bluuebunny/crossref_metadata_2025_split huggingface dataset:
UV-C decontamination for N95 emergency reuse: Quantitative dose validation with photochromic indicators
Authors: Su Alison , Grist Samantha M. , Geldert Alisha , Gopal Anjali , Herr Amy E. 
Published: July 2020

AbstractWith COVID-19 N95 respirator shortages, frontline medical personnel are forced to reuse this disposable – but sophisticated – multilayer textile respirator. Widely used for decontamination of nonporous surfaces, UV-C light has germicidal efficacy on porous, non-planar N95 respirators when ≥1.0 J/cm2 dose is applied across all surfaces. Here, we address outstanding limitations of photochromic indicators (qualitative readout and insufficient dynamic range) and introduce a photochromic UV-C dose quantification technique for: (1) design of UV-C treatments and (2) in-process UV-C dose validation. Our methodology establishes that color-changing dosimetry can achieve the necessary accuracy (>90%), uncertainty (<10%), and UV-C specificity (>95%). Furthermore, we adapt consumer electronics for accessible quantitative readout and extend the dynamic range >10× using optical attenuators. In a measurement infeasible with radiometers, we observe striking 20× dose variation over 3D N95 facepieces. By transforming photochromic indicators into quantitative dosimeters, we illuminate critical design considerations for both photochromic indicators and UV-C decontamination.
COVID-19 Case Series at UnityPoint Health St. Luke’s Hospital in Cedar Rapids, IA
Authors: Edwards Dianna , McGrail Daniel 
Published: July 2020

AbstractA retrospective, descriptive study of all patients tested for SARS-CoV2 on admission for illness to a community hospital in Iowa from 3/21/20 thru 6/14/20 consisted of evaluation as to demographics, presentation and hospital course. Ninety-one patients were SARS-CoV2 PCR+ with 63% being male and a median age of 60. Cardiovascular disease was a significant comorbidity in the PCR+ group. Fever, cough, dyspnea, nausea, emesis, diarrhea, headache and myalgias were significantly more common in that group, as was an elevated CRP, LDH, serum ferritin and transaminases. Overall survival of the COVID-19 patients was 88%, 77% in the critically ill, 59% of those mechanically ventilated and 33% of those requiring new dialysis. Survival was 93% in those not receiving any antivirals. Survival of those treated with hydroxychloroquine-azithromycin was 92%, compared to 86% of those treated with hydroxychloroquine alone. The latter two groups were significantly more ill than the untreated group. A transition from an early intubation strategy to aggressive utilization of high flow nasal cannula and noninvasive ventilation(i.e BiPAP) was successful in freeing up ICU resources.
On the organization of the locomotor CPG: insights from split-belt locomotion and mathematical modeling
Authors: Latash Elizaveta M. , Lecomte Charly , Danner Simon M. , Frigon Alain , Rybak Ilya A. , Molkov Yaroslav I. 
Published: July 2020

AbstractRhythmic limb movements during locomotion are controlled by a central pattern generator (CPG) circuits located in the spinal cord. It is considered that these circuits are composed of individual rhythm generators (RGs) for each limb interacting with each other through multiple commissural and long propriospinal circuits. The organization and operation of each RG are not fully understood, and different competing theories exist about interactions between its flexor and extensor components, as well as about left-right commissural interactions between the RGs. The central idea of circuit organization proposed in this study is that with an increase of excitatory input to each RGs (or an increase in locomotor speed) the rhythmogenic mechanism within the RGs changes from “flexor-driven” rhythmicity to a “classical half-center” mechanism. We test this hypothesis using our experimental data on changes in duration of stance and swing phases in the intact and spinal cats walking on the ground or tied-belt treadmills (symmetric conditions) or split-belt treadmills with different left and right belt speeds (asymmetric conditions). We compare these experimental data with the results of mathematical modeling, in which simulated CPG circuits operate in similar symmetric and asymmetric conditions with matching or differing control drives to the left and right RGs. The obtained results support the proposed concept of state-dependent changes in RG operation and specific commissural interactions between the RGs. The performed simulations and mathematical analysis of model operation under different conditions provide new insights into CPG network organization and limb coordination during locomotion.Key Point SummaryLimb movements during locomotion are controlled by neural circuits located within the spinal cord. These circuits include rhythm generators (RGs) controlling each limb interacting through multiple commissural pathways.The organization and operation of spinal RGs are not fully understood, and different competing concepts exists. We suggest that the operation of RGs is state-dependent, so that with an increase of external excitation the rhythmogenesis changes from “flexor-driven” oscillations to a “classical half-center” mechanism.A mathematical model of spinal circuits representing bilaterally-interacting RGs has been developed based on the above suggestion and used to interpret experimental data from intact and spinal cats walking on the ground or tied-belt treadmills (symmetric conditions) as well as on split-belt treadmills with different left and right belt speeds (asymmetric conditions).The performed simulations and mathematical analysis of the model under different conditions provide new insights into operation of spinal circuits and limb coordination during locomotion.
Untangling the animacy organization of occipitotemporal cortex
Authors: Ritchie J. Brendan , Zeman Astrid A. , Bosmans Joyce , Sun Shuo , Verhaegen Kirsten , Op de Beeck Hans P. 
Published: July 2020

AbstractSome of the most impressive functional specialization in the human brain is found in occipitotemporal cortex (OTC), where several areas exhibit selectivity for a small number of visual categories, such as faces and bodies, and spatially cluster based on stimulus animacy. Previous studies suggest this animacy organization reflects the representation of an intuitive taxonomic hierarchy, distinct from the presence of face- and body-selective areas in OTC. Using human fMRI, we investigated the independent contribution of these two factors – the face-body division and taxonomic hierarchy – in accounting for the animacy organization of OTC, and whether they might also be reflected in the architecture of several deep neural networks. We found that graded selectivity based on animal resemblance to human faces and bodies masquerades as an apparent animacy continuum, which suggests that taxonomy is not a separate factor underlying the organization of the ventral visual pathway.
Neutralization Assay with SARS-CoV-1 and SARS-CoV-2 Spike Pseudotyped Murine Leukemia Virions
Authors: Zheng Yue , Larragoite Erin T. , Lama Juan , Cisneros Isabel , Delgado Julio C. , Slev Patricia , Rychert Jenna , Innis Emily A. , Williams Elizabeth S.C.P. , Coiras Mayte , Rondina Matthew T. , Spivak Adam M. , Planelles Vicente 
Published: July 2020

AbstractAntibody neutralization is an important prognostic factor in many viral diseases. To easily and rapidly measure titers of neutralizing antibodies in serum or plasma, we developed pseudovirion particles composed of the spike glycoprotein of SARS-CoV-2 incorporated onto murine leukemia virus capsids and a modified minimal MLV genome encoding firefly luciferase. These pseudovirions provide a practical means of assessing immune responses under laboratory conditions consistent with biocontainment level 2.
A novel approach for assessing hypoperfusion in stroke using spatial independent component analysis of resting-state fMRI
Authors: Hu Jiun-Yiing , Kirilina Evgeniya , Nierhaus Till ,   Dr. rer. medic. Dipl.-Ing.(FH), Ovadia-Caro Smadar , Livne Michelle , Villringer Kersten , Margulies Daniel , Fiebach Jochen B. , Villringer Arno , Khalil Ahmed A. 
Published: July 2020

AbstractIndividualized treatment of acute stroke depends on the timely detection of ischemia and potentially salvageable tissue in the brain. Using functional MRI (fMRI), it is possible to characterize cerebral blood flow from blood-oxygen-level-dependent (BOLD) signals without the administration of exogenous contrast agents. In this study, we applied spatial independent component analysis to resting-state fMRI data of 37 stroke patients scanned within 24 hours of symptom onset, 17 of whom received follow-up scans the next day. Our analysis revealed “Hypoperfusion spatially-Independent Components” (HICs) whose spatial patterns of BOLD signal resembled regions of delayed perfusion depicted by dynamic susceptibility contrast MRI. These HICs were detected even in the presence of excessive patient motion, and disappeared following successful tissue reperfusion. The unique spatial and temporal features of HICs allowed them to be distinguished with high accuracy from other components in a user-independent manner (AUC = 0.95, accuracy = 0.96, sensitivity = 1.00, specificity = 0.96). Our study therefore presents a new, non-invasive method for assessing blood flow in acute stroke that minimizes interpretative subjectivity and is robust to severe patient motion.
Evaluating the Simple Arrhenius Equation for the Temperature Dependence of Complex Developmental Processes
Authors: Crapse Joseph , Pappireddi Nishant , Gupta Meera , Shvartsman Stanislav Y. , Wieschaus Eric , Wühr Martin 
Published: July 2020

SummaryThe famous Arrhenius equation is well motivated to describe the temperature dependence of chemical reactions but has also been used for complicated biological processes. Here, we evaluate how well the simple Arrhenius equation predicts complex multistep biological processes, using frog and fruit fly embryogenesis as two canonical models. We find the Arrhenius equation provides a good approximation for the temperature dependence of embryogenesis, even though individual developmental stages scale differently with temperature. At low and high temperatures, however, we observed significant departures from idealized Arrhenius Law behavior. When we model multistep reactions of idealized chemical networks we are unable to generate comparable deviations from linearity. In contrast, we find the single enzyme GAPDH shows non-linearity in the Arrhenius plot similar to our observations of embryonic development. Thus, we find that complex embryonic development can be well approximated by the simple Arrhenius Law and propose that the observed departure from this law results primarily from non-idealized individual steps rather than the complexity of the system.
The Step-Wise C-Truncation and Transport of ESyt3 to Lipid Droplets Reveals a Mother Primordial Cisterna
Authors: Lalioti Vasiliki , Beznoussenko Galina V. , Mironov Alexander A. , Sandoval Ignacio V. 
Published: July 2020

AbstractExtended synaptotagmins (E-Syts) are endoplasmic reticulum (ER) proteins consisting of an SMP domain and multiple C2 domains that bind phospholipids and Ca2+. E-Syts create contact junctions between the ER and plasma membrane to facilitate lipid exchange. During adipocyte differentiation, the proteasome-based removal of the C2C domain results in targeting of E-Syt3 to the primordial cisterna, a previously undescribed giant annular organelle that mothers the LDs. Further cleavage causes the E-Syt3 relocation to the surface of LDs. Fragmentation of the primordial cisterna and LD budding into its lumen are early events in the biogenesis of LDs in the 3T3-L1 adipocyte. Electron tomography-based 3D reconstruction of the fragmented primordial cisterna revealed patches of a tightly packed E-Syt3-rich network of varicose tubules in close contact with young LDs. Esyt3 binds avidly phosphatidylethanolamine through its SMP domain, a main component of the LD membrane that fosters LD biogenesis. Repression of E-Syt3 effectively inhibits LD biogenesis and growth.
The impact of commercially available ale and lager yeast strains on the fermentative diversity of beers
Authors: Bonatto Diego 
Published: July 2020

AbstractYeasts from the speciesSaccharomyces cerevisiae(ale yeast) andSaccharomyces pastorianus(lager yeast) are the main component of beer fermentation. It is known that different beer categories depend on the use of specific ale or lager strains, where the yeast imprint its distinctive fermentative profile to the beer. Despite this, there are no studies reporting how diverse, rich, and homogeneous the beer categories are in terms of commercially available brewing yeast strains. In this work, the diversity, richness, and evenness of different beer categories and commercial yeast strains available for brewing were evaluated by applying quantitative concepts of ecology analysis in a sample of 121,528 beer recipes. For this purpose, the frequency of ale or lager and dry or liquid yeast formulations usage was accessed and its influence in the fermentation temperature, attenuation profile, and number of recipes for a beer category were analyzed. The results indicated that many beer categories are preferentially fermented with dry yeast strains formulations instead of liquid yeasts, despite considering the high number of available liquid yeast formulations. Moreover, ale dry strains are preferentially used for lager brewing. The preferential use of specific yeast formulations drives the diversity, richness, and evenness of a beer category, showing that many yeast strains are potentially and industrially underexplored.
Functional differentiation in the language network revealed by lesion-symptom mapping
Authors: Matchin William , Basilakos Alexandra , den Ouden Dirk-Bart , Stark Brielle C. , Hickok Gregory , Fridriksson Julius 
Published: July 2020

AbstractTheories of language organization in the brain commonly posit that different regions underlie distinct linguistic mechanisms. However, such theories have been criticized on the grounds that many neuroimaging studies of language processing find similar effects across regions. Moreover, condition by region interaction effects, which provide the strongest evidence of functional differentiation between regions, have rarely been offered in support of these theories. Here we address this by using lesion-symptom mapping in three large, partially-overlapping groups of aphasia patients with left hemisphere brain damage due to stroke (N=121, N=92, N= 218). We identified multiple measure by region interaction effects, associating damage to the posterior middle temporal gyrus with syntactic comprehension deficits, damage to posterior inferior frontal gyrus with expressive agrammatism, and damage to inferior angular gyrus with semantic category word fluency deficits. Our results are inconsistent with recent hypotheses that regions of the language network are undifferentiated with respect to high-level linguistic processing.
Lysozyme resistance inC. difficileis dependent on two peptidoglycan deacetylases
Authors: Kaus Gabriela M. , Snyder Lindsey F. , Müh Ute , Flores Matthew J. , Popham David L. , Ellermeier Craig D. 
Published: July 2020

AbstractClostridioides (Clostridium) difficileis a major cause of hospital-acquired infections leading to antibiotic-associated diarrhea.C. difficileexhibits a very high level of resistance to lysozyme. Bacteria commonly resist lysozyme through modification of the cell wall. InC. difficileσVis required for lysozyme resistance and σVis activated in response to lysozyme. Once activated σV, encoded bycsfV, directs transcription of genes necessary for lysozyme resistance. Here we analyze the contribution of individual genes in thecsfVregulon to lysozyme resistance. Using CRISPR-Cas9 mediated mutagenesis we constructed in-frame deletions of single genes in thecsfVoperon. We findpdaV, which encodes a peptidoglycan deacetylase, is partially responsible for lysozyme resistance. We then performed CRISPR inhibition (CRISPRi) to identify a second peptidoglycan deacetylase,pgdA, that is important for lysozyme resistance. Deletion of eitherpgdAorpdaVresulted in modest decreases in lysozyme resistance. However, deletion of bothpgdAandpdaVresulted in a 1000-fold decrease in lysozyme resistance. Further, muropeptide analysis revealed loss of either PgdA or PdaV had modest effects on peptidoglycan deacetylation but loss of both PgdA and PdaV resulted in almost complete loss of peptidoglycan deacetylation. This suggests that PgdA and PdaV are redundant peptidoglycan deacetylases. We also use CRISPRi to compare other lysozyme resistance mechanisms and conclude that peptidoglycan deacetylation is the major mechanism of lysozyme resistance inC. difficile.ImportanceClostridioides difficileis the leading cause of hospital-acquired diarrhea.C. difficileis highly resistant to lysozyme. We previously showed that thecsfVoperon is required for lysozyme resistance. Here we use CRISPR-Cas9 mediated mutagenesis and CRISPRi knockdown to show that peptidoglycan deacetylation is necessary for lysozyme resistance and is the major lysozyme resistance mechanism inC. difficile. We show that two peptidoglycan deacetylases inC. difficileare partially redundant and are required for lysozyme resistance. PgdA provides an intrinsic level of deacetylation and PdaV, encoded as part of thecsfVoperon, provides lysozyme-induced peptidoglycan deacetylation.
Unpicking the mysterious symbiosis ofMycoplasmain salmonids
Authors: Cheaib B , Yang P , Kazlauskaite R , Lindsay E , Heys C , De Noa M , Schaal Patrick , Dwyer T , Sloan W , Ijaz UZ , Llewellyn MS 
Published: July 2020

AbstractLacking a peptidoglycan cell wall, mycoplasmas are the smallest self-replicating life forms. Members of this bacterial genus are known to parasitise a wide array of metazoans including vertebrates. Whilst much research has been significant targeted at parasitic mammalian mycoplasmas, very little is known about their role in other vertebrates. In the current study, we aim to explore the biology and evolution ofMycoplasmain salmonids, including cellular niche, genome size structure and gene content. Using Fluorescencein-situhybridisation (FISH),mycoplasmaswere identified in epithelial tissues across the digestive tract (stomach, pyloric caecum and midgut) during the developmental stages (eggs, parr, subadult) of farmed Atlantic salmon (Salmo salar), showing a high abundance in acidic compartments. With high throughput sequencing from subadults farmed Atlantic salmon, we assembled a nearly complete genome (~0.57 MB) via shotgun-metagenomics. The phylogenetic inference from the recovered genome revealed successful taxonomic proximity toMycoplasma penetrans(~1.36 Mb) from the recovered genome. Although, no significant correlation between genome size and its phylogeny was observed, we recovered functional signatures, especially, riboflavin encoding genes pathway and sugars transporters, suggesting a symbiotic relationship betweenMycoplasmaand the host. Though 247 strains ofMycoplasmaare available in public databases, to the best of our knowledge, this is the first study to demonstrate ecological and functional association betweenMycoplasmaandSalmo salarwhich delineates symbiotic reductive evolution and genome erosion primarily and also serves as a proxy for salmonid health in aquaculture processes (cell lines,in vitrogut models).
The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins
Authors: Ghosh Souvik , Börsch Anastasiya , Zavolan Mihaela 
Published: July 2020

AbstractThe behavior of cells in vivo is complex and highly dynamic, as it results from an interplay between components of the intercellular matrix proteins with surface receptor and other microenvironmental cues. Although the effects of the cellular niche have been investigated for a number of cell types using different molecular approaches, comprehensive assessments of how the global transcriptome responds to 3D scaffolds composed of various extracellular matrix (ECM) constituents are still lacking. In this study, we explored the effect of the biomechanical parameters of Collagen I and Matrigel (ECM) on transcriptional gene regulation in a cell culture system. Using Huh-7 cells cultured on traditional cell culture plates or on the components of the ECM at different concentrations to modulate microenvironment properties, we have generated transcriptome sequencing data that may be further explored to understand the differentiation and growth potential of this cell for the development of 3D cultures. Assessment of the hepatocyte phenotype in relation to our transcriptomic data set would be very useful for the development of systems mimicking the in vivo structure and function of liver cells which still remains a challenge.
Respiratory Syncytial Virus Infections Induce Hypermetabolism in Pediatric Upper Airways
Authors: Rezinciuc Svetlana , Bezavada Lavanya , Bahadoran Azadeh , Ingels Jesse F. , Kim Young-Yin , Cormier Stephania A. , Devincenzo John P. , Shulkin Barry L. , Smallwood Heather S. 
Published: July 2020

AbstractTo determine whether respiratory syncytial virus (RSV) regulates human metabolism, we used positron emission tomography (PET) of patient lungs along with bioenergetics and metabolomics of patient upper airway cells and fluids. We previously found a significant negative monotonic relationship between glucose uptake and respiratory viral infection in 20 pediatric patients (e.g., 70% of infected patients had glucose uptake within 0–3 days). In our recent study, 3 out of 4 patients positive for glucose uptake at later times (>5 days) were positive for RSV infection. At present, the bioenergetics of upper respiratory cells (URCs) from nasal pharyngeal aspirates have not been investigated, andin vitrostudies indicate RSV reduces metabolism in cell lines. To define metabolic changes in RSV-infected pediatric patients, we acquired fresh aspirates from 6 pediatric patients. Immediately following aspiration of URCs, we measured the two major energy pathways using an XFe flux analyzer. Glycolysis and mitochondrial respiration were significantly increased in URCs from RSV-infected patients, and mitochondrial respiration was operating at near maximal levels, resulting in loss of cellular capacity to increase respiration with impaired coupling efficiency. Metabolomics analysis of metabolites flushed from the upper airways confirmed a significant increase in TCA cycle intermediates. Taken together, these studies demonstrate RSV induces significant hypermetabolism in pediatric patients’ lungs and respiratory tract. Thus, hypermetabolism is a potential anti-viral drug target and reveals RSV can regulate human metabolism.Contributions to the fieldMetabolic changes in humans in response to viral infection are largely unknown. In this brief clinical report, we find metabolism is markedly increased in live upper respiratory cells from infants infected with respiratory syncytial virus (RSV) concomitant to changes in metabolites in their upper airway fluids. This sheds light on viral induced hypermetabolism in the airways and offers potential biomarkers for RSV. In addition, this identifies potential therapeutic targets for host directed therapies of aberrant metabolism in RSV. This work has clinical impact as biomarkers and therapeutics for RSV are needed for this pervasive virus that causes infections with long term consequence for some children. Further, advancements in molecular mechanisms underpinning RSV infection biology are constrained by the difficulties in translating model systems to humans as well as relating human studies in adults to infants (Mestas and Hughes, 2004; Papin et al., 2013).