bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gone in 40 years, the curious case of the Himalayan Quail: an attempt at rediscovery and implications for conservation
Authors: Pop Paul , Pandey Puneet , Singh Randeep 
Published: July 2020

AbstractHimalayan Quail (Ophrysia superciliosa) is a Galliforme species currently classified as Critically Endangered by the IUCN. Given the fact that the species has only been recorded over a period of 40 years in the 19thcentury, this classification needs more scrutiny. The aim of this study was to explore the possibility of detecting the species in their known historical distribution in the lower Himalayas, and understand if possible, the factors which led to their decline or extinction. The potential habitats in districts of Nainital and Dehradun of Uttrakhand (India), where the species which has been recorded between 1836 to 1876, have been scoured thoroughly insofar as logistics and other factors permitted using trail and point transects. We did not detect any sign of the species in any of the areas, thereby corroborating the results of past surveys/expeditions in search of this species. Domesticated/feral species (grazing pressure and hunting by dogs), natural predation by species such as Yellow-throated Marten (Martes flavigula), hunting by humans, population growth and resulting land-use change, biogeochemical events, and tourism may all have contributed in varying degrees to their decline or extinction. It was found that most, if not all, proposals of strategies to find the species have been thus far unemployed or futile. We suggest improving the chances of re-discovering this species using tools such as molecular/genetic analysis and Unmanned Aerial Vehicles. Management recommendations include stress on grazing laws, sterilization of dogs, awareness about unchecked human population growth and measures for limiting the effects of unsustainable tourism.
What executive function network is that? An image-based meta-analysis of network labels
Authors: Witt Suzanne T. , van Ettinger-Veenstra Helene , Salo Taylor , Riedel Michael C. , Laird Angela R. 
Published: July 2020

AbstractThe current state of label conventions used to describe brain networks related to executive functions is highly inconsistent, leading to confusion among researchers regarding network labels. Visually similar networks are referred to by different labels, yet these same labels are used to distinguish networks within studies. We performed a literature review of fMRI studies and identified nine frequently-used labels that are used to describe topographically or functionally similar neural networks: central executive network (CEN), cognitive control network (CCN), dorsal attention network (DAN), executive control network (ECN), executive network (EN), frontoparietal network (FPN), working memory network (WMN), task positive network (TPN), and ventral attention network (VAN). Our aim was to meta-analytically determine consistency of network topography within and across these labels. We hypothesized finding considerable overlap in the spatial topography among the neural networks associated with these labels. An image-based meta-analysis was performed on 158 group-level statistical maps (SPMs) received from authors of 69 papers listed on PubMed. Our results indicated that there was very little consistency in the SPMs labeled with a given network name. We identified four clusters of SPMs representing four spatially distinct executive function networks. We provide recommendations regarding label nomenclature and propose that authors looking to assign labels to executive function networks adopt this template set for labeling networks.
MAVE-NN: learning genotype-phenotype maps from multiplex assays of variant effect
Authors: Tareen Ammar , Kooshkbaghi Mahdi , Posfai Anna , Ireland William T. , McCandlish David M. , Kinney Justin B. 
Published: July 2020

AbstractMultiplex assays of variant effect (MAVEs) are a family of methods that includes deep mutational scanning (DMS) experiments on proteins and massively parallel reporter assays (MPRAs) on gene regulatory sequences. However, a general strategy for inferring quantitative models of genotype-phenotype (G-P) maps from MAVE data is lacking. Here we introduce MAVE-NN, a neural-network-based Python package that implements a broadly applicable information-theoretic framework for learning G-P maps—including biophysically interpretable models—from MAVE datasets. We demonstrate MAVE-NN in multiple biological contexts, and highlight the ability of our approach to deconvolve mutational effects from otherwise confounding experimental nonlinearities and noise.
Fast scanning high optical invariant two-photon microscopy for monitoring a large neural network activity with cellular resolution
Authors: Ota Keisuke , Oisi Yasuhiro , Suzuki Takayuki , Ikeda Muneki , Ito Yoshiki , Ito Tsubasa , Kobayashi Kenta , Kobayashi Midori , Odagawa Maya , Matsubara Chie , Kuroiwa Yoshinori , Horikoshi Masaru , Matsushita Junya , Hioki Hiroyuki , Ohkura Masamichi , Nakai Junichi , Oizumi Masafumi , Miyawaki Atsushi , Aonishi Toru , Ode Takahiro , Murayama Masanori 
Published: July 2020

AbstractFast and wide imaging with single-cell resolution, high signal-to-noise ratio and no optical aberration has the potential to open up new avenues of investigation in biology. However, this imaging is challenging because of the inevitable tradeoffs among those parameters. Here, we overcome the tradeoffs by combining a resonant scanning system, a large objective with low magnification and high numerical aperture, and highly sensitive large-aperture photodetectors. The result is a practically aberration-free, fast scanning high optical invariant two-photon microscopy (FASHIO-2PM) that enables calcium imaging from a large network composed of ∼16k neurons at 7.5 Hz in a 9 mm2contiguous image plane including more than 10 sensory-motor and higher-order regions of the cerebral cortex in awake mice. Through a network analysis based on single-cell activities, we discover that the brain exhibits small-world-ness rather than scale-freeness. FASHIO-2PM will enable revealing biological dynamics by simultaneous monitoring of macroscopic activity and its composing elements.
Dynamic tracking of variant frequencies depicts the evolution of mutation sites amongst SARS-CoV-2 genomes from India
Authors: Hudson B. Shenu , Kolte Vaishnavi , Khan Azra , Sharma Gaurav 
Published: July 2020

AbstractWith the exponential spread of the COVID-19 pandemic across the world within the twelve months, SARS-CoV-2 strains are continuously trying to adapt themselves in the host environment by random mutations. While doing so, some variants with evolutionary advantages such as better human to human transmissibility potential might get naturally selected. This short communication demonstrates how the mutation frequency patterns are evolving in 2,457 SAR-CoV-2 strains isolated from COVID-19 patients across diverse Indian states. We have identified 19 such variants showing contrasting mutational probabilities in the span of seven months. Out of these, 14 variants are showing increasing mutational probabilities suggesting their propagation with time due to their unexplored evolutionary advantages. Whereas mutational probabilities of five variants have significantly decreased in June onwards as compared to March/April, suggesting their termination with time. Further in-depth investigation of these identified variants will provide valuable knowledge about the evolution, infection strategies, transmission rates, and epidemiology of SARS-CoV-2.
The antibody response to the glycan α-Gal correlates with COVID-19 disease symptoms
Authors: Urra José Miguel , Ferreras-Colino Elisa , Contreras Marinela , Cabrera Carmen M. , Fernández de Mera Isabel G. , Villar Margarita , Cabezas-Cruz Alejandro , Gortázar Christian , de la Fuente José 
Published: July 2020

AbstractThe coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide. The characterization of the immunological mechanisms involved in disease symptomatology and protective response is important to advance in disease control and prevention. Humans evolved by losing the capacity to synthesize the glycan Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal), which resulted in the development of a protective response against pathogenic viruses and other microorganisms containing this modification on membrane proteins mediated by anti-α-Gal IgM/IgG antibodies produced in response to bacterial microbiota. In addition to anti-α-Gal antibody-mediated pathogen opsonization, this glycan induces various immune mechanisms that have shown protection in animal models against infectious diseases without inflammatory responses. In this study, we hypothesized that the immune response to α-Gal may contribute to the control of COVID-19. To address this hypothesis, we characterized the antibody response to α-Gal in patients at different stages of COVID-19 and in comparison with healthy control individuals. The results showed that while the inflammatory response and the anti-SARS-CoV-2 (Spike) IgG antibody titers increased, reduction in anti-α-Gal IgE, IgM and IgG antibody titers and alteration of anti-α-Gal antibody isotype composition correlated with COVID-19 severity. The results suggested that the inhibition of the α-Gal-induced immune response may translate into more aggressive viremia and severe disease inflammatory symptoms. These results support the proposal of developing interventions such as probiotics based on commensal bacteria with α-Gal epitopes to modify the microbiota and increase the α-Gal-induced protective immune response and reduce the severity of COVID-19.
Syncytia formation by SARS-CoV-2 infected cells
Authors: Buchrieser Julian , Dufloo Jeremy , Hubert Mathieu , Monel Blandine , Planas Delphine , Rajah Maaran Michael , Planchais Cyril , Porrot Françoise , Guivel-Benhassine Florence , Van der Werf Sylvie , Casartelli Nicoletta , Mouquet Hugo , Bruel Timothée , Schwartz Olivier 
Published: July 2020

AbstractSevere cases of COVID-19 are associated with extensive lung damage and the presence of infected multinucleated syncytial pneumocytes. The viral and cellular mechanisms regulating the formation of these syncytia are not well understood. Here, we show that SARS-CoV-2 infected cells express the viral Spike protein (S) at their surface and fuse with ACE2-positive neighbouring cells. Expression of S without any other viral proteins triggers syncytia formation. Type-I interferon (IFN)-induced transmembrane proteins (IFITMs), a family of restriction factors that block the entry of many viruses, inhibit S-mediated fusion, with IFITM1 being more active than IFITM2 and IFITM3. On the contrary, the TMPRSS2 serine protease, which is known to enhance infectivity of cell-free virions, processes both S and ACE2 and increases syncytia formation by accelerating the fusion process. TMPRSS2 thwarts the antiviral effect of IFITMs. Our results show that the pathological effects of SARS-CoV-2 are modulated by cellular proteins that either inhibit or facilitate syncytia formation.One Sentence SummarySyncytia produced by SARS-CoV-2 infected cells and regulation of their formation by IFITMs and TMPRSS2.
10 years of EPOC: A scoping review of Emotiv’s portable EEG device
Authors: Williams Nikolas S , McArthur Genevieve M , Badcock Nicholas A 
Published: July 2020

AbstractBACKGROUNDCommercially-made low-cost electroencephalography (EEG) devices have become increasingly available over the last decade. One of these devices, Emotiv EPOC, is currently used in a wide variety of settings, including brain-computer interface (BCI) and cognitive neuroscience research.PURPOSEThe aim of this study was to chart peer-reviewed reports of Emotiv EPOC projects to provide an informed summary on the use of this device for scientific purposes.METHODSWe followed a five-stage methodological framework for a scoping review that included a systematic search using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) guidelines. We searched the following electronic databases: PsychINFO, MEDLINE, Embase, Web of Science, and IEEE Xplore. We charted study data according to application (BCI, clinical, signal processing, experimental research, and validation) and location of use (as indexed by the first author’s address).RESULTSWe identified 382 relevant studies. The top five publishing countries were the United States (n = 35), India (n = 25), China (n = 20), Poland (n = 17), and Pakistan (n = 17). The top five publishing cities were Islamabad (n = 11), Singapore (n = 10), Cairo, Sydney, and Bandung (n = 7 each). Most of these studies used Emotiv EPOC for BCI purposes (n = 277), followed by experimental research (n = 51). Thirty-one studies were aimed at validating EPOC as an EEG device and a handful of studies used EPOC for improving EEG signal processing (n = 12) or for clinical purposes (n = 11).CONCLUSIONSIn its first 10 years, Emotiv EPOC has been used around the world in diverse applications, from control of robotic limbs and wheelchairs to user authentication in security systems to identification of emotional states. Given the widespread use and breadth of applications, it is clear that researchers are embracing this technology.
Characteristics of viable but nonculturableVibrio parahaemolyticusinduced under extended periods of cold-starvation with various NaCl concentrations
Authors: Yoon Jae-Hyun , Hyun Jeong-Eun , Moon Sung-Kwon , Lee Sun-Young 
Published: July 2020

AbstractThis study was undertaken to examine the induction of VBNC states ofVibrio parahaemolyticusunder prolonged cold-starvation with various NaCl concentrations and their responsive characteristics to maintain cell viability.V. parahaemolyticusentered the viable but nonculturable (VBNC) state in artificial sea water at 4°C within 80 day and persisted in the VBNC state for 150 days. During cold-starvation, bacterial cells were used to estimate their cell functions, including cytotoxicity, fatty acid composition, membrane potential, and morphology. Cytotoxic effect ofV. parahaemolyticuscells against animal cell lines was decreased to below 50% after 80 days. VBNCV. parahaemolyticuscells showed decreasing levels of palmitic, vaccenic, and hexadecenoic acid on membrane, concomitantly with the formation of empty gaps between the cytoplasmic and outer membrane, in comparison with those of the pure cultures. Starvation at 4°C for 30 days resulted in a high increase inN-phenyl-1-napthylamine intensity withinV. parahaemolyticuscells. Membrane potential and cellular composition were strongly affected by increasing NaCl contents of the microcosms after its evolution into the VBNC state. VBNCV. parahaemolyticuscells may undergo selected physiological changes such as the modulation of membrane potential and re-arrangement of cellular composition.
MITF reprograms the extracellular matrix and focal adhesion in melanoma
Authors: Dilshat Ramile , Fock Valerie , Kenny Colin , Gerritsen Ilse , Lasseur Romain Maurice Jacques , Travnickova Jana , Eichhoff Ossia , Cerny Philipp , Möller Katrin , Sigurbjörnsdóttir Sara , Kirty Kritika , Einarsdottir Berglind Ósk , Cheng Phil F. , Levesque Mitchell , Cornell Robert , Patton E. Elizabeth , Larue Lionel , de Tayrac Marie , Magnúsdóttir Erna , Ogmundsdottir Margrét H. , Steingrímsson Eiríkur 
Published: July 2020

AbstractThe microphthalmia associated transcription factor (MITF) is a critical regulator of melanocyte development and differentiation. It also plays an important role in melanoma where it has been described as a molecular rheostat that, depending on activity levels, allows reversible switching between different cellular states. Here we show that MITF directly represses the expression of genes associated with the extracellular matrix (ECM) and focal adhesion pathways in human melanoma cells as well as of regulators of epithelial to mesenchymal transition (EMT) such as CDH2, thus affecting cell morphology and cell-matrix interactions. Importantly, we show that these effects of MITF are reversible, as expected from the rheostat model. The number of focal adhesion points increased upon MITF knockdown, a feature observed in drug resistant melanomas. Cells lacking MITF are similar to the cells of minimal residual disease observed in both human and zebrafish melanomas. Our results suggest that MITF plays a critical role as a repressor of gene expression and is actively involved in shaping the microenvironment of melanoma cells in a cell-autonomous manner.
Identification of areas of very high biodiversity value to achieve the EU Biodiversity Strategy for 2030 key commitments
Authors: Miu Iulia V. , Rozylowicz Laurentiu , Popescu Viorel D. , Anastasiu Paulina 
Published: July 2020

AbstractBackgroundThe European Union strives to increase protected areas of the EU terrestrial surface to 30% by year 2030, of which one third should be strictly protected. Designation of the Natura 2000 network, the backbone of nature protection in the EU, was mostly an expert-opinion process with little systematic conservation planning. The designation of the Natura 2000 network in Romania followed the same non-systematic approach, resulting in a suboptimal representation of invertebrates and plants. To help identify areas with very high biodiversity without repeating past planning missteps, we present a reproducible example of spatial prioritization using Romania’s current terrestrial Natura 2000 network and coarse-scale terrestrial species occurrence.MethodsWe used 371 terrestrial Natura 2000 Sites of Community Importance (Natura 2000 SCI), designated to protect 164 terrestrial species listed under Annex II of Habitats Directive in Romania in our spatial prioritization analyses (marine Natura 2000 sites and species were excluded). Species occurrences in terrestrial Natura 2000 sites were aggregated at a Universal Traverse Mercator spatial resolution of 1 km2. To identify priority terrestrial Natura 2000 sites for species conservation, and to explore if the Romanian Natura 2000 network sufficiently represents species included in Annex II of Habitats Directive, we used Zonation v4, a decision support software tool for spatial conservation planning. We carried out the analyses nationwide (all Natura 2000 sites) as well as separately for each biogeographic region (i.e., Alpine, Continental, Pannonian, Steppic and Black Sea).ResultsThe results of spatial prioritization of terrestrial Natura 2000 vary greatly by planning scenario. The performance of national-level planning of top priorities is minimal. On average, when 33% of the landscape of Natura 2000 sites is protected, only 20% of the distribution of species listed in Annex II of Habitats Directive are protected. As a consequence, the representation of species by priority terrestrial Natura 2000 sites is lessened when compared to the initial set of species. When planning by taxonomic group, the top-priority areas include only 10% of invertebrate distribution in Natura 2000. When selecting top-priority areas by biogeographical region, there are significantly fewer gap species than in the national level and by taxa scenarios; thusly, the scenario outperforms the national-level prioritization. The designation of strictly protected areas as required by the EU Biodiversity Strategy for 2030 should be followed by setting clear objectives, including a good representation of species and habitats at the biogeographical region level.
Chimpanzee (Pan troglodytes verus) density and environmental gradients at their biogeographical range edge
Authors: Wessling Erin G. , Dieguez Paula , Llana Manuel , Pacheco Liliana , Pruetz Jill D. , Kühl Hjalmar S. 
Published: July 2020

ABSTRACTIdentifying ecological gradients at the range edge of a species is an essential step in revealing the underlying mechanisms and constraints that limit the species’ geographic range. We aimed to describe the patterns of variation in chimpanzee (Pan troglodytes verus) density and habitat characteristics perpendicular to the northern edge of their range and to investigate potential environmental mechanisms underlying chimpanzee distribution in a savanna-mosaic habitat. We estimated chimpanzee densities at six sites forming a 126 km latitudinal gradient at the biogeographical range edge of the western chimpanzee in the savanna-mosaic habitats of southeastern Senegal. To accompany these data, we used systematically placed vegetation plots to characterize the habitats at each site for habitat heterogeneity, tree density and size, floral assemblages, among other variables. We found that both biotic and abiotic factors are potential determinants of the chimpanzee range limit in this ecoregion. Specifically, chimpanzee-occupied landscapes at the limit had smaller available floral assemblages, less habitat heterogeneity, and contained fewer closed canopy habitats in which chimpanzees could seek refuge from high temperatures than landscapes farther from the range limit. This pattern was accompanied by a decline in chimpanzee density with increasing proximity to the range limit. Our results provide several indications of the potential limits of food species diversity, thermal refuge, and water availability to the chimpanzee niche and the implications of these limits for chimpanzee biogeography, especially in the face of climate change predictions, as well as to species distributional modeling more generally.