bluuebunny/crossref_metadata_2025_split huggingface dataset:
Key informant perceptions on wildlife hunting in India during the COVID-19 lockdown
Authors: Mendiratta Uttara , Khanyari Munib , Velho Nandini , Suryawanshi Kulbhushansingh Ramesh , Kulkarni Nirmal 
Published: May 2021

AbstractLockdowns intended to control the COVID-19 pandemic resulted in major socioeconomic upheavals across the world. While there were numerous reports of these lockdowns benefiting wildlife by reducing human movement and habitat disturbance, increased hunting during these lockdowns emerged as a conservation concern, particular in tropical Asia and Africa. We used online interviews with key informants including wildlife researchers, enforcement staff and NGO employees (N=99), and media reports (N=98), to examine the impacts of India’s COVID-19 lockdown (March-May 2020) on wildlife hunting across the country. We asked whether and how hunting patterns changed during the lockdown, and explored socioeconomic and institutional factors underlying these changes. Over half the interviewees spread over 43 administrative districts perceived hunting (mammals, in particular) to have increased during the lockdown relative to a pre-lockdown reference period. Interviewees identified household consumption (53% of respondents) and sport and recreation (34%) as main motivations for hunting during the lockdown, and logistical challenges for enforcement (36%), disruption of food supply (32%), and need for recreational opportunities (32%) as key factors associated with hunting during this period. These insights were corroborated by statements by experts extracted from media articles. Collectively, our findings suggest that the COVID-19 lockdown potentially increased hunting across much of India, and emphasize the role of livelihood and food security in mitigating threats to wildlife during such periods of acute socioeconomic perturbation.
Mind the gap: performance metric evaluation in brain-age prediction
Authors: de Lange Ann-Marie G. , Anatürk Melis , Rokicki Jaroslav , Han Laura K.M. , Franke Katja , Alnæs Dag , Ebmeier Klaus P. , Draganski Bogdan , Kaufmann Tobias , Westlye Lars T. , Hahn Tim , Cole James H. 
Published: May 2021

AbstractEstimating age based on neuroimaging-derived data has become a popular approach to developing markers for brain integrity and health. While a variety of machine-learning algorithms can provide accurate predictions of age based on brain characteristics, there is significant variation in model accuracy reported across studies. We predicted age based on neuroimaging data in two population-based datasets, and assessed the effects of age range, sample size, and age-bias correction on the model performance metrics r, R2, Root Mean Squared Error (RMSE), and Mean Absolute Error (MAE). The results showed that these metrics vary considerably depending on cohort age range; r and R2 values are lower when measured in samples with a narrower age range. RMSE and MAE are also lower in samples with a narrower age range due to smaller errors/brain age delta values when predictions are closer to the mean age of the group. Across subsets with different age ranges, performance metrics improve with increasing sample size. Performance metrics further vary depending on prediction variance as well as mean age difference between training and test sets, and age-bias corrected metrics indicate high accuracy - also for models showing poor initial performance. In conclusion, performance metrics used for evaluating age prediction models depend on cohort and study-specific data characteristics, and cannot be directly compared across different studies. Since age-bias corrected metrics in general indicate high accuracy, even for poorly performing models, inspection of uncorrected model results provides important information about underlying model attributes such as prediction variance.
Social Housing Status Impacts Rhesus Monkeys’ Affective Responding in Classic Threat Processing Tasks
Authors: Charbonneau Joey A. , Amaral David G. , Bliss-Moreau Eliza 
Published: May 2021

AbstractThe established literature clearly demonstrates that whether or not monkeys are socially reared has long term consequences for their affective behavior. Yet, in the context of behavioral neuroscience and pharmacological studies, social context of adult animals is often ignored. When social context has been studied in adult monkeys, such studies have typically focused on welfare-related issues, as social isolation often leads to the development of abnormal behavior, rather than the impact on outcomes in behavioral neuroscience studies. Variation in social housing conditions for adult animals could have an impact on affective responding and may have significant implications for the interpretation of data from biopsychiatry and behavioral neuroscience studies. We evaluated the affective reactivity of rhesus monkeys (Macaca mulatta) maintained in one of four housing conditions (individually-housed, grate-paired, intermittently-paired, and continuously-paired) using two classic threat processing tasks—a test of responsivity to objects and the Human Intruder Test. Individually-housed monkeys exhibited consistently blunted sensitivity to ostensibly threatening stimuli as compared to socially-housed monkeys. Within the three socially-housed conditions, intermittently- and continuously-paired monkeys behaved similarly to each other and grate-paired monkeys exhibited relatively enhanced sensitivity to threatening stimuli. These findings suggest that the adult housing conditions of monkeys can robustly modulate affective responding in a way that may be consistent with behavioral phenotypes observed in human psychiatric conditions. Results are considered in the context of the broad behavioral and psychiatric neuroscience literatures, which have historically used individually-housed animals, pointing to the potential need to reconsider inferences drawn from those studies.
Flexibility of Functional Neuronal Assemblies Supports Human Memory
Authors: Umbach Gray , Tan Ryan , Jacobs Joshua , Pfeiffer Brad E. , Lega Bradley 
Published: May 2021

Summary ParagraphEpisodic memories, or consciously accessible memories of unique events, represent a key aspect of human cognition. Evidence from rodent models suggests that the neural representation of these complex memories requires cooperative firing of groups of neurons on short time scales1, organized by gamma oscillations2, 3. These co-firing groups, termed “neuronal assemblies,”4 represent a fundamental neurophysiological unit supporting memory. Using microelectrode data from neurosurgical patients5, we identify neuronal assemblies in the human MTL and show that they exhibit consistent organization in their firing pattern based on gamma phase information. We connect these properties to memory performance across recording sessions. Finally, we describe how human neuronal assemblies flexibly adjust6-9 over longer time scales. Our findings provide key evidence linking assemblies to human episodic memory for the first time.
Rho Kinase regulates neutrophil NET formation that is involved in UVB-induced skin inflammation
Authors: Li Minghui , Lyu Xing , Liao James , Werth Victoria P. , Liu Ming-Lin 
Published: May 2021

AbstractObjectiveUltraviolet B (UVB) is an important trigger of skin inflammation and lupus with leukocyte recruitment to inflamed skin. We recently reported the involvement of neutrophil NETosis in UVB-induced skin inflammation, and that NETotic nuclear envelope rupture is driven by PKCα-mediated nuclear lamin B disassembly. To address the role of Actin cytoskeleton in NETosis, we investigated the effects of Rho kinase (ROCK) and its downstream actomyosin cytoskeletal networks on PKCα nuclear translocation and NET formation, as well as their involvement in UVB-induced skin inflammation.MethodsWe studied the dynamic changes of ROCK and actomyosin cytoskeletal networks during NETosis induction and their involvement in PKCα nuclear translocation. Using mice with hematopoietic-specific ROCK1 deficiency, we investigated the effects of ROCK1 deficiency on NETosis, and its involvement in UVB-induced skin inflammation.ResultsOur time course studies demonstrated the dynamic changes of actin polymerization and ROCK activation, support the role of actin cytoskeleton in nuclear translocation of cytosolic PKCα in early stage of NETosis induction. Inhibition of actin polymerization or key molecules of the ROCK/MLCK/myosin pathway decreased PKCα nuclear translocation and NET formation. Genetic deficiency of ROCK1, inhibited NETosisex vivoandin vivo, decreased extracellular display of NET-associated IL-17A, TNFα, IFNγ, and IFNα in inflamed skin, which were correlated with the ameliorated skin inflammation in UVB-irradiated mice with hematopoietic-specific ROCK1 deficiency.ConclusionsROCK regulated NETosis through modulation of PKCα nuclear translocation via actomyosin cytoskeletal networks in neutrophils. ROCK1 deficiency ameliorated UVB- induced skin inflammation by attenuation of NETosis and NET-associated cytokines.
Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions
Authors: Sugimoto Naoki , Fukasawa Keita , Asahara Akio , Kasada Minoru , Matsuba Misako , Miyashita Tadashi 
Published: May 2021

AbstractLand abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with climatic niches and habitat preferences. Hierarchical models that unified species occurrence and habitat preferences revealed that negative responses to land abandonment were associated with species that have cold climatic niches and utilize open habitats, suggesting that species negatively impacted by land abandonment will decline more due to future climate warming. Maps representing species gains and losses due to land abandonment, which were created from the model estimates, showed similar geographic patterns, but some areas exhibited high species losses relative to gains. Our hierarchical modelling approach was useful for scaling up local-scale effects of land abandonment to a macro-scale assessment, which is crucial to developing spatial conservation strategies in the era of depopulation.
The bitter end: T2R bitter receptor agonists elevate nuclear calcium and induce apoptosis in non-ciliated airway epithelial cells
Authors: McMahon Derek B. , Kuek Li Eon , Johnson Madeline E. , Johnson Paige O. , Horn Rachel L.J. , Carey Ryan M. , Adappa Nithin D. , Palmer James N. , Lee Robert J. 
Published: May 2021

AbstractBitter taste receptors (T2Rs) localize to airway motile cilia and initiate innate immune responses in retaliation to bacterial quorum sensing molecules (acyl-homoserine lactones and quinolones). Activation of T2Rs leads to calcium-driven NO production that increases cilia beating and directly kills bacteria. Several airway diseases, including chronic rhinosinusitis, COPD, and cystic fibrosis, are characterized by epithelial remodeling, including loss of motile cilia and/or squamous metaplasia. To understand the function of T2Rs within the altered landscape of airway disease, we studied T2Rs in non-ciliated airway cell lines and primary cells de-differentiated to a squamous phenotype. In differentiated cells, T2Rs localize to cilia, however in de-differentiated, non-ciliated cells they localize to the nucleus. Cilia and nuclear import utilize many shared proteins, thus in the absence of motile cilia some T2Rs may target to the nucleus. T2R agonists selectively elevated both nuclear and mitochondrial calcium through a G-protein-coupled receptor, phospholipase C, and InsP3receptor-dependent mechanism. Additionally, T2R agonists decreased nuclear cAMP, increased nitric oxide, and increased cGMP, consistent with T2R signaling. Furthermore, exposure to T2R agonists led to nuclear calcium-induced mitochondrial depolarization and caspase activation. T2R agonists induced apoptosis in primary bronchial and nasal cells differentiated at air-liquid interface but then induced to a squamous phenotype by apical submersion. Air-exposed well-differentiated cells did not die. This T2R-induced apoptosis may be a last-resort defense against infection, possibly when bacteria have breached the epithelial barrier and reach non-ciliated cells below. However, it may also increase susceptibility of de-differentiated or remodeled epithelia to damage by bacterial metabolites. Moreover, the T2R-activated apoptosis pathway occurs in airway cancer cells. T2Rs may thus contribute to microbiome-tumor cell crosstalk in airway cancers. T2R agonists may also be useful topical therapeutics (e.g., delivered by nasal rinse or nebulizer) for activating airway cancer cell apoptosis without killing surrounding differentiated tissue.
DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering
Authors: Zeng Xiangrui , Kahng Anson , Xue Liang , Mahamid Julia , Chang Yi-Wei , Xu Min 
Published: May 2021

AbstractCryo-electron tomography directly visualizes heterogeneous macromolecular structures in complex cellular environments, but existing computer-assisted sorting approaches are low-throughput or inherently limited due to their dependency on available templates and manual labels.We introduce a high-throughput template-and-label-free deep learning approach that automatically discovers subsets of homogeneous structures by learning and modeling 3D structural features and their distributions.Diverse structures emerging from sorted subsets enable systematic unbiased recognition of macro-molecular complexes in situ.
Growth and division mode plasticity is dependent on cell density in marine-derived black yeasts
Authors: Goshima Gohta 
Published: May 2021

AbstractThe diversity and ecological contribution of the fungus kingdom in the marine environment remain under-studied. A recent survey in the Atlantic (Woods Hole, MA, USA) brought to light the diversity and unique biological features of marine fungi. The study revealed that black yeast species undergo an unconventional cell division cycle, which has not been documented in conventional model yeast species such as Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast). The prevalence of this unusual property is unknown. Here, I collected and identified 65 marine fungi species across 40 genera from the surface ocean water, sediment, and the surface of macroalgae (seaweeds) in the Pacific (Sugashima, Toba, Japan). The Sugashima collection largely did not overlap with the Woods Hole collection and included several unidentifiable species, further illustrating the diversity of marine fungi. Three black yeast species were isolated, two of which were commonly found in Woods Hole (Aureobasidium pullulans, Hortaea werneckii). Surprisingly, their cell division mode was dependent on cell density, and the previously reported unconventional division mode was reproduced only at a certain cell density. For all three black yeast species, cells underwent filamentous growth with septations at low cell density and immediately formed buds at high cell density. At intermediate cell density, two black yeasts (H. werneckii and an unidentifiable species) showed rod cells undergoing septation at the cell equator. In contrast, all eight budding yeast species showed a consistent division pattern regardless of cell density. This study suggests the plastic nature of the growth/division mode of marine-derived black yeast.
Species turnover between age groups of horses and positive network of co-occurrences define the structure of horse strongylid communities: a meta-analysis
Authors: Boisseau Michel , Mach Núria , Basiaga Marta , Kornaś Sławomir , Kuzmina Tetiana , Laugier Claire , Sallé Guillaume 
Published: May 2021

AbstractGrazing horses are infected by a wide range of strongylid species mostly located in the large intestine. Despite their impact on equine health and the emergence of drug resistant isolates, the phenology of these nematodes has been poorly characterized and the rules structuring their assembly as a community are not understood. Here, we compiled data on 46 equine strongylid species collected worldwide at the regional or horse scales (upon deworming or after necropsy) to analyse their richness, diversity and associated factors of variation. Worldwide, twelve species from the Cylicocyclus (n = 4), Cylicostephanus (n = 3), Coronocyclus (n = 2) and Cyathostomum (n = 2) genera were found in at least 75% of sites. Geoclimatic conditions had a limited effect on strongylid communities, but reduced species richness was found under the temperate European area. The recovery method did not affect species richness and differences on the temporal and sampling effort scales between studies applying either methods underpinned heterogeneous variances in community diversity.At the horse level, rarefaction curves correlated poorly to parasite egg excretion, suggesting little contribution of community diversity to this trait. Using a diversity partitioning approach, we found that within-host diversity represented half of overall diversity underscoring the importance of host density and environmental contamination to the diversity of strongylid communities. While this is expected to erase diversity across communities, species turnover between age classes was the second most important contributor to overall diversity (23.9%). This was associated with a network of positive co-occurrences between the four most prevalent genera that we resolved at the anatomical niche level. Altogether this pattern of β-diversity maintenance across age classes combined with positive co-occurrences may be grounded by priority effects between major species. Our findings set the first assembly rules of equine strongylid communities.
Functional analysis of Ost3p and Ost6p containing yeast oligosaccharyltransferases
Authors: Neuhaus Julia D. , Wild Rebekka , Eyring Jillianne , Irobalieva Rossitza N. , Kowal Julia , Lin Chia-wei , Locher Kaspar P. , Aebi Markus 
Published: May 2021

AbstractThe oligosaccharyltransferase (OST) is the central enzyme in theN-glycosylation pathway. It transfers a defined oligosaccharide from a lipid-linker onto the asparagine side chain of proteins. The yeast OST consists of eight subunits and exists in two catalytically distinct isoforms that differ in one subunit, Ost3p or Ost6p. The cryo-electron microscopy structure of the Ost6p containing complex was found to be highly similar to the Ost3p containing OST. OST enzymes with altered Ost3p/Ost6p subunits were generated and functionally analysed. The three C-terminal transmembrane helices were responsible for the higher turnover-rate of the Ost3p vs. the Ost6p containing enzymein vitroand the more severe hypoglycosylation in Ost3p lacking strainsin vivo. Glycosylation of specific OST target sites required the N-terminal thioredoxin domain of Ost3p or Ost6p. This Ost3p/Ost6p dependence was glycosylation site but not protein specific. We concluded that the Ost3p/Ost6p subunits modulate the catalytic activity of OST and provide additional specificity for OST substrate recognition.
3D matrix adhesion composition facilitates nuclear force coupling to drive invasive cell migration
Authors: Newman Daniel , Young Lorna , Waring Thomas , Brown Louise , Wolanska Katarzyna , Macdonald Ewan , Orszag Arthur Charles , Caswell Patrick , Sakuma Tetsushi , Yamamoto Takashi , Machesky Laura , Morgan Mark , Zech Tobias 
Published: May 2021

AbstractCell invasion and metastasis is a multi-step process, initialised through the acquisition of a migratory phenotype and the ability to move through differing and complex 3D extracellular environments. In this study we set out to identify the parameters required for invasive cell migration in 3D environments. Cells interact with the extracellular matrix via transmembrane-spanning integrin adhesion complexes, which are well characterised in cells plated on 2D surfaces, yet much less is known about them in cells embedded in 3D matrices. We establish a technique to determine the composition of cell matrix adhesion complexes of invasive breast cancer cells in 3D matrices and on 2D surfaces and we identify an interaction complex enriched in 3D adhesive sites required for 3D invasive migration. Depletion of β-PIX-Myosin18A (Myo18A) abolishes cancer cell invasion, without negatively affecting matrix degradation, Rho GTPase signalling, or protrusion formation in collagen matrices. Instead, in a mechanism only seen in cells moving through 3D matrix, β-PIX and Myo18A drive the polarised recruitment of non-muscle Myosin 2A (NM2A) to the tips of protrusions. This recruitment of NM2A is required for the creation of an NM2A-NM2B isoform gradient, which ranges from the protrusion to the nucleus. We observe a requirement for active force transmission to the nucleus during invasive migration that is needed to pull the nucleus forward. We postulate that the establishment of the NM2A-NM2B actomyosin gradient facilitates the coupling of cell-matrix interactions at the protrusive cell front with nuclear movement, enabling effective invasive migration and front-rear cell polarity.
Hidden viral sequences in public sequencing data and warning for future emerging diseases
Authors: Kawasaki Junna , Kojima Shohei , Tomonaga Keizo , Horie Masayuki 
Published: May 2021

AbstractRNA viruses cause numerous emerging diseases, mostly due to transmission from mammalian and avian reservoirs. Large-scale surveillance of RNA viral infections in these animals is a fundamental step for controlling viral infectious diseases. Metagenomic analysis is a powerful method for virus identification with low bias and has substantially contributed to the discovery of novel viruses. Deep sequencing data have been collected from diverse animals and accumulated in public databases, which can be valuable resources for identifying unknown viral sequences. Here, we screened for infections of 33 RNA viral families in publicly available mammalian and avian sequencing data and found approximately 900 hidden viral infections. We also discovered six nearly complete viral genomes in livestock, wild, and experimental animals: hepatovirus in a goat, hepeviruses in blind mole-rats and a galago, astrovirus in macaque monkeys, parechovirus in a cow, and pegivirus in tree shrews. Some of these viruses were phylogenetically close to human pathogenic viruses, suggesting the potential risk of causing disease in humans upon infection. Furthermore, the infections of five novel viruses were identified in several different individuals, indicating that their infections may have already spread in the natural host population. Our findings demonstrate the reusability of public sequencing data for surveying viral infections and identifying novel viral sequences, presenting a warning about a new threat of viral infectious disease to public health.ImportanceMonitoring the spread of viral infections and identifying novel viruses capable of infecting humans through animal reservoirs are necessary to control emerging viral diseases. Massive amounts of sequencing data collected from various animals are publicly available, and these data may contain sequences originating from a wide variety of viruses. Here, we analyzed more than 46,000 public sequencing data and identified approximately 900 hidden RNA viral infections in mammalian and avian samples. Some viruses discovered in this study were genetically similar to pathogens that cause hepatitis, diarrhea, or encephalitis in humans, suggesting the presence of new threats to public health. Our study demonstrates the effectiveness of reusing public sequencing data to identify known and unknown viral infections, indicating that future continuous monitoring of public sequencing data by metagenomic analyses would help prepare and mitigate future viral pandemics.