bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bark beetles locate fungal symbionts by detecting volatile fungal metabolites of host tree resin monoterpenes
Authors: Kandasamy Dineshkumar , Zaman Rashaduz , Nakamura Yoko , Zhao Tao , Hartmann Henrik , Andersson Martin N , Hammerbacher Almuth , Gershenzon Jonathan 
Published: July 2021

AbstractOutbreaks of the Eurasian spruce bark beetle (Ips typographus) have decimated millions of hectares of conifer forests in Europe in recent years. The ability of these 3-6 mm long insects to kill mature trees over a short period has been ascribed to two main factors: (1) mass attacks on the host tree to overcome tree defenses and (2) the presence of fungal symbionts that support successful beetle development in the tree. While the role of pheromones in coordinating mass attacks has been well studied, the role of chemical communication in maintaining the fungal symbiosis is poorly understood. We previously demonstrated thatI. typographuscan recognize beneficial fungal symbionts of the generaGrosmannia,EndoconidiophoraandOphiostomaby theirde novosynthesized volatile compounds. Here, we hypothesize that the fungal symbionts of the bark beetles might metabolize spruce resin monoterpenes of the beetle’s host tree, Norway spruce (Picea abies), and that the volatile products could be used as cues by beetles for locating breeding sites with beneficial symbionts. We show thatGrosmannia penicillataand other fungal symbionts altered the profile of spruce bark volatiles by converting the major monoterpenes into an attractive blend of oxygenated derivatives. Bornyl acetate was metabolized to camphor, and α- and β-pinene totrans-4-thujanol and other oxygenated products. Other co-occurring non-beneficial fungi (Trichoderma sp.)also produce oxygenated monoterpenes, but in non-attractive ratios. Extensive electrophysiological measurements showed that the bark beetle possesses dedicated olfactory sensory neurons for oxygenated metabolites. Compounds such as camphor andtrans-4-thujanol attracted beetles at specific doses in olfactory experiments, and the presence of symbiotic fungi enhanced attraction of females to pheromones. Finally, we show that colonization of fungal symbionts on spruce bark diet stimulated beetles to make tunnels into the diet. Collectively, our study suggests that the blends of oxygenated metabolites of conifer monoterpenes produced by fungal symbionts are used by bark beetles as attractive cues to find breeding or feeding sites containing their essential microbial symbionts. The oxygenated metabolites may aid beetles in assessing the presence of the fungus, the defense status of the host tree and the density of conspecifics at potential feeding and breeding sites.
Allotypic variation in antigen processing controls antigenic peptide generation from SARS-CoV-2 S1 Spike Glycoprotein
Authors: Stamatakis George , Samiotaki Martina , Temponeras Ioannis , Panayotou George , Stratikos Efstratios 
Published: July 2021

ABSTRACTPopulation genetic variability in immune system genes can often underlie variability in immune responses to pathogens. Cytotoxic T-lymphocytes are emerging as critical determinants of both SARS-CoV-2 infection severity and long-term immunity, either after recovery or vaccination. A hallmark of COVID-19 is its highly variable severity and breadth of immune responses between individuals. To address the underlying mechanisms behind this phenomenon we analyzed the proteolytic processing of S1 spike glycoprotein precursor antigenic peptides by 10 common allotypes of ER aminopeptidase 1 (ERAP1), a polymorphic intracellular enzyme that can regulate cytotoxic T-lymphocyte responses by generating or destroying antigenic peptides. We utilized a systematic proteomic approach that allows the concurrent analysis of hundreds of trimming reactions in parallel, thus better emulating antigen processing in the cell. While all ERAP1 allotypes were capable of producing optimal ligands for MHC class I molecules, including known SARS-CoV-2 epitopes, they presented significant differences in peptide sequences produced, suggesting allotype-dependent sequence biases. Allotype 10, previously suggested to be enzymatically deficient, was rather found to be functionally distinct from other allotypes. Our findings suggest that common ERAP1 allotypes can be a major source of heterogeneity in antigen processing and through this mechanism contribute to variable immune responses to COVID-19.
Synchronized swarming: Harmonic convergence and acoustic mating dynamics in the malaria mosquito Anopheles gambiae
Authors: Garcia Castillo Stefano S. , Pritts Kevin S. , Krishnan Raksha S. , Harrington Laura C. , League Garrett P. 
Published: July 2021

AbstractThe mosquito Anopheles gambiae is a major African malaria vector, transmitting parasites responsible for significant mortality and disease burden. Malaria declines have stagnated recently due to widespread insecticide resistance among vector populations. Flight acoustics are essential to mosquito mating biology and represent promising alternative targets for mosquito control. However, mosquito swarm acoustics data are limited. Here, for the first time, we present detailed analyses of free-flying male and female An. gambiae flight tones and their harmonization (harmonic convergence) over a complete swarm sequence. Audio analysis of single-sex swarms showed elevated male or female flight tone frequencies and amplitudes during swarming flight with gradual declines to pre-swarm levels over an approximately 35-min period. Analysis of mixed-sex swarms revealed additional increases in flight tone frequencies and amplitudes due to mating activity. Data from mixed-sex swarms suggest harmonic convergence during swarming enhances the efficiency of female detection by synchronizing male and female baseline swarm tones. Further, data from experiments using female swarm tone playbacks to males indicate that harmonic convergence during mating interactions coordinates male scramble competition by acoustically masking mating couple flight tones. These findings advance our knowledge of mosquito swarm acoustics, providing vital information for reproductive control strategies.
Effect of artificial light at night on sleep and metabolism in weaver birds
Authors: Yadav Anupama , Kumar Raj , Tiwari Jyoti , Vaish Vaibhav , Malik Shalie , Rani Sangeeta 
Published: July 2021

AbstractArtificial light at night is constantly minimizing the span of dark nights’ from the natural light-dark cycle of earth. Over the past century, the ‘lightscape’ of earth has completely changed owing to technological advancements which subsequently changed the lifestyle of human as well as the nearby animal species. This motivated the present study, wherein we investigated the impact of light at night (LAN) on behavior and physiology of a diurnal passerine finch, baya weaver (Ploceus philippinus). A group of bird (N=10) exposed to 12L:12D photoperiod was initially subjected to dark nights (0 lux) for a period of 10 days followed by 5 lux; night light for a span of 4 weeks. First week in LAN served as acute treatment with respect to fourth week (chronic). Acute exposure had more pronounced impact on the behavioral and physiological observations when compared with chronic treatment. The results reveal significant increase in nighttime activity, sleep loss, significant inclusion of drowsiness behavior during the day in response to LAN. Beside these behavioral alterations, changes in physiological parameters such as; reduction in body mass, loss of gradient between pre- and post-prandial blood glucose levels, elevation in plasma corticosterone levels were more prominent during acute exposure of LAN. Plasma metabolites such as triglycerides, total protein, serum glutamic-oxaloacetic transaminase (SGOT) and creatinine concentrations also hiked in response to LAN treatment. Thus, the study broadly enumerates the impact of acute and chronic exposure of LAN on behavior (rest/sleep) and physiology (metabolism) of birds’.
Assessing our capability to predict the presence of respiratory diseases at the age of four using data available at one month of age
Authors: Han Xinyi , Gray Lawrence E. K. , Mahar Robert K. , Carlin John B. , Ranganathan Sarath , Vuillermin Peter J. , Vukcevic Damjan 
Published: July 2021

AbstractChronic respiratory diseases are often difficult to cure and are likely to originate early in life. Therefore, early identification of such diseases is of interest for early prevention.We explored the potential to predict these almost from birth; using data at 1 month of age, we attempted to predict disease occurrence 4 years later in life. Our data came from the Barwon Infant Study; after cleaning and processing, we had measurements on 41 variables from 401 participants.We considered three respiratory diseases: asthma, wheeze and hay fever. As predictors, we used a variety of information that would be available in a clinical setting. Of particular interest to our investigation was whether lung function measurements (newly available at such an early age) would helpfully improve predictive accuracy. We also investigated whether maternal smoking (previously associated with respiratory illnesses) is a helpful predictor.Our methods included logistic regression as the main model, multiple imputation to deal with missing values, stepwise selection and LASSO to select variables, and cross-validation to assess performance. We measured predictive performance using AUC (area under the receiver operating characteristic curve), sensitivity and specificity.Broadly, we found that the best models had only modest predictive power for each disease. For example, for asthma we achieved an AUC of 0.67, a sensitivity of 68% and a corresponding specificity of 63%. Performance for the other two diseases was similar.We also found that our lung function measurements didnotimprove predictive performance; some-what surprisingly, this was also true for maternal smoking. The most useful predictors included, among others, family history of these diseases and variables relating to the size of the infants.Given the modest performance of these models, our findings suggest that very early prediction of respiratory illnesses is still a challenging task.
Investigation on the current situation of stroke patients in northernern Henan Province of China
Authors: Li Zhenhua , Yang Qingcheng , Zhang Xiangdong , Guo Yanping , Zhang Jiangang , Sun Ke , Yang Junzheng 
Published: July 2021

AbstractObjectivesTo analyze the basic situations and clinical characteristics of stroke patients in our hospital from May 2018 to April 2021, lay a foundation for the prevention and reasonable treatment of stroke patients in northern Henan Province.MethodsThe basic information of 835 stroke patients in our hospital was collected and classified according to age, gender, bad habits, accompanied diseases and drug use before admission to hospital, and severity of the stroke patients were also evaluated according to mRS scoring standard.ResultsA total of 835 stroke patients were collected from May 2018 to April 2021 in our hospital. The age range of stroke patients was 28-95 years old, 96.29% stroke patients was above 40 years old; there were 202 stroke patients with smoking history and 225 stroke patients with drinking history; Among the 835 stroke patients, hypertension, cerebral infarction and diabetes mellitus were the main accompanied diseases. Antihypertensive drugs (506 cases), antiplatelet drugs (208 cases), statins (173 cases) and antidiabetic drugs (143 cases) were the main therapeutic drugs in stroke patients before admission in the northern Henan Province; the results of mRS scoring standard showed that among 835 stroke patients, there were 609 cases with milder symptoms, accounting for 82.84% (there were 330 stroke patients with 1 points, 279 stroke patients with 2 points, and 83 stroke patients with 3 points), and 120 cases with severe symptoms, accounting for 14.37% (55 cases with 4 points, 65 cases with 5 points).ConclusionThe age of stroke patients in northern Henan Province was mainly over 40 years old, most of stroke patients were in the early stage of stroke; smoking, drinking, hypertension and diabetes mellitus were main risk factors of stroke. And there was a sex difference between male stroke patients and female stroke patients in stroke risk factors smoking and hypertension. those data may help us for active prevention and rational drug use for stroke in clinic.
Single-cell sequencing unravels the cellular diversity that shapes neuro- and gliogenesis in the fast aging killifish (N. furzeri) brain
Authors: Ayana Rajagopal , Zandecki Caroline , Van houcke Jolien , Mariën Valerie , Seuntjens Eve , Arckens Lutgarde 
Published: July 2021

SummaryThe African turquoise killifish combines a short lifespan with spontaneous age-dependent loss of neuroregenerative capacity. The stem cell niches driving neuroregeneration and their molecular signatures remain elusive. To investigate this, we performed scRNA-seq of the adult telencephalon, combined with full-length transcriptomics using ISO-seq. Our results unveil about 25 cell types including neurons and progenitors of glial-and non-glial nature. Subclustering of progenitors identifies four radial glia (RG), and two non-glial progenitor (NGP) cell states. Combining the molecular profiles with spatial mapping of the RG clusters, reveals two spatially divergent astroglia, one ependymal, and one neuroepithelial-like subtype. We propose neuroepithelial-like RG and NGPs to be the start and intercessor populations of both neuro- and gliogenic lineages. Neuronal classification reveals distinct subtypes and lineages corresponding to excitatory and inhibitory neurons. This catalogue of telencephalon cell types is an extensive resource to understand the molecular basis of intrinsic plasticity shaping adult neuro- and gliogenesis.HighlightsScRNA-seq and ISO-seq identified a complete cell catalogue of the adult killifish telencephalonProgenitor diversity revealed the presence of spatially-defined (astro)glial subtypesA neuroepithelial radial glia population marks the start point of neurogenesis, accompanied by proliferative non-glial progenitorsImmature neurons form transcriptional subgroups that correspond to excitatory and inhibitory mature neuronal cell typesThis cellular atlas is a basis for studying neurogenesis and neuro-regeneration upon injury, disease and aging
Single-cell analysis uncovers differential regulation of lung γδ T cell subsets by the co-inhibitory molecules, PD-1 and TIM-3
Authors: Edwards Sarah C. , Hedley Ann , Hoevenaar Wilma H. M. , Glauner Teresa , Wiesheu Robert , Kilbey Anna , Shaw Robin , Boufea Katerina , Batada Nizar , Blyth Karen , Miller Crispin , Kirschner Kristina , Coffelt Seth B. 
Published: July 2021

ABSTRACTIL-17A-producing γδ T cells within the lung consist of both Vγ6+tissue-resident cells and Vγ4+circulating cells that play important roles in homeostasis, inflammation, infection, tumor progression and metastasis. How these γδ T cell subsets are regulated in the lung environment during homeostasis and cancer remains poorly understood. Using single-cell RNA sequencing and flow cytometry, we show that lung Vγ6+cells express a repertoire of cell surface molecules distinctive from Vγ4+cells, including PD-1 and ICOS. We found that PD-1 functions as a co-inhibitory molecule on Vγ6+cells to reduce IL-17A production, whereas manipulation of ICOS signaling fails to affect IL-17A in Vγ6+cells. In a mammary tumor model, ICOS and PD-1 expression on lung Vγ6+cells remained stable. However, Vγ6+and Vγ4+cells within the lung pre-metastatic niche increased expression of IL-17A, IL-17F, amphiregulin (AREG) and TIM-3 in response to tumor-derived IL-1β and IL-23, where the upregulation of TIM-3 was specific to Vγ4+cells. Inhibition of either PD-1 or TIM-3 in mammary tumor-bearing mice further increased IL-17A by Vγ6+and Vγ4+cells, indicating that both PD-1 and TIM-3 function as negative regulators of IL-17A-producing γδ T cell subsets. Together, these data demonstrate how lung γδ T cell subsets are differentially controlled by co-inhibitory molecules in steady-state and cancer.
Mice and primates use distinct strategies for visual segmentation
Authors: Luongo Francisco J. , Liu Lu , Ho Chun Lum Andy , Hesse Janis K. , Wekselblatt Joseph B. , Lanfranchi Francesco , Huber Daniel , Tsao Doris Y. 
Published: July 2021

AbstractThe rodent visual system has attracted great interest in recent years due to its experimental tractability, but the fundamental mechanisms used by the mouse to represent the visual world remain unclear. In the primate, researchers have argued from both behavioral and neural evidence that a key step in visual representation is “figure-ground segmentation,” the delineation of figures as distinct from backgrounds [1–4]. To determine if mice also show behavioral and neural signatures of figure-ground segmentation, we trained mice on a figure-ground segmentation task where figures were defined by gratings and naturalistic textures moving counterphase to the background. Unlike primates, mice were severely limited in their ability to segment figure from ground using the opponent motion cue, with segmentation behavior strongly dependent on the specific carrier pattern. Remarkably, when mice were forced to localize naturalistic patterns defined by opponent motion, they adopted a strategy of brute force memorization of texture patterns. In contrast, primates, including humans, macaques, and mouse lemurs, could readily segment figures independent of carrier pattern using the opponent motion cue. Consistent with mouse behavior, neural responses to the same stimuli recorded in mouse visual areas V1, RL, and LM also did not support texture-invariant segmentation of figures using opponent motion. Modeling revealed that the texture dependence of both the mouse’s behavior and neural responses could be explained by a feedforward neural network lacking explicit segmentation capabilities. These findings reveal a fundamental limitation in the ability of mice to segment visual objects compared to primates.
Examining the effects of an anti-Salmonella bacteriophage preparation, BAFASAL, on ex vivo human gut microbiome composition and function using a multi-omics approach
Authors: Mayne Janice , Zhang Xu , Butcher James , Walker Krystal , Ning Zhibin , Wójcik Ewelina , Dastych Jarosław , Stintzi Alain , Figeys Daniel 
Published: July 2021

AbstractSalmonella infections (salmonellosis) pose serious health risks to humans, usually via contamination in our food chain. This foodborne pathogen causes major food losses and human illnesses that result in significant economic impacts. Pathogens such as Salmonella have traditionally been kept at bay through the use of antibiotics, but antibiotic overuse within the food industry has led to the development of numerous multidrug-resistant bacterial strains. Thus, governments are now restricting antibiotic use, forcing the industry to search for alternatives to secure safe food chains. Bacteriophages, viruses that infect and kill bacteria, are currently being investigated and used as replacement treatments and prophylactics due to their specificity and efficacy. They are generally regarded as safe alternatives to antibiotics as they are natural components of the ecosystem. One example is BAFASEL, a commercial bacteriophage mixture that specifically targets Salmonella and is currently approved for use in poultry farming. However, when specifically used in the industry they can also make their way into humans through our food chain or exposure as is the case for antibiotics. In particular, agricultural workers could be repeatedly exposed to bacteriophages supplemented in animal feeds. To the best of our knowledge, no studies have investigated the effects of such exposure to bacteriophages on the human gut microbiome. In this study, we used a novel in vitro assay called RapidAIM to investigate BAFASAL’s potential impact on five individual human gut microbiomes. Multi-omics analyses, including 16S rRNA gene sequencing and metaproteomic, revealed that ex vivo human gut microbiota composition and function were unaffected by BAFASAL treatment providing an additional measure for its safety. Due to the critical role of the gut microbiome in human health and the known role of bacteriophages in regulation of microbiome composition and function, we suggest assaying the impact of bacteriophage-cocktails on the human gut microbiome as a part of their safety assessment.Graphical Abstract
Divergent effects of absolute evidence magnitude on decision accuracy and confidence in perceptual judgements
Authors: Ko Yiu Hong , Feuerriegel Daniel , Turner William , Overhoff Helen , Niessen Eva , Stahl Jutta , Hester Robert , Fink Gereon R. , Weiss Peter H. , Bode Stefan 
Published: July 2021

AbstractWhether people change their mind after making a perceptual judgement may depend on how confident they are in their decision. Recently, it was shown that, when making perceptual judgements about stimuli containing high levels of ‘absolute evidence’ (i.e., the overall magnitude of sensory evidence across choice options), people make less accurate decisions and are also slower to change their mind and correct their mistakes. Here we report two studies that investigated whether high levels of absolute evidence also lead to increased decision confidence. We used a luminance judgment task in which participants decided which of two dynamic, flickering stimuli was brighter. After making a decision, participants rated their confidence. We manipulated relative evidence (i.e., the mean luminance difference between the two stimuli) and absolute evidence (i.e., the summed luminance of the two stimuli). In the first experiment, we found that higher absolute evidence was associated with decreased decision accuracy but increased decision confidence. In the second experiment, we additionally manipulated the degree of luminance variability to assess whether the observed effects were due to differences in perceived evidence variability. We replicated the results of the first experiment but did not find substantial effects of luminance variability on confidence ratings. Our findings support the view that decisions and confidence judgments are based on partly dissociable sources of information, and suggest that decisions initially made with higher confidence may be more resistant to subsequent changes of mind.
ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data
Authors: Guydosh Nicholas R. 
Published: July 2021

AbstractRibosome profiling is a valuable methodology for measuring changes in a cell’s translational program. The approach can report how efficiently mRNA coding sequences are translated and pinpoint positions along mRNAs where ribosomes slow down or arrest. It can also reveal when translation takes place outside coding regions, often with important regulatory consequences. While many useful software tools have emerged to facilitate analysis of these data, packages can become complex and challenging to adapt to specialized needs. In particular, the results of meta analysis of average footprint data around sequence motifs of interest can vary substantially depending on the normalization method that is utilized. We therefore introduce ribofootPrinter, a suite of Python tools designed to offer an accessible and modifiable set of code for analysis of ribosome profiling data. Footprint alignments are made to a simplified transcriptome, keeping the code intuitive, and multiple normalization options help facilitate interpretation of meta analysis, particularly outside coding regions. We believe this tool has promise to carry out sophisticated analysis yet offer simplicity to make it readily understandable and adaptable.