Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates non-gradual expansion of the disease vector

Background Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. Results By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Ae. aegypti, sampled along an altitudinal temperature gradient in Nepal (200- 1300m), we identify adaptive traits and describe the species’ genomic footprint of climate adaptation to colder ecoregions. We found two clusters of differentiation with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300m) and all other lowland populations (≤ 800 m). We revealed non-synonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. Conclusion Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. This finding either indicates a differential invasion history to Nepal or local high-altitude adaptation explaining the population’s phenotypic cold tolerance. In any case, this highland population can be assumed to carry pre-adapted alleles relevant for the species’ invasion into colder ecoregions worldwide that way expanding their climate niche.
A neurocomputational theory of action regulation predicts motor behavior in neurotypical individuals and patients with Parkinson’s disease

Surviving in an uncertain environment requires not only the ability to select the best action, but also the flexibility to withhold inappropriate actions when the environmental conditions change. Although selecting and withholding actions have been extensively studied in both human and animals, there is still lack of consensus on the mechanism underlying these action regulation functions, and more importantly, how they inter-relate. A critical gap impeding progress is the lack of a computational theory that will integrate the mechanisms of action regulation into a unified framework. The current study aims to advance our understanding by developing a neurodynamical computational theory that models the mechanism of action regulation that involves suppressing responses, and predicts how disruption of this mechanism can lead to motor deficits in Parkinson’s disease (PD) patients. We tested the model predictions in neurotypical individuals and PD patients in three behavioral tasks that involve free action selection between two opposed directions, action selection in the presence of conflicting information and abandoning an ongoing action when a stop signal is presented. Our results and theory suggest an integrated mechanism of action regulation that affects both action initiation and inhibition. When this mechanism is disrupted, motor behavior is affected, leading to longer reaction times and higher error rates in action inhibition. Author Summary Humans can rapidly regulate actions according to updated demands of the environment. A key component of action regulation is action inhibition, the failure of which contributes to various neuropsychiatric disorders. When faced with multiple choices, dealing with conflicting information, or current actions become inappropriate or unwanted, we should be able to pause or completely abandon actions. Despite extensive efforts to understand how the brain selects, pauses, and abandons actions based on environmental demands, the mechanisms underlying these action regulation functions and, perhaps more importantly, how they inter-relate remain elusive. Part of this challenge lies in the fact that these mechanisms were rarely explored together, making it difficult to develop a unified theory that explains the computational aspects of action regulation functions. The current study introduces a large-scale model that better characterizes the computations of action regulation functions, how they are implemented within brain networks that involve frontal, motor and basal ganglia (BG) circuits, and how disruption of these circuits can lead to deficits in motor behavior seen in Parkinson’s disease (PD). The model was developed by studying the motor behavior of healthy individuals and PD patients in three motor tasks that involve action inhibition. Overall, the model explains many key aspects on how the brain regulates actions that involve inhibitory processes, opening new avenues for improving and developing therapeutic interventions for diseases that may involve these circuits.
Whole-Genome Profiling of Ethyl Methanesulfonate Mutagenesis in Tomato

The induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but having an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of mutagenized individuals uncovers the complete spectrum of mutations in the genome. We sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected ca. 41 million SNPs and 5.5 million short-INDELs. We found a very high average density of mutations 1/3.05 Kb compared to other species. About 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than 1/3rd of genes in the mutagenized population had one or more deleterious mutations predicted by SIFT. Nearly 1/4th of deleterious genes mapped on tomato metabolic pathways modulating multiple pathway steps. Contrary to the reported GC>AT transition bias for EMS, we found EMS also produced nearly equal AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is least mutagenic towards EMS. The reduction in carotenoids in ζ-carotene isomerase mutant fruits and chloroplasts relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our study makes a large repertoire of mutations accessible to genetic studies and the breeding of tomato.
Gut microbiota analysis of the western honeybee (Apis mellifera L.) infested with the mite Varroa destructor reveals altered bacterial and archaeal community

The western honeybee, Apis mellifera L. , is a crop pollinator that makes royal jelly and other hive products. However, widespread concerns arise about opportunistic diseases (e.g., bacteria, fungi, or mites) or chemicals that have an effect on the health and number of colonies, as well as their activity. The relationships between the gut microbiota and its host are currently being researched extensively. The effects of Varroa destructor infection on the gut microbial community, in particular, have received little investigation. This work utilized amplicon sequencing of the bacterial and archaeal 16S rRNA genes to assess the bacterial and archaeal communities of adult bee groups (healthy and affected by Varroa designed in NG and VG, respectively) and larvae from Varroa destructor-infected hives. Our results suggest that the genus Bombella was substantially dominant in larvae, while the genera Gillamella, unidentified Lactobacillaceae, and Snodgrassella were significantly dominant in adult bees. NG and VG, on the other hand, did not differ statistically significantly. The PICRUSt study revealed a significant difference in the KEGG classifications of larvae and adult bee groups. A greater number of genes involved in cofactor and vitamin production were identified in larvae. Additionally, despite the complexity of the honeybee’s bacterial community, all groups exhibited a straightforward archaeal community structure. Surprisingly, methanogen was detected in low abundance in the microbiota of honeybees. In summary, larvae and adult bees infected with Varroa destructor exhibit altered gut microbiota composition and function.
Stress fibers orient traction forces on micropatterns: A hybrid cellular Potts model study

Adhering cells exert traction forces on the underlying substrate. We numerically investigate the intimate relation between traction forces, the structure of the actin cytoskeleton, and the shape of cells adhering to adhesive micropatterned substrates. By combining the Cellular Potts Model with a model of cytoskeletal contractility, we reproduce prominent anisotropic features in previously published experimental data on fibroblasts, endothelial cells, and epithelial cells on adhesive micropatterned substrates. Our work highlights the role of cytoskeletal anisotropy in the generation of cellular traction forces, and provides a computational strategy for investigating stress fiber anisotropy in dynamical and multicellular settings. Author summary Cells that make up multicellular life perform a variety of mechanical tasks such as pulling on surrounding tissue to close a wound. The mechanisms by which cells perform these tasks are, however, incompletely understood. In order to better understand how they generate forces on their environment, cells are often studied in vitro on compliant substrates, which deform under the so called “traction forces” exerted by the cells. Mathematical models complement these experimental approaches because they help to interpret the experimental data, but most models for traction forces on adhesive substrates assume that cells contract isotropically, i.e., they do not contract in a specific direction. However, many cell types contain organized structures of stress fibers - strong contracting cables inside the cell - that enable cells to exert forces on their environment in specific directions only. Here we present a computational model that predicts both the orientations of these stress fibers as well as the forces that cells exert on the substrates. Our model reproduces both the orientations and magnitudes of previously reported experimental traction forces, and could serve as a starting point for exploring mechanical interactions in multicellular settings.
Inspeção de Usabilidade em Organizações de Desenvolvimento de Software - Uma Experiência Prática

Users’ acceptability of Web applications relies strictly on these applications’ usability, which can be improved through the use of inspections. This paper reports an industrial case study of usability inspection, where developers and requirements assessors applied an inspection technique to evaluate the usability of newly developed modules. The results of this case study indicate the feasibility of performing usability inspections with the participation of a software project’s stakeholders, even when stakeholders are not usability experts.
Teaching and Learning Enhancement Based on Telegram Social Media Tool

This study investigates a perception of students on the implementation of a Telegram application as an enhancement tool for teaching and learning. The population of this study is 66 students who are studying a Bachelor of Electrical and Electronic Engineering programme at Universiti Teknologi MARA (Pulau Pinang). The study has been conducting on Mac – September 2015 academic semester. The students have been using the Telegram tool in their teaching and learning process during the academic semester. Next, an online survey consisting of a number of agreement-level questions and open-ended questions are developed in google form. At the end of the semester, the form has been distributed to students via a link created in Telegram discussion groups to collect students’ valuable feedback. The student feedbacks have been analyzed to obtain the results of their perception on the Telegram application as an enhancement tool for teaching and learning process. The results show that Telegram application support teaching and learning enhancement by providing a quick way and easy platform for sharing information.
Analysis of factors influencing first year University Undergraduate performance in selected pure Mathematics courses at the National University of Science and Technology – Zimbabwe

In 2012, the National University of Science and Technology (NUST) in Zimbabwe reviewed the University qualification entry cut-off points downwards in the Applied Mathematics Department. Following the review, there has been a worrisome and distinct change in student performance in first year mathematics courses. To explore the possible causes of the poor performance amongst students, a two-stage probability sampling technique was used to collect secondary data covering mainly admission entry level qualification for each student. A one-way Sir Ronald Fisher’s Analysis of Variance model (ANOVA) was used to explore the contribution of various hypothesised factors to performance in first year undergraduate courses. Mathematics grade at advance level and overall performance in all subjects done at Advanced level by a student have a significant influence on his or her first year pure Mathematics courses performance at NUST. We recommend that the Department should employ remedial strategies to first year pure Mathematics courses if students with low scores in advance level mathematics are to be admitted. Instead of focusing on service courses with large classes only, the Department should prioritise allocating extra tutorial hours to pure Mathematics courses. Furthermore the effects of brain drain cannot be ignored, hence the University should find ways to curb or deal with the gap that the highly experienced staff who left, created.
Tax Incentive Policy and Enterprise Innovation: From Enterprise Heterogeneous Perspective

In the study, data of Chinese listed companies in city Hangzhou, Ningbo and Wenzhou from 2012 to 2019 are used for detailed analysis. According to the data analysis, we have got several results: (1) the tax incentive policy has a significant promoting effect on the innovation activities of enterprises. (2) For such microlevel data, we also can get more detailed conclusion by enterprise heterogeneity. Heterogeneous factors do affect the effect of tax incentives on enterprise innovation input. Based on these findings, we can provide well-directed suggestions for future actions of enterprises and policy makers.
Behind Front Pembela Islam (FPI) Movement: Can Social Value Orientation Influence Religious Prejudice?

Abstrak: This research aims to identify the roles of social value orientation on religious prejudice in Front Pembela Islam (FPI) towards others religious community. The sample was several members of Front Pembela Islam (FPI) in East Java involving 113 people and it was collected by accidental sampling technique. Measure instrument used was Social Value Orientation scale adopted from Akhrani (2016) with the theory of Eek and Garling (2008), for Religious Prejudice scale was designed by Ahmadi (1991) theory. Reliability of Social Value Orientation was 0.81 and Religious Prejudice was 0.94. The data was analyzed using dummy variable in regression technique. The results of analysis show that social value orientation does not affect the religious prejudice so that the alternative hypothesis (Ha) in this study is rejected. It can be seen from coefficient of p value 0.83 (p>0.05). In addition, coefficient value between variables obtained can be categorized as low (-0.02).
ExpressionInversely Regulates Fas Ligand and Bcl6 and Germinal Center Formation and JAB1 Is Essential for B Cell Development

Jun activation domain-binding protein 1 (JAB1) regulates ubiquitin-dependent protein degradation by deneddylation of cullin-based ubiquitin ligases and, therefore, plays a central role in regulating proliferation and apoptosis. Because these processes are decisive for B cell development, we investigated JAB1 functions in B cells by establishing a mouse strain with a B cell-speciﬁc JAB1 deletion. We show that JAB1 is essential for early B cell development, because the ablation of JAB1 expression blocks B cell development between the pro-B and pre-B cell stages. Furthermore, JAB1 deletion leads to aberrant expression of the apoptosis-triggering protein Fas ligand in pro-B cells. Concomitant B cell-speciﬁc overexpression of the antiapoptotic protein Bcl2 partially reverses the block in B cell development; rescued JAB1-deﬁcient B cells reachtheperiphery and produce protective class-switched Abs after Borrelia burgdorferi infection. Interestingly, B cell-rescued mice exhibit no germinal centers but a striking extrafollicular plasma cell accumulation. In addition, JAB1 is essential for Bcl6 expression, a transcriptional repressor required for germinal center formation. These ﬁndings identify JAB1 as an important factor in checkpoint control during early B cell development, as well as in fate decisions in mature Ag-primed B cells. The Journal of Immunology , 2012, 188: 2677–2686.
No Evidence of Benefits of Host Nano-Carbon Materials for Practical Lithium Anode-Free Cells

Nano-carbon-based materials are widely reported as lithium host materials in lithium metal batteries (LMBs); however, researchers report contradictory claims as to where the lithium plating occurs. Herein, the use of pure hollow core-carbon spheres coated on Cu (PHCCSs@Cu) to study the lithium deposition behavior with respect to this type of structure in lithium anode-free cells is described. It is demonstrated that the lithium showed some initial and limited intercalation into the PHCCSs and then plated on the external carbon walls and the top surface of the carbon coating during the charging process. The unfavorable deposition of lithium inside the PHCCSs is discussed from the viewpoint of lithium-ion transport and lithium nucleation. The application potential of PHCCSs and the data from these LMB studies are also discussed.
MACHINE LEARNING APPROACH FOR ATTRIBUTE IDENTIFICATION AND QUALITY PREDICTION OF RED WINE

: The paper focuses on quality prediction analysis of red wine which contains the attributes such as fixed acidity, volatile acidity, citric acid, residual sugar, chlorides, free sulfuric acids, total sulfuric acid, density, pH, sulphates, alcohol - quantity. The Prediction is evaluated through various machine learning algorithms such as Logistic Regression, Support Vector Machine, Decision Tree Classifier and Random Forest Classifier. By applying these algorithms, a detailed view of the tested results and the trained results of the machines were obtained. The results were visualized using Boxplot, Correlation matrix, joint plot. The Support Vector Machine (SVM) algorithm yields highest Accuracy of 87.5%, when used with grid search CV the accuracy was approximately equal to 90%.
Evidence-Based Nutrition Interventions Improved Adolescents’ Knowledge and Behaviors in Indonesia

Adolescence is a nutritionally vulnerable and critical life stage. However, few programs and policies focus on improving adolescent nutrition in Indonesia. To address this gap, we implemented a gender-responsive package of interventions: (1) breakfast and weekly iron-folic acid supplementation (WIFS), (2) a school-based nutrition education program, and (3) a social behavior change communication strategy. We surveyed 514 adolescents at baseline (2019) and endline (2020) in Klaten and Lombok Barat districts in Indonesia. The survey included a knowledge assessment on nutrition, as well as indicators of attitudes and behaviors on diet, physical activity, and WIFS. We employed multivariable linear and logistic regression to test for pre–post intervention differences. Overall knowledge was significantly higher post-intervention (β: 3.3; 95% confidence interval [CI]: 2.6, 3.9). Diet diversity was high at both timepoints, however, at post-intervention there was significantly higher odds of consuming vitamin A-rich fruits and vegetables (Odds Ratio [OR]: 1.5; 95% CI: 1.1, 2.0) and lower odds of consuming sugar-sweetened beverages (OR: 0.4; 95% CI: 0.3, 0.5). Post-intervention, there was higher odds of reporting 60 min of daily physical activity (OR: 2.3; 95% CI: 1.7, 3.2) and WIFS among girls (OR: 6.7; 95% CI: 1.5, 30.9). The package of interventions may be a promising first step to improving adolescent nutrition in Indonesia.
Biological and Clinical Attributes of Sporothrix globosa, a Causative Agent of Sporotrichosis

Abstract Sporotrichosis is an important subcutaneous mycosis with high prevalence and threat to human and animal health worldwide. Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa are the main etiological agents of this disease; and even though many efforts have been made recently to understand the Sporothrix-host interaction, little is known about S. globosa, an underestimated species. This organism shows the lowest virulence among the members of the Sporothrix pathogenic clade and represents an important pathogenic agent due to its global distribution. Here, we offer a review with all the known information about S. globosa, including its genome and proteomic information, and compare it with S. schenckii and S. brasiliensis, to explain the differences observed among these species, in terms of virulence, the host immune response, and the antifungal sensitivity. Also, we provide the gene prediction of some S. globosa putative virulence factors.
Integrated geophysical technique for groundwater salinity delineation, an approach to agriculture sustainability for Nankana Sahib Area, Pakistan

Abstract Owing to the climatic dryness and shortage of surface water, Pakistani farmers have been forced to rely on groundwater resources to meet the irrigation demand for crops. Pumping an excessive amount of water from the aquifers is turning it brackish. Our study aims to select a suitable depth of freshwater for installing tube wells in a study area, Tehsil Nankana Sahib. Sixteen vertical electrical soundings (VES) were arrayed in this study area, and water samples were also collected to record their electrical conductivity. The interpolation maps for different parameters were generated by using the inverse distance weighted interpolation method. The obtained results depict that the central and southeastern region has good groundwater at depths from 60 to 90 m, the northeastern region has marginally fit water, while the northwestern region is marked as having an unfit groundwater zone. This research article is not only a case study but also can be used for other areas of Punjab, Pakistan, facing similar groundwater problems. However, the comparison of VES results with borehole data is critical to achieve better accuracy. An extensive exploratory borehole study of the area is recommended to further characterize the subsurface lithology.