Miracle-dz/UniFAR-FTUs huggingface dataset:
Deletion of an intronic polypyrimidine tract of porcine DNAH17 perturbs splicing and causes defective sperm flagella

Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P=4.22 x 10−15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1:c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.
Drainage-structuring of ancestral variation and a common functional pathway shape limited genomic convergence in natural high- and low-predation guppies

Studies of convergence in wild populations have been instrumental in understanding adaptation by providing strong evidence for natural selection. At the genetic level, we are beginning to appreciate that the re-use of the same genes in adaptation occurs through different mechanisms and can be constrained by underlying trait architectures and demographic characteristics of natural populations. Here, we explore these processes in naturally adapted high- (HP) and low-predation (LP) populations of the Trinidadian guppy, Poecilia reticulata. As a model for phenotypic change this system provided some of the earliest evidence of rapid and repeatable evolution in vertebrates; the genetic basis of which has yet to be studied at the whole-genome level. We collected whole-genome sequencing data from ten populations (176 individuals) representing five independent HP-LP river pairs across the three main drainages in Northern Trinidad. We evaluate population structure, uncovering several LP bottlenecks and variable between-river introgression that can lead to constraints on the sharing of adaptive variation between populations. Consequently, we found limited selection on common genes or loci across all drainages. Using a pathway type analysis, however, we find evidence of repeated selection on different genes involved in cadherin signalling. Finally, we found a large repeatedly selected haplotype on chromosome 20 in three rivers from the same drainage. Taken together, despite limited sharing of adaptive variation among rivers, we found evidence of convergent evolution associated with HP-LP environments in pathways across divergent drainages and at a previously unreported candidate haplotype within a drainage.
High Phase Synchronization in Alpha Band Activity in Older Subjects With High Creativity

Despite growing evidence that high creativity leads to mental well-being in older individuals, the neurophysiological bases of creativity remain elusive. Creativity reportedly involves multiple brain areas and their functional interconnections. In particular, functional magnetic resonance imaging (fMRI) is used to investigate the role of patterns of functional connectivity between the default network and other networks in creative activity. These interactions among networks play the role of integrating various neural processes to support creative activity and involve attention, cognitive control, and memory. The electroencephalogram (EEG) enables researchers to capture a pattern of band-specific functional connectivity, as well as moment-to-moment dynamics of brain activity; this can be accomplished even in the resting-state by exploiting the excellent temporal resolution of the EEG. Furthermore, the recent advent of functional connectivity analysis in EEG studies has focused on the phase-difference variable because of its fine spatio-temporal resolution. Therefore, we hypothesized that the combining method of EEG signals having high-temporal resolution and the phase synchronization analysis having high-spatio-temporal resolutions brings a new insight of functional connectivity regarding high creative activity of older participants. In this study, we examined the resting-state EEG signal in 20 healthy older participants and estimated functional connectivities using the phase lag index (PLI), which evaluates the phase synchronization of EEG signals. Individual creativity was assessed using the S-A creativity test in a separate session before the EEG recording. In the analysis of associations of EEG measures with the S-A test scores, the covariate effect of the intelligence quotient was evaluated. As a result, higher individual S-A scores were significantly associated with higher node degrees, defined as the average PLI of a node (electrode) across all links with the remaining nodes, across all nodes at the alpha band. A conventional power spectrum analysis revealed no significant association with S-A scores in any frequency band. Older participants with high creativity exhibited high functional connectivity even in the resting-state, irrespective of intelligence quotient, which supports the theory that creativity entails widespread brain connectivity. Thus, PLIs derived from EEG data may provide new insights into the relationship between functional connectivity and creativity in healthy older people.
VWCE Functions as a Tumor Suppressor in Breast Cancer Cells

Breast cancer remains a leading cause of cancer-related death, for which the majority of deaths result from metastases. Von Willebrand factor C and EGF domain (VWCE) is a member of the Von Willebrand factor (VWF) gene family; however, its function, regulatory mechanism, and clinical value in breast cancer remain unclear. In the present study, we sought to elucidate the role of VWCE in breast cancer metastasis. We examined the expression of VWCE in breast cancer tissues and normal control tissues of 50 breast cancer patients. We found that VWCE expression was downregulated in breast cancer cells and tissues compared to normal breast epithelial cells or the adjacent normal tissues. To explore the role of VWCE in human breast cancer development, we introduced a VWCE-overexpressing or control lentiviral vector into the breast cancer MDA-MB-453 and MDA-MB-231 lines in vitro. The overexpression of VWCE inhibited the proliferation, migration, invasion, and chemoresistance of the breast cancer cell lines. More importantly, the forced expression of VWCE suppressed tumor formation and metastasis in nude mice. iTRAQ-based quantitative proteomic analysis revealed that VWCE overexpression induced a 10-fold decrease in the level of WD-repeat domain 1 (WDR1) protein expression. Rescue experiments further verified that WDR1 was a downstream molecule of VWCE, and WDR1 overexpression reversed the above effects of VWCE overexpression on tumor growth. Therefore, VWCE may represent a novel tumor suppressor, for which its deregulation promotes breast cancer progression via the upregulation of WDR1.
Gut Microbiota Approach—A New Strategy to Treat Parkinson’s Disease

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by neuronal loss and dysfunction of dopaminergic neurons located in the substantia nigra, which contain a variety of misfolded α-synuclein (α-syn). Medications that increase or substitute for dopamine can be used for the treatment of PD. Recently, numerous studies have shown gut microbiota plays a crucial role in regulating and maintaining multiple aspects of host physiology including host metabolism and neurodevelopment. In this review article, the role of gut microbiota in the etiological mechanism of PD will be reviewed. Furthermore, we discussed current pharmaceutical medicine-based methods to prevent and treat PD, followed by describing specific strains that affect the host brain function through the gut-brain axis. We explained in detail how gut microbiota directly produces neurotransmitters or regulate the host biosynthesis of neurotransmitters. The neurotransmitters secreted by the intestinal lumen bacteria may induce epithelial cells to release molecules that, in turn, can regulate neural signaling in the enteric nervous system and subsequently control brain function and behavior through the brain-gut axis. Finally, we proved that the microbial regulation of the host neuronal system. Endogenous α-syn can be transmitted long distance and bidirectional between ENS and brain through the circulatory system which gives us a new option that the possibility of altering the community of gut microbiota in completely new medication option for treating PD.
Transcription termination and antitermination of bacterial CRISPR arrays

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences (“repeats”) interspersed with short, variable sequences (“spacers”). CRISPR arrays are transcribed and processed into individual CRISPR RNAs (crRNAs) that each include a single spacer, and direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho termination functionally limits the length of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of Rho termination in the evolution of bacterial CRISPR-Cas systems.
Peptide vaccine candidate mimics the heterogeneity of natural SARS-CoV-2 immunity in convalescent humans and induces broad T cell responses in mice models

We developed a global peptide vaccine against SARS-CoV-2 that addresses the dual challenges of heterogeneity in the immune responses of different individuals and potential heterogeneity of the infecting virus. PolyPEPI-SCoV-2 is a polypeptide vaccine containing nine 30-mer peptides derived from all four major structural proteins of the SARS-CoV-2. Vaccine peptides were selected based on their frequency as HLA class I and class II personal epitopes (PEPIs) restricted to multiple autologous HLA alleles of individuals in an in silico cohort of 433 subjects of different ethnicities. PolyPEPI-SCoV-2 vaccine administered with Montanide ISA 51VG adjuvant generated robust, Th1-biased CD8+ and CD4+ T cell responses against all four structural proteins of the virus, as well as binding antibodies upon subcutaneous injection into BALB/c and CD34+ transgenic mice. In addition, PolyPEPI-SCoV-2-specific, polyfunctional CD8+ and CD4+ T cells were detected ex vivo in each of the 17 asymptomatic/mild COVID-19 convalescents’ blood investigated, 1–5 months after symptom onset. The PolyPEPI-SCoV-2-specific T cell repertoire used for recovery from COVID-19 was extremely diverse: donors had an average of seven different peptide-specific T cells, against the SARS-CoV-2 proteins; 87% of donors had multiple targets against at least three SARS-CoV-2 proteins and 53% against all four. In addition, PEPIs determined based on the complete HLA class I genotype of the convalescent donors were validated, with 84% accuracy, to predict PEPI-specific CD8+ T cell responses measured for the individuals. Extrapolation of the above findings to a US bone marrow donor cohort of 16,000 HLA-genotyped individuals with 16 different ethnicities (n=1,000 each ethnic group) suggest that PolyPEPI-SCoV-2 vaccination in a general population will likely elicit broad, multi-antigenic CD8+ and CD4+ T cell responses in 98% of individuals, independent of ethnicity, including Black, Asian, and Minority Ethnic (BAME) cohorts.
Identification of Denatured Biological Tissues Based on Compressed Sensing and Improved Multiscale Dispersion Entropy during HIFU Treatment

Identification of denatured biological tissue is crucial to high-intensity focused ultrasound (HIFU) treatment, which can monitor HIFU treatment and improve treatment efficiency. In this paper, a novel method based on compressed sensing (CS) and improved multiscale dispersion entropy (IMDE) is proposed to evaluate the complexity of ultrasonic scattered echo signals during HIFU treatment. In the analysis of CS, the method of orthogonal matching pursuit (OMP) is employed to reconstruct the denoised signal. CS-OMP can denoise the ultrasonic scattered echo signal effectively. Comparing with traditional multiscale dispersion entropy (MDE), IMDE improves the coarse-grained process in the multiscale analysis, which improves the stability of MDE. In the analysis of simulated signals, the entropy value of the IMDE method has less fluctuation compared with MDE, indicating that the IMDE method has better stability. In addition, MDE and IMDE are applied to the 300 cases of ultrasonic scattered echo signals after denoising (including 150 cases of normal tissues and 150 cases of denatured tissues). The experimental results show that the MDE and IMDE values of denatured tissues are higher than normal tissues. Both the MDE and IMDE method can be used to identify whether biological tissue is denatured. However, the multiscale entropy curve of IMDE is smoother and more stable than MDE. The interclass distance of IMDE is greater than MDE, and the intraclass distance of IMDE is less than MDE at different scale factors. This indicates that IMDE can better distinguish normal tissues and denatured tissues to obtain more accurate clinical diagnosis during HIFU treatment.
Okra ( Abelmoschus esculentus Linn) inhibits lipopolysaccharide-induced inflammatory mediators in BV2 microglial cells

Purpose: To investigate the inhibitory effects of okra ( Abelmoschus esculentus Linn.) extract on the production of reactive oxygen species (ROS) and pro-inflammatory cytokines in lipopolysaccharide (LPS)-stimulated BV2 microglia. Methods: Okra was extracted with ethanol by Soxhlet extraction. Non-cytotoxic doses of okra at concentrations of 50, 100 and 200 μg/mL were used in this study. BV2 cells were cultured and treated with LPS in the presence or absence of okra at the concentrations indicated above. ROS, nitric oxide (NO), tumor necrotic factor alpha (TNF-α), interleukin 1 beta (IL-1β), phosphorylation levels of nuclear factor-kappa B (NF-kB) p65 and Akt were determined. Results: Treatment of BV2 cells with okra concentrations of 50, 100 and 200μg/mL significantly suppressed LPS-induced NO as well as ROS compared to untreated cells. There was also a significant decrease in the production of TNF-α and IL-1β in okra-treated BV2 microglia cells. The level of LPSinduced NF-kB p65 phosphorylation was significantly decreased by okra treatment. In addition, okra inhibited LPS-induced Akt phosphorylation, which is an upstream molecule of NF-kB. Conclusion: Okra exerts anti-oxidative and anti-inflammatory effects in LPS-stimulated BV2 microglial cells by suppressing Akt-mediated NF-κB pathway. This suggests that okra might be a valuable agent for the treatment of anti-neuroinflammatory diseases mediated by microglial cells. Keywords: Abelmoschus esculentus Linn, Inflammatory cytokines, Lipopolysaccharide, Neuroinflammation, Microglia, Reactive oxygen species
Detection of Algorithmically Generated Domain Names Using the Recurrent Convolutional Neural Network with Spatial Pyramid Pooling

Domain generation algorithms (DGAs) use specific parameters as random seeds to generate a large number of random domain names to prevent malicious domain name detection. This greatly increases the difficulty of detecting and defending against botnets and malware. Traditional models for detecting algorithmically generated domain names generally rely on manually extracting statistical characteristics from the domain names or network traffic and then employing classifiers to distinguish the algorithmically generated domain names. These models always require labor intensive manual feature engineering. In contrast, most state-of-the-art models based on deep neural networks are sensitive to imbalance in the sample distribution and cannot fully exploit the discriminative class features in domain names or network traffic, leading to decreased detection accuracy. To address these issues, we employ the borderline synthetic minority over-sampling algorithm (SMOTE) to improve sample balance. We also propose a recurrent convolutional neural network with spatial pyramid pooling (RCNN-SPP) to extract discriminative and distinctive class features. The recurrent convolutional neural network combines a convolutional neural network (CNN) and a bi-directional long short-term memory network (Bi-LSTM) to extract both the semantic and contextual information from domain names. We then employ the spatial pyramid pooling strategy to refine the contextual representation by capturing multi-scale contextual information from domain names. The experimental results from different domain name datasets demonstrate that our model can achieve 92.36% accuracy, an 89.55% recall rate, a 90.46% F1-score, and 95.39% AUC in identifying DGA and legitimate domain names, and it can achieve 92.45% accuracy rate, a 90.12% recall rate, a 90.86% F1-score, and 96.59% AUC in multi-classification problems. It achieves significant improvement over existing models in terms of accuracy and robustness.
First Record of Loggerhead Sea Turtles (Caretta caretta) in the Southern Gulf of California, Sinaloa, Mexico

Abstract Loggerhead turtles (Caretta caretta) are characterized by their transoceanic migratory patterns in the North Pacific Ocean, as individuals of this species originating from nesting beaches in Japan are known to forage along the Baja California Peninsula (BCP), Mexico. The nearshore waters of BCP serve as important foraging habitat for growth and development; however, the implementation of appropriate management strategies has been hindered by the paucity of data on the biology and distribution of the species, particularly for juveniles during their developmental migrations. We report for the first time the occurrence and distribution of loggerhead turtles in Sinaloa, Mexico, in the southernmost portion of the Gulf of California.
A Survey on Privacy Preserving Location Transfer for mobile users

Location-based services are quickly becoming immensely popular. In addition to services based on users current location, many potential services rely on users location history, or their spatial-temporal provenance.Literature survey deals with study of three method dealing with privacy preserving location transfer for mobile users;they are VeriPlace is a location proof architecture which is designed with privacy protection and collusion resilience Spatial-Temporal provenance Assurance with Mutual Proofs (STAMP) scheme.STAMP is designed for ad-hoc mobile users generating location proofs for each other in a distributed setting. However, it can easily accommodate trusted mobile users and wireless access points. A Privacy-Preserving Location proof Updating System (APPLAUS) in which co-located Blue tooth enabled mobile devices mutually generate location proofs and send updates to a location proof server. The method using for privacy preservation in above method are achieved through encryption with suitable protocol.
GENOMIC DNA ISOLATION OFGAJAH SUMATERA (Elephas maximus sumatrensis) IN ELEPHANT TRAINING CENTER, WAY KAMBAS NATIONAL PARK, EAST LAMPUNG

Elephant Training Center, Way Kambas National Park holds 44 captive sumatran elephants(Elephasmaximussumatrensis). This critically endangered species small population is in high risk of inbreeding. Its genomic DNA isolation was done to provide DNA amplification material for phylogenetic analysis. Individual blood sampels were collected from 8 different individuals based on age and sex characteristics and stored at EDTA-anticoagulated blood tubes. Qualitative test by 1% agarose gell electrophoresis, visualized by UV transiluminator Isolated genomic DNA was kept in -200C elution buffer solution.
A prediction-correction primal-dual hybrid gradient method for convex programming with linear constraints

: In recent years, the primal-dual hybrid gradient (PDHG) method has been widely used. However, the original PDHG method may diverge without additional conditions. Here we propose a convergent prediction-correction PDHG (PD-PDHG) method for canonical convex programming with linear constraints. The most important characteristic of the PD-PDHG method is that it adopts a new descent direction in the correction step, which does not converge to zero in general. Convergence of the new method is proved under mild assumptions. Finally, its efﬁciency is veriﬁed by compressive sensing
Effect of bioagents on the growth of rice against blast disease caused by Pyricularia oryzae

Rice (Oryza sativa L.) is the most important sources of food which provide diet more than 50% of the world population. Blast disease caused by Pyricularia oryzae, contributes a major reduction in rice production. The rampant use of fungicides causes deleterious effect on the environment. To minimise side effects of fungicides alternative means are opted. To concern about climate change, environment pollution and sustainable crop production disease management on sustainable basis is crucial. Thus, bioagents use as an alternative to chemical fungicides for the management of diseases. Effect of bio control agents (BCAs) evaluated against pathogen Pyricularia oryzae causing blast disease of rice in vitro and field condition. The result revealed that after three days of inoculation Trichoderma harzianum found most effective against Pyricularia oryzae which inhibited mycelial growth around 63%. Meanwhile Trichoderma viride inhibited 60% radial growth of Pyricularia oryzae. The best result shown by Trichoderma harzianum which inhibited pathogen by 63%, 56% and 41% at consecutive interval of three, five and seven days respectively. Dry shoot weight was found increased by T. harzianum (48.24%) followed by T. viride (45.98%) with respect to seed treated with pathogen. Among treatment of different bioagents the best yield was found 15.01 q/hac and 14.88 q/hac treatment with T. harzianum and T. viride against crop infected with pathogen. Seed treated with T. harzianum and T. viride the disease severity was found decreasing of 51.33% and 48.52% respectively. The application of bio control agents not only reduced the disease severity, promoted the plant growth and ultimately increased the grain yield significantly compared to control without any hazardous effect on environment.