Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms of Innate Immune Sensing of HTLV-1 and Viral Immune Evasion

Human T lymphotropic virus-1 (HTLV-1) was the first identified oncoretrovirus, which infects and establishes a persistent infection in approximately 10–20 million people worldwide. Although only ~5% of infected individuals develop pathologies such as adult T-cell leukemia/lymphoma (ATLL) or a neuroinflammatory disorder termed HTLV-1-asssociated myelopathy/tropical spastic paraparesis (HAM/TSP), asymptomatic carriers are more susceptible to opportunistic infections. Furthermore, ATLL patients are severely immunosuppressed and prone to other malignancies and other infections. The HTLV-1 replication cycle provides ligands, mainly nucleic acids (RNA, RNA/DNA intermediates, ssDNA intermediates, and dsDNA), that are sensed by different pattern recognition receptors (PRRs) to trigger immune responses. However, the mechanisms of innate immune detection and immune responses to HTLV-1 infection are not well understood. In this review, we highlight the functional roles of different immune sensors in recognizing HTLV-1 infection in multiple cell types and the antiviral roles of host restriction factors in limiting persistent infection of HTLV-1. We also provide a comprehensive overview of intricate strategies employed by HTLV-1 to subvert the host innate immune response that may contribute to the development of HTLV-1-associated diseases. A more detailed understanding of HTLV-1-host pathogen interactions may inform novel strategies for HTLV-1 antivirals, vaccines, and treatments for ATLL or HAM/TSP.
The Evaluation Forms of International Passenger Airport Hub in Southeast Asia

This research aims to present the selection of Asean international airports in order to establish the international passenger airport hub in Southeast Asia. The study focused on the airports in Southeast Asia region which most passengers travelling through as follows : Singapore’s Changi International Airport (SIN),Cambodia’s Phnom Pehn International Airport (PNH),Brunei’s Brunei international Airport (BWN), Indonesia’s Sugarno Hatta International Airport (CGK), Lao PDR’s Wattay International Airport (VTE), Malaysia’s Kuala Lumpur International Airport (KUL), Myanmar’s Rangoon International Airport (RGN), the Philippines’ Ninoy Aquino International Airport (MNL), Thailand’s Suvarnabhumi International Airport (BKK), and Vietnam’s Tan Son Nhat International Airport (SGN) as the optional airports. In order to acquire the most suitable areas in the engineering perspective, the Multiple Criteria Decision Making (MCDM) has been applied by using both Technique for Order Preference by Similarity to Ideal Solution-TOPSIS and Analytic Hierachy Process-AHP. There are 5 main criterions to be considered consisting of Geographical factors, Economic Factors, Functional Factors, Operational Factors and other factors. The two main research methodology to gain these factors which effecting the establishment of airport hubs consist of Delphi method and Regression analysis. The research will be the benefits for managing airports and developing their airport hub. Moreover the study of the research will be useful for Southeast Asia governments to determine the relevant policies and planning for aviation business development of the country.
AKT2 Loss Impairs BRAF-Mutant Melanoma Metastasis

Despite recent advances in treatment, melanoma remains the deadliest form of skin cancer, due to its highly metastatic nature. Melanomas harboring oncogenic BRAFV600E mutations combined with PTEN loss exhibit unrestrained PI3K/AKT signaling and increased invasiveness. However, the contribution of different AKT isoforms to melanoma initiation, progression, and metastasis has not been comprehensively explored, and questions remain whether individual isoforms play distinct or redundant roles in each step. We investigate the contribution of individual AKT isoforms to melanoma initiation using a novel mouse model of AKT isoform-specific loss in a murine melanoma model, and investigate tumor progression, maintenance, and metastasis among a panel of human metastatic melanoma cell lines using AKT-isoform specific knockdown studies. We elucidate that AKT2 is dispensable for primary tumor formation but promotes migration and invasion in vitro and metastatic seeding in vivo, while AKT1 is uniquely important for melanoma initiation and cell proliferation. We propose a mechanism whereby inhibition of AKT2 impairs glycolysis and reduces an EMT-related gene expression signature in PTEN-null BRAF-mutant human melanoma cells to limit metastatic spread. Our data suggest that elucidation of AKT2-specific functions in metastasis could inform therapeutic strategies to improve treatment options for melanoma patients. Graphical Abstract
High Resolution Face Editing with Masked GAN Latent Code Optimization

—Face editing is a popular research topic in the computer vision community that aims to edit a speciﬁc characteristic of a face image. Recent proposed methods are based on either training a conditional encoder-decoder Generative Adversarial Network (GAN) in an end-to-end fashion or on deﬁning an operation in the latent space of a pre-trained vanilla GAN generator model. However, these methods exhibit a certain degree of visual degradation and lack disentanglement properties in the edited images. Moreover, they usually operate on lower image resolution. In this paper, we propose a GAN embedding optimization procedure with spatial and semantic constraints. We optimize a latent code of a GAN, pre-trained on face dataset, to embed a ﬁxed region of the image, while imposing constraints on the inpainted regions with face parsing and attribute classiﬁcation networks. By latent code optimization, we constrain the result to follow an image probability distribution, as deﬁned by the GAN model. We use such framework to produce high image quality face edits. Due to the spatial constraints introduced, the edited images exhibit higher degree of disentanglement between the desired facial attributes and the rest of the image than other methods. The approach is validated in experiments on three datasets and in comparison with four state-of-the-art approaches. The results demonstrate that the proposed approach is able to edit face images with respect to several facial attributes with unprecedented image quality, while disentangling the undesired factors of variation. Code will be made available.
Racial and Ethnic Disparities in Accidental and Undetermined Drug Overdose Deaths - Rhode Island, 2016-2021.

BACKGROUND Over the last 21 years, drug overdose deaths have increased nationwide, particularly in Rhode Island (RI). The goal of this work is to identify populations that are disproportionately impacted by accidental drug overdose deaths to guide future intervention efforts. Methods: We obtained data on accidental and undetermined drug overdose deaths from the RI State Unintentional Drug Overdose Reporting System (SUDORS) database from 2016 to 2021. We compared basic demographic factors stratified by decedent race and ethnicity. Chi Square and Fisher's exact tests were used to determine differences in characteristics across racial groups. FINDINGS Across all race and ethnic groups, cocaine-involved (64.5%) fatal overdoses were higher among Black non-Hispanics. White, non-Hispanics (31.4%) were more likely to receive treatment for substance use disorder (SUD) when compared to minority groups. CONCLUSION To help address the gaps in treatment for SUD among minority groups, culturally responsive intervention efforts should prioritize connecting minority groups to treatment.
Surgeon factors but not hospital factors associated with length of stay after colorectal surgery – A population based study

Length of stay (LOS) after colorectal surgery (CRS) is a significant driver of healthcare utilization and adverse patient outcomes. To date, there is little high‐quality evidence in the literature examining how individual surgeon and hospital factors independently impact LOS. We aimed to identify and quantify the independent impact of surgeon and hospital factors on LOS after CRS.
A short peptide protects from age‐onset proteotoxicity

Aberrant protein aggregation jeopardizes cellular functionality and underlies the development of a myriad of late‐onset maladies including Alzheimer's disease (AD) and Huntington's disease (HD). Accordingly, molecules that mitigate the toxicity of hazardous protein aggregates are of great interest as potential future therapeutics. Here we asked whether a small peptide, composed of five amino acids (5MER peptide) that was derived from the human pro‐inflammatory CD44 protein, could protect model nematodes from the toxicity of aggregative proteins that underlie the development of neurodegenerative disorders in humans. We found that the 5MER peptide mitigates the toxicity that stems from both; the AD‐causing Aβ peptide and a stretch of poly‐glutamine that is accountable for the development of several disorders including HD, while minimally affecting lifespan. This protection was dependent on the activity of aging‐regulating transcription factors and associated with enhanced Aβ and polyQ35‐YFP aggregation. A transcriptomic analysis unveiled that the peptide modifies signaling pathways, thereby modulating the expression of various genes, including these, which are known as protein homeostasis (proteostasis) regulators such as txt‐13 and modifiers of proteasome activity. The knockdown of txt‐13 protects worms from proteotoxicity to the same extent as the 5MER peptide, suggesting that the peptide activates the transcellular chaperone signaling to promote proteostasis. Together, our results propose that the 5MER peptide should be considered as a component of future therapeutic cocktails for the treatment of neurodegenerative maladies.
Differentiating patients with obstructive sleep apnea from healthy controls based on heart rate - blood pressure coupling quantified by entropy-based indices

We introduce an entropy-based classification method for pairs of sequences (ECPS) for quantifying mutual dependencies in heart rate and beat-to-beat blood pressure recordings. The purpose of the method is to build a classifier for data in which each item consists of two intertwined data series taken for each subject. The method is based on ordinal patterns and uses entropy-like indices. Machine learning is used to select a subset of indices most suitable for our classification problem in order to build an optimal yet simple model for distinguishing between patients suffering from obstructive sleep apnea and a control group.
Dynamics in a behavioral–epidemiological model for individual adherence to a nonpharmaceutical intervention

Significance While SARS-CoV-2 transmission continues, adherence to nonpharmaceutical interventions (NPIs) is now largely based on individual decision-making, which itself depends on infection levels, adherence cost, and perceived risk of an infection. With a cross-scale behavioral–epidemiological model, we find that when partial adherence is the stable outcome, the transmission rate has no influence on endemic infection levels because individuals tend to adhere less to NPIs when infection levels decrease (and vice versa). However, we show that vaccination decreases infecteds and susceptibles in this setting. Furthermore, we find that a very effective NPI is only partially adhered to, whereas moderate efficacy can lead to complete adherence. Overall, our results illustrate the importance of vaccination and of the rational deployment of additional NPIs.
Early life factors associated with childhood trajectories of violence among the Birth to Twenty-Plus Cohort in Soweto, South Africa.

Violence against children (VAC) has devastating and long-term negative consequences on individuals' and society's health, social and economic well-being. There is limited research on the life course experience of VAC, especially in Africa. This study aimed to identify sub-groups of physical & sexual violence victimization patterns separately in childhood, and evaluate early life factors predicting violence trajectories. This study used data from ages 5 to 18 years from the ongoing prospective Birth to Twenty Plus cohort (Bt20+). Children with data on physical and sexual violence in at least 2-time points between 5 and 18 years were included in the analyses. Group-based trajectory modelling was employed to identify groups of children with similar patterns of violence over time, while multivariable logistic regression was used to identify early life factors associated with violence trajectory group membership. Separately, two trajectory groups of physical violence (adolescent limited (65.1%) and chronic increasing (34.9%)) and sexual violence (adolescent limited (74.1%) and late increasing (25.9%)) victimization were identified. Early life factors associated with a higher risk of chronic increasing trajectory group membership, after adjusting for covariates, were being male (aOR 1.67, 95% CI 1.31; 2.10) and having a mother with at least secondary education compared to higher education (aOR 1.73, 95% CI 1.08; 2.76). In addition, residing in middle, compared to low, socioeconomic households (aOR 0.68, 95% CI 0.50; 0.92) was protective against membership in this group. Residing in high compared to low socioeconomic households, was the only early life factor with marginally significant (aOR 0.63, 95% CI 0.42; 0.95) association with membership in the late-increasing sexual violence victimization trajectory group. In conclusion, children follow different violence victimization trajectories over childhood. Identifying early life factors predicting violence trajectories provides key prevention intervention areas that can mitigate childrens violence experience.
Cachexia and head and neck squamous cell carcinoma: A scoping review.

OBJECTIVE The objective of this paper was to provide an understanding of cachexia in relation to oral squamous cell carcinoma relevant to oral health care. The paper is a scoping review of aspects of the clinical presentation, aetiology and management of cachexia in relation to oral health and oral health care. METHODS A combined search of MEDLINE and EMBASE databases (via OVID) was conducted using the terms ([Head and Neck] OR [Oral Squamous Cell Carcinoma]) AND (Cachexia). Duplicates were removed and results were subsequently limited to studies published between 2000 and 2023, humans and English language. After screening and full-text assessment a total number of 87 studies were included in the review. RESULTS It is evident that cachexia is a not uncommon feature of patients with advanced malignancy of the head and neck driven by a multitude of mechanisms, induced by the tumour itself, that lead to reduced nutritional intake, increased metabolism and loss of adipose and skeletal tissue. CONCLUSION While a variety of nutritional, physical, psychological and pharmacological interventions may improve quality and duration of life, ultimately the diagnosis of cachexia in relation to head and neck cancer remains an indicator of poor life expectancy.
An End-to-End Deep Hybrid Autoencoder Based Method for Single-Cell RNA-Seq Data Analysis

Single-cell RNA sequencing technology provides powerful support for researchers to understand the complex mechanisms of cells at the single-cell level. Due to the high sparsity, technical noise, and computational complexity of single-cell transcriptome data, the existing data analysis methods are unable to effectively extract the fine-grained characteristics of scRNA-seq data, resulting in inaccurately analyze the heterogeneity of the individual cell from a great quantity of cell mixtures. To address these shortcomings, we proposed an end-to-end analysis method called dhaSCA, which integrates the Graph convolutional neural network (GCN) feature learning and downstream tasks such as classification and imputation into a unified deep learning manner. dhaSCA uses hybrid GCN-MLP deep autoencoder and to capture structural information between cells, and learn the low dimensional cell representation. It also introduces downstream tasks as constraints to guide the model to learn more accurate cell features. We conducted various experiments to evaluate the performance of dhaSCA based on eight real RNA-Seq datasets, including classification, imputation, clustering, and visualization. The results show that dhaSCA outperforms other state-of-the-art methods in these downstream tasks. Therefore, dhaSCA is able to obtain a richer representation of cells, and provides strong support for efficient analysis of single-cell data.
Study of Developmental Pattern of Tea Shoot Tenderness on the Base of Texture Analyser

Texture analyser was utilized to study shoot tenderness in tea cultivar Longjing 43 and Zhongcha 108.The evaluation method was established by taking maximum shearing force to determine shoot tenderness.Low maximum shearing force represents high shoot tenderness.The results showed that it is feasible to use texture analyser to determine shoot tenderness.There was a sharp decrease of shoot tenderness from the third to fifth node.Furthermore,the tenderness of the first and second nodes was relatively high.The shoot tenderness was correlated with maturity,spatial location,plucking time and variety.Pruning significantly increased the tenderness of the third and fourth nodes.A consistently changing pattern of tea shoot tenderness was found by texture analyser in this study,which provided a useful method to evaluate shoot tenderness and its keeping ability in tea plant.
Genome-Wide Identiﬁcation and Expression Analysis of the MADS Gene Family in Tulips ( Tulipa gesneriana )

: To investigate the cold response mechanism and low temperature regulation of ﬂowering in tulips, this study identiﬁed 32 MADS-box transcription factor family members in tulips based on full-length transcriptome sequencing, named TgMADS1-TgMADS32. Phylogenetic analysis revealed that these genes can be divided into two classes: type I and type II. Structural analysis showed that TgMADS genes from different subfamilies have a similar distribution of conserved motifs. Quantitative real-time PCR results demonstrated that some TgMADS genes (e.g., TgMADS3 , TgMADS15 , TgMADS16 , and TgMADS19 ) were signiﬁcantly upregulated in buds and stems under cold conditions, implying their potential involvement in the cold response of tulips. In summary, this study systematically identiﬁed MADS family members in tulips and elucidated their evolutionary relationships, gene structures, and cold-responsive expression patterns, laying the foundation for further elucidating the roles of these transcription factors in ﬂowering and the cold adaptability of tulips.
Spray-Dried Oregano Oil and Lavender Oil Microcapsules for Antibacterial Sports and Leisurewear

In this research, an industrially adaptable method is designed for antibacterial clothing. The essential oils of oregano and lavender were extracted using water vapor distillation, then they were spray-dried to form microcapsules. Comprehensive morphological analysis revealed the round shape of the microcapsules with smooth surfaces. The mean size of the optimum oregano and lavender microcapsules were 5.2 µm and 2.2 µm. The essential oils were detected in the polymeric matrix as peaks of microcapsules’ infrared spectra resembled both oils and polymer. Thermal analyses showed that encapsulation delays the degradation of the essential oil. The microcapsules were applied to six different fabrics used in sports and leisurewear by exhaustion. Scanning electron microscopy images indicated the existence of capsules after 10 washes. The antibacterial properties of cotton fabrics were assessed against Escherichia coli and Staphylococcus aureus in terms of the oil and washings. The developed products can serve as a long-lasting, natural antibacterial alternative to other products on the market.
A checklist of birds recorded in Guam's marine habitats

This checklist contains 77 species of birds that have been recorded in marine habitats on Guam (13o28’N, 144o45’E), Mariana Islands (Table 1). Included are 27 species of seabirds, 41 shorebirds and herons, four ducks, and five land birds. Only five of the species currently nest on the island, while 68 others are visitors that arrive annually or less frequently. Four land birds that were extirpated from the island or became extinct during the 1980s are listed because of their past use of mangroves. Five additional species are included as hypothetical species or were identified to genus only because definitive documentation of their occurrence is lacking. Guam is the largest (541 km), most populous (about 155,000 people), and southernmost island in the Marianas. For this report, I recognize five types of marine habitats that are used by birds, as follows: Offshore waters: These extend from the island’s fringing reef margins into deep open water. Within this zone are six submerged banks located 22-85 km southwest of Guam, and Rota Banks 19 km to the north, that are attractive to pelagic seabirds because of their baitfish populations. These pinnacles range in size from about 0.5-35 km and rise to within 30-150 m of the ocean’s surface. Lagoons: Apra Harbor (14.7 km) and Cocos Lagoon (10.7 km) are two sizable areas of relatively shallow and calm water enclosed by barrier reefs or breakwaters. Water depths reach 55 m. Reef flats: This habitat comprises the intertidal and subtidal zones between the shoreline and outer reef edge. Guam’s largest reef flats occur along its southern and central coasts and reach widths of up to 800 m. About 69 km of reef flat are present on the island.
IoTNetEMU - A Framework to Emulate and Test IoT Applications

Testing and validating IoT applications is inherently complex due to the number of devices involved that should communicate with each other and with cloud infrastructures. Models, emulators and testbeds are used to validate parts of the solution, but the gap between simulations and live experiences is still deep. To minimize this gap, we propose IoTNetEMU, a modular framework that combines several open-source components to provide a validation tool for developers and researchers. This paper describes the framework, shows how it can be used to test and validate an IoT application with minimal changes, and compares results collected using it with results from real devices.
A Systematic Analysis of Problems in Open Collaborative Data Engineering

Collaborative workflows are common in open-source software development. They reduce individual costs and improve the quality of work results. Open data shares many characteristics with open-source software, as it can be used, modified, and redistributed by anyone, for free. However, in contrast to open-source software engineering, collaborative data engineering on open data lacks a shared understanding of processes, methods, and tools. This article presents a systematic literature review of collaboration processes, methods, and tools in data engineering as performed by open data users. An additional interview study with practitioners confirms and enhances the findings and strengthens the resulting insights. We find an ecosystem with heterogeneous participants and no standardized processes, methods, and tools. Participants face a variety of technical and social challenges during their work. Our work provides a structured overview of collaboration systems in open collaborative data engineering, enabling further research. Additionally, we contribute preliminary guidelines for successful open collaborative data engineering projects and recommendations to increase its adoption for open data ecosystems.