,836 added annum energy cost per NP room). For XP-UV, the annum kilowatt-hours and costs were 438 ($45), 493 ($50), 548 ($56) for small, medium, and large hospitals. There are other initial costs associated with the purchase and installation of the equipment, with XP-UV having a higher initial cost. XP-UV had a greater reduction in secondary COVID-19 infections in large and medium hospitals. NP rooms had a greater reduction in secondary SARS-CoV-2 transmission in small hospitals. Early implementation of interventions can result in realized cost savings through reduced hospital-acquired infections.
Genomic surveillance revealed prevalence of unique SARS-CoV- 2 variants bearing mutation in the RdRp gene among Nevada patients
Authors: Hartley Paul D. , Tillett Richard L. , AuCoin David P. , Sevinsky Joel R. , Xu Yanji , Gorzalski Andrew , Pandori Mark , Buttery Erin , Hansen Holly , Picker Michael A. , Rossetto Cyprian C. , Verma Subhash C. 
Published: August 2020

ABSTRACTPatients with signs of COVID-19 were tested with CDC approved diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from nasopharyngeal/nasal swabs. In order to determine the variants of SARS-CoV-2 circulating in the state of Nevada, 200 patient specimens from positively identified cases were sequenced through our robust protocol for sequencing SARS-CoV-2 genomes from the nasopharyngeal or nasal swabs. This protocol enabled the identification of specific nucleotide variants including those coding for D614G and clades defining mutations. Additionally, these sequences were used for determining the phylogenetic relationships of SARS-CoV-2 genomes of public health importance occurring in the state of Nevada. Our study reports the occurrence of a novel variant in the nsp12 (RdRp-RNA dependent RNA Polymerase) protein at residue 323 (314aa of orf1b) to Phenylalanine (F) from Proline (P), present in the original isolate of SARS-CoV-2 (Wuhan-Hu-1). This 323F variant is found at a very high frequency (46% of the tested specimen) in Northern Nevada, possibly because the virus accumulated this mutation while circulating in the community and the shelter in place orders restricted the introduction and spread of other variants into this region. Structural modeling of the RdRp with P323F variant did not show any significant difference in protein conformation, but the phenotypic effect is unknown and an area of active investigation. In conclusion, our results highlight the introduction and spread of specific SARS-CoV-2 variants at very high frequency within a distinct geographic location that is important for clinical and public health perspectives in understanding the evolution and transmission of SARS-CoV-2.IMPORTANCESARS-COV-2 genomes accumulate nucleotide mutations while passing in the human population and these mutations may confer phenotypic differences including altered immune response and anti-viral drug resistance. We developed a robust workflow to sequence SARS-CoV-2 directly from the nasal/nasopharyngeal swabs containing even a very low viral loads (>35 Ct value samples). Our protocol does not rely on amplicon based sequencing strategies nor the need of passing the virus into tissue culture thus reduces the possibility of an introduction of laboratory-adapted mutations. Sequences of SARS-CoV-2 from the patients of the state of Nevada during early months of the pandemic identified a rare mutation in the RdRp protein (P323F). This mutation occurred at a very high frequency in the variants of SARS-CoV-2 circulating Northern Nevada. Identification of such variants is important for clinical and public health perspectives in understanding transmission mediated evolution of SARS-CoV-2 variants and their implications on therapeutics and diagnostics.
Development and validation of 2D-LiDAR-based gait analysis instrument and algorithm
Authors: Yoon Seongjun , Jung Hee-Won , Jung Heeyoune , Kim Keewon , Koo Hong Suk , Roh Hyunchul , Oh Byung-Mo 
Published: August 2020

AbstractAcquiring gait parameters from usual walking is important to predict clinical outcomes, including life expectancy, risk of fall, and neurocognitive performance, in older people. For comprehensive gait analysis, instruments such as marker-based motion analysis systems and walkways with pressure sensor arrays are necessary. Traditional instruments are bulky, complex, expensive, and intrinsically intrusive. Requirements of dedicated spaces for installation and specialized staff make it difficult to utilize traditional gait analysis instruments in most outpatient clinics. We present a novel gait analysis tool that is small, highly accurate, easy-to-use, and non-intrusive and is based on two-dimensional light detection and ranging technology. Using an object-tracking algorithm, we conducted a validation study of spatiotemporal tracking of ankle locations of subjects by comparing our tool with a gold standard modality. Our tool showed successful acquisition of gait parameters from usual walking motions and trackability with multiple targets in noisy conditions, including typical clinical environments.
Dynamics of the Gut Microbiota in MEBO and PATM conditions: Protocol of a fully remote clinical study
Authors: Gabashvili Irene S. 
Published: August 2020

AbstractSummaryThe proposed study will identify microbial communities associated with flare ups and remissions of MEBO (systemic malodor of metabolic origin) or PATM (“People allergic to me”) conditions.BackgroundHuman odor-prints, mostly owing to the microbiome, have proven their value as biomarkers of health and environmental exposures.In recent years, microbial networks responsible for localized malodors (e.g., halitosis [1,2], groin area, foot and axillary odor [3,4]) have been mapped by using next generation sequencing approaches.Intestinal microbes responsible for psychologically debilitating systemic malodor (whole-body and extraoral halitosis), however, remain to be identified. Even a relatively straightforward disorder of choline metabolism trimethylaminuria (TMAU) is thought to exhibit complex host-gene microbiome interactions [5] and has not been sufficiently studied.Mapping gut microbiome is needed to understand human metabolic disfunction, make proper dietary recommendations and develop targeted treatments such as microbial therapies [6–8]. Our preliminary analysis of culture-, PCR- and 16S-RNA-based data found several Operational Taxonomic Units (OTUs) potentially linked to systemic malodor. Proposed controlled pilot study will provide a more comprehensive evaluation and, combined with our prior data [9–12], will help to develop new therapies and treatments.
Distinct clinical and biological characteristics of acute myeloid leukemia with higher expression of long noncoding RNA KIAA0125
Authors: Wang Yu-Hung , Lin Chien-Chin , Hsu Chia-Lang , Hung Sheng-Yu , Yao Chi-Yuan , Lee Sze-Hwei , Tsai Cheng-Hong , Hou Hsin-An , Chou Wen-Chien , Tien Hwei-Fang 
Published: August 2020

AbstractExpression of long non-coding RNA KIAA0125 has been incorporated in various gene expression signatures for prognostic prediction in acute myeloid leukemia (AML) patients, yet its functions and clinical significance remain unclear. This study was aimed to investigate the clinical and biological characteristics of AML bearing different levels of KIAA0125. We profiled KIAA0125 expression levels in bone marrow cells from 347 de novo AML patients and found higher KIAA0125 expression was closely associated with FLT3-ITD, RUNX1, and DNMT3A mutations, and M1 subtype by the French-American-British classification, but inversely correlated with t(8;21) and t(15;17). Among the 227 patients who received standard chemotherapy, those with higher KIAA0125 expression had a lower complete remission rate, shorter overall survival (OS) and disease-free survival (DFS) than those with lower expression. The prognostic significance was validated in both TCGA and GSE12417 cohorts. Subgroup analyses showed that higher KIAA0125 expression also predicted shorter DFS and OS in patients with normal karyotype or non-M3 AML. In multivariable analysis, higher KIAA0125 expression remained an adverse risk factor independent of age, WBC counts, karyotypes, and mutation patterns. Bioinformatics analyses revealed that higher KIAA0125 expression was associated with hematopoietic and leukemic stem cell signatures and ATP-binding cassette transporters, two predisposing factors for chemoresistance.
Untuned antiviral immunity in COVID-19 revealed by temporal type I/III interferon patterns and flu comparison
Authors: Galani Ioanna-Evdokia , Rovina Nikoletta , Lampropoulou Vicky , Triantafyllia Vasiliki , Manioudaki Maria , Pavlos Eleftherios , Koukaki Evangelia , Fragkou Paraskevi C. , Panou Vasiliki , Rapti Vasiliki , Koltsida Ourania , Mentis Andreas , Koulouris Nikolaos , Tsiodras Sotirios , Koutsoukou Antonia , Andreakos Evangelos 
Published: August 2020

AbstractA central paradigm of immunity is that interferon (IFN) mediated antiviral responses precede the pro-inflammatory ones, optimizing host protection and minimizing collateral damage1,2. Here, we report that for COVID-19 this does not apply. By investigating temporal IFN and inflammatory cytokine patterns in 32 COVID-19 patients hospitalized for pneumonia and longitudinally followed for the development of respiratory failure and death, we reveal that IFN-λ and type I IFN production is both diminished and delayed, induced only in a fraction of patients as they become critically ill. On the contrary, pro-inflammatory cytokines such as TNF, IL-6 and IL-8 are produced before IFNs, in all patients, and persist for a prolonged time. By comparison, in 16 flu patients hospitalized for pneumonia with similar clinicopathological characteristics to COVID-19 and 24 milder non-hospitalized flu patients IFN-λ and type I IFN are robustly induced, earlier, at higher levels and independently of disease severity, while pro-inflammatory cytokines are only acutely and transiently produced. Notably, higher IFN-λ levels in COVID-19 patients correlate with lower viral load in bronchial aspirates and faster viral clearance, and a higher IFN-λ:type I IFN ratio with improved outcome of critically ill patients. Moreover, altered cytokine patterns in COVID-19 patients correlate with longer hospitalization time and higher incidence of critical disease and mortality compared to flu. These data point to an untuned antiviral response in COVID-19 contributing to persistent viral presence, hyperinflammation and respiratory failure.
Differential shared genetic influences on anxiety with problematic alcohol use compared to alcohol consumption
Authors: Colbert Sarah M. C. , Funkhouser Scott A. , Johnson Emma C. , Hoeffer Charles , Ehringer Marissa A. , Evans Luke M. 
Published: August 2020

AbstractAnxiety disorders and alcohol use disorders are common psychiatric illnesses. Comorbidity of the two disorders can have a tremendous effect on treatment of one or both disorders, as well as an individual’s social, economic, and physical well-being. We estimated genome-wide genetic correlations between anxiety and alcohol use traits using linkage disequilibrium score regression (LDSC) and found strong and positive correlations of anxiety with problematic alcohol use (PAU), but not with most alcohol consumption (AC) measures. We observed strong, positive between-sex genetic correlations for all traits, but found suggestive evidence that the genetic correlation between alcohol use and anxiety might differ between males and females. Estimates of local genetic covariance demonstrated divergent genetic covariance profiles of PAU and AC with anxiety phenotypes and localized 12 specific genomic regions that likely contribute to both anxiety and alcohol use. Finally, partitioning the genetic covariance among functional annotations also identified the amygdala, caudate basal ganglia and frontal cortex as contributing significantly to positive genetic covariance between anxiety and PAU phenotypes. This study serves as a framework for an approach to be used in future analyses of the genetics of comorbid disorders.
The unintended consequences of inconsistent pandemic control policies
Authors: Althouse Benjamin M. , Wallace Brendan , Case Brendan , Scarpino Samuel V. , Berdahl Andrew M. , White Easton R. , Hébert-Dufresne Laurent 
Published: August 2020

ABSTRACTControlling the spread of COVID-19 – even after a licensed vaccine is available – requires the effective use of non-pharmaceutical interventions, e.g., physical distancing, limits on group sizes, mask wearing, etc.. To date, such interventions have neither been uniformly nor systematically implemented in most countries. For example, even when under strict stay-at-home orders, numerous jurisdictions granted exceptions and/or were in close proximity to locations with entirely different regulations in place. Here, we investigate the impact of such geographic inconsistencies in epidemic control policies by coupling search and mobility data to a simple mathematical model of SARS-COV2 transmission. Our results show that while stay-at-home orders decrease contacts in most areas of the United States of America (US), some specific activities and venues often see an increase in attendance. Indeed, over the month of March 2020, between 10 and 30% of churches in the US saw increases in attendance; even as the total number of visits to churches declined nationally. This heterogeneity, where certain venues see substantial increases in attendance while others close, suggests that closure can cause individuals to find an open venue, even if that requires longer-distance travel. And, indeed, the average distance travelled to churches in the US rose by 13% over the same period. Strikingly, our mathematical model reveals that, across a broad range of model parameters, partial measures can often be worse than no measures at all. In the most severe cases, individuals not complying with policies by traveling to neighboring jurisdictions can create epidemics when the outbreak would otherwise have been controlled. Taken together, our data analysis and modelling results highlight the potential unintended consequences of inconsistent epidemic control policies and stress the importance of balancing the societal needs of a population with the risk of an outbreak growing into a large epidemic.
Formation of an Aminovinyl-Cysteine Residue in Thioviridamide Non-Lanthipeptides Occurs through a Path Independent of Known Lanthionine Synthetase Activity inStreptomyces sp. NRRL S-87
Authors: Qiu Yanping , Liu Jingyu , Li Yuqing , Xue Yanqing , Wang Huan , Liu Wen 
Published: August 2020

ABSTRACT2-Aminovinyl-cysteine (AviCys) is an unusual thioether amino acid shared by a variety of ribosomally synthesized and posttranslationally modified peptides (RiPPs), as part of a macrocyclic ring system that contains theC-terminal 4 or 6 residues of a precursor peptide. This amino acid is nonproteinogenic and arises from processing theC-terminal Cys residue and an internal Ser/Thr residue to form an unsaturated thioether linkage. Enzyme activities for forming lanthionine (Lan), a distinct saturated thioether residue characteristic of lanthipeptide-related RiPPs, has long been speculated to be necessary for AviCys formation. Based on investigations into the biosynthesis of thioviridamide non-lanthipeptdes inStreptomyces sp. NRRL S-87, we here report an alternative path for AviCys formation that is independent of known Lan synthetase activity. This path relies on four dedicated enzymes for posttranslational modifications of the precursor peptide, in which TvaES-87, a phosphotransferase homolog, plays a critical role. It works with LanD-like flavoprotein TvaFS-87to form a minimum AviCys synthetase complex that follows the combined activity of TvaCDS-87for Thr dehydration and catalyzes Cys oxidative decarboxylation and subsequent Michael addition of the resulting enethiol nucleophile onto the newly formed dehydrobutyrine residue for cyclization. With TvaES-87, TvaFS-87activity for Cys processing can be coordinated with TvaCDS-87activity for minimizing competitive or unexpected spontaneous reactions and forming AviCys effectively.
Do substrate roughness and gap distance impact gap-bridging strategies in arboreal chameleons
Authors: Luger Allison M. , Vincent Vermeylen , Anthony Herrel , Dominique Adriaens 
Published: August 2020

AbstractChameleons are well-equipped for an arboreal lifestyle, having ‘zygodactylous’ hands and feet as well as a fully prehensile tail. However, to what degree tail use is preferred over autopod prehension has been largely neglected. Using an indoor experimental set-up, where chameleons had to cross gaps of varying distances, we tested the effect of substrate diameter and roughness on tail use inChamaeleo calyptratus. Our results show that when crossing greater distances,C. calyptratusis more likely to use its tail for additional stability. The animals were able to cross greater distances (up to 1 75 times the shoulder-hip length) on perches with a rougher surface. We saw that depending on the distance of the gap, chameleons would change how they use their prehensile tails when crossing. With shorter gaps the tails either do not touch, or only touch the perch without coiling around it. With larger distances the tails are fully coiled around the perch, and with the largest distances additionally they reposition the hind legs, shifting them towards the end of the perch. Males were able to cross relatively greater distances than females, likely due to their larger size and strength.
MotiMul: A significant discriminative sequence motif discovery algorithm with multiple testing correction
Authors: Mori Koichi , Ozaki Haruka , Fukunaga Tsukasa 
Published: August 2020

AbstractSequence motifs play essential roles in intermolecular interactions such as DNA-protein interactions. The discovery of novel sequence motifs is therefore crucial for revealing gene functions. Various bioinformatics tools have been developed for finding sequence motifs, but until now there has been no software based on statistical hypothesis testing with statistically sound multiple testing correction. Existing software therefore could not control for the type-1 error rates. This is because, in the sequence motif discovery problem, conventional multiple testing correction methods produce very low statistical power due to overly-strict correction. We developed MotiMul, which comprehensively finds significant sequence motifs using statistically sound multiple testing correction. Our key idea is the application of Tarone’s correction, which improves the statistical power of the hypothesis test by ignoring hypotheses that never become statistically significant. For the efficient enumeration of the significant sequence motifs, we integrated a variant of the PrefixSpan algorithm with Tarone’s correction. Simulation and empirical dataset analysis showed that MotiMul is a powerful method for finding biologically meaningful sequence motifs. The source code of MotiMul is freely available athttps://github.com/ko-ichimo-ri/MotiMul.
Identifying Taxonomic Units in Metagenomic DNA Streams
Authors: Zheng Vicky , Sariyuce Ahmet Erdem , Zola Jaroslaw 
Published: August 2020

AbstractWith the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagenomic DNA analysis is computationally and memory intensive, and the current methods are designed for batch processing, the current metagenomic tools are not well suited for mobile devices.In this paper, we propose a new memory-efficient method to identify Operational Taxonomic Units (OTUs) in metagenomic DNA streams. Our method is based on finding connected components in overlap graphs constructed over a real-time stream of long DNA reads as produced by MinION platform. We propose an efficient algorithm to maintain connected components when an overlap graph is streamed, and show how redundant information can be removed from the stream by transitive closures. Through experiments on simulated and real-world metagenomic data, we demonstrate that the resulting solution is able to recover OTUs with high precision while remaining suitable for mobile computing devices.
Route following by one-eyed ants suggests a revised model of normal route following
Authors: Woodgate Joseph L. , Perl Craig , Collett Thomas S. 
Published: August 2020

SummaryThe prevailing account of visually controlled routes is that an ant learns views as it follows a route, while guided by other path-setting mechanisms. Once a set of route views is memorised, the insect follows the route by turning and moving forwards when the view on the retina matches a stored view. We have engineered a situation in which this account cannot suffice in order to discover whether there may be additional components to the performance of routes. One-eyed wood ants were trained to navigate a short route in the laboratory guided by a single black, vertical bar placed in the blinded visual field. Ants thus had to turn away from the route to see the bar. They often turned to look at or beyond the bar and then turned to face in the direction of the goal. Tests in which the bar was shifted to be more peripheral or more frontal than in training produced a corresponding change in the ants’ paths, demonstrating that they were guided by the bar, presumably obtaining information during scanning turns towards the bar. Examination of the endpoints of turns away from the bar suggest that ants use the bar for guidance by learning how large a turn-back is needed to face the goal. We suggest that the ants’ zigzag paths are an integral part of visually guided route following. In addition, on some runs in which ants did not take a direct path to the goal, they still turned to face and sometimes approach the goal for a short stretch. This off-route goal facing indicates that they store a vector from start to goal and use path integration to track their position relative to the endpoint of the vector.