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Ghimire, P.

Publications and source records attributed to Ghimire, P..

8 recordsLinked to original sources

ASD-FER: An Annotated Multi-Class Benchmark and Comparative Study for Facial Emotion Recognition in Children with Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) affects social interaction and communication, and automatically recognizing emotions from the facial expressions of children with ASD remains challenging. A key barrier to facial emotion recognition (FER) in children with ASD is the absence of ASD-specific datasets with proper emotion-level annotations. To address this, we present ASD-FER, a benchmark of 2,779 facial images of children with ASD annotated across six emotion categories by three independent annotators using majority voting. We evaluate nine models -- CNN, SVM, AlexNet, ResNet34, ResNet50, MobileNetV2, and three backbone configurations of our proposed task-specific architecture, EQFormer: ViT, Swin-T, and a compact Hybrid CNN-Transformer (HybridT) -- under stratified 10-fold cross-validation and a held-out 90/10 evaluation. ResNet50 led conventional models at 84.89% mean cross-validation accuracy; among transformer-based models, ViT led with 88.27%, followed by Swin-T at 88.02% and HybridT at 86.58%. On the held-out set, ViT achieved the highest overall accuracy (91.01%), while Swin-T obtained the best balanced accuracy (74.47%) and macro-F1 (0.7078); HybridT remained competitive at 89.57% accuracy with a fraction of the parameters. To support explainability, Grad-CAM visualizations highlighted attention on emotion-relevant facial regions -- eyes, eyebrows, and mouth -- with Swin-T the most spatially focused and the HybridT the most parameter-efficient (2.66M). Class imbalance and cross-dataset generalization remain open challenges.

neuroscience↗

Integrated landscape genomics reveals biogeography and climate-driven local adaptation in high-altitudes

High-elevation environments harbor unique species adapted to altitudinal and environmental extremes. However, due to logistical challenges of sampling such species throughout their distribution across steep and varied terrains, studies often lack comprehensive evidence to understand patterns of population divergence, local adaptation, and how current adaptations may influence future vulnerability. In this study, we utilized Tibetan Partridge (Perdix hodgsoniae), a high-altitude endemic bird found between 2800-5000 meters across the arid western and humid northeastern regions of the Sino-Himalayan landscape. This regions complex topography-characterized by tall mountains, deep valleys, and contrasting climatic conditions provided opportunities for investigating population divergence, local adaptation, and climate-related vulnerability. We integrated population-scale whole-genome sequencing with ecological, climatic, landscape, and morphological data to examine current patterns of local adaptation and forecast future risks. Our findings show that both biogeographic barriers and climatic variation drive rapid population divergence in P. hodgsoniae, reflected in distinct morphological traits and population genetic structure. Western populations, inhabiting dry and fragmented landscapes, exhibit adaptations to temperature extremes with low genetic diversity, reduced habitat suitability, limited gene flow, and weak connectivity--factors that increase their vulnerability to future environmental changes. In contrast, northeastern populations, living in more humid regions, show genetic adaptations linked to precipitation, maintain high genetic diversity and habitat connectivity, and may serve as evolutionary refugia under future climate scenarios. This study underscores the value of integrating genomic, ecological, and landscape data to reveal mechanisms of divergence and adaptation, and to develop robust predictions for conservation planning under rapidly changing environmental conditions.

evolutionary biology↗

A complete reference genome assembly and annotation of the Black Redstart (Phoenicurus ochruros)

The Black Redstart (Phoenicurus ochruros) is one of the most widely distributed species, occupying diverse habitats and exhibiting remarkable altitudinal migration, making it suitable model for studying altitudinal migration and high-altitude adaptation. In this study, we present the first reference genome of Phoenicurus ochruros, generated using PacBio HiFi long-read sequencing. The nuclear genome is 1.37 Gb in length, assembled into 296 scaffolds with a scaffold N50 of 29.9 Mb. Multiple complementary genome validation approaches - including BUSCO analysis, mapping of raw PacBio HiFi reads, and comparative genomics analysis - confirmed the high contiguity and gene-space completeness of the genome. The Black Redstart genome contains one of the highest proportions of transposable elements among passerines (30.58%), second only to Bells Sparrow (Artemisiospiza belli), 31.2%. We further integrated RNA-seq data, protein homology evidence, and ab initio gene prediction to build high-quality genome annotation of 18,609 genes in the P. ochruros genome. This genomic resource provides invaluable resource for evolutionary genomics studies of passerines and explore genetic basis of high-altitude adaptation.

genomics↗

Unraveling cryptic diversity: Genomic approaches to study the taxonomy and evolution of Woolly-necked storks using museum specimens

The availability of large-scale genomics data for current research in evolutionary biology has enabled a comprehensive examination of the intricate interplay between diverse evolutionary processes associated with speciation. Despite these advancements, the genomic basis of taxonomic classification remains challenging in many species, one such example being the Woolly-necked storks (Ciconia sps.). The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification (C. episcopus and C. microcelis) that has been a matter of contention and ambiguity. Asian and African Woollynecks were just recently recognized as different species based on their morphological differences, however genetic/genomic studies on Woolly-necked storks are lacking. In this study, we have used [~]70-year-old museum samples to explore the taxonomy and evolution of the Woolly-necked storks. We used a whole-genome sequencing strategy and generated 13.5 million single nucleotide polymorphisms (SNPs) that were polymorphic among populations of Asian and African Woollynecks. Our study has revealed that Asian and African Woollyneck are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies C. e. neglecta and C. e. episcopus suggesting this classification harbors cryptic diversity that requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results suggest populations-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds. Moreover, our study also provides historical genomic resources to examine genomic signatures of local adaptation associated with the distribution, ecology, and evolution of African and Asian Woollynecks.

evolutionary biology↗

Role of multiple pericentromeric repeats on heterochromatin assembly

Although the length and constituting sequences for pericentromeric repeats are highly variable across eukaryotes, the presence of multiple pericentromeric repeats is one of the conserved features of the eukaryotic chromosomes. Pericentromeric heterochromatin is often misregulated in human diseases, with the expansion of pericentromeric repeats in human solid cancers. In this article, we have developed a mathematical model of the RNAi-dependent methylation of H3K9 in the pericentromeric region of fission yeast. Our model, which takes copy number as an explicit parameter, predicts that the pericentromere is silenced only if there are many copies of repeats. It becomes bistable or desilenced if the copy number of repeats is reduced. This suggests that the copy number of pericentromeric repeats alone can determine the fate of heterochromatin silencing in fission yeast. Through sensitivity analysis, we identified parameters that favor bistability and desilencing. Stochastic simulation shows that faster cell division and noise favor the desilenced state. These results show the unexpected role of pericentromeric repeat copy number in gene silencing and elucidate how the copy number of silenced genomic regions may impact genome stability. Author SummaryPericentromeric repeats vary in length and sequences, but their presence is a conserved feature of eukaryotes. This suggests that the repetitive nature of pericentromeric sequences is an evolutionarily conserved feature of centromeres, which is under selective pressure. Here we developed a quantitative model for gene silencing at the fission yeast pericentromeric repeats. Our model is one of the first models which incorporates the copy number of pericentromeric repeats and predicts that the number of repeats can solely govern the dynamics of pericentromeric gene silencing. Our results suggest that the repeat copy number is a dynamic parameter for gene silencing, and copy-number-dependent silencing is an effective machinery to repress the repetitive part of the genome.

systems biology↗

Coexistence between similar invaders: The case of two cosmopolitan exotic insects

Biological invasions are usually examined in the context of their impacts on native species. However, few studies have examined the dynamics between invaders when multiple exotic species successfully coexist in a novel environment. Yet, long-term coexistence of now established exotic species has been observed in North American lady beetle communities. Exotic lady beetles Harmonia axyridis and Coccinella septempunctata were introduced for biological control in agricultural systems and have since become dominant species within these communities. In this study, we investigated coexistence via spatial and temporal niche partitioning among H. axyridis and C. septempunctata using a 31-year dataset from southwestern Michigan, USA. We found evidence of long-term coexistence through a combination of small-scale environmental, habitat, and seasonal mechanisms. Across years, H. axyridis and C. septempunctata experienced patterns of cyclical dominance likely related to yearly variation in temperature and precipitation. Within years, populations of C. septempunctata peaked early in the growing season at 550 degree days, while H. axyridis populations grew in the season until 1250 degree days, and continued to have high activity after this point. Coccinella septempunctata was generally most abundant in herbaceous crops, whereas H. axyridis did not display strong habitat preferences. These findings suggest that within this region H. axyridis has broader habitat and abiotic environmental preferences, while C. septempunctata thrives under more specific ecological conditions. These ecological differences have contributed to the continued coexistence among these two invaders. Understanding mechanisms that allow coexistence of dominant exotic species contributes to native biodiversity conservation management of invaded ecosystems. Open research statementData are already published and publicly available, with those items properly cited in this submission. This submission uses novel code, which is provided, per our requirements, in an external repository to made available in perpetuity, and are available at https://github.com/ReproducibleQM/space_invader. Data sets utilized for this research (Landis 2020) are housed at EDI here: https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-kbs.23.30 (doi:10.6073/pasta/f0776c1574808b08c484c1f7645a7357). Weather data was downloaded directly from the Kellogg Biological Station data repository (https://lter.kbs.msu.edu/datatables/7) and downloading the full record. An archival record of these data are available at https://portal.edirepository.org/nis/mapbrowse?packageid=knb-lter-kbs.2.107 (doi:10.6073/pasta/4c30523bae14c4340e4d9c90e72f90c4). Because both databases are living and subject to update as data is collected, databases as used within this study are mirrored within the code repository as CSV files.

ecology↗

Epidemiology of Dengue viral infection in Nepal: 2006-2019

BackgroundDengue is one of the newest emerging diseases in Nepal with increasing burden and geographic spread over the last 14 years. The main objective of this study was to explore the spatio-temporal epidemiological patterns of Dengue since its first report (2006) till 2019 in Nepal. MethodsThis study is a retrospective analysis of dengue data available from the Epidemiological Disease Control Division (EDCD) of Government of Nepal. The data in this study cover the last 14 years (2006-2019) of reported dengue cases in Nepal. Epidemiological trend and spatio-temporal analyses were performed. Maps of reported case incidence were created using QGIS version 3.4. ResultsSince the first report of dengue in a foreigner in 2004, Nepal reported a total of 17,992 dengue cases in 68 districts of Nepal in 2019. The incidence was approximately five times higher in 2018 (Incidence Rate Ratio (IRR): 4.8; 95% CI: 1.5 - 15.3) and over 140 times higher in 2019 (IRR: 141.6; CI: 45.8 - 438.4). Population density was not a statistically significant predictor of case incidence. Mean elevation had a negative association with case incidence. A one standard deviation increase in elevation was associated with a 90% decrease in reported case incidence (IRR: 0.10; CI: 0.01 - 0.20). However, the association with mean elevation varied across the years. In comparison to 2016, incidence was greater at higher elevations in 2018 (IRR: 22.7; CI: 6.0 - 86.1) and 2019 (IRR: 9.6; CI: 2.6 - 36.1). ConclusionThere is a high risk of dengue outbreak in the Terai region with increasing spread towards the mid-mountains and beyond as seen over the last 14 years. Urgent measures are required to increase the availability of diagnostics and resources to mitigate future dengue epidemics. Findings from this study can inform the spatio-temporal distribution of dengue and can help in resource allocation and priority setting for future epidemic. Author summaryDengue in humans is caused by four different serotypes (DENV-1, DENV-2, DENV-3 & DENV-4). Globally it is the most pervasive vector borne diseases with increasing number of cases in recent years. Dengue is one of the youngest emerging diseases in Nepal with increasing cases and spread from the tropical lowland to the highland (hilly) regions. We conducted a spatio-temporal analysis of national data to consolidate the information using QGIS to measure the dengue incidence at district levels of Nepal. Spatio-temporal analysis exploring the incidence and distribution of dengue cases aids in identification of high-risk areas which can ultimately enable national dengue programme to mobilize and allocate resources for the control and treatment. This study shows, the persistent high risk of dengue outbreak in lowland Terai region with annual rise in the risk of spread towards the mid-mountains and beyond. Urgent measures are required to increase the diagnostics and resources to mitigate the epidemic burden of dengue in Terai and peripheral regions.

microbiology↗