bluuebunny/crossref_metadata_2025_split huggingface dataset:
Precision as a metric for acoustic survey design using occupancy or spatial capture-recapture
Authors: Juodakis Julius , Castro Isabel , Marsland Stephen 
Published: October 2020

AbstractPassive acoustic surveys provide a convenient and cost-effective way to monitor animal populations. Methods for conducting and analysing such surveys, especially for performing automated call recognition from sound recordings, are undergoing rapid development. However, no standard metric exists to evaluate the proposed changes. Furthermore, most metrics that are currently used are specific to a single stage of the survey workflow, and therefore may not reflect the overall effects of a design choice.Here, we attempt to define and evaluate the effectiveness of surveys conducted in two common frameworks of population inference – occupancy modelling and spatially explicit capture-recapture (SCR). Specifically, we investigate precision (standard error of the final estimate) as a possible metric of survey performance, but we show that it does not lead to generally optimal designs in occupancy modelling. In contrast, precision of the SCR density estimate can be optimised with fewer experiment-specific parameters. We illustrate these issues using simulations.We further demonstrate how SCR precision can be used to evaluate design choices on a field survey of little spotted kiwi (Apteryx owenii). We show that precision correctly measures tradeoffs involving sampling effort. As a case study, we compare automated call recognition software with human annotations. The proposed metric captured the tradeoff between missed calls (8% loss of precision when using the software) and faster data through-put (60% gain), while common metrics based on per-second agreement failed to identify optimal improvements and could be inflated by deleting data.Due to the flexibility of SCR framework, the approach presented here can be applied to a wide range of different survey designs. As the precision is directly related to the power of detecting temporal trends or other effects in the subsequent inference, this metric evaluates design choices at the application level, and can capture tradeoffs that are missed by stage-specific metrics, thus enabling reliable comparison between different experimental designs and analysis methods.
Sensory experience selectively reorganizes the late component of evoked responses
Authors: Bermudez-Contreras Edgar , Schjetnan Andrea Gomez-Palacio , Luczak Artur , Mohajerani Majid H. 
Published: October 2020

AbstractIn response to sensory stimulation, the cortex exhibits an early transient response followed by a late and slower activation pattern. Recent studies suggest that the early component represents features of the stimulus while the late component is associated with stimulus perception. Although very informative, these studies only focus on the amplitude of the evoked responses to study its relationship with sensory perception. In this work we expand upon the study of how patterns of evoked and spontaneous activity are modified by experience at mesoscale level using voltage and extracellular glutamate transient recordings over widespread regions of mice dorsal neocortex. We find that repeated tactile or auditory stimulation selectively modifies the spatiotemporal patterns of cortical activity, mainly of the late evoked response in anesthetized mice injected with amphetamine and also in awake mice. This modification lasted up to 60 minutes and results not only in an increase in amplitude of the late response after repeated stimulation, but also in an increase in the similarity between the spatiotemporal patterns of the late and the early evoked response patterns in anesthetized mice. This similarity increase occurs only for the evoked responses of the sensory modality that received the repeated stimulation. Thus, this selective long-lasting spatiotemporal modification of the cortical activity patterns might provide evidence that evoked responses are a cortex-wide phenomenon. This work opens new questions about how perception-related cortical activity changes with sensory experience across the cortex.
A Hilbert-based method for processing respiratory timeseries
Authors: Harrison Samuel J. , Bianchi Samuel , Heinzle Jakob , Stephan Klaas Enno , Iglesias Sandra , Kasper Lars 
Published: October 2020

AbstractIn this technical note, we introduce a new method for estimating changes in respiratory volume per unit time (RVT) from respiratory bellows recordings. By using techniques from the electrophysiological literature, in particular the Hilbert transform, we show how we can better characterise breathing rhythms, with the goal of improving physiological noise correction in functional magnetic resonance imaging (fMRI). Specifically, our approach leads to a representation with higher time resolution and better captures atypical breathing events than current peak-based RVT estimators. Finally, we demonstrate that this leads to an increase in the amount of respiration-related variance removed from fMRI data when used as part of a typical preprocessing pipeline.Our implementation will be publicly available as part of the PhysIO package, which is distributed as part of the open-source TAPAS toolbox (translationalneuromodeling.org/tapas).HighlightsWe introduce a new estimator for respiratory volume per unit time from respiratory recordings.We demonstrate how this is able to accurately characterise atypical breathing events.This removes significantly more variance when used as a confound regressor for fMRI data.Our implementation will be included in PhysIO, released as part of TAPAS:translationalneuromodeling.org/tapas.
Sex-Dependent Age Trajectories of Subcortical Brain Structures: Analysis of Large-Scale Percentile Models and Shape Morphometry
Authors: Ching Christopher R. K. , Abaryan Zvart , Santhalingam Vigneshwaran , Zhu Alyssa H. , Bright Joanna K. , Jahanshad Neda , Thompson Paul M. 
Published: October 2020

ABSTRACTModeling of structural brain variation over the lifespan is important to better understand factors contributing to healthy aging and risk for neurological conditions such as Alzheimer’s disease. Even so, we lack normative data on brain morphometry across the adult lifespan in large, well-powered samples. Here, in a large population-based sample of 26,440 adults from the UK Biobank (age: 44-81 yrs.), we created normative percentile charts for MRI-derived subcortical volumes. Next, we investigated associations between these morphometric measures and the strongest known genetic risk factor for late-onset Alzheimer’s disease (APOEgenotype) and mapped the spatial distribution of age-by-sex interactions using computational surface mesh modeling and shape analysis. Vertex-wise shape mapping supplements traditional gross volumetric approaches to reveal finer-grained variations across functionally important brain subcompartments. Normative curves revealed volumetric loss with age, as expected, for all subcortical brain structures except for the lateral ventricles, which expanded with age. Surprisingly, no volumetric associations withAPOEgenotype were detected, despite the very large sample size. Age-related trajectories for volumes differed in women versus men, and surface-based statistical maps revealed the spatial distribution of the age-by-sex interaction. Subcortical volumes declined faster in men than women over the full age range, but after age 60, fewer structures showed sex-dependent trajectories, indicating similar volumetric changes in older men and women. Large-scale statistical modeling of age effects on brain structures may drive new insights into individual differences in brain aging and help to identify factors that promote healthy brain aging and risk for disease.
History modulates early sensory processing of salient distractors
Authors: Adam Kirsten C.S. , Serences John T. 
Published: October 2020

AbstractTo find important objects, we must focus on our goals, ignore distractions, and take our changing environment into account. This is formalized in models of visual search whereby goal-driven, stimulus-driven and history-driven factors are integrated into a priority map that guides attention. Stimulus history robustly influences where attention is allocated even when the physical stimulus is the same: when a salient distractor is repeated over time, it captures attention less effectively. A key open question is how we come to ignore salient distractors when they are repeated. Goal-driven accounts propose that we use an active, expectation-driven mechanism to attenuate the distractor signal (e.g., predictive coding), whereas stimulus-driven accounts propose that the distractor signal is attenuated due to passive changes to neural activity and inter-item competition (e.g., adaptation). To test these competing accounts, we measured item-specific fMRI responses in human visual cortex during a visual search task where trial history was manipulated (colors unpredictably switched or were repeated). Consistent with a stimulus-driven account of history-based distractor suppression, we found that repeated singleton distractors were suppressed starting in V1, and distractor suppression did not increase in later visual areas. In contrast, we observed signatures of goal-driven target enhancement that were absent in V1, increased across visual areas, and were not modulated by stimulus history. Our data suggest that stimulus history does not alter goal-driven expectations, but rather modulates canonically stimulus-driven sensory responses to contribute to a temporally-integrated representation of priority.Significance StatementVisual search refers to our ability to find what we are looking for in a cluttered visual world (e.g., finding your keys). To perform visual search, we must integrate information about our goals (e.g., ‘find the red key-chain’), the environment (e.g., salient items capture your attention), and changes to the environment (i.e., stimulus history). Although stimulus history impacts behavior, the neural mechanisms that mediate history-driven effects remain debated. Here, we leveraged fMRI and multivariate analysis techniques to measure history-driven changes to the neural representation of items during visual search. We found that stimulus history influenced the representation of a salient ‘pop-out’ distractor starting in V1, suggesting that stimulus history operates via modulations in early sensory processing rather than goal-driven expectations.
Genomic features underlying the evolutionary transitions ofApibacterto honey bee gut symbionts
Authors: Zhang Wenjun , Zhang Xue , Su Qinzhi , Tang Min , Zheng Hao , Zhou Xin 
Published: October 2020

AbstractThe symbiotic bacteria associated with honey bee gut have likely transformed from a free-living or parasitic lifestyle, through a close evolutionary association with the insect host. However, little is known about the genomic mechanism underlying bacterial transition to exclusive adaptation to the bee gut. Here we compared the genomes of bee gut symbiontsApibacterwith their close relatives living in different lifestyles. We found that despite of general reduction in theApibactergenome, genes involved in amino acid synthesis and monosaccharide detoxification were retained, which were likely beneficial to the host. Interestingly, the microaerobicApibacterspecies have specifically acquired genes encoding for the nitrate respiration (NAR). The NAR system is also conserved in the cohabiting bee microbeSnodgrassella, although with a differed structure. This convergence implies a crucial role of respiratory nitrate reduction for microaerophilic microbiomes to colonize bee gut epithelium. Genes involved in lipid, histidine degradation are substantially lost inApibacter, indicating a transition of the energy source utilization. Particularly, genes involved in the phenylacetate degradation to generate host toxic compounds, as well as other virulence factors were lost, suggesting the loss of pathogenicity. Antibiotic resistance genes were only sporadically distributed amongApibacterspecies, but condensed in their pathogenic relatives, which may be related to the remotely living feature and less exposure to antibiotics of their bee hosts. Collectively, this study advances our understanding of genomic transition underlying specialization in bee gut symbionts.ImportanceInvestigations aiming to uncover the genetic determinants underlying the transition to a gut symbiotic lifestyle were scarce. The vertical transmitted honey bee gut symbionts of genusApibacterprovided an rare opportunity to tackle this, as evolving from family Flavobacteriaceae, they had phylogenetic close relatives living various lifestyles. Here, we documented thatApibacterhave both preserved and horizontally acquired host beneficial genes including monosaccharides detoxification that may have seeded a mutualistic relationship with the host. In contrast, multiple virulence factors and antibiotic resistance genes have been lost. Importantly, an highly efficient and genomic well organized respiratory nitrate reduction pathway is conserved across allApibacterspp., as well as in majority ofSnodgrassella, which colonize the same habitat asApibacter, suggesting an crucial role it played in living inside the gut. These findings highlight genomic changes paving ways to the transition to a honey bee gut symbiotic lifestyle.
Circulating levels of calcitonin gene-related peptide (CGRP) are lower in COVID-19 patients
Authors: Ochoa-Callejero Laura , García-Sanmartín Josune , Villoslada-Blanco Pablo , Íñiguez María , Pérez-Matute Patricia , Brody Rachel , Oteo José A. , Martínez Alfredo 
Published: October 2020

AbstractBackgroundTo better understand the biology of COVID-19, we have explored the behavior of calcitonin gene-related peptide (CGRP), an angiogenic, vasodilating, and immune modulating peptide, in SARS-CoV-2 positive patients.MethodsLevels of CGRP in the serum of 57 COVID-19 patients (24 asymptomatic, 23 hospitalized in the general ward, and 10 admitted to the intensive care unit) and healthy donors (n=24) were measured by ELISA. In addition, to better understand the physiological consequences of the observed variations, we investigated by immunofluorescence the distribution of RAMP1, one of the components of the CGRP receptor, in autopsy lung specimens.ResultsCGRP levels greatly decreased in COVID-19 patients (p<0.001) when compared to controls, and there were no significant differences due to disease severity, sex, age, or comorbidities. We found that COVID-19 patients treated with proton pump inhibitors had lower levels of CGRP than other patients not taking this treatment (p=0.001). RAMP1 immunoreactivity was found in smooth muscle cells of large blood vessels and the bronchial tree, and in the airways epithelium. In COVID-19 samples, RAMP1 was also found in proliferating type II pneumocytes, a common finding in these patients.ConclusionsThe lower levels of CGRP should negatively impact the respiratory physiology of COVID-19 patients due to vasoconstriction, improper angiogenesis, less epithelial repair, and faulty immune response. Therefore, restoring CGRP levels in these patients may represent a novel therapeutic approach for COVID-19.
Biomathematical models for genetic diversity analyses in complete genomes of SARS-CoV-2
Authors: Ramos Robson da Silva , Felix Pierre Teodósio , Ramos Venâncio Dallynne Bárbara , Nascimento Filho Cícero Batista do , Paulino Antônio João 
Published: October 2020

AbstractIn this work, we evaluated the levels of genetic diversity in 38 complete genomes of SARS-CoV-2, publicly available on the National Center for Biotechnology Information (NCBI) platform and from six countries in South America (Brazil, Chile, Peru, Colombia, Uruguay and Venezuela with 16, 11, 1, 1, 1, 7 haplotypes, respectively), all with an extension of 29,906 bp and Phred values ≥ 40. These haplotypes were previously used for phylogenetic analyses, following the alignment protocols of the MEGA X software; where all gaps and unconserved sites were extracted for the construction of phylogenetic trees. The specific methodologies for Paired FSTestimators, Molecular Variance (AMOVA), Genetic Distance, mismatch, demographic and spatial expansion analyses, molecular diversity and evolutionary divergence time analyses, were obtained using 20,000 random permutation.
Vulnerability to rumors during the COVID-19 pandemic: Results of a national survey
Authors: En Long Victoria Jane , Koh Wei Shien , Saw Young Ern , Liu Jean CJ 
Published: October 2020

AbstractAmidst the COVID-19 pandemic, many rumors have emerged. Given prior research linking rumor exposure to mental well-being, we conducted a nation-wide survey to document the base rate of rumor exposure and factors associated with rumor vulnerability. Between March to July 2020, 1237 participants were surveyed on 5 widely-disseminated COVID-19 rumors (that drinking water frequently could be preventive, that eating garlic could be preventive, that the outbreak arose because of bat soup consumption, that the virus was created in an American lab, and that the virus was created in a Chinese lab). For each rumor, participants reported whether they had heard, shared or believed each rumor. Although most participants had been exposed to COVID-19 rumors, few shared or believed these. Sharing behaviors sometimes occurred in the absence of belief; however, education emerged as a protective factor for both sharing and belief. Together, our results suggest that campaigns targeting skills associated with higher education (e.g. epistemology) may prove more effective than counter-rumor messages.HighlightsPrior studies linked exposure to COVID-19 rumors with poor mental health.In a community sample, most participants reported having heard rumors.Few participants shared or believed rumors.Sharing sometimes occurred in the absence of belief.More educated individuals believed and shared fewer rumors.
Cardiovascular risk factors are independently associated with COVID-19 mortality: a prospective cohort study
Authors: Collard Didier , Nurmohamed Nick S. , Kaiser Yannick , Reeskamp Laurens F. , Dormans Tom , Moeniralam Hazra , Simsek Suat , Douma Renée A. , Eerens Annet , Reidinga Auke C. , Elbers Paul , Beudel Martijn , Vogt Liffert , Stroes Erik S.G. , van den Born Bert-Jan H. 
Published: October 2020

AbstractObjectivesRecent reports suggest a high prevalence of hypertension and diabetes in COVID-19 patients, but the role of cardiovascular disease (CVD) risk factors in the clinical course of COVID-19 is unknown. We evaluated the time-to-event relationship between hypertension, dyslipidemia, diabetes, and COVID-19 outcomes.DesignWe analyzed data from the prospective Dutch COVID-PREDICT cohort, an ongoing prospective study of patients admitted for COVID-19 infection.SettingPatients from 8 participating hospitals, including two university hospitals from the COVID-PREDICT cohort were included.ParticipantsAdmitted, adult patients with a positive COVID-19 polymerase chain reaction (PCR) or high suspicion based on CT-imaging of the thorax. Patients were followed for major outcomes during hospitalization. CVD risk factors were established via home medication lists and divided in antihypertensives, lipid lowering therapy, and antidiabetics.Primary and secondary outcomes measuresThe primary outcome was mortality during the first 21 days following admission, secondary outcomes consisted of ICU-admission and ICU-mortality. Kaplan-Meier and Cox-regression analyses were used to determine the association with CVD risk factors.ResultsWe included 1604 patients with a mean age of 66±15 of whom 60.5% were men. Antihypertensives, lipid lowering therapy, and antidiabetics were used by 45%, 34.7%, and 22.1% of patients. After adjustment for age and sex, the presence of ≥2 risk factors was associated with increased mortality risk (HR 1.52, 95%CI 1.15-2.02), but not with ICU-admission. Moreover, the use of ≥2 antidiabetics and ≥2 antihypertensives was associated with mortality independent of age and sex with HRs of respectively 2.09 (95%CI 1.55-2.80) and 1.46 (95%CI 1.11-1.91).ConclusionsThe accumulation of hypertension, dyslipidemia and diabetes leads to a stepwise increased risk for short-term mortality in hospitalized COVID-19 patients independent of age and sex. Further studies investigating how these risk factors disproportionately affect COVID-19 patients are warranted.Strengths and limitations of this studyWhile previous data reported a high prevalence of CVD risk factors in COVID-19 patients, this study investigated whether diabetes, dyslipidemia and hypertension predict adverse outcomes.This study is limited by the use of medication as surrogate for cardiovascular risk factorsThe causality of the investigated risk factors remains to be addressed in future studies.
Differential inhibition of GABA release from mouse hippocampal interneuron subtypes by the volatile anesthetic isoflurane
Authors: Speigel Iris A. , Hemmings Hugh C. 
Published: October 2020

AbstractGeneral anesthesia is critical to modern medicine and animal research, but the cellular and molecular actions of general anesthetics on the central nervous system remain poorly understood. Volatile anesthetics such as isoflurane disrupt synaptic transmission and inhibit synaptic vesicle release in a neurotransmitter-selective manner. For example, GABA release from interneurons is less sensitive to isoflurane inhibition than are glutamate or dopamine release. Hippocampal and cortical interneuron subpopulations have diverse neurophysiological and synaptic properties, and their individual subtype-specific responses to isoflurane are unknown. We used live-cell optical imaging of exocytosis using fluorescent biosensors expressed in transgenic mouse hippocampal neuron cultures to delineate interneuron subtype-specific effects of isoflurane on synaptic vesicle exocytosis. We found that a clinically relevant concentration of isoflurane (0.5 mM) differentially modulated action potential-mediated exocytosis from GABAergic interneurons: parvalbumin-expressing interneurons were inhibited to 83.1±11.7% of control, whereas somatostatin-expressing and interneurons glutamatergic neurons were inhibited to 58.6±13.3% and 64.5±8.5% of control, respectively. The role of presynaptic voltage-gated sodium channel (Nav) subtype expression in determining isoflurane sensitivity was probed by overexpression or knockdown of specific Navsubtypes, which have distinct sensitivities to isoflurane and are differentially expressed between glutamatergic and GABAergic neurons. We found that the sensitivity of exocytosis to isoflurane was determined by the relative expression of Nav1.1 (associated with lower sensitivity) and Nav1.6 (associated with higher sensitivity). Thus the selective effects of isoflurane on synaptic vesicle exocytosis from hippocampal interneuron subtypes is determined by synaptic diversity in the relative expression of Nav1.1 and Nav1.6.Significance statementThe volatile anesthetic isoflurane inhibits hippocampal GABAergic interneuron synaptic vesicle exocytosis with differences in potency between interneuron subtypes. This neuron subtype-specific pharmacology derives in part from synaptic diversity in the expression of presynaptic voltage-gated sodium channels that have different sensitivities to anesthetic modulation of channel function. GABAergic interneurons are generally more resistant to the presynaptic effects of isoflurane owing to predominant Nav1.1 expression, whereas glutamatergic neurons are more sensitive owing to predominant Nav1.6 expression, which supports heterogenous pharmacologic effects on specific neural circuits.