bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Cloth Facemask Causes No Major Respiratory or Cardiovascular Perturbations during Moderate to Heavy Exercise
Authors: Guardieiro Natália Mendes , Barreto Gabriel , Marticorena Felipe Miguel , Oliveira Tamires Nunes , de Oliveira Luana Farias , de Sá Pinto Ana Lucia , do Prado Danilo Marcelo Leite , Saunders Bryan , Gualano Bruno 
Published: December 2021

AbstractObjectivesTo investigate whether wearing a cloth facemask could affect physiological and perceptual responses to exercise at distinct exercise intensities in non-trained men and women.MethodsIn a crossover design, participants (17 men and 18 women) underwent a progressive square-wave test at four intensities (i. at 80% of the ventilatory anerobic threshold [80%VAT]; ii. at VAT; iii. at the respiratory compensation point [RCP]; iv. at exercise peak [Peak] to exhaustion), with or without a triple-layered cloth mask (Mask or No-Mask). Several physiological, metabolic and perceptual measures were analyzed.ResultsMask reduced inspiratory capacity at all exercise intensities vs. No-Mask (p<0.0001), irrespective of sex. Mask reduced respiratory frequency vs. No-Mask (p=0.001) at Peak (−8.3 breaths·min-1; CI: -5.8, -10.8), RCP (−6.9 breaths·min-1; CI: -4.6, -9.2) and VAT (−6.5 breaths·min-1; CI: -4.1, -8.8), but not at Baseline or at 80%VAT. Mask also reduced tidal volume (p<0.0001) at both RCP (−0.5L; CI: -0.3, -0.6) and Peak (−0.8L; CI: -0.6, -0.9), but not at Baseline, 80%VAT or VAT. Shallow breathing index was increased with Mask at Peak compared to No-Mask (11.3; CI: 7.5, 15.1), but not at any other intensities. Mask did not change heart rate, lactate, ratings of perceived exertion, blood pressure or oxygen saturation.ConclusionsWearing a cloth facemask during exercise at moderate to heavy intensities is unlikely to incur significant respiratory or cardiovascular changes, irrespective of sex. These data can inform new exercise recommendations for health during the COVID-19 pandemic and debunk unfounded allegations of harmful effects of masks during exercise. ClinicalTrials.gov: NCT04887714What are the new findings?✓Using a progressive square-wave test, we showed that wearing a cloth facemask during exercise increased breathing difficulty, but this was dependent upon the exercise intensity.✓Respiratory variables (e.g., inspiratory capacity, respiratory frequency, shallow breathing index) were affected at higher rather than lower intensities.✓Mask wearing did not change heart rate, lactate, ratings of perceived exertion, blood pressure or oxygen saturation at any exercise intensity.✓There were no substantial sex differences on the effects of mask wearing during exercise.How might it impact on clinical practice in the future?✓These data can debunk unfounded allegations on harmful effects of masks during exercise, and help inform new exercise recommendations for health during the COVID-19 pandemic, particularly where facemasks remain necessary.
Analytical Solution of a New SEIR Model Based on Latent Period-Infectious Period Chronological Order
Authors: Liu Xiaoping 
Published: December 2021

ABSTRACTThe Susceptible-Infectious-Recovered (SIR) and SIR derived epidemic models have been commonly used to analyze the spread of infectious diseases. The underlying assumption in these models, such as Susceptible-Exposed-Infectious-Recovered (SEIR) model, is that the change in variables E, I or R at time t is dependent on a fraction of E and I at time t. This means that after exposed on a day, this individual may become contagious or even recover on the same day. However, the real situation is different: an exposed individual will become infectious after a latent period (l) and then recover after an infectious period (i). In this study, we proposed a new SEIR model based on the latent period-infectious period chronological order (Liu X., Results Phys. 2021; 20:103712). An analytical solution to equations of this new SEIR model was derived. From this new SEIR model, we obtained a propagated curve of infectious cases under conditions l>i. Similar propagated epidemic curves were reported in literature. However, the conventional SEIR model failed to simulate the propagated epidemic curves under the same conditions. For l<i, the new SEIR models generated bell-shaped curves for infectious cases, and the curve is near symmetrical to the vertical line passing the curve peak. This characteristic can be found in many epidemic curves of daily COVID-19 cases reported from different countries. However, the curve generated from the conventional SEIR model is a right-skewed bell-shaped curve. An example for applying the analytical solution of the new SEIR model equations to simulate the reported daily COVID-19 cases was also given in this paper.
Label-free Cell Tracking Enables Collective Motion Phenotyping in Epithelial Monolayers
Authors: Gu Shuyao , Lee Rachel M. , Benson Zackery , Ling Chenyi , Vitolo Michele I. , Martin Stuart S. , Chalfoun Joe , Losert Wolfgang 
Published: December 2021

SummaryCollective cell migration is an umbrella term for a rich variety of cell behaviors, whose distinct character is essential for biological function, notably for cancer metastasis. One essential feature of collective behavior is the motion of cells relative to their immediate neighbors. We introduce an AI-based pipeline to segment and track cell nuclei from phase contrast images. Nuclei segmentation is based on a U-Net convolutional neural network trained on images with nucleus staining. Tracking, based on the Crocker-Grier algorithm, quantifies nuclei movement and allows for robust downstream analysis of collective motion. Since the AI algorithm required no new training data, our approach promises to be applicable to and yield new insights for vast libraries of existing collective motion images. In a systematic analysis of a cell line panel with oncogenic mutations, we find that the collective rearrangement metric, D2min, which reflects non-affine motion, shows promise as an indicator of metastatic potential.Graphical AbstractHighlightsVersatile AI-based algorithm can robustly identify individual cells and track their motion from phase contrast images.Analysis of motion of cells relative to nearby neighbors distinguishes weakly tumorigenic (KRas) and metastatic (KRas/PTEN-/-) cell lines.
Identifying C. elegans Lifespan Mutants by Screening for Early-Onset Protein Aggregation
Authors: Midkiff Daniel F. , San-Miguel Adriana 
Published: December 2021

SummaryGenetic screens have been widely used to identify genetic pathways that control specific biological functions. In C. elegans, forward genetic screens rely on the isolation of reproductively active mutants that can self-propagate clonal populations. Since aged individuals are unable to generate clonal populations, screens that target post-reproductive phenotypes, such as longevity, are challenging. In this work, we developed an approach that combines microfluidic technologies and image processing to perform a high-throughput, automated screen for mutants with shortened lifespan using protein aggregation as a marker for aging. We take advantage of microfluidics for maintaining a reproductively-active adult mutagenized population and for performing serial high-throughput analysis and sorting of animals with increased protein aggregation, using fluorescently labeled PAB-1 as a readout. We identified five mutants with increased aggregation levels, of which two exhibited a reduced lifespan. We demonstrate that lifespan mutants can be identified by screening for accelerated protein aggregation through quantitative analysis of fluorescently-labeled aggregates in populations that do not require conditional sterilization or manual separation of parental and progeny populations. We further analyzed the morphology of protein aggregates and reveal that patterns of aggregation in naturally-aging animals differ from mutants with increased aggregation, suggesting aggregate growth is time-dependent. This screening approach can be customized to other non-developmental phenotypes that appear during adulthood, as well as to other aging markers to identify additional longevity-regulating genetic pathways.
Prefrontal top-down projections control context-dependent strategy selection
Authors: Gschwend Olivier , Yang Tao , van de Lisdonk Daniëlle , Zhang Xian , Sharma Radhashree , Li Bo 
Published: December 2021

AbstractThe rules governing behavior often vary with behavioral contexts. As a consequence, an action rewarded in one context may be discouraged in another. Animals and humans are capable of switching between behavioral strategies under different contexts and acting adaptively according to the variable rules, a flexibility that is thought to be mediated by the prefrontal cortex (PFC)1–4. However, how the PFC orchestrates context-dependent switch of strategies remains unclear. Here we show that pathway-specific projection neurons in the medial PFC (mPFC) differentially contribute to context-instructed strategy selection. In a decision-making task in which mice have been trained to flexibly switch between a previously established rule and a newly learned rule in a context-dependent manner, the activity of mPFC neurons projecting to the dorsomedial striatum encodes the contexts, and further represents decision strategies conforming to the old and new rules. Moreover, the activity of these neuron is required for context-instructed strategy selection. In contrast, the activity of mPFC neurons projecting to the ventral midline thalamus does not discriminate between the contexts, and represents the old rule even if mice have adopted the new one; furthermore, these neurons act to prevent the strategy switch under the new rule. Our results suggest that the mPFC→striatum pathway promotes flexible strategy selection guided by contexts, whereas the mPFC→thalamus pathway favors fixed strategy selection by preserving old rules. Balanced activity between the two pathways may be critical for adaptive behaviors.
Sampling motion trajectories during hippocampal theta sequences
Authors: Ujfalussy Balázs B , Orbán Gergő 
Published: December 2021

AbstractEfficient planning in complex environments requires that uncertainty associated with current inferences and possible consequences of forthcoming actions is represented. Representation of uncertainty has been established in sensory systems during simple perceptual decision making tasks but it remains unclear if complex cognitive computations such as planning and navigation are also supported by probabilistic neural representations. Here we capitalized on gradually changing uncertainty along planned motion trajectories during hippocampal theta sequences to capture signatures of uncertainty representation in population responses. In contrast with prominent theories, we found no evidence of encoding parameters of probability distributions in the momentary population activity recorded in an open-field navigation task in rats. Instead, uncertainty was encoded sequentially by sampling motion trajectories randomly in subsequent theta cycles from the distribution of potential trajectories. Our analysis is the first to demonstrate that the hippocampus is well equipped to contribute to optimal planning by representing uncertainty.
The perceived position of a moving object is reset by temporal, not spatial limits
Authors: Liu Sirui , Tse Peter U. , Cavanagh Patrick 
Published: December 2021

AbstractWhen the internal texture of a Gabor patch drifts orthogonally to its physical path, its perceived motion deviates dramatically from its physical path. The local position shifts accumulate to such an extent that a 45° oblique physical path appears to be vertical. However, at some point, a limit is reached and the path resets back to its veridical location, whereupon a new accumulation starts, making the new perceived path segment appear parallel to the pre-reset segment, but offset horizontally from it. Here, we tested whether spontaneous resets of this motion-induced position shift depend on the time or the distance over which position errors accrue, or both. We introduced a temporal gap in the middle of the path that forced the illusory path to reset back to its veridical physical position. This gap-triggered reset allowed us to measure the magnitude of the illusory offset up to that point. We found that perceived offset was less than expected for the angle of illusory drift, indicating that spontaneous resets had occurred prior to the gap-induced reset. The position offset decreased when the pre-gap duration increased but approximately doubled when the path length doubled. This pattern of perceived offsets is best accounted for by spontaneous resets that occur randomly over time at a constant rate, independently of the distance traveled. Our results suggest a temporal, not spatial, limit for the accumulation of position errors that underlies this illusion.
Prolyl-hydroxylase inhibitor-induced regeneration of alveolar bone and soft tissue in a mouse model of ligature-induced periodontitis
Authors: Zebrowitz Elan , Kajikawa Tetsuhiro , Bedelbaeva Kamila , Aslanukov Azamat , Bollinger Sam , Zhang Yong , Sarfatti David , Cheng Jing , Messersmith Phillip B. , Hajishengallis George , Heber-Katz Ellen 
Published: December 2021

AbstractBone injuries and fractures reliably heal through a process of regeneration with restoration to original structure and function when the gap between adjacent sides of a fracture site is small. However, when there is significant volumetric loss of bone, bone regeneration usually does not occur.In the present studies, we explore a particular case of volumetric bone loss in a mouse model of human periodontal disease (PD) in which alveolar bone surrounding teeth is permanently lost and not replaced. This model employs the placement a ligature around the upper second molar which leads to inflammation and bone breakdown and faithfully replicates the bacterially-induced inflammatory etiology of human PD to induce bone degeneration. After 10 days, the ligature is removed and the mice are treated with a timed-release formulation of a small molecule inhibitor of prolylhydroxylases (PHDi; 1,4-DPCA) previously shown to induce epimorphic regeneration of soft tissue in non-regenerating mice. This PHDi induces high expression of HIF-1α and the regenerative response is completely blocked by siHIF1a. Here, we observe that timed-release 1,4-DPCA rapidly and completely restores bone and soft tissue with normal anatomic fidelity and with increased stem cell markers due to stem cell migration into the site and/or de-differentiation of local tissue, PDL cell proliferation, and increased vascularization. In-vitro studies using gingival tissue show that 1,4-DPCA indeed induces de-differentiation and the expression of stem cell markers but does not exclude the role of migrating stem cells.
Areas Important for Ecological Connectivity Throughout Canada
Authors: Pither Richard , O’Brien Paul , Brennan Angela , Hirsh-Pearson Kristen , Bowman Jeff 
Published: December 2021

ABSTRACTGovernments around the world have acknowledged the importance of conserving ecological connectivity to help reverse the decline of biodiversity. In this study we employed recent methodological developments in circuit theory to conduct the first pan-Canadian analysis of multi-species connectivity for all terrestrial regions of the country, at a spatial grain sufficient to support local land-management decisions. We developed a movement cost surface with a limited number of thematic categories using the most recently updated land cover data available for the country. We divided the country into 17 tiles and used a wall-to-wall, omnidirectional mode of Circuitscape on each tile in order to assess ecological connectivity throughout entire landscapes as opposed to strictly among protected areas. The resulting raw current density map of Canada revealed heterogenous patterns of current density across the country, strongly influenced by geography, natural barriers, and human development. We included a validation analysis of the output current density map with independent wildlife data from across the country and found that mammal and herpetofauna locations were predicted by areas of high current density. We believe our current density map can be used to identify areas important for connectivity throughout Canada and thereby contribute to efforts to conserve biodiversity.
Genetic diversity patterns of human ethnic groups as inferred from the 1000 genomes
Authors: Xia Zhiyi , Huang Shi 
Published: December 2021

AbstractHuman genetic diversity remains to be better understood. We here analyzed data from the 1000 Genomes Project and defined group specific fixed alleles (GSFAs) as those that are likely fixed in one ethnic group but non-fixed in at least one other group. The fraction of derived alleles in GSFAs indicates relative distance to apes because such alleles are absent in apes. Our results show that different groups differed in GSFA numbers consistent with known genetic diversity patterns, but also differed in the fraction of derived alleles in GSFAs throughout the entire genome, with East Asians having the largest fraction, followed by South Asians, Europeans, Native Americans, and Africans. Fast evolving sites such as intergenic regions were enriched with derived alleles and showed greater differences in GSFA numbers between East Asians and Africans. Furthermore, GSFAs in East Asians are mostly not fixed in other groups especially Africans, which was particularly more pronounced for fast evolving noncoding variants, while GSFAs in Africans are mostly also fixed in East Asians. Finally, variants that are likely non-neutral such as those leading to stop codon gain/loss and splice donor/acceptor gain/loss showed patterns similar to those of fast-evolving noncoding variants. These results can be accounted for by the maximum genetic diversity theory but not by the neutral theory or its inference that Eurasians suffered bottlenecks, and have implications for better management of group specific genetic diseases.
Asymmetric Structure of the Native Rhodobacter sphaeroides Dimeric LH1-RC Complex
Authors: Tani K. , Kanno R. , Kikuchi R. , Kawamura S. , Nagashima K. V. P. , Hall M. , Takahashi A. , Yu L.-J. , Kimura Y. , Madigan M. T. , Mizoguchi A. , Humbel B. M. , Wang-Otomo Z.-Y. 
Published: December 2021

AbstractThe light-harvesting-reaction center (LH1-RC) core complex of purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides is characterized by the presence of both a dimeric form and a monomeric form. Following structure determination of the monomeric LH1-RC including its previously unrecognized component designated protein-U (Nat. Commun. 12, 6300, 2021), here we present cryo-EM structures of the dimeric LH1-RC from native Rba. sphaeroides IL106 at 2.75 Å resolution and from an LH1-RC monomer lacking protein-U (ΔU) at 2.64 Å resolution. The native dimeric core complex reveals many asymmetric features in the arrangement of its two monomeric components including the structural integrity of protein-U, the overall LH1 organization, and the rigidities of the proteins and pigments that form the complex. PufX polypeptides play a critical role in connecting two monomers, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in another monomer, in good agreement with biochemical analyses. One of the proteins-U was only partially identified in the dimeric structure, signaling significantly different degrees of disorder in the two monomers. The ΔU LH1-RC monomer revealed a half-moon-shaped structure containing 11 α- and 10 β-polypeptides (compared with 14 of each in the wild type), indicating a critical role for protein-U in controlling the number of αβ-subunits required for correct assembly and stabilization of the LH1-RC dimer. The structural features are discussed in relation to the unusual topology of intracytoplasmic photosynthetic membranes and an assembly model proposed for the native Rba. sphaeroides dimeric LH1-RC complex in membranes of wild-type cells.
Evolution of stickleback spines through independentcis-regulatory changes atHOXDB
Authors: Wucherpfennig Julia I. , Howes Timothy R. , Au Jessica N. , Au Eric H. , Roberts Kingman Garrett A. , Brady Shannon D. , Herbert Amy L. , Reimchen Thomas E. , Bell Michael A. , Lowe Craig B. , Dalziel Anne C. , Kingsley David M. 
Published: December 2021

SummaryUnderstanding the genetic mechanisms leading to new traits is a fundamental goal of evolutionary biology. We show thatHOXDBregulatory changes have been used repeatedly in different stickleback fish species to alter the length and number of bony dorsal spines. InGasterosteus aculeatus, a variantHOXDBallele is genetically linked to shortening an existing spine and adding a spine. InApeltes quadracus, a variant allele is associated with lengthening an existing spine and adding a spine. The alleles alter the same conserved non-codingHOXDBenhancer by diverse molecular mechanisms, including SNPs, deletions, and transposable element insertions. The independentcis-acting regulatory changes are linked to anterior expansion or contraction ofHOXDBexpression. Our findings support the long-standing hypothesis that naturalHoxgene variation underlies key morphological patterning changes in wild populations and illustrate how different mutational mechanisms affecting the same region may produce opposite gene expression changes with similar phenotypic outcomes.Abstract Figure
Simulation of the omicron variant of SARS-CoV-2 shows broad antibody escape, weakened ACE2 binding, and modest increase in furin binding
Authors: Jawaid M. Zaki , Baidya A. , Mahboubi-Ardakani R. , Davis Richard L. , Cox Daniel L. 
Published: December 2021

AbstractThe recent emergence of the omicron variant of the SARS-CoV-2 virus with large numbers of mutations has raised concern about a potential new surge in infections. Here we use molecular dynamics to study the biophysics of the interface of the omicron spike protein binding to (i) the ACE2 receptor protein, (ii) antibodies from all known binding regions, and (iii) the furin binding domain. Our simulations suggest that while there is significant reduction of antibody binding strength corresponding to escape, the omicron spike pays a cost in terms of weaker receptor binding. The furin cleavage domain is the same or weaker binding than the alpha variant, suggesting less viral load and disease intensity than the extant delta variant.
Ethyl-Iophenoxic acid as a serum marker for oral baiting of carnivorous marsupials
Authors: Pye Ruth , Nichols David , Gilbert Amy T. , Flies Andrew S. 
Published: December 2021

ABSTRACTContextEthyl-Iophenoxic acid (Et-IPA) has been widely used as a bait biomarker to determine oral bait consumption by vertebrate wildlife species. Oral bait vaccines have been delivered to numerous wildlife species to protect them from disease. The Tasmanian devil (Sarcophilis harrisii), the largest extant carnivorous marsupial species, is threatened by the transmissible cancers known as devil facial tumour disease (DFTD). Development of a protective DFTD vaccine is underway, and an oral bait has been proposed to deliver the vaccine in the wild. The bait delivery system requires a biomarker that can be detected for several months post-consumption in Tasmanian devils.AimTo determine the suitability of Et-IPA as a bait biomarker in the Tasmanian devil.MethodTwo Tasmanian devils were fed 50 mg Et-IPA (4.5 to 7.1 mg Et-IPA/kg bodyweight). Liquid chromatography with tandem mass spectrometry (LC-MS/-MS) was used to directly measure Et-IPA in baseline serum samples and samples collected on days 1, 14, 26 and 56 post-baiting.Key resultBoth devils retained serum Et-IPA concentrations at two orders of magnitude above negative control sera when this study concluded.ConclusionsEt-IPA is a useful bait biomarker for Tasmanian devils and can be included in future DFTD bait vaccine field trials to determine bait vaccine uptake.