Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiology and molecular detection of Anaplasma spp. in goats from Chattogram district, Bangladesh

Abstract Objectives Anaplasmosis is an economically important disease affecting cattle, buffalo, sheep, goat etc. The study was conducted to determine the prevalence, potential risk factors and molecular identification of circulating Anaplasma spp. in goats in Chattogram district, Bangladesh. Material and methods Four hundred blood samples were collected from goats of different ages, breeds, sex, coat color and body condition. These goats were selected based on some inclusion criteria through the period of July 2017 to June 2018. Samples were examined microscopically (Giemsa staining method) followed by polymerase chain reaction (PCR) and sequencing to identify of Anaplasma spp. Results The overall prevalences were estimated 5.75% (23/400) and 15.75% (63/400) by microscopy and PCR, respectively. Anaplasma ovis (A. ovis) and Anaplasma marginale (A. marginale) were identified with the prevalence of 14.75% (59/400) and 1.0% (4/400), respectively through PCR. Among different risk factors, jamnapari breed (p = 0.027), no use of acaricide (p = 0.025) and presence of tick (p < 0.01) were found to be significantly associated with anaplasmosis. Sequence analysis of msp4 gene revealed that, Anaplasma spp. detected in the present study were highly similar with those of China, Venezuela, Mongolia, Spain, Tunisia, Cyprus, Italy, Brazil, Argentina, Australia, Japan and Columbia. Conclusions In conclusion, strategic use of acaricide can control tick that ultimately will control the anaplasmosis in goats. Besides, rearing local goats in compare to cross and exotic breed are also recommended for the farmer to prevent the disease.
An assessment of the impact of 1.5 versus 2 and 2.5°C global temperature increase on flooding in Jamaica: a case study from the Hope watershed

Climate change models project that, within the Caribbean basin, rainfall intensity is likely to increase toward the end of this century, although the region is projected to be drier overall. This may affect the frequency and severity of floods in Jamaica and the Caribbean Small Island Developing States. We investigate how flood hazards may be affected by increases in global mean surface temperature of 1.5, 2.0 and 2.5°C above pre-industrial levels using a case study of a Jamaican watershed. Rainfall projections from the PRECIS regional climate model for the Caribbean are analysed. Six members from the Quantifying Uncertainty in Model Predictions (AENWH, AEXSA, AEXSC, AEXSK, AEXSL and AEXSM) were used to create 100-year flood inundation maps for the Hope river for different global warming levels using hydrological and hydraulic models. Model runs projected peak discharges at 2.0, 2.5 and 1.5°C warming that were higher than discharges in the historical record of events that damaged sections of the watershed. Projections from the hydraulic model show increased flow area, depth and extent for 1.5 followed by 2.0 and 2.5°C rises in temperature. These results imply continued flood risk for the vulnerable areas of the watershed. This article is part of the theme issue 'Developing resilient energy systems'.
Risk of Pneumothorax Requiring Pleural Drainage after Drainless VATS Pulmonary Wedge Resection: A Systematic Review and Meta-Analysis

Objective Omitting pleural drainage after video-assisted thoracic surgery (VATS) for pulmonary wedge resections has been shown to be a safe approach to enhance recovery. However, major concerns remain regarding the risk of postoperative pneumothoraces requiring surgical interventions. Therefore, our objective was to provide conclusive evidence whether chest tube omission after VATS wedge resection is safe and does not increase the risk of pneumothoraces requiring pleural drainage. Methods Five scientific databases were searched. Studies comparing patients with (CT group) and without chest tube drainage (NCT group) after VATS wedge resection were evaluated. Outcomes included radiographically diagnosed pneumothoraces and pneumothoraces requiring pleural drainage, postoperative complications, hospitalization, and pain scores. Results Overall, 9 studies (3 randomized controlled trials) were included (N = 928). Meta-analysis showed significantly more radiographically diagnosed pneumothoraces in the NCT group (risk ratio [RR] = 2.58, 95% confidence interval [CI]: 1.56 to 4.29, P < 0.001; I 2 = 0%). However, no significant differences were found in postoperative pneumothoraces requiring pleural drainage (RR = 1.72, 95% CI: 0.63 to 4.74, P = 0.29; I2 = 0%) or complications (RR = 0.77, 95% CI: 0.39 to 1.52, P = 0.46; I 2 = 0%). Furthermore, the NCT group showed significantly shorter hospitalization (mean difference = −1.26, 95% CI: −1.56 to −0.95, P < 0.001) with high heterogeneity (I 2 = 58%, P = 0.02), and lower pain scores on postoperative day 1 (standard mean difference [SMD] = −0.98, 95% CI: −1.71 to −0.25, P = 0.009; I 2 = 92%) and postoperative day 2 (SMD = −1.28, 95% CI: −2.55 to −0.01, P = 0.05; I 2 = 96%) compared with the CT group. Conclusions VATS wedge resection without routine chest tube placement is suggested as a safe and less invasive approach in selected patients that does not increase the risk of a pneumothorax requiring pleural drainage.
Surveillance of synthetic acaricide efficacy against Varroa destructor in Ontario, Canada

Abstract The parasitic mite Varroa destructor (Mesostigmata: Varroidae) is the main culprit of honey bee (Hymenoptera: Apidae) colony mortality in Ontario, Canada. Most beekeepers use synthetic acaricides to control V. destructor infestations in their colonies, but the use of these products increases the risk of V. destructor developing resistance to the active ingredients, which is a growing concern. This study sought to determine the efficacy of three synthetic acaricides approved for use in Canada for control of V. destructor infestations, amitraz (Apivar™), tau-fluvalinate (Apistan®), and flumethrin (Bayvarol®), using the Pettis test. The mite mortality rate in populations of V. destructor differed for the acaricides tested. Amitraz caused a significantly higher mite mortality rate (92%) than flumethrin (78%) and tau-fluvalinate (72%) did. Amitraz was classified as “mostly effective” (90–97%), whereas flumethrin and tau-fluvalinate were classified as “minimally effective” (< 80%) for V. destructor control in the mite populations studied. Variation in mite mortality due to acaricide exposure was observed between apiaries and regions. The results highlight the importance of periodically assessing the varroacidal activity of acaricides to inform decisions to control the parasite when implementing integrated pest management strategies.
Critical indicators of dynamic stall vortex

Abstract During a dynamic stall process, various flow structures leave their pressure footprints on a wing surface, through which it is possible to understand the development of different flow stages and predict the critical flow events. Based on a classical airfoil ramp-up pitching motion, proper orthogonal decomposition analysis of pressure on the suction surface is carried out in this study. Accordingly, the surface pressure evolution during dynamic stall is summarized into three basic physical schemas, based on which several real-time critical indicators for predicting the flow events related to the dynamic stall vortex (DSV) are constructed. These critical indicators include the spatial distribution coefficient of pressure (SDCP), the high-order central moment of pressure (HCMP), the location of peak pressure (LPP) and the modulated location of peak pressure (MLPP). These indicators can predict the formation of laminar separation bubbles, DSV initiation, DSV centre position and the detachment of DSV. Therefore, the real-time whole-life monitoring of DSV has been realized. Moreover, the effectiveness of these indicators has also been confirmed under different parameters, and testing using wind tunnel experimental data proves their noise robustness. Studies show that the SDCP and HCMP may also be effective even if only two transducers are used. Finally, a modification method of SDCP based on Z-score standardized pressure is proposed. It is found that the modified SDCP can effectively reduce sensitivity to kinematic parameters and the Reynolds number. The critical indicators in this study can be used as a reference for the standardized mathematical and physical description of DSV evolution, thus laying a foundation for constructing a universal theoretical framework of dynamic stall.
Irisin response to acute moderate intensity exercise and high intensity interval training in youth of different obesity statuses: A randomized crossover trial

Limited data exist regarding the impact of an acute bout of exercise with varying intensities on irisin levels in the youth of different obesity statuses. The objectives were to (1) compare an acute bout of moderate continuous intensity (MCI) exercise and an acute bout of high‐intensity interval training (HIIT) on irisin response in youth with different obesity statuses and, (2) investigate whether changes in irisin levels are correlated with exploratory outcomes. A randomized crossover design study was conducted on 25 youth aged 12–18 years old. Participants were classified as either healthy weight (BMI percentile <85; n = 14) or overweight/obese (BMI percentile ≥85; n = 11). Participants performed an MCI exercise session at 50% of heart rate reserve for 35 min and a HIIT exercise session for 35 min, with intervals every 5 min increasing from 50% heart rate reserve to 85–90% for 2 min. Irisin was measured using an enzyme‐linked immunoabsorbent assay from plasma sampling obtained throughout the exercise (at times 0, 7, 14, 21, 28, and 35 min). A time effect was observed throughout the HIIT session [F(1,5) = 6.478, p < 0.001]. Bonferonni post‐hoc analysis revealed significant differences in irisin levels post‐exercise (35 min) compared to times 7, 14, 21, and 28 min. Irisin increased during HIIT (81.0% ± 71.3; p = 0.012) in youth with a healthy weight. No differences were observed for youth living as overweight or with obesity. Overall, HIIT elicits a higher peak irisin response compared to MCI exercise training in youth.
A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding

T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. This approach identifies binders missed by computational prediction and serves as a framework for diverse objectives, including examining relationships between viral conservation and MHC binding.
PanGraph: scalable bacterial pan-genome graph construction

The genomic diversity of microbes is commonly parameterized as single nucleotide polymorphisms relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the wide-spread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. Traditional computational approaches towards whole-genome analysis either scale poorly with the number of genomes, or treat genomes as dissociated “bags of genes”, and thus are not suited for this new era. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as an undirected path along vertices, which in turn, encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into a several common formats for either downstream analysis or immediate visualization.
Phenotypic and transcriptional response of Daphnia pulicaria to the combined effects of temperature and predation

Daphnia, an ecologically important zooplankton species in lakes, shows both genetic adaptation and phenotypic plasticity in response to temperature and fish predation, but little is known about the molecular basis of these responses and their potential interactions. We performed a factorial experiment exposing laboratory-propagated Daphnia pulicaria clones from two lakes in the Sierra Nevada mountains of California to normal or high temperature (15°C or 25°C) in the presence or absence of fish kairomones, then measured changes in life history and gene expression. Exposure to kairomones increased upper thermal tolerance limits for physiological activity in both clones. Cloned individuals matured at a younger age in response to higher temperature and kairomones, while size at maturity, fecundity and population intrinsic growth were only affected by temperature. At the molecular level, both clones expressed more genes differently in response to temperature than predation, but specific genes involved in metabolic, cellular, and genetic processes responded differently between the two clones. Although gene expression differed more between clones from different lakes than experimental treatments, similar phenotypic responses to predation risk and warming arose from these clone-specific patterns. Our results suggest that phenotypic plasticity responses to temperature and kairomones interact synergistically, with exposure to fish predators increasing the tolerance of Daphnia pulicaria to stressful temperatures, and that similar phenotypic responses to temperature and predator cues can be produced by divergent patterns of gene regulation.
Age influences audiovisual speech processing in multi-talker scenarios – Evidence from cortical oscillations

Age-related differences in the processing of audiovisual speech in a multi-talker environment were investigated analyzing event-related spectral perturbations (ERSPs), focusing on theta, alpha, and beta oscillations that are assumed to reflect conflict processing, multisensory integration, and attentional mechanisms, respectively. Eighteen older and 21 younger healthy adults completed a two-alternative forced-choice word discrimination task, responding to audiovisual speech stimuli. In a cocktail-party scenario with two competing talkers (located at-15° and 15° azimuth), target words (/yes/ or /no/) appeared at a pre-defined (attended) position, distractor words at the other position. In two audiovisual conditions, acoustic speech was combined either with congruent or uninformative visual speech. While a behavioral benefit for congruent audiovisual speech occurred for both age groups, differences between audiovisual conditions in the theta and beta band were only present for older adults. A stronger increase in theta perturbations for stimuli containing uninformative visual speech could be associated with early conflict processing, while a stronger suppression in beta perturbations for congruent audiovisual speech could be associated to audiovisual integration. Compared to the younger group, the older group showed generally stronger beta perturbations. No condition differences in the alpha band were found. Overall, the findings suggest age-related differences in audiovisual speech integration in a multi-talker environment. While the behavioral benefit of congruent audiovisual speech was unaffected by age, older adults had a stronger need for cognitive control when processing conflicting audiovisual speech input. Furthermore, mechanisms of audiovisual integration are differently activated depending on the informational content of the visual information.
Changes in body shape implicate cuticle stretch in C. elegans growth control

Growth control establishes organism size, requiring mechanisms to sense and adjust growth during development. Studies of single cells revealed that size homeostasis uses distinct control methods. In multicellular organisms, mechanisms that regulate single cell growth must integrate control across organs and tissues during development to generate adult size and shape. We leveraged the roundworm Caenorhabditis elegans as a scalable and tractable model to collect precise growth measurements of thousands of individuals, measure feeding behavior, and quantify changes in animal size and shape during a densely sampled developmental time course. As animals transitioned from one developmental stage to the next, we observed changes in body aspect ratio while body volume remained constant. Then, we modeled a physical mechanism by which constraints on cuticle stretch could cause changes in C. elegans body shape. The model-predicted shape changes are consistent with those observed in the data. Theoretically, cuticle stretch could be sensed by the animal to initiate larval-stage transitions, providing a means for physical constraints to influence developmental timing and growth rate in C. elegans. Highlights Body size measurements of thousands of animals in a dense developmental time course Growth rate exhibits nonlinear dynamics in both length and width Changes in body shape but not volume occur during periods of increased quiescence Dynamics of animal shape consistent with a length-based threshold in cuticle stretch Modeling of cuticle stretch dynamics suggests a novel mode for growth control
Cell-to-cell variations in subcellular localisation of V2R are independent of its expression level

G protein coupled receptors (GPCRs) translate the actions of hormones into intracellular signalling events. Mutations in GPCRs can prevent their correct expression and trafficking to the cell surface and cause disease. We use single cell measurements in HEK293 cells to show that the balance between endoplasmic reticulum (ER) and cell surface localisation of the Vasopressin 2 receptor (V2R) varies significantly from cell to cell. We find that mutations in the V2R affect the proportion of cells able to send this GPCR to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. These findings reveal that the ability of cells to correctly traffic V2R to the cell surface depends not only on the expressed V2R mutant but also on the individual cell environment. Significance statement Missense mutations in the Vasopressin 2 Receptor (V2R) cause Nephrogenic Diabetes Insipidus. Some of these mutations prevent correct expression and trafficking of V2R to the cell surface resulting in a loss-of-function. We show -using single cell measurements-that the balance between endoplasmic reticulum and cell surface localisation of the V2R varies significantly from cell to cell, independent from its expression level. Mutations affect the proportion of cells able to send V2R to the cell surface but do not prevent all cells in the population from correctly trafficking the mutant receptors. Hence, the ability of cells to correctly traffic V2R to the cell surface depends not only on expressed V2R mutant but also on the cell environment.
Arousal state affects perceptual decision-making by modulating hierarchical sensory processing in a large-scale visual system model

Arousal levels strongly affect task performance. Yet, what arousal level is optimal for a task depends on its difficulty. Easy task performance peaks at higher arousal levels, whereas performance on difficult tasks displays an inverted U-shape relationship with arousal, peaking at medium arousal levels, an observation first made by Yerkes and Dodson in 1908. It is commonly proposed that the noradrenergic locus coeruleus system regulates these effects on performance through a widespread release of noradrenaline resulting in changes of cortical gain. This account, however, does not explain why performance decays with high arousal levels only in difficult, but not in simple tasks. Here, we present a mechanistic model that revisits the Yerkes-Dodson effect from a sensory perspective: a deep convolutional neural network augmented with a global gain mechanism reproduced the same interaction between arousal state and task difficulty in its performance. Investigating this model revealed that global gain states differentially modulated sensory information encoding across the processing hierarchy, which explained their differential effects on performance on simple versus difficult tasks. These findings offer a novel hierarchical sensory processing account of how, and why, arousal state affects task performance. Author’s summary Over a hundred years ago, it was first observed that the effect of arousal on performance depends on task difficulty: the Yerkes-Dodson effect. Difficult tasks are best solved at intermediate arousal levels, whereas easy tasks benefit from a high arousal state. Current theories on how arousal affects neural processing cannot explain this effect of task difficulty. Here, we implement a key effect of arousal on cortical processing, a change in neuronal gain, in a computational model of visual processing capable of object recognition. Across a series of experiments, we find that our model can reproduce the Yerkes-Dodson effect behaviorally and that this effect can be explained by where in the processing hierarchy different arousal states optimize sensory information encoding.
Cytokine Profiles of Head and Neck Squamous Cell Carcinoma Undergoing Dual Immunotherapy With Cetuximab and Pembrolizumab Identify Interferon Gamma-Induced Protein 10 as Novel Biomarker

Background Pembrolizumab and cetuximab are antibodies under investigation in head and neck squamous cell carcinoma (HNSCC) either as single agents or combined with cisplatin and other chemotherapeutic drugs, e.g., 5-fluorouracil and/or docetaxel. However, also the combination of both antibodies may have potential in recurrent/metastatic (R/M) HNSCC, in particular in cisplatin-resistant or -refractory cases or patients with comorbid disease, e.g. patients with impaired renal function. Methods To clarify potential benefit that may result from such combination, we used the FLAVINO assay, a short-time ex vivo assay to compare responsiveness of HNSCC to pembrolizumab, cetuximab and both combined regarding colony formation of epithelial cells of biopsy-derived tumor samples and their cytokine production within three days either without or with stimulation with 10 ng/mL interferon gamma (IFN-γ). Vascular endothelial growth factor A (VEGF), monocyte chemoattractant protein 1 (MCP-1 or CCL2), interleukin 6 (IL-6), IL-8, IFN-γ, and interferon gamma-induced protein 10 (IP-10 or CXCL10) in supernatants were measured by ELISA. Results We detected huge heterogeneity in response to cetuximab, pembrolizumab and both combined with and without IFN-γ stimulation. Moreover, we detected a link between IFN-γ induced IP-10 release and improved outcome in those HNSCC patients who were capable to respond to IFN-γ and pembrolizumab, cetuximab and both combined with a further increase in IP-10 production. We derived an “IP-10 score” that independent from clinical characteristics of HNSCC patients and therapy regimens applied was able to predict their outcome. Conclusions The heterogeneity in the ex vivo response of cetuximab, pembrolizumab and both combined with and without IFN-γ stimulation identifies subgroups of HNSCC patients with deviating OS.