bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of using personal protective equipment during the COVID-19 pandemic on the quality indicators of screening colonoscopies
Authors: Chirayath Subin , Bahirwani Janak , Kaur Parampreet , Martins Noel , Modi Ronak 
Published: May 2021

AbstractBackgroundCoronavirus Disease 2019 (COVID-19) has affected many facets of the practice of medicine including screening colonoscopies.AimsOur study looks to observe if there has been an effect on the quality of colonoscopies, as indicated by quality measures such as cecal intubation rate (CIR), cecal intubation time (CIT), scope withdrawal time (SWT) and adenoma detection rate (ADR) with the adoption of standard COVID-19 precautions.MethodsWe conducted a retrospective chart review to analyze the effects of the COVID-19 pandemic on screening colonoscopies. The study utilized data on CIR, CIT, SWT and ADR from outpatient, non-emergent procedures conducted at 3 endoscopy suites of St Luke’s University Health Network. All inpatient and emergent procedures were excluded.ResultsOur study demonstrated that the total number of screening colonoscopies was decreased between 2019 to 2020 (318 in 2019 vs 157 in 2020, p= 0.005). CIT (320±105 seconds in 2019 vs 392±107 seconds in 2020, p=0.001) and SWT (706±232 seconds in 2019 vs 830±241 seconds in 2020, p=0.001) were increased while CIR (98.2% in 2019 vs 96.6% in 2020, p=0.04) was decreased between 2019 and 2020 likely due to PPE introduction. ADR was similar between the two groups (38.23 (12.50-66.66) in 2019 vs 38.18(16.66-66.00) in 2020, p=0.8).ConclusionOur study showed that quality indices for screening colonoscopies like CIR, CIT, and SWT were negatively impacted during the COVID-19 time period. ADR, however, were similar. Thus, the efficiency of the procedures was affected by the use of PPE but it did not affect the colonoscopy’s clinical benefit.
Cross-sectional study of the association between perceived organizational support and COVID-19 vaccine intention
Authors: Kobayashi Yuichi , Nagata Tomohisa , Fujino Yoshihisa , Hino Ayako , Tateishi Seiichiro , Ogami Akira , Tsuji Mayumi , Matsuda Shinya , Mori Koji ,   CORoNaWork project
Published: May 2021

AbstractObjectivesThis study examined the association between perceived organizational support (POS) and COVID-19 vaccine intention and the influence of the implementation of workplace infection prevention measures.MethodsWe analyzed 23,846 workers using data from an Internet survey of workers aged 20–65 years conducted in December 2020, during a period of widespread COVID-19 infection in Japan.ResultsA higher POS was associated with a higher intention to vaccinate. The relationship between POS and vaccine intention was attenuated when adjusted for infection prevention measures in the workplace.ConclusionsIn workplaces where POS is present, a sense of responsibility to the group and altruistic behavior may arise. This means employees act to acquire herd immunity to protect others, which may result in increased vaccine intention. The association between POS and vaccination intention was attenuated by adjusting for workplace infection prevention measures, which suggested that infection prevention measures may be a confounding factor or that POS created a health climate that promoted infection prevention measures. The results suggest that working to improve employee well-being and implementing appropriate workplace infection prevention measures during infectious disease outbreaks may promote vaccination behavior and contribute to the acquisition of herd immunity in the community.
Benchmarking 50 classification algorithms on 50 gene-expression datasets
Authors: Piccolo Stephen R. , Mecham Avery , Golightly Nathan P. , Johnson Jérémie L. , Miller Dustin B. 
Published: May 2021

AbstractBy classifying patients into subgroups, clinicians can provide more effective care than using a uniform approach for all patients. Such subgroups might include patients with a particular disease subtype, patients with a good (or poor) prognosis, or patients most (or least) likely to respond to a particular therapy. Diverse types of biomarkers have been proposed for assigning patients to subgroups. For example, DNA variants in tumors show promise as biomarkers; however, tumors exhibit considerable genomic heterogeneity. As an alternative, transcriptomic measurements reflect the downstream effects of genomic and epigenomic variations. However, high-throughput technologies generate thousands of measurements per patient, and complex dependencies exist among genes, so it may be infeasible to classify patients using traditional statistical models. Machine-learning classification algorithms can help with this problem. However, hundreds of classification algorithms exist—and most support diverse hyperparameters—so it is difficult for researchers to know which are optimal for gene-expression biomarkers. We performed a benchmark comparison, applying 50 classification algorithms to 50 gene-expression datasets (143 class variables). We evaluated algorithms that represent diverse machine-learning methodologies and have been implemented in general-purpose, open-source, machine-learning libraries. When available, we combined clinical predictors with gene-expression data. Additionally, we evaluated the effects of performing hyperparameter optimization and feature selection in nested cross-validation folds. Kernel- and ensemble-based algorithms consistently outperformed other types of classification algorithms; however, even the top-performing algorithms performed poorly in some cases. Hyperparameter optimization and feature selection typically improved predictive performance, and univariate feature-selection algorithms outperformed more sophisticated methods. Together, our findings illustrate that algorithm performance varies considerably when other factors are held constant and thus that algorithm selection is a critical step in biomarker studies.Author Summary
Re-evaluating rhythmic attentional switching: Spurious oscillations from shuffling-in-time
Authors: Brookshire Geoffrey 
Published: May 2021

AbstractHow does attention help to focus perceptual processing on the important parts of a visual scene? Although the neural and perceptual effects of attention were traditionally assumed to be sustained over time, the field is converging on a dramatically different view: that covert attention rhythmically switches between objects at 3-8 Hz. Here I demonstrate that ubiquitous analyses in this literature conflate rhythmic oscillations with aperiodic temporal structure. Using computational simulations, I show that the behavioral oscillations reported in this literature could reflect aperiodic dynamics in attention, rather than periodic rhythms. I then propose two analyses (one novel and one widely used in climate science) that discriminate between periodic and aperiodic structure in behavioral time-series. Finally, I apply these alternative analyses to published data-sets, and find no evidence for rhythms in attentional switching after accounting for aperiodic temporal structure. Attention shows rich temporal structure. The techniques presented here will help to clarify the periodic and aperiodic dynamics of perception and cognition.
“Destructive fishing” – a ubiquitously used but vague term? Usage and impacts across academic research, media, and policy
Authors: Willer David F. , Brian Joshua I. , Derrick Christina J. , Hicks Marcus , Pacay Alerick , McCarthy Arlie H. , Benbow Sophie , Brooks Holly , Hazin Carolina , Mukherjee Nibedita , McOwen Chris J , Walker Jessica , Steadman Daniel 
Published: May 2021

AbstractThe term “destructive fishing” appears in multiple international policy instruments intended to improve outcomes for marine biodiversity, coastal communities and sustainable fisheries. However, the meaning of “destructive fishing” is often vague, limiting effectiveness in policy. Therefore, in this study we systematically reviewed the use of “destructive fishing” in three record types: academic literature, media articles, and policy documents between 1976-2020. A more detailed analysis was performed on sub-sets of these records, considering the extent to which the term is characterised, geographic distribution of use, and specific impacts and practices associated with the term. We found that use of “destructive fishing” relative to the generic term ‘fisheries’ has increased since the 1990s. Records focused predominantly on fishing practices in South-eastern Asia, followed by Southern Asia and Europe. The term was characterised in detail in only 15% of records. Habitat damage and blast/poison fishing were the most associated ecological impacts and gear/practices, respectively. Bottom trawling and unspecified net fishing were regularly linked to destructive fishing. Importantly, the three record types use the term differently. Academic literature tends to specifically articulate the negative impacts, while media articles focus generally on associated gears/practices. Significant regional variation also exists in how the term is used and what phenomena it is applied to. This study provides evidence and recommendations to inform stakeholders in any future pursuit of a unified definition of “destructive fishing” to support more meaningful implementation of global sustainability goals.
The effects of predator odor (TMT) exposure and mGlu3NAM pretreatment on lasting behavioral and molecular adaptations in the insular cortex and BNST
Authors: Tyler Ryan E. , Bluitt Maya N. , Engers Julie L. , Lindsley Craig W. , Besheer Joyce 
Published: May 2021

AbstractA stressor can trigger adaptations that contribute to neuropsychiatric disorders. Predator odor (TMT) exposure is an innate stressor that produces lasting adaptations. TMT exposure may activate metabotropic glutamate receptor 3 (mGlu3), triggering excitatory corticolimbic adaptations that underlie behavioral changes. To evaluate functional involvement, the mGlu3negative allosteric modulator (NAM, VU6010572; 3 mg/kg, i.p.) was administered before TMT exposure in male, Long Evans rats. Two weeks after stressor, rats underwent behavioral testing (context re-exposure, zero maze and acoustic startle response) followed by RT-PCR gene expression in the insular cortex and BNST. During the TMT exposure, rats displayed stress-reactive behaviors that were not affected by the VU6010572. During the context re-exposure, prior TMT exposure and VU6010572 pretreatment both produced a hyperactive response. TMT exposure did not affect zero maze or ASR measures, but VU6010572 increased time spent in the open arms and habituation to ASR, indicating anxiolytic-like effects. In the insular cortex, TMT exposure resulted in excitatory adaptations as shown by increased expression of mGlu (Grm3, Grm5), NMDA (GriN2A, GriN2B, GriN2C, GriN3A, GriN3B) and AMPA (GriA3) receptor transcripts. Interestingly, mGlu3signaling during stressor mediatedGriN3Bupregulation. Stress reactivity during TMT exposure was associated withGrm5, GriN2A, GriN2C, andGriA3upregulation in the insular cortex and context re-exposure reactivity in the TMT/vehicle, but not the TMT/mGlu3NAM group. In the BNST,GriN2A, GriN2BandGriN3Bwere increased by VU6010572, but TMT prevented these effects. These data demonstrate that mGlu3signaling contributes to the lasting behavioral and molecular adaptations of predator odor stressor.
Tree diversity effects on forest productivity: disentangling the effects of tree species addition vs. substitution
Authors: Maude Toïgo , Bastien Castagneyrol , Hervé Jactel , Xavier Morin , Celine Meredieu 
Published: May 2021

ABSTRACTMixture effect on stand productivity is usually apprehended through a substitutive approach, whereby productivity in mixed stands is compared to productivity in monocultures, at equivalent stand density. This approach has proved that in many cases mixed stands perform better than monospecific forests, however, we do not yet have a solid theory about species behaviour in the mixture or even guidelines for combining species. The addition of a second tree species to an existing mono-specific stand has received much less consideration. Yet, this approach has the potential to separate the facilitation effect from the complementarity effect.We compared the effect of tree species substitution vs. addition on the productivity of maritime pine and silver birch in a young tree diversity experiment implemented in 2008 in SW France.Substituting pines with birches to create two-species mixtures resulted in an increase of tree productivity at stand level beyond what was expected from monocultures (i.e., overyielding). In contrast, creating mixture through the addition of birches to pine stands had no effect on the maritime pine stand productivity (transgressive mixture effect not significant). This absence of effect is produced by two distinct density-dependence responses at an individual level.Our results allow clarifying the cases in which a mixed stand can be considered as an alternative to a monoculture of a productive species. In particular, the addition of a pioneer and soil low-demanding species during young developmental stages is a possibility to diversify the stand and potentially to increase ecosystem services without altering the productivity of the target species.
Genetic variation associated with plastic and homeostatic growth responses to drought in Arabidopsis
Authors: Ferrero-Serrano Ángel , Assmann Sarah M. 
Published: May 2021

AbstractNatural genetic variation influences plant responses to environmental stressors. However, the extent to which such variation underlies plastic versus homeostatic response phenotypes deserves more attention. We quantified the extent of drought-induced changes in leaf area in a set of Iberian Arabidopsis accessions and then performed association studies correlating plasticity and homeostasis in this phenotype with genomic and transcriptomic variation. Drought-induced plastic reductions in relative leaf area typified accessions originating from productive environments. In contrast, homeostasis in relative leaf area typified accessions originating from unproductive environments. Genome-Wide Association Studies (GWAS), Transcriptome Wide Association Studies (TWAS), and expression GWAS (eGWAS) highlighted the importance of auxin-related processes in conferring leaf area plasticity. Homeostatic responses in relative leaf area were associated with a diverse gene set and positively associated with a higher intrinsic water use efficiency (WUEi), as confirmed in a TWAS metanalysis of previously published δ13C measurements. Thus, we have identified not only candidate “plasticity genes” but also candidate “homeostasis genes” controlling leaf area. Our results exemplify the value of a combined GWAS, TWAS, and eGWAS approach to identify mechanisms underlying phenotypic responses to stress.HighlightInformation on phenotype, genotype, and transcript abundance is integrated to identify candidate plasticity and homeostasis genes and processes associated with local adaptation to drought stress in Arabidopsis accessions of the Iberian Peninsula.
Increasing phagocytosis of microglia through targeting CD33 with liposomes displaying glycan ligands
Authors: Bhattacherjee Abhishek , Daskhan Gour Chand , Bains Arjun , Watson Adrianne E. S. , Eskandari-Sedighi Ghazaleh , St. Laurent Chris D. , Voronova Anastassia , Macauley Matthew S. 
Published: May 2021

AbstractCD33 is an immunomodulatory receptor expressed on microglia and genetically linked to Alzheimer’s disease (AD) susceptibility. While antibodies targeting CD33 have entered clinical trials to treat neurodegeneration, it is unknown whether the glycan-binding properties of CD33 can be exploited to modulate microglia. Here, we use liposomes that multivalently display glycan ligands of CD33 (CD33L liposomes) to engage CD33. We find that CD33L liposomes increase phagocytosis of cultured monocytic cells and microglia in a CD33-dependent manner. Enhanced phagocytosis strongly correlates with loss of CD33 from the cell surface and internalization of liposomes. Increased phagocytosis by treatment with CD33L liposomes is dependent on a key intracellular signaling motif on CD33 as well as the glycan-binding ability of CD33. These effects are specific totransengagement of CD33 by CD33L liposomes, ascisengagement through insertion of lipid-linked CD33L into cells produces the opposite effect on phagocytosis. Moreover, intracerebroventricular injection of CD33L liposomes in mice enhances phagocytosis of microglia in a CD33-dependent manner. These results demonstrate that multivalent engagement of CD33 with glycan ligands can modulate microglial cell function.
Resource Profile and User Guide of the Polygenic Index Repository
Authors: Becker Joel , Burik Casper A.P. , Goldman Grant , Wang Nancy , Jayashankar Hariharan , Bennett Michael , Belsky Daniel W. , Linnér Richard Karlsson , Ahlskog Rafael , Kleinman Aaron , Hinds David A. ,   23andMe Research Group, Caspi Avshalom , Corcoran David L. , Moffitt Terrie E. , Poulton Richie , Sugden Karen , Williams Benjamin S. , Harris Kathleen Mullan , Steptoe Andrew , Ajnakina Olesya , Milani Lili , Esko Tõnu , Iacono William G. , McGue Matt , Magnusson Patrik K.E. , Mallard Travis T. , Harden K. Paige , Tucker-Drob Elliot M. , Herd Pamela , Freese Jeremy , Young Alexander , Beauchamp Jonathan P. , Koellinger Philipp , Oskarsson Sven , Johannesson Magnus , Visscher Peter M. , Meyer Michelle N. , Laibson David , Cesarini David , Benjamin Daniel J. , Turley Patrick , Okbay Aysu 
Published: May 2021

AbstractPolygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is rapidly growing. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs’ prediction accuracies, we constructed them using genome-wide association studies—some of which are novel—from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the “additive SNP factor.” Regressions in which the true regressor is the additive SNP factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.
Emerged human-like facial expression representation in a deep convolutional neural network
Authors: Zhou Liqin , Meng Ming , Zhou Ke 
Published: May 2021

AbstractFace identity and expression play critical roles in social communication. Recent research found that the deep convolutional neural networks (DCNNs) trained to recognize facial identities spontaneously learn features that support facial expression recognition, and vice versa, suggesting an integrated representation of facial identity and expression. In the present study, we found that the expression-selective units spontaneously emerged in a VGG-Face trained for facial identity recognition and tuned to distinct basic expressions. Importantly, they exhibited typical hallmarks of human expression perception, i.e., the facial expression confusion effect and categorical perception effect. We then investigated whether the emergence of expression-selective units is attributed to either face-specific experience or domain-general processing, by carrying out the same analysis on a VGG-16 trained for object classification and an untrained VGG-Face without any visual experience, both of them having the identical architecture with the pretrained VGG-Face. Although Similar expression-selective units were found in both DCNNs, they did not exhibit reliable human-like characteristics of facial expression perception. Taken together, our computational findings revealed the necessity of domain-specific visual experience of face identity for the development of facial expression perception, highlighting the contribution of nurture to form human-like facial expression perception. Beyond the weak equivalence between human and DCNNS at the input-output behavior, emerging simulated algorithms between models and humans could be established through domain-specific experience.
Estimating the glutamate transporter surface density in distinct sub-cellular compartments of mouse hippocampal astrocytes
Authors: Rădulescu Anca R. , Todd Gabrielle C. , Williams Cassandra L. , Bennink Benjamin A. , Lemus Alex A. , Chesbro Haley E. , Bourgeois Justin R. , Kopec Ashley M. , Zuloaga Damian G. , Scimemi Annalisa 
Published: May 2021

AbstractGlutamate transporters preserve the spatial specificity of synaptic transmission by limiting glutamate diffusion away from the synaptic cleft, and prevent excitotoxicity by keeping the extracellular concentration of glutamate at low nanomolar levels. Glutamate transporters are abundantly expressed in astrocytes, and previous estimates have been obtained about their surface expression in astrocytes of the rat hippocampus and cerebellum. Analogous estimates for the mouse hippocampus are currently not available. In this work, we derive the surface density of astrocytic glutamate transporters in mice of different ages via quantitative dot blot. We find that the surface density of glial glutamate transporters is similar in 7-8 week old mice and rats. In mice, the levels of glutamate transporters increase until about 6 months of age and then begin to decline slowly. Our data, obtained from a combination of experimental and modeling approaches, show that there are stark differences in the density of expression of glutamate transporters across different sub-cellular compartments, indicating that the extent to which astrocytes limit extrasynaptic glutamate diffusion depends not only on their level of synaptic coverage, but also on the identity of the astrocyte compartment in contact with the synapse. Together, these findings provide information on how heterogeneity in the spatial distribution of glutamate transporters in the plasma membrane of hippocampal astrocytes my alter glutamate receptor activation out of the synaptic cleft.Author summaryIn this work, we use experimental and modeling approaches to estimate the surface density of the glial glutamate transporters GLAST and GLT-1 in mouse hippocampal astrocytes. The results show that the surface density of glutamate transporters in hippocampal astrocytes is similar in 7-8 week old mice and rats. In mice, GLAST and GLT-1 reach their peak expression at ~ 6 months of age. Their expression, however, varies widely across different sub-cellular compartments. These findings indicate that the identity of the sub-cellular compartment of an astrocyte in contact with a glutamatergic synapses, in addition to the extent of its synaptic coverage, is a main factor to limit glutamate spillover and receptor activation at a distance from the release site.