Miracle-dz/UniFAR-FTUs huggingface dataset:
The Prognostic Signature and Potential Target Genes of Six Long Non-coding RNA in Laryngeal Squamous Cell Carcinoma

Studies have shown that long non-coding RNA (lncRNA) may act as the carcinogenic factor or tumor suppressor of laryngeal squamous cell carcinoma (LSCC). This study aims to identify the prognostic value and potential target protein-coding genes (PCGs) of lncRNAs in LSCC. The LSCC datasets were collected from The Cancer Genome Atlas (TCGA). Statistical and bioinformatic methods were used to establish and evaluate the prognostic model, identify the correlation between lncRNAs and clinical characteristics, and screen for PCGs co-expressed with lncRNAs. Weighted gene co-expression network analysis (WGCNA) identified PCG modules associated with clinical characteristics. The expression of lncRNAs and PCGs was analyzed using our LSCC patients by RT-qPCR. LINC02154, LINC00528, SPRY4-AS1, TTTY14, LNCSRLR, and KLHL7-DT were selected to establish the prognostic model. The overall survival (OS) of low-risk patients forecasted by the model was significantly better than high-risk patients. Receiver operating characteristic (ROC) curve and concordance index (C-index) validated the accuracy of the prognostic model. Chi-square test showed that six lncRNAs were associated with one of the clinical characteristics, i.e., gender, clinical stage, T and N stage, respectively. WGCNA identified PCG modules associated with gender, clinical stage, T and N stage. We took the intersection of the PCG modules of WGCNA, the differentially expressed PCGs between LSCC and normal samples, and the PCGs co-expressed with six lncRNAs. The intersection PCGs survival analysis showed that four PCGs, i.e., STC2, TSPAN9, SMS, and TCEA3 affected the OS of LSCC. More importantly, the differential expression of six lncRNAs and four PCGs between LSCC and normal samples was verified by our LSCC patients. In conclusion, we successfully established a prognostic model based on six-lncRNA RiskScore and initially screened the potential target PCGs of six lncRNAs for further basic and clinical research.
Host Induced Gene Silencing Targeting Aspergillus flavus aflM Reduced Aflatoxin Contamination in Transgenic Maize Under Field Conditions

Maize (Zea mays L.) is one of the major crops susceptible to Aspergillus flavus infection and subsequent contamination with aflatoxins, the most potent naturally produced carcinogenic secondary metabolites. This pathogen can pose serious health concerns and cause severe economic losses due to the Food and Drug Administration (FDA) regulations on permissible levels of aflatoxins in food and feed. Although biocontrol has yielded some successes in managing aflatoxin contamination, enhancing crop resistance is still the preferred choice of management for long-term sustainability. Hence, host induced gene silencing (HIGS) strategy was explored in this study. The A. flavus gene aflM encoding versicolorin dehydrogenase, a key enzyme involved in the aflatoxin biosynthetic pathway, was selected as a possible target for suppression through HIGS. An RNAi vector containing a portion of the aflM gene was constructed and introduced into immature B104 maize zygotic embryos through Agrobacterium transformation. PCR analysis of the genomic DNA from T0 leaf tissue confirmed the presence of the transgene in six out of the seven events. The seeds from the lines that showed reduced aflatoxin production in laboratory aflatoxin kernel screening assay (KSA) have been increased from T1 to T4 generation in the past four years. Changes in aflatoxin resistance in these transgenic kernels have been evaluated under both field and laboratory conditions. The T2 generation kernels containing the transgene from two events out of four examined had less aflatoxin (P ≤ 0.01 and P ≤ 0.08) than those without the transgene. Field-inoculated homozygous T3 and T4 transgenic kernels also revealed lower levels of aflatoxins (P ≤ 0.04) than kernels from the null (segregated non-transgenic samples) or B104 controls. A similar result was observed when the harvested T3 and T4 homozygous transgenic kernels were evaluated under KSA conditions without inoculation (P ≤ 0.003–0.05). These two events were crossed with LH195, LH197, LH210, and PHW79 elite breeding lines and the resulting crosses supported less aflatoxin (P ≤ 0.02) than the crosses made with non-transgenic lines. In addition, significantly higher levels of aflM gene-specific small RNAs were detected in the transgenic leaf and kernel tissues, indicating that the enhanced aflatoxin resistance in the homozygous transgenic kernels is likely due to suppression of aflM expression through HIGS.
TRP Channels as Interior Designers: Remodeling the Endolysosomal Compartment in Natural Killer Cells

Cytotoxic lymphocytes, including natural killer (NK) cells and T cells are distinguished by their ability to eliminate target cells through release of secretory lysosomes. Conventional lysosomes and secretory lysosomes are part of the pleomorphic endolysosomal system and characterized by its highly dynamic nature. Several calcium-permeable TRP calcium channels play an essential role in endolysosomal calcium signaling to ensure proper function of these organelles. In NK cells, the expression of self MHC-specific inhibitory receptors dynamically tunes their secretory potential in a non-transcriptional, calcium-dependent manner. New insights suggest that TRPML1-mediated lysosomal calcium fluxes are tightly interconnected to NK cell functionality through modulation of granzyme B and perforin content of the secretory lysosome. Lysosomal TRP channels show a subset-specific expression pattern during NK differentiation, which is paralleled with gradually increased loading of effector molecules in secretory lysosomes. Methodological advances, including organellar patch-clamping, specific pharmacological modulators, and genetically-encoded calcium indicators open up new possibilities to investigate how TRP channels influence communication between intracellular organelles in immune cells. This review discusses our current understanding of lysosome biogenesis in NK cells with an emphasis on the TRP mucolipin family and the implications for NK cell functionality and cancer immunotherapy.
Langerhans Cells From Mice at Birth Express Endocytic- and Pattern Recognition-Receptors, Migrate to Draining Lymph Nodes Ferrying Antigen and Activate Neonatal T Cells in vivo

Antigen capturing at the periphery is one of the earliest, crucial functions of antigen-presenting cells (APCs) to initiate immune responses. Langerhans cells (LCs), the epidermal APCs migrate to draining lymph nodes (DLNs) upon acquiring antigens. An arsenal of endocytic molecules is available to this end, including lectins and pathogen recognition receptors (PRRs). However, cutaneous LCs are poorly defined in the early neonatal period. We assessed endocytic molecules expression in situ: Mannose (CD206)-, Scavenger (SRA/CD204)-, Complement (CD2l, CDllb)-, and Fc-Receptors (CD16/32, CD23) as well as CD1d, CD14, CD205, Langerin (CD207), MHCII, and TLR4 in unperturbed epidermal LCs from both adult and early neonatal mice. As most of these markers were negative at birth (day 0), LC presence was revealed with the conspicuous, epidermal LC-restricted ADPase (and confirmed with CD45) staining detecting that they were as numerous as adult ones. Unexpectedly, most LCs at day 0 expressed CD14 and CD204 while very few were MHCII+ and TLR4+. In contrast, adult LCs lacked all these markers except Langerin, CD205, CD11b, MHCII and TLR4. Intriguingly, the CD204+ and CD14+ LCs predominant at day 0, apparently disappeared by day 4. Upon cutaneous FITC application, LCs were reduced in the skin and a CD204+MHCII+FITC+ population with high levels of CD86 subsequently appeared in DLNs, with a concomitant increased percentage of CD3+CD69+ T cells, strongly suggesting that neonatal LCs were able both to ferry the cutaneous antigen into DLNs and to activate neonatal T cells in vivo. Cell cycle analysis indicated that neonatal T cells in DLNs responded with proliferation. Our study reveals that epidermal LCs are present at birth, but their repertoire of endocytic molecules and PRRs differs to that of adult ones. We believe this to be the first description of CDl4, CD204 and TLR4 in neonatal epidermal LCs in situ. Newborns’ LCs express molecules to detect antigens during early postnatal periods, are able to take up local antigens and to ferry them into DLNs conveying the information to responsive neonatal T cells.
Get Moving! Increases in Physical Activity Are Associated With Increasing Functional Connectivity Trajectories in Typically Aging Adults

Background: Physical activity closely relates to cognition and brain structure as we age. However, the neural mechanisms underlying this relationship in humans remain less clear. Functional connectivity (FC), measured by task-free functional MRI (tf-fMRI) is a dynamic marker of network activity and may be a sensitive indicator of the brain’s response to exercise over time. We aimed to test the longitudinal relationship between physical activity and FC trajectories in functionally normal older adults. Methods: Two hundred and twelve functionally normal, longitudinally-followed older adults completed the Physical Activity Scale for the Elderly (PASE) and tf-fMRI scans at each visit [mean = 1.5 visits (range:1–3)]. We studied FC of the default mode network (DMN), frontal-parietal (FP), subcortical networks (SubCort), and frontal-subcortical inter-network connectivity (FS), given that previous studies implicate these regions in age-related changes. Linear mixed-effects models examined the relationship between within-person changes in PASE and FC (in SD units), covarying for age, sex, education and systemic cardiovascular risk factors (heart rate, BMI and systolic blood pressure). We additionally examined models covarying for DTI fractional anisotropy (FA) and mean diffusivity (MD) of tracts underlying networks of interest, as a marker of cerebrovascular disease. Furthermore, we examined the longitudinal relationship between PASE and neuropsychological trajectories. Results: In our first model, within-subject increases in physical activity tracked with increasing SubCort (β = 0.33, p = 0.007) and FS inter-network (β = 0.27, p = 0.03) synchrony, while between-subject parameters did not reach significance (β = −0.042 to −0.07, ps > 0.37). No significant longitudinal associations were observed between PASE and DMN (β = −0.02 p = 0.89) or FP networks (β = 0.15, p = 0.23). Adjusting for markers of cerebrovascular health (FA/MD) did not change estimated effects (SubCort: β = 0.31, p = 0.01, FS inter-network: β = 0.28, p = 0.03). Associations between changes in physical activity and neuropsychological trajectories were small (β = −0.14 to 0.002) and did not reach statistical significance (p-values >0.42). Conclusions: Our findings suggest that changes in exercise over time are specifically associated with frontal-subcortical processes in older adults. This relationship appears to be independent of cardio- or cerebrovascular disease, possibly driven by a more direct neural response to exercise.
The Role of the Flagellar Protein FlgJ in the Virulence of Brucella abortus

Brucella abortus is a facultative intracellular pathogen that causes a zoonosis called brucellosis. This disease leads to abortion and infertility in cattle, and diverse complications in humans. B. abortus is a successful intracellular bacterium that has developed the ability to evade the host's immune system and it replicates in professional and non-professional phagocytic cells, persisting in the different tissues, and organs of its hosts. It has been described that Brucella expresses a polar flagellum under certain conditions, but its function is still unknown. In this study we evaluated the role of the FlgJ, a protein, presumably a peptidoglycan hydrolase involved in flagellum formation and in the virulence of B. abortus strain 2308. B. abortus 2308 ΔflgJ mutant and complemented strains were constructed to study the function of the FlgJ protein in the context of the virulence of this pathogen in in vitro and in vivo assays. The results showed that the elimination of the flgJ gene delays the growth rate of B. abortus in culture, reduces its intracellular survival capacity in professional and non-professional phagocytic cells, rendering it unable to escape from the endocytic route and not reaching the endoplasmic reticulum. It also negatively affects their persistence in BALB/c mice. Functionally, the B. abortus 2308 flgJ gene restored motility to an E. coli flgJ mutant gene. Furthermore, it was discovered that the production of FlgJ protein is associated with the bacterial adherence by B. abortus. Therefore, although the specific function of the polar flagellum for Brucella is unknown, the data indicates that the flagellar flgJ gene and its product are required for full virulence of B. abortus 2308, since its deletion significantly reduces the fitness of this pathogen in vitro and in vivo.
Design of Muscle Reflex Control for Upright Standing Push-Recovery Based on a Series Elastic Robot Ankle Joint

In physical human–robot interaction environment, ankle joint muscle reflex control remains significant and promising in human bipedal stance. The reflex control mechanism contains rich information of human joint dynamic behavior, which is valuable in the application of real-time decoding motion intention. Thus, investigating the human muscle reflex mechanism is not only meaningful in human physiology study but also useful for the robotic system design in the field of human–robot physical interaction. In this paper, a specialized ankle joint muscle reflex control algorithm for human upright standing push-recovery is proposed. The proposed control algorithm is composed of a proportional-derivative (PD)-like controller and a positive force controller, which are employed to mimic the human muscle stretch reflex and muscle tendon force reflex, respectively. Reflex gains are regulated by muscle activation levels of contralateral ankle muscles. The proposed method was implemented on a self-designed series elastic robot ankle joint (SERAJ), where the series elastic actuator (SEA) has the potential to mimic human muscle–tendon unit (MTU). During the push-recovery experimental study, the surface electromyography (sEMG), ankle torque, body sway angle, and velocity of each subject were recorded in the case where the SERAJ was unilaterally kneed on each subject. The experimental results indicate that the proposed muscle reflex control method can easily realize upright standing push-recovery behavior, which is analogous to the original human behavior.
Genetic Privacy and Data Protection: A Review of Chinese Direct-to-Consumer Genetic Test Services

Background The existing literature has not examined how Chinese direct-to-consumer (DTC) genetic testing providers navigate the issues of informed consent, privacy, and data protection associated with testing services. This research aims to explore these questions by examining the relevant documents and messages published on websites of the Chinese DTC genetic test providers. Methods Using Baidu.com, the most popular Chinese search engine, we compiled the websites of providers who offer genetic testing services and analyzed available documents related to informed consent, the terms of services, and the privacy policy. The analyses were guided by the following inquiries as they applied to each DTC provider: the methods available for purchasing testing products; the methods providers used to obtain informed consent; privacy issues and measures for protecting consumers’ health information; the policy for third-party data sharing; consumers right to their data; and the liabilities in the event of a data breach. Results 68.7% of providers offer multiple channels for purchasing genetic testing products, and that social media has become a popular platform to promote testing services. Informed consent forms are not available on 94% of providers’ websites and a privacy policy is only offered by 45.8% of DTC genetic testing providers. Thirty-nine providers stated that they used measures to protect consumers’ information, of which, 29 providers have distinguished consumers’ general personal information from their genetic information. In 33.7% of the cases examined, providers stated that with consumers’ explicit permission, they could reuse and share the clients’ information for non-commercial purposes. Twenty-three providers granted consumer rights to their health information, with the most frequently mentioned right being the consumers’ right to decide how their data can be used by providers. Lastly, 21.7% of providers clearly stated their liabilities in the event of a data breach, placing more emphasis on the providers’ exemption from any liability. Conclusions Currently, the Chinese DTC genetic testing business is running in a regulatory vacuum, governed by self-regulation. The government should develop a comprehensive legal framework to regulate DTC genetic testing offerings. Regulatory improvements should be made based on periodical reviews of the supervisory strategy to meet the rapid development of the DTC genetic testing industry.
Probabilistic models for phylogenetic classification of Mycobacterium tuberculosis complex genotyping data

This thesis presents a semi-supervised hierarchical Bayesian network to classify strains of Mycobacterium Tuberculosis complex (MTBC) into a three-tier set of genetic lineages and sublineages. MTBC is the causative agent of the infectious disease Tuberculosis (TB), which resulted in over 1.4 million deaths in 2011. Two main types of DNA fingerprinting techniques—spacer oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive units (MIRUs)—are regularly used by public health officials and TB researchers to track and control TB. The model and algorithms presented in this thesis use spoligotype and MIRU data combined from multiple heterogeneous data sources labeled by different experts to provide a model that is able to classify MTBC isolates into a hierarchical phylogenetic structure. The model is trained on over 117064 isolate DNA fingerprints collected by the United States Centers for Disease Control and Prevention, the SITVITWEB database at Institut Pasteur de Guadeloupe, and the MIRU-VNTRplus collection of MTBC strains. The model achieves high classification accuracy, confirming many well-established lineages at all hierarchy levels, and provides visualizations of spoligotype and MIRU signatures for each lineage. In addition, the model discovers some inconsistencies in MTBC labels between data sources, and suggests possible resolutions of these inconsistencies. After further study and refinement, this approach will form the basis for a new tool for MTBC lineage identification freely available online.
Comportamento ingestivo de cordeiros alimentados com dietas contendo feno de amoreira

The experiment was conducted to evaluate the feeding behavior of lambs fed with diets containing 0, 12.5 and 25.0% of mulberry hay as a substitute for the concentrate. Twenty four Ile de France lambs, non castrated, with 25 kg of body weight and four months old, confined, in a completely randomized design, were used. The feeding daily time (242.01 minutes), rumination (435.48 minutes) and leisure (762.50 minutes), the numbers of cakes ruminated per day (658.36) and the time spent per cake (40.03 sec) were not affected (P>0.05) by different levels of hay in mulberry concentrate. The dry matter voluntary intake (1.258 kg/day) and neutral detergent fiber intake (0.302 kg/day), as well as the efficiency of dry matter intake and rumination (316.24 and 173.54 g/h, respectively) and efficiency of neutral detergent fiber intake and rumination (75.89 and 41.68 g/h, respectively) were similar in all treatments. The ruminating chew expressed in hour/day (11.29) and the number of chews expressed per cake (72.65) and per day (47.638.06), as well as the number and the feeding time (22.02 meals and 11.23 min/meal), rumination (25.95 ruminations and 17.29 min/rumination) and idle (41.81 idle and 18.30 min/idle time), were also not affected (P>0.05). The inclusion of mulberry hay did not change the rumination expressed in g of DM and NDF/cake (1.91 and 0.46, respectively) and min/kg of DM and NDF (361.51 and 1.505.78, respectively), as well as the total chew expressed in min/kg of DM and NDF (563.70 and 2.347.19, respectively). The use of mulberry hay partially replacing the concentrated, does not change the feeding behavior of feedlot lambs.
Improving Archival Records and Service of Traditional Korean Performing Arts in a Semantic Web Environment

Abstract Purpose This research project aims to organize the archival information of traditional Korean performing arts in a semantic web environment. Key requirements, which the archival records manager should consider for publishing and distribution of gugak performing archival information in a semantic web environment, are presented in the perspective of linked data. Design/methodology/approach This study analyzes the metadata provided by the National Gugak Center’s Gugak Archive, the search and browse menus of Gugak Archive’s website and K-PAAN, the performing arts portal site. Findings The importance of consistency, continuity, and systematicity—crucial qualities in traditional record management practices—is undiminished in a semantic web environment. However, a semantic web environment also requires new tools such as web identifiers (URIs), data models (RDF), and link information (interlinking). Research limitations The scope of this study does not include practical implementation strategies for the archival records management system and website services. The suggestions also do not discuss issues related to copyright or policy coordination between related organizations. Practical implications: The findings of this study can assist records managers in converting a traditional performing arts information archive into a semantic web environment-based online archival service and system. This can also be useful for collaboration with record managers who are unfamiliar with relational or triple database system. Originality/value This study analyzed the metadata of the Gugak Archive and its online services to present practical requirements for managing and disseminating gugak performing arts information in a semantic web environment. In the application of the semantic web services’ principles and methods to an Gugak Archive, this study can contribute to the improvement of information organization and services in the field of Korean traditional music.
Characteristics of Petroleum Compounds and their Removal from the Aquatic Environment

Abstract The aim of the study was to characterize the components of crude oil, with particular emphasis on those that have a toxic effect on organisms, and to describe the sources of pollution and the methodology for determining these compounds in aqueous solutions. In addition, the study presents the legal provisions in the field of petroleum compounds and practical methods for their removal in the event of uncontrolled emission of these compounds into the aquatic environment as well as methods used in the treatment of wastewater loaded with these compounds.