bluuebunny/crossref_metadata_2025_split huggingface dataset:
In situnovel environment assay reveals acoustic exploration as a repeatable behavioral response in migratory bats
Authors: Schabacker Theresa , Lindecke Oliver , Rizzi Sofia , Marggraf Lara , Pētersons Gunārs , Voigt Christian C. , Snijders Lysanne 
Published: April 2021

AbstractIntegrating information on species-specific sensory perception together with spatial activity provides a high-resolution understanding of how animals explore environments, yet frequently used exploration assays commonly ignore sensory acquisition as a measure for exploration. Echolocation is an active sensing system used by hundreds of mammal species, primarily bats. As echolocation call activity can be reliably quantified, bats present an excellent animal model to investigate intra-specific variation in environmental cue sampling. Here, we developed anin situroost-like novel environment assay for tree-cave roosting bats. We repeatedly tested 52 individuals of the migratory bat species,Pipistrellus nathusii, across 24 hours, to examine the role of echolocation when crawling through a maze-type arena and test for consistent intra-specific variation in sensory-based exploration. We reveal a strong correlation between echolocation call activity and spatial activity. Moreover, we show that during the exploration of the maze, individuals consistently differed in spatial activity as well as echolocation call activity given their spatial activity, a behavioral response we term ‘acoustic exploration’. Acoustic exploration was correlated with other exploratory behaviors, but not with emergence latency. We here present a relevant new measure for exploration behavior and provide evidence for consistent (short-term) intra-specific variation in the level at which wild bats collect information from a novel environment.
Miami-Dade: A Case Study of Domestic Violence Arrests During the COVID-19 Pandemic
Authors: Kurland Justin , Piquero Alex R. , Piquero Nicole Leeper 
Published: April 2021

AbstractThe global health crisis that started early in 2020 has triggered a surge of interest in the effect (if any) of COVID-19 on patterns of domestic violence.1 The first systematic review and meta-analysis examining domestic violence during the pandemic revealed quite a lot of diversity in the approaches used to measure potential effects. Drawing on the time series forecasting literature, this brief report contributes to the growing body of evidence around the issue of domestic violence during the pandemic. Arrest data from Miami-Dade County (US) are leveraged along with a robust approach towards model identification, which is used to generate a suitably accurate forecast against which the observed pandemic period domestic violence data can be compared. The pattern uncovered for Miami-Dade County was similar what was found in other U.S. cities that during the pandemic experienced spikes (+95 CI) in the level of domestic violence arrests that were greater than expected. Interestingly these spikes appeared shortly after dips (−95 CI) in observed arrests fell below the expected level.
The dark side of SARS-CoV-2 rapid antigen testing: screening asymptomatic patients
Authors: Caruana Giorgia , Lebrun Laure-Line , Aebischer Oriane , Opota Onya , Urbano Luis , de Rham Mikael , Marchetti Oscar , Greub Gilbert 
Published: April 2021

AbstractMost of the reports describing SARS-CoV-2 rapid antigen tests (RATs) performances derive from COVID-19 symptomatic subjects in outpatient settings during periods of highest incidence of infections and high rates of hospital admissions. Here we investigated the role of RATs in an Emergency Department, as a screening tool before admission for COVID-19 asymptomatic patients. Each patient was screened with two simultaneous nasopharyngeal swabs: one immediately analyzed at the bedside using RAT and the other sent to the laboratory for RT-PCR analysis. A total of 116 patients were screened at hospital admission in a 250-bed community hospital in Morges (EHC), Switzerland. With a disease prevalence of 6% based on RT-PCR results, RAT detected only two out of seven RT-PCR positive patients (sensitivity 28.6%) and delivered two false positive results (specificity 98.2%), thus resulting not fiable enough to be used as a screening method in this clinical scenario.
Sex differences in TB treatment outcomes: Retrospective cohort study and meta-analysis
Authors: Chidambaram Vignesh , Tun Nyan Lynn , Majella Marie Gilbert , Castillo Jennie Ruelas , Ayeh Samuel K. , Kumar Amudha , Neupane Pranita , Sivakumar Ranjith Kumar , Win Ei Phyo , Abbey Enoch J. , Wang Siqing , Zimmerman Alyssa , Blanck Jaime , Gupte Akshay , Wang Jann-Yuan , Karakousis Petros C. 
Published: April 2021

AbstractRationaleAlthough the incidence of tuberculosis (TB) is higher in males compared to females, the relationship of sex with TB treatment outcomes has not been adequately studied.Objectives and MethodsWe performed a retrospective cohort study and a systematic review and meta-analysis of observational studies during the last 10 years to assess the sex differences in clinical and microbiological outcomes in tuberculosis.Measurements and Main ResultsIn our cohort of 2,894 patients with drug-susceptible pulmonary TB (1,975 males and 919 females), males had higher adjusted hazards of mortality due to all causes (HR 1·43,95%CI 1.03-1.98) and infections (HR 1.70, 95%CI 1.09-2.64) at 9 months and higher adjusted odds ratio for sputum culture (OR 1.56,95%CI 1.05-2.33) and similar odds ratio for smear positivity (OR 1.27, 0.71-2.27) at 2 months compared to females. Among 7896 articles retrieved, 398 articles were included in our systematic review with a total of 3,957,216 patients. The odds of all-cause mortality was higher in males compared to females in the pooled unadjusted (OR 1.26, 95%CI 1.19-1.34) and adjusted (OR 1.31, 95%CI 1.18-1.45) analyses. Relative to females, males had higher pooled odds of sputum culture (OR 1.44,95% CI 1.14-1.81) and sputum smear (OR 1.58,95%CI 1.41-1.77) positivity at the end of the intensive phase, and upon completion of treatment.ConclusionsDuring TB treatment, males have higher all-cause-, infection- and TB-related mortality, as well as higher rates of sputum smear and culture positivity, both after the intensive phase and at the completion of TB treatment, after adjusting for confounding factors.
Stingless bee floral visitation in the global tropics and subtropics
Authors: Garcia Bulle Bueno Francisco , Kendall Liam , Araujo Alves Denise , Lequerica Tamara Manuel , Heard Tim , Latty Tanya , Gloag Rosalyn 
Published: April 2021

AbstractBees play a key role in maintaining healthy terrestrial ecosystems by pollinating plants. Stingless bees (Apidae: Meliponini) are a diverse clade of social bees (>500 species) with a pantropical distribution spanning South and Central America, Africa, India, Australia and Asia. They are garnering increasing attention as commercially-beneficial pollinators of some crops, yet their contribution to the pollination of native plants in the tropics and subtropics remains poorly understood. Here we conduct a global review of the plants visited by stingless bees. We compile a database of reported associations (flower visits) between stingless bees and plants, from studies that have made either direct observations of foraging bees or analysed the pollen stored in nests. Worldwide, we find stingless bees have been reported to visit the flowers of plants from at least 220 different families and 1465 genera, with frequently reported interactions for many of the tropic’s most species-diverse plant families including Fabaceae, Asteraceae, Rubiaceae, Malvaceae, Lamiaceae, Arecaceae, Euphorbiaceae, Poaceae, Apocinaceae, Bignoniaceae, Melastomataceae and Myrtaceae. The list of commonly-visited plant families was similar for the stingless bee fauna of each of three major biogeographic regions (Neotropical, Afrotropical and Indo-Malayan-Australasian), though we detected differences in the proportional use of plant families by the stingless bees of the Indo-Malayan-Australasian and Neotropical regions, likely reflecting differences in the available flora of those regions. Stingless bees in all regions visit a range of exotic species in their preferred plant families (crops, ornamental plants and weeds), in addition to native plants. Although most reports of floral visitation on wild plants do not confirm effective pollen transfer, it is likely that stingless bees make at least some contribution to pollination for the majority of plants they visit. In all, our database supports the view that stingless bees play an important role in the ecosystems of the global tropics and subtropics as pollinators of an exceptionally large and diverse number of plants. This database also highlights important gaps in our knowledge of stingless bee resource use that may help focus future research efforts.
Stress granules are shock absorbers that prevent excessive innate immune responses to dsRNA
Authors: Paget Max , Cadena Cristhian , Ahmad Sadeem , Wang Hai-Tao , Jordan Tristan X. , Kim Ehyun , Koo Beechui , Lyons Shawn M. , Ivanov Pavel , tenOever Benjamin , Mu Xin , Hur Sun 
Published: April 2021

SummaryProper defense against microbial infection depends on the controlled activation of the immune system. This is particularly important for the RIG-I-like receptors (RLRs), which recognize viral dsRNA and initiate antiviral innate immune responses with the potential of triggering systemic inflammation and immunopathology. Here we show that stress granules (SGs), molecular condensates that form in response to various stresses including viral dsRNA, play key roles in controlled activation of RLR signaling. Without the SG nucleators G3BP1/2 and UBAP2L, dsRNA triggers excessive inflammation and immune-mediated apoptosis. In addition to exogenous dsRNA, we find that host-derived dsRNA generated in response to ADAR1 deficiency is also controlled by SG biology. Intriguingly, SGs can function beyond immune control by suppressing viral replication independent of the RLR pathway. These observations thus highlight the multi-functional nature of SGs as cellular “shock absorbers” that converge on protecting cell homeostasis–by dampening both toxic immune response and viral replication.
Surface-Shaving Proteomics ofMycobacterium marinumIdentifies Biofilm Subtype-Specific Changes Affecting Virulence, Tolerance and Persistence
Authors: Savijoki Kirsi , Myllymäki Henna , Luukinen Hanna , Paulamäki Lauri , Vanha-aho Leena-Maija , Svorjova Aleksandra , Miettinen Ilkka , Fallarero Adyary , Ihalainen Teemu O. , Yli-Kauhaluoma Jari , Nyman Tuula A. , Parikka Mataleena 
Published: April 2021

ABSTRACTThe complex cell wall and biofilm matrix (ECM) act as key barriers to antibiotics in mycobacteria. Here, the ECM-proteins ofMycobacterium marinumATCC927, a non-tuberculous mycobacterial model, was monitored over three months by label-free proteomics and compared with cell-surface proteins on planktonic cells to uncover pathways leading to virulence, tolerance, and persistence. We show that ATCC927 forms pellicle-type (PBFs) and submerged-type (SBFs) biofilms after two weeks and two days of growth, respectively, and that the increased CelA1 synthesis in this strain prevents biofilm formation and leads to reduced rifampicin tolerance. The proteomic data suggests that specific changes in mycolic acid synthesis (cord factor), Esx1-secretion, and cell-wall adhesins explain the appearance of PBFs as ribbon-like cords and SBFs as lichen-like structures. A subpopulation of cells resisting the 64 × MIC rifampicin (persisters) were detected in both biofilm subtypes, and already in one-week-old SBFs. The key forces boosting their development could include subtype-dependent changes in asymmetric cell division, cell wall biogenesis, tricarboxylic acid/glyoxylate cycle activities, and energy/redox/iron metabolisms. The effect of varying ambient oxygen tensions on each cell type and non-classical protein secretion are likely factors explaining majority of the subtype-specific changes. The proteomic findings also imply that Esx1-type protein secretion is more efficient in PL and PBF cells, while SBF may prefer both the Esx5- and non-classical pathways to control virulence and prolonged viability/persistence. In conclusion, this study reports a first proteomic insight into aging mycobacterial biofilm-ECMs and indicates biofilm subtype-dependent mechanisms conferring increased adaptive potential and virulence on non-tuberculous mycobacteria.IMPORTANCEMycobacteria are naturally resilient and mycobacterial infections are notoriously difficult to treat with antibiotics, with biofilm formation being the main factor complicating the successful treatment of TB. The present study shows that non-tuberculousMycobacterium marinumATCC927 forms submerged- and pellicle-type biofilms with lichen- and ribbon-like structures, respectively, as well as persister cells under the same conditions. We show that both biofilm subtypes differ in terms of virulence-, tolerance- and persistence-conferring activities, highlighting the fact that both subtypes should be targeted to maximize the power of antimycobacterial treatment therapies.
In vitroefficacy of gentamicin against multidrug-resistantNeisseria gonorrhoeae: synergy of three gentamicin antimicrobial combinations
Authors: Li Xuechun , Le Wenjing , Lou Xiangdi , Wang Biwei , Genco Caroline A. , Rice Peter A. , Su Xiaohong 
Published: April 2021

ABSTRACTObjectivesTo determinein vitroactivities of gentamicin alone and in combination with ceftriaxone, ertapenem and azithromycin against multidrug-resistant (MDR)N. gonorrhoeaeisolates.Methods407 isolates from Nanjing, China, obtained in 2016 and 2017, had minimum inhibitory concentrations (MICs) determined for gentamicin using the agar dilution method. Antimicrobial combinations were also tested in 97 MDR strains using the antimicrobial gradient epsilometer test (Etest); results ranging from synergy to antagonism were interpreted using the fractional inhibitory concentration (FICI).ResultsAll 407 gonococcal isolates were susceptible to gentamicin. MICs ranged from 2 mg/L to 16 mg/L. Synergy was demonstrated in 16.5%(16/97), 27.8%(27/97) and 8.2%(8/97) MDR strains when gentamicin was combined with ceftriaxone [geometric mean (GM) FICI; 0.747], ertapenem (GM FICI; 0.662) and azithromycin (GM FICI; 1.021), respectively. No antimicrobial antagonism was observed with any combination. The three antimicrobial combinations were indifferent overall. The overall GM MICs of gentamicin were reduced by 2.63-, 3.80- and 1.98-fold when tested in combination with ceftriaxone, ertapenem and azithromycin, respectively. The GM MICs of the three antimicrobials by themselves were reduced by 3-, 2.57- and 1.98-fold respectively, when each was tested in combination with gentamicin. No antimicrobial antagonism was observed with any combination.ConclusionsGentamicin alone was effectivein vitroagainst MDRN. gonorrhoeaeand in combination with ceftriaxone, ertapenem or azithromycin. Combination testing of resistant strains, overall, showed lower effective MICs against gentamicin itself and each of the three antimicrobials when used in combination with gentamicin.
A Stable Nano-Vaccine for the Targeted Delivery of Tumor-Associated Glycopeptide Antigens
Authors: Trabbic Kevin R. , Kleski Kristopher A. , Barchi Joseph J 
Published: April 2021

AbstractWe have developed a novel antigen delivery system based on polysaccharide-coated gold nanoparticles (AuNPs) targeted to antigen presenting cells (APCs) expressing Dectin-1. AuNPs were synthesized de-novo using yeast-derived β-1,3-glucans (B13Gs) as the reductant and passivating agent in a microwave-catalyzed procedure yielding highly uniform and serum-stable particles. These were further functionalized with both peptides and glycopeptides from the tandem repeat sequence of mucin 4 (MUC4), a glycoprotein overexpressed in pancreatic tumors. The glycosylated sequence contained the Thomsen-Friedenreich disaccharide, a pan-carcinoma, Tumor-Associated Carbohydrate Antigen (TACA), which has been a traditional target for antitumor vaccine design. These motifs were prepared with a cathepsin B protease cleavage site (Gly-Phe-Leu-Gly), loaded on the B13Gs-coated particles and these constructs were examined for Dectin-1 binding, APC processing and presentation in a model in vitro system and for immune responses in mice. We showed that these particles elicit strong in vivo immune responses through the production of both high-titer antibodies and priming of antigen-recognizing T-cells. Further examination showed that a favorable antitumor balance of expressed cytokines was generated, with limited expression of immunosuppressive Il-10. This system is modular in that any range of antigens can be conjugated to our particles and efficiently delivered to APCs expressing Dectin-1.
Quantification of volumetric morphometry and optical property in the cortex of human cerebellum at micrometer resolution
Authors: Liu Chao J. , Ammon William , Siless Viviana , Fogarty Morgan , Wang Ruopeng , Atzeni Alessia , Aganj Iman , Iglesias Juan Eugenio , Zöllei Lilla , Fischl Bruce , Schmahmann Jeremy D. , Wang Hui 
Published: April 2021

AbstractThe surface of the human cerebellar cortex is much more tightly folded than the cerebral cortex. Volumetric analysis of cerebellar morphometry in magnetic resonance imaging studies suffers from insufficient resolution, and therefore has had limited impact on disease assessment. Automatic serial polarization-sensitive optical coherence tomography (as-PSOCT) is an emerging technique that offers the advantages of microscopic resolution and volumetric reconstruction of large-scale samples. In this study, we reconstructed multiple cubic centimeters ofex vivohuman cerebellum tissue using as-PSOCT. The morphometric and optical properties of the cerebellar cortex across five subjects were quantified. While the molecular and granular layers exhibited similar mean thickness in the five subjects, the thickness varied greatly between the crown of the folium and the depth of the fissure in the granular layer within subjects. Layer-specific optical property remained homogenous within individual subjects but showed higher cross-subject variability than layer thickness. High-resolution volumetric morphometry and optical property maps of human cerebellar cortex revealed by as-PSOCT have great potential to advance our understanding of cerebellar function and diseases.HighlightsWe reconstructed cubic centimeters of human cerebellar samples at micrometer resolution in five subjects.Thickness of the granular layer varies greatly between the crowns and depths of cerebellar fissures.Cross-subject variability is higher in optical property than cortical morphology.Our results suggest homogenous cell and myelin density in the cortical layers of human cerebellum despite the highly convoluted folding patterns.
Olfactory receptor-dependent receptor repression inDrosophila
Authors: Mika Kaan , Cruchet Steeve , Chai Phing Chian , Prieto-Godino Lucia L. , Auer Thomas O. , Pradervand Sylvain , Benton Richard 
Published: April 2021

AbstractIn olfactory systems across phyla, most sensory neurons transcribe a single olfactory receptor gene selected from a large genomic repertoire. We describe novel receptor gene-dependent mechanisms that ensure singular expression of receptors encoded by a tandem gene array inDrosophila. Transcription from upstream genes in the cluster runs through the coding region of downstream loci to inhibit their expression incis, via transcriptional interference. Moreover, one receptor blocks expression of other receptor proteins intransthrough a post-transcriptional mechanism. These repression mechanisms operate in endogenous neurons to ensure their unique expression. Our data provide evidence for inter-olfactory receptor regulation in invertebrates, and highlight unprecedented, but potentially widespread, mechanisms for ensuring exclusive expression of chemosensory receptors, and other protein families, encoded by tandemly-arranged genes.
CYCLeR– a novel tool for the full isoform assembly and quantification of circRNAs
Authors: Stefanov Stefan R. , Meyer Irmtraud M. 
Published: April 2021

AbstractSplicing is one key mechanism determining the state of any eukaryotic cell. Apart from linear splice variants, circular splice variants (circRNAs) can arise via non-canonical splicing involving aback-splice junction(BSJ). Most existing methods only identifycircRNAs via the corresponding BSJ, but do not aim to estimate their full sequence identity or to identify different, alternatively spliced circular isoforms arising from the same BSJ. We here present CYCLeR, the first computational method for identifying the full sequence identify of new and alternatively splicedcircRNAs and their abundances while simultaneously co-estimating the abundances of known linear splicing isoforms. We show that CYCLeR significantly out-performs existing methods in terms of sensitivity, precision and quantification of transcripts. When analysingD. melanogasterdata, CYCLeR uncovers biological patterns of circRNA expression that other methods fail to observe.
Nasal BCG Exposure Accelerates Dural Lymphatics Development via Macrophages’ Role in Newborn Mice
Authors: Yang Junhua , Yuan Lifang , Song Linyang , Qi Fangfang , Zuo Zejie , Xu Jie , Yao Zhibin 
Published: April 2021

AbstractThe dural lymphatics develop mainly during the first postnatal month. Lymphatics may be shaped by immune activation when bacterial infection happens. BCG, a strong immune activator, is widely injected to newborns. Moreover, human beings are nasally exposed in daily life to bacterial stimuli. These background prompted us to investigate whether neonatal BCG injection combined with nasally exposure exerts an influence on dural lymphatics develop. Here, mice received a single dose intracutaneous (i.c.) BCG injection immediately after birth followed by repeated nasal BCG challenge once a day (i.c./nasal group). These mice had an accelerated dural lymphatics growth and increased levels of several cytokines and VEGFR-3. Furthermore, macrophages were identified as a key mediator of these alterations. Mice that received mere one dose i.c. BCG injection showed no significant alterations in these indexes. Additionally, mere repeated nasal BCG challenge induced similar effects to i.c./nasal challenge but with a slighter extent. Taken together, these findings show that repeated nasal BCG vaccination accelerates dural lymphatics development in neonatal mice, especially in the presence of neonatal i.c. BCG injection.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes
Authors: Durant Éloi , Sabot François , Conte Matthieu , Rouard Mathieu 
Published: April 2021

AbstractMotivationPangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations comes with their own challenges, and linearity remains a suitable option for user-friendliness.ResultsWe introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective.AvailabilityPanache is available at github.com/SouthGreenPlatform/panache under the MIT License.Contacteloi.durant@ird.fr,m.rouard@cgiar.org