bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy of face masks, neck gaiters and face shields for reducing the expulsion of simulated cough-generated aerosols
Authors: Lindsley William G. , Blachere Francoise M. , Law Brandon F. , Beezhold Donald H. , Noti John D. 
Published: October 2020

AbstractFace masks are recommended to reduce community transmission of SARS-CoV-2. One of the primary benefits of face masks and other coverings is as source control devices to reduce the expulsion of respiratory aerosols during coughing, breathing, and speaking. Face shields and neck gaiters have been proposed as an alternative to face masks, but information about face shields and neck gaiters as source control devices is limited. We used a cough aerosol simulator with a pliable skin headform to propel small aerosol particles (0 to 7 µm) into different face coverings. An N95 respirator blocked 99% of the cough aerosol, a medical grade procedure mask blocked 59%, a 3-ply cotton cloth face mask blocked 51%, and a polyester neck gaiter blocked 47% as a single layer and 60% when folded into a double layer. In contrast, the face shield blocked 2% of the cough aerosol. Our results suggest that face masks and neck gaiters are preferable to face shields as source control devices for cough aerosols.
Model-based ordination for species with unequal niche widths
Authors: van der Veen Bert , Hui Francis K.C. , Hovstad Knut A. , Solbu Erik B. , O’Hara Robert B. 
Published: October 2020

SummaryIt is common practice for ecologists to examine species niches in the study of community composition. The response curve of a species in the fundamental niche is usually assumed to be quadratic. The center of a quadratic curve represents a species’ optimal environmental conditions, and the width its ability to tolerate deviations from the optimum.Most multivariate methods assume species respond linearly to the environment of the niche, or with a quadratic curve that is of equal width and height for all species. However, it is widely understood that some species are generalists who tolerate deviations from their optimal environment better than others. Rare species often tolerate a smaller range of environments than more common species, corresponding to a narrow niche.We propose a new method, for ordination and fitting Joint Species Distribution Models, based on Generalized Linear Mixed-Effects Models, which relaxes the assumptions of equal tolerances and equal maxima.By explicitly estimating species optima, tolerances, and maxima, per ecological gradient, we can better predict change in species communities, and understand how species relate to each other.
Activation of the membrane-bound Nrf1 transcription factor by USP19, a ubiquitin-specific protease C-terminally tail-anchored in the endoplasmic reticulum
Authors: Hu Shaofan , Xiang Yuancai , Qiu Lu , Wang Meng , Zhang Yiguo 
Published: October 2020

AbstractThe membrane-bound transcription factor Nrf1 (i.e., encoded byNfe2l1) is activated by sensing glucose deprivation, cholesterol excess, proteasomal inhibition and oxidative stress, and then mediates distinct signaling responses in order to maintain cellular homeostasis. Herein, we found that Nrf1 stability and transactivity are both enhanced by USP19, a ubiquitin-specific protease tail-anchored in the endoplasmic reticulum (ER) through its C-terminal transmembrane domain. Further experiments revealed that USP19 directly interacts with Nrf1 in proximity to the ER and topologically acts as a deubiquitinating enzyme to remove ubiquitin moieties from this protein, and hence allows it to circumvent the potential proteasomal degradation. Such USP19-mediated effect takes place only after Nrf1 is retrotranslocated by p97 out of ER membranes to dislocate the cytoplasmic side. Conversely, knockout of USP19 causes significant decreases in the Nrf1 abundance and its active isoform entering the nucleus, resulting in down-regulation of its target proteasomal subunits. This led to a modest reduction ofUSP19−/−-derived tumor growth in xenograft mice, when compared with wild-type controls. Altogether, these demonstrate that USP19 serves as a novel mechanistic modulator of Nrf1, but not Nrf2, enabling Nrf1 to be rescued from putative ubiquitin-directed ER-associated degradation pathway. In turn, our additional experimental evidence has unraveled that transcriptional expression of endogenousUSP19and its promoter-driven reporter genes is differentially regulated by Nrf2, as well by Nrf1, at distinct layers within a complex hierarchical regulatory network.
“The stressed bird in the hand”: Influence of sampling design on the physiological stress response in a free-living songbird
Authors: Huber Nikolaus , Mahr Katharina , Tóth Zsófia , Szarka Endre Z. , Çınar Yusuf Ulaş , Salmón Pablo , Lendvai Ádám Z. 
Published: October 2020

AbstractDespite the widely used application of standardized capture-handling protocols to collect blood and assess the physiological stress response, the effect of the actual sampling design (e.g. timing and the number of blood samples) often differs between studies, and the potential implications for the measured physiological endpoints remain understudied. We, therefore, experimentally tested the effects of repeated handling and multiple blood sampling on the stress response in wintering free-living great tits (Parus major). We modified a well-established sampling protocol of avian studies by adding either an additional blood sample or a “sham-manipulation” (i.e. handling associated with the blood sampling procedure without venepuncture), to disentangle the effects of handling stress and blood loss. We combined three different stress metrics along the endocrine-immune interface to investigate the acute short-term stress response: total corticosterone levels (CORT), the heterophil/lymphocyte ratio (H:L), and the Leukocyte Coping Capacity (LCC). Our study provided three key results: i) no relationship between CORT-levels, LCC and H:L, confirming that these three parameters represent different physiological endpoints within the stress response; ii) contrasting dynamics in response to stress by the measured parameters and iii) no difference in stress levels 30 minutes after capture due to one additional blood sampling or handling event. By optimising the sampling design, our results provide implications for animal welfare and planning experimental procedures on stress physiology in passerine species.Summary StatementWhen testing the short-term stress response in free living passerines, both – the scientist and the bird may be better off with a 15-minute stress protocol.
Genome evolution in an agricultural pest following adoption of transgenic crops
Authors: Fritz Megan L. , Hamby Kelly A. , Taylor Katherine , DeYonke Alexandra M. , Gould Fred 
Published: October 2020

AbstractReplacement of synthetic insecticides with transgenic crops for pest management has been both economically and environmentally beneficial. These benefits have often eroded as pests evolved resistance to transgenic crops, but a broad understanding of the timing and complexity of adaptive changes which lead to field-evolved resistance in pest species is lacking. Wild populations ofHelicoverpa zea, a major lepidopteran crop pest and the target of transgenic Cry toxin-expressing cotton and corn, have recently evolved widespread, damaging levels of resistance. Here, we quantified patterns of genomic change in wildH. zeacollected between 2002 and 2017 when adoption rates of Cry-expressing crops expanded in North America. Using a combination of genomic approaches, we identified significant temporal changes in allele frequency throughout the genomes of field-collectedH. zea. Many of these changes occurred concurrently with increasingly damaging levels of resistance to Cry toxins between 2012 and 2016, in a pattern consistent with polygenic selection. Surprisingly, none of the eleven previously described Cry resistance genes showed signatures of selection in wildH. zea. Furthermore, we observed evidence of a very strong selective sweep in one region of theH. zeagenome, yet this strongest change was not additively associated with Cry resistance. This first, whole genome analysis of field-collected specimens to study evolution of Cry resistance demonstrates the potential and need for a more holistic approach to examining pest adaptation to changing agricultural practices.Significance StatementEvolution of pest resistance to management approaches in agricultural landscapes is common and results in economic losses. Early detection of pest resistance evolution prior to significant crop damage would benefit the agricultural community. It has been hypothesized that new genomic approaches could track molecular signals of emerging resistance problems and trigger efforts to pre-empt widespread damage. We tested this hypothesis by quantifying genomic changes in the pestHelicoverpa zeaover a 15 year period concurrent with commercialization and subsequent loss of efficacy of transgenic Bt-expressing crops. Our results demonstrate the complex nature of evolution in agricultural ecosystems and provide insight into the potential for and pitfalls associated with use of genomic approaches for resistance monitoring. We discuss approaches for improvement.
Dynamic and reversible remapping of network representations in an unchanging environment
Authors: Low Isabel I. C. , Williams Alex H. , Campbell Malcolm G. , Linderman Scott W. , Giocomo Lisa M. 
Published: October 2020

AbstractIn response to environmental changes, the medial entorhinal cortex alters its single-cell firing properties. This flexibility in neural coding is hypothesized to support navigation and memory by dividing sensory experience into unique contextual episodes. However, it is unknown how the entorhinal circuit transitions between different representations, particularly when sensory information is not delineated into discrete contexts. Here, we describe spontaneous and abrupt transitions between multiple spatial maps of an unchanging task and environment. These remapping events were synchronized across hundreds of medial entorhinal neurons and correlated with changes in running speed. While remapping altered spatial coding in individual neurons, we show that features of the environment were statistically preserved at the population-level, enabling simple decoding strategies. These findings provoke a reconsideration of how medial entorhinal cortex dynamically represents space and broadly suggest a remarkable capacity for higher-order cortical circuits to rapidly and substantially reorganize their neural representations.
Diffusion MRI Changes in the Healthy Aging Canine Brain
Authors: Barry Erica F. , Loftus John P. , Luh Wen-Ming , de Leon Mony J. , Niogi Sumit N. , Johnson Philippa J. 
Published: October 2020

AbstractWhite matter dysfunction and degeneration have been a topic of great interest in healthy and pathological aging. While ex vivo studies have investigated age-related changes in canines, little in vivo canine aging research exists. Quantitative diffusion MRI such as diffusion tensor imaging (DTI) has demonstrated aging and neurodegenerative white matter changes in humans. However, this method has not been applied and adapted in vivo to canine populations. This study aimed to test the hypothesis that white matter diffusion changes frequently reported in human aging are also found in aged canines. The study used Tract Based Spatial Statistics (TBSS) and a region of interest (ROI) approach to investigate age related changes in fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AxD) and radial diffusivity (RD). The results show that, compared to younger animals, aged canines have significant decreases in FA in parietal and temporal regions as well as the corpus callosum and fornix. Additionally, AxD decreases were observed in parietal, frontal and midbrain regions. Similarly, an age-related increase in RD was observed in the right parietal lobe while MD decreases were found in the midbrain. These findings suggest that canine samples offer a model for healthy human aging as they exhibit similar white matter diffusion tensor changes with age.
Human placental-derived stem cell therapy ameliorates experimental necrotizing enterocolitis and supports restoration of the intestinal stem cell niche
Authors: Weis Victoria G. , Deal Anna C. , Mekkey Gehad , Clouse Cara , Gaffley Michaela , Whitaker Emily , Weis Jared A. , Schwartz Marshall Z. , Atala Anthony 
Published: October 2020

AbstractNecrotizing enterocolitis (NEC), a life-threatening intestinal disease, is becoming a larger proportionate cause of morbidity and mortality in premature infants. To date, therapeutic options remain elusive. Based on recent cell therapy studies, we investigated the effect of a human placental-derived stem cell (hPSC) therapy on intestinal damage in an experimental NEC rat pup model. NEC was induced in newborn Sprague-Dawley rat pups for 4 days via formula feeding, hypoxia, and LPS. NEC pups received intraperitoneal (ip) injections of either saline or hPSC (NEC-hPSC) at 32 and 56 hours into NEC induction. At 4 days, intestinal macroscopic and histological damage, epithelial cell composition, and inflammatory marker expression of the ileum was assessed. Breastfed (BF) littermates were used as controls. NEC pups developed significant bowel dilation and fragility in the ileum. Further, NEC induced loss of normal villi-crypt morphology, disruption of epithelial proliferation and apoptosis, and loss of Paneth cells and LGR5+ stem cells in the crypt. hPSC treatment improved macroscopic intestinal health with reduced ileal dilation and fragility. Histologically, hPSC administration had a significant reparative effect on the villi-crypt morphology and epithelium. In addition to a trend of decreased inflammatory marker expression, hPSC-NEC pups had increased epithelial proliferation and decreased apoptosis when compared to NEC littermates. Further, the intestinal stem cell niche of Paneth cells and LGR5+ stem cells was increased with hPSC therapy. Together, these data demonstrate hPSC can promote epithelial healing of NEC intestinal damage in part through support of the intestinal stem cell niche.New and NoteworthyThese studies demonstrate a human placental-derived stem cell (hPSC) therapeutic strategy for necrotizing enterocolitis (NEC). In an experimental model of NEC, hPSC administration improved macroscopic intestinal health, ameliorated epithelial morphology, and supported the intestinal stem cell niche. Our data suggest that hPSC are a potential therapeutic approach to attenuate established intestinal NEC damage. Further, we show hPSC are a novel research tool that can now be utilized to elucidate critical neonatal repair mechanisms to overcome NEC disease.
Evolutionary dynamics at the tumor edge reveals metabolic imaging biomarkers
Authors: Jiménez-Sánchez Juan , Bosque Jesús J. , Jiménez Londoño Germán A. , Molina-García David , Martínez Álvaro , Pérez-Beteta Julián , Ortega-Sabater Carmen , Martínez Antonio F. Honguero , García Vicente Ana M. , Calvo Gabriel F. , Pérez-García Víctor M. 
Published: October 2020

Human cancers are biologically and morphologically heterogeneous. A variety of clonal populations emerge within these neoplasms and their interaction leads to complex spatio-temporal dynamics during tumor growth. We studied the reshaping of metabolic activity in human cancers by means of continuous and discrete mathematical models, and matched the results to positron emission tomography (PET) imaging data. Our models revealed that the location of increasingly active proliferative cellular spots progressively drifted from the center of the tumor to the periphery, as a result of the competition between gradually more aggressive phenotypes. This computational finding led to the development of a metric, the NPAC, based on the distance from the location of peak activity (proliferation) to the tumor centroid. The NPAC metric can be computed for human patients using 18F-FDG PET/CT images where the voxel of maximum uptake (SUVmax) is taken as the point of peak activity. Two datasets of 18F-FDG PET/CT images were collected, one from 61 breast cancer patients and another from 161 non-small-cell lung cancer patients. In both cohorts, survival analyses were carried out for the NPAC and for other classical PET/CT-based biomarkers, finding that the former had a high prognostic value, outperforming the latter. In summary, our work offers new insights into the evolutionary mechanisms behind tumor progression and provides a PET/CT-based biomarker with clinical applicability.Significance StatementThrough the use of different in silico modeling approaches capturing tumor heterogeneity, we predicted that areas of high metabolic activity would shift towards the periphery as tumors become more malignant. To confirm the prediction and provide clinical value for the finding, we took 18F-FDG PET images of breast cancers and non-small-cell lung cancers, where we measured the distance from the point of maximum activity to the tumor centroid, and normalized it by a surrogate of the volume. We show that this metric has a high prognostic value for both malignancies and outperforms other classical PET-based metabolic biomarkers used in oncology.
Low-density lipoprotein cholesterol levels are associated with poor clinical outcomes in COVID-19
Authors: Aparisi Álvaro , Iglesias-Echeverría Carolina , Ybarra-Falcón Cristina , Cusácovich Iván , Uribarri Aitor , García-Gómez Mario , Ladrón Raquel , Fuertes Raúl , Candela Jordi , Hinojosa Williams , Dueñas Carlos , González Roberto , Nogales Leonor , Calvo Dolores , Carrasco-Moraleja Manuel , Román J. Alberto San , Amat-Santos Ignacio J. , Andaluz-Ojeda David 
Published: October 2020

STRUCTURED ABSTRACTBackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the sole causative agent of coronavirus infectious disease-19 (COVID-19).MethodsWe performed a retrospective single-center study of consecutively admitted patients between March 1st and May 15th, 2020, with a definitive diagnosis of SARS-CoV-2 infection. The primary end-point was to evaluate the association of lipid markers with 30-days all-cause mortality in COVID-19.ResultsA total of 654 patients were enrolled, with an estimated 30-day mortality of 22.8% (149 patients). Non-survivors had lower total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-c) levels during the entire course of the disease with complete resolution among survivors. Both showed a significant inverse correlation with inflammatory markers and a positive correlation with lymphocyte count. In a multivariate analysis, LDL-c ≤ 69 mg/dl (hazard ratio [HR] 1.94; 95% confidence interval [CI] 1.14-3.31), C-reactive protein > 88 mg/dl (HR 2.44; 95% CI, 1.41-4.23) and lymphopenia < 1,000 (HR 2.68; 95% CI, 1.91-3.78) at admission were independently associated with 30-day mortality. This association was maintained 7 days after admission.ConclusionHypolipidemia in SARS-CoV-2 infection may be secondary to an immune-inflammatory response, with complete recovery in survivors. Low LDL-c serum levels are independently associated with higher 30-day mortality in COVID-19 patients.
Clinical, laboratory, and temporal predictors of neutralizing antibodies to SARS-CoV-2 after COVID-19
Authors: Boonyaratanakornkit Jim , Morishima Chihiro , Selke Stacy , Zamora Danniel , McGuffin Sarah , Shapiro Adrienne E. , Campbell Victoria L. , McClurkan Christopher L. , Jing Lichen , Gross Robin , Liang Janie , Postnikova Elena , Mazur Steven , Chaudhary Anu , Das Marie K. , Fink Susan L. , Bryan Andrew , Greninger Alex L. , Jerome Keith R. , Holbrook Michael R. , Gernsheimer Terry B. , Wener Mark H. , Wald Anna , Koelle David M. 
Published: October 2020

ABSTRACTBackgroundSARS-CoV-2-specific antibodies may protect from reinfection and disease, providing the rationale for administration of plasma containing SARS-CoV-2 neutralizing antibodies (nAb) as a treatment for COVID-19. The clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood.MethodsAdults with virologically-documented SARS-CoV-2 infection in a convalescent plasma donor screening program were tested for serum IgG to SARS-CoV-2 spike protein S1 domain, nucleoprotein (NP), and for nAb.ResultsAmongst 250 consecutive persons studied a median of 67 days since symptom onset, 243/250 (97%) were seropositive on one or more assays. Sixty percent of donors had nAb titers ≥1:80. Correlates of higher nAb titer included older age (adjusted OR [AOR] 1.03/year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during acute illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic (ROC) analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. NAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range, 77-120) apart (P<0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses.ConclusionsNab titers correlated with COVID-19 severity, age, and sex. Standard commercially available SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels were found to decline and a small proportion of COVID-19 survivors lack adaptive immune responses.
Mask mandates can limit COVID spread: Quantitative assessment of month-over-month effectiveness of governmental policies in reducing the number of new COVID-19 cases in 37 US States and the District of Columbia
Authors: Maloney Michael J. , Rhodes Nathaniel J. , Yarnold Paul R. 
Published: October 2020

ABSTRACTIntroductionSARS-CoV-2 is the beta-coronavirus responsible for COVID-19. Facemask use has been qualitatively associated with reduced COVID-19 cases, but no study has quantitatively assessed the impact of government mask mandates (MM) on new COVID-19 cases across multiple US States.Data and MethodsWe utilized a non-parametric machine-learning algorithm to test the a priori hypothesis that MM were associated with reductions in new COVID-19 cases. Publicly available data were used to analyze new COVID-19 cases from 37 States and the District of Columbia (i.e., “38 States”). We conducted confirmatory All-States and State-Wise analyses, validity analyses [e.g., leave-one-out (LOO) and bootstrap resampling], and covariate analyses.ResultsNo statistically significant difference in the daily number of new COVID-19 infections was discernable in the All-States analysis. In State-Wise LOO validity analysis, 11 States exhibited reductions in new COVID-19 and the reductions in four of these States (AK, MA, MN, VA) were significant in bootstrap resampling. Only the Social Capital Index predicted MM success (training p<0.028 and LOO p<0.013).ConclusionResults obtained when studying the impact of MM on COVID-19 cases varies as a function of the heterogeneity of the sample being considered, providing clear evidence of Simpson’s Paradox and thus of confounded findings. As such, studies of MM effectiveness should be conducted on disaggregated data. Since transmissions occur at the individual rather than at the collective level, additional work is needed to identify optimal social, psychological, environmental, and educational factors which will reduce the spread of SARS-CoV-2 and facilitate MM effectiveness across diverse settings.