Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapamycin Improves the Response of Effector and Memory CD8+ T Cells Induced by Immunization With ASP2 of Trypanosoma cruzi

Deficiency in memory formation and increased immunosenescence are pivotal features of Trypanosoma cruzi infection proposed to play a role in parasite persistence and disease development. The vaccination protocol that consists in a prime with plasmid DNA followed by the boost with a deficient recombinant human adenovirus type 5, both carrying the ASP2 gene of T. cruzi, is a powerful strategy to elicit effector memory CD8+ T-cells against this parasite. In virus infections, the inhibition of mTOR, a kinase involved in several biological processes, improves the response of memory CD8+ T-cells. Therefore, our aim was to assess the role of rapamycin, the pharmacological inhibitor of mTOR, in CD8+ T response against T. cruzi induced by heterologous prime-boost vaccine. For this purpose, C57BL/6 or A/Sn mice were immunized and daily treated with rapamycin for 34 days. CD8+ T-cells response was evaluated by immunophenotyping, intracellular staining, ELISpot assay and in vivo cytotoxicity. In comparison with vehicle-injection, rapamycin administration during immunization enhanced the frequency of ASP2-specific CD8+ T-cells and the percentage of the polyfunctional population, which degranulated (CD107a+) and secreted both interferon gamma (IFNγ) and tumor necrosis factor (TNF). The beneficial effects were long-lasting and could be detected 95 days after priming. Moreover, the effects were detected in mice immunized with ten-fold lower doses of plasmid/adenovirus. Additionally, the highly susceptible to T. cruzi infection A/Sn mice, when immunized with low vaccine doses, treated with rapamycin, and challenged with trypomastigote forms of the Y strain showed a survival rate of 100%, compared with 42% in vehicle-injected group. Trying to shed light on the biological mechanisms involved in these beneficial effects on CD8+ T-cells by mTOR inhibition after immunization, we showed that in vivo proliferation was higher after rapamycin treatment compared with vehicle-injected group. Taken together, our data provide a new approach to vaccine development against intracellular parasites, placing the mTOR inhibitor rapamycin as an adjuvant to improve effective CD8+ T-cell response.
In vivo Functional Genomics for Undiagnosed Patients: The Impact of Small GTPases Signaling Dysregulation at Pan-Embryo Developmental Scale

While individually rare, disorders affecting development collectively represent a substantial clinical, psychological, and socioeconomic burden to patients, families, and society. Insights into the molecular mechanisms underlying these disorders are required to speed up diagnosis, improve counseling, and optimize management toward targeted therapies. Genome sequencing is now unveiling previously unexplored genetic variations in undiagnosed patients, which require functional validation and mechanistic understanding, particularly when dealing with novel nosologic entities. Functional perturbations of key regulators acting on signals’ intersections of evolutionarily conserved pathways in these pathological conditions hinder the fine balance between various developmental inputs governing morphogenesis and homeostasis. However, the distinct mechanisms by which these hubs orchestrate pathways to ensure the developmental coordinates are poorly understood. Integrative functional genomics implementing quantitative in vivo models of embryogenesis with subcellular precision in whole organisms contribute to answering these questions. Here, we review the current knowledge on genes and mechanisms critically involved in developmental syndromes and pediatric cancers, revealed by genomic sequencing and in vivo models such as insects, worms and fish. We focus on the monomeric GTPases of the RAS superfamily and their influence on crucial developmental signals and processes. We next discuss the effectiveness of exponentially growing functional assays employing tractable models to identify regulatory crossroads. Unprecedented sophistications are now possible in zebrafish, i.e., genome editing with single-nucleotide precision, nanoimaging, highly resolved recording of multiple small molecules activity, and simultaneous monitoring of brain circuits and complex behavioral response. These assets permit accurate real-time reporting of dynamic small GTPases-controlled processes in entire organisms, owning the potential to tackle rare disease mechanisms.
Expression Profiling of Glioblastoma Cell Lines Reveals Novel Extracellular Matrix-Receptor Genes Correlated With the Responsiveness of Glioma Patients to Ionizing Radiation

Glioblastoma (GBM) is the most lethal and frequent type of brain tumor, leading patients to death in approximately 14 months after diagnosis. GBM treatment consists in surgical removal followed by radio and chemotherapy. However, tumors commonly relapse and the treatment promotes only a slight increase in patient survival. Thus, uncovering the cellular mechanisms involved in GBM resistance is of utmost interest, and the use of cell lines has been shown to be an extremely important tool. In this work, the exploration of RNAseq data from different GBM cell lines revealed different expression signatures, distinctly correlated with the behavior of GBM cell lines regarding proliferation indexes and radio-resistance. U87MG and U138MG cells, which presented expressively reduced proliferation and increased radio-resistance, showed a particular expression signature encompassing enrichment in many extracellular matrix (ECM) and receptor genes. Contrasting, U251MG and T98G cells, that presented higher proliferation and sensibility to radiation, exhibited distinct signatures revealing consistent enrichments for DNA repair processes and although several genes from the ECM-receptor pathway showed up-regulation, enrichments for this pathway were not detected. The ECM-receptor is a master regulatory pathway that is known to impact several cellular processes including: survival, proliferation, migration, invasion, and DNA damage signaling and repair, corroborating the associations we found. Furthermore, searches to The Cancer Genome Atlas (TCGA) repository revealed prognostic correlations with glioma patients for the majority of genes highlighted in the signatures and led to the identification of 31 ECM-receptor genes individually correlated with radiation responsiveness. Interestingly, we observed an association between the number of upregulated genes and survivability greater than 5 years after diagnosis, where almost all the patients that presented 21 or more upregulated genes were deceased before 5 years. Altogether our findings suggest the clinical relevance of ECM-receptor genes signature found here for radiotherapy decision and as biomarkers of glioma prognosis.
Acoustic Vulnerability, Hydraulic Capacitance, and Xylem Anatomy Determine Drought Response of Small Grain Cereals

Selection of high-yielding traits in cereal plants led to a continuous increase in productivity. However, less effort was made to select on adaptive traits, favorable in adverse and harsh environments. Under current climate change conditions and the knowledge that cereals are staple foods for people worldwide, it is highly important to shift focus to the selection of traits related to drought tolerance, and to evaluate new tools for efficient selection. Here, we explore the possibility to use vulnerability to drought-induced xylem embolism of wheat cultivars Excalibur and Hartog (Triticum aestivum L.), rye cultivar Duiker Max (Secale cereale L.), and triticale cultivars Dublet and US2014 (x Triticosecale Wittmack) as a proxy for their drought tolerance. Multiple techniques were combined to underpin this hypothesis. During bench-top dehydration experiments, acoustic emissions (AEs) produced by formation of air emboli were detected, and hydraulic capacitances quantified. By only looking at the AE50 values, one would classify wheat cultivar Excalibur as most tolerant and triticale cultivar Dublet as most vulnerable to drought-induced xylem embolism, though Dublet had significantly higher hydraulic capacitances, which are essential in terms of internal water storage to temporarily buffer or delay water shortage. In addition, xylem anatomical traits revealed that both cultivars have a contrasting trade-off between hydraulic safety and efficiency. This paper emphasizes the importance of including a cultivar’s hydraulic capacitance when evaluating its drought response and vulnerability to drought-induced xylem embolism, instead of relying on the AE50 as the one parameter.
Future Land Use for Insect Meat Production Among Countries: A Global Classification

A potentially suitable alternative to reduce land use by livestock production is insect meat production. However, land use predictions for insect meat production, which are important in the planning of food production strategies in each country, have not been well-performed. To consider the strategy of insect meat production with regard to land use, the categorical perspectives of countries would be highly useful. Here, using previous simulation results, we used random forest machine learning to classify the potential land use of 157 countries for insect meat production under future climate change. From the categorical maps, we showed the global distribution of five different country categories and found that the land area of the countries may be an important factor in considering the future increase in insect meat production. Our classification could be used to help formulate future food policies by considering the increase in insect meat production in each country, as well as regionally and/or globally.
Integrating miRNA and mRNA Profiling to Assess the Potential miRNA–mRNA Modules Linked With Testicular Immune Homeostasis in Sheep

Beyond its well-known role in spermatogenesis and androgen production, mammalian testes are increasingly recognized as an immune-privileged organ for protecting autoantigenic germ cells, especially meiotic and postmeiotic germ cells, from systemic immune responses. Despite its importance, the molecular mechanisms underlying this regulation in mammals, including sheep, are far from known. In this study, we searched for the genes associated with testicular immune privilege and assessed their possible modulating mechanisms by analyzing systematic profiling of mRNAs and miRNAs on testicular tissues derived from prepubertal and postpubertal Tibetan sheep acquired by RNA sequencing. We identified 1,118 differentially expressed (DE) mRNAs associated with immunity (245 increased mRNAs and 873 decreased mRNAs) and 715 DE miRNAs (561 increased miRNAs and 154 decreased miRNAs) in postpubertal testes compared with prepuberty. qPCR validations for 20 DE mRNAs and 16 miRNAs showed that the RNA-seq results are reliable. By using Western blot, the postpubertal testes exhibited decreased protein abundance of CD19 and TGFBR2 (two proteins encoded by DE mRNAs) when compared with prepuberty, consistent with mRNA levels. The subsequent immunofluorescent staining showed that the positive signals for the CD19 protein were observed mainly in Sertoli cells and the basement membrane of pre- and postpubertal testes, as well as the prepubertal testicular vascular endothelium. The TGFBR2 protein was found mostly in interstitial cells and germ cells of pre- and postpubertal testes. Functional enrichment analysis indicated that DE mRNAs were mainly enriched in biological processes or pathways strongly associated with the blood–testis barrier (BTB) function. Many decreased mRNAs with low expression abundance were significantly enriched in pathways related to immune response. Also, multiple key miRNA-target negative correlation regulatory networks were subsequently established. Furthermore, we verified the target associations between either oar-miR-29b or oar-miR-1185-3p and ITGB1 by dual-luciferase reporter assay. Finally, a putative schematic model of the miRNA-mRNA-pathway network mediated by immune homeostasis-related genes was proposed to show their potential regulatory roles in sheep testicular privilege. Taken together, we conclude that many immune-related genes identified in this study are negatively regulated by potential miRNAs to participate in the homeostatic regulation of testicular immune privilege of sheep by sustaining BTB function and inhibiting immune responses under normal physiological conditions. This work offers the first global view of the expression profiles of miRNAs/mRNAs involved in sheep testicular immune privilege and how the genes potentially contribute to immune-homeostatic maintenance.
Identification of Resistance Sources and Genome-Wide Association Mapping of Septoria Tritici Blotch Resistance in Spring Bread Wheat Germplasm of ICARDA

Septoria tritici blotch (STB) of wheat, caused by the ascomycete Zymoseptoria tritici (formerly Mycosphaerella graminicola), is one of the most important foliar diseases of wheat. In Morocco, STB is a devastating disease in temperate wheat-growing regions, and the yield losses can exceed up to 50% under favorable conditions. The aims of this study were to identify sources of resistance to STB in Septoria Association Mapping Panel (SAMP), which is composed of 377 advanced breeding lines (ABLs) from spring bread wheat breeding program of ICARDA, and to identify loci associated with resistance to STB at seedling (SRT) as well as at the adult plant (APS) stages using genome-wide association mapping (GWAM). Seedling resistance was evaluated under controlled conditions with two virulent isolates of STB (SAT-2 and 71-R3) from Morocco, whereas adult plant resistance was assessed at two hot spot locations in Morocco (Sidi Allal Tazi, Marchouch) under artificial inoculation with a mixture of STB isolates. At seedling stage, 45 and 32 ABLs were found to be resistant to 71-R3 and SAT-2 isolates of STB, respectively. At adult plant stage, 50 ABLs were found to be resistant at hot spot locations in Morocco. Furthermore, 10 genotypes showed resistance in both locations during two cropping seasons. GWAM was conducted with 9,988 SNP markers using phenotypic data for seedling and the adult plant stage. MLM model was employed in TASSEL 5 (v 5.2.53) using principal component analysis and Kinship Matrix as covariates. The GWAM analysis indicated 14 quantitative trait loci (QTL) at the seedling stage (8 for isolate SAT-2 and 6 for isolate 71-R3), while 23 QTL were detected at the adult plant stage resistance (4 at MCH-17, 16 at SAT-17, and 3 at SAT-18). SRT QTL explained together 33.3% of the phenotypic variance for seedling resistance to STB isolate SAT-2 and 28.3% for 71-R3, respectively. QTL for adult plant stage resistance explained together 13.1, 68.6, and 11.9% of the phenotypic variance for MCH-17, SAT-17, and SAT-18, respectively. Identification of STB-resistant spring bread wheat germplasm in combination with QTL detected both at SRT and APS stage will serve as an important resource in STB resistance breeding efforts.
Content-Based TV Sports Video Retrieval Based on Audio-Visual Features and Text Information

In this paper, we propose content-based video retrieval, which is a kind of retrieval by its semantical contents. Because video data is composed of multimodal information streams such as visual, auditory and textual streams, we describe a strategy of using multimodal analysis for automatic parsing sports video. The paper first defines the basic structure of sports video database system, and then introduces a new approach that integrates visual streams analysis, speech recognition, speech signal processing and text extraction to realize video retrieval. The experimental results for TV sports video of football games indicate that multimodal analysis is effective for video retrieval by quickly browsing tree-like video clips or inputting keywords within predefined domain.
Novel disease-causing variant in RDH12 presenting with autosomal dominant retinitis pigmentosa

Aim To describe the clinical and molecular features of a novel, autosomal dominant RDH12-retinopathy. Methods Retrospective cross-sectional study. Twelve individuals from a four-generation British pedigree underwent ophthalmic examination, genotyping using next generation sequencing, including whole genome sequencing and multimodal retinal imaging including fundus photography, optical coherence tomography (OCT), autofluorescence imaging and adaptive optics (AO) scanning light ophthalmoscopy were performed. Visual electrophysiology was performed in a subset. Results Eight family members were confirmed as affected by genotyping heterozygous for RDH12 c.763delG. Visual acuity ranged from −0.1 to 0.2 logMAR. Affected individuals had constricted visual fields. A parafoveal and peripapillary ring of hyper-autofluorescence was seen initially, and with progression the area of perifoveal hypo-autofluorescence increased to involve the parafoveal area. Mild retinal thinning was identified on OCT imaging with reduction in both foveal total retinal and outer nuclear layer thickness. Cone densities along the temporal meridian were reduced in affected individuals compared with normative values at all temporal eccentricities studied. One individual with incomplete penetrance, was identified as clinically affected primarily on the basis of AO imaging. Full-field electroretinography demonstrated a rod-cone pattern of dysfunction and large-field pattern electroretinography identified peripheral macular dysfunction. Conclusions This novel heterozygous variant RDH12 c.763delG is associated with a rod-cone dystrophy with variable expression. Determination of the degree of penetrance may depend on the modality employed to phenotypically characterise an individual. This rare and specific heterozygous (dominant) variant is predicted to result in a gain of function, that causes disease in a gene typically associated with biallelic (recessive) variants.
New perspectives on Aspersentis Megarhynchus (Acanthocephala: Heteracanthocephalidae) from Notothenia Coriiceps Richardson (Nototheniidae) in the West Antarctic, with emended generic diagnosis

Abstract A number of variable descriptive accounts of Aspersentis megarhynchus (von Linstow, 1892) Golvan, 1960 have been reported from specimens collected from many species of fish in various locations off Antarctic islands. We have described a new population from Notothenia coriiceps Richardson (Nototheniidae) off Galindez Island, West Antarctica, and features not previously reported, resolved the taxonomic controversies and nomenclature, and emended and updated the generic diagnosis taking into account the newly observed structures. These are depicted in microscopic images and include the outer spiral wall of the proboscis receptacle, the thicker dorsal wall of the receptacle compared to the ventral wall, parts of the female reproductive system, the separate cement gland ducts, the dorsal position of the male gonopore and more detail of proboscis hooks and trunk spines. It is surprising that the newly observed features were missed from the many descriptions of A. megarhynchus created since the original description. The variability in A. megarhynchus is noted with a comparison of the morphometrics of our specimens vs. those in six other descriptions. We also analysed the metal composition of hooks and spines using energy-dispersive X-ray analysis and concluded a molecular characterization of the species based on 18S DNA gene, with related phylogenetic analyses.
Stainless-Steel-Mediated Quantitative Hydrogen Generation from Water under Ball Milling Conditions

A robust and quantitative gaseous hydrogen generation method has been developed in an effort to achieve efficient H2 generation derived from H2O. The present reaction could be achieved by a simple ball friction (milling) reaction of H2O using a planetary ball mill machine with a stainless-steel vessel and balls. It was mediated by metals as an element of stainless steel of the ball mill and also promoted by mechanochemical processing.
Photocatalytic Removal of 2,4-D Herbicide on Lanthanum Oxide-Modified Titanium Dioxide

Titanium dioxide (TiO2) has been recognized as an active photocatalyst for degradation of various organic pollutants. In this study, in order to improve the photocatalytic activity of TiO2, the effect of lanthanum oxide modification was investigated by using commercial P25 as the benchmark. Lanthanum oxide/P25 TiO2 composites with 0.1, 0.5, 1 and 5 mol% of La loadings were prepared via an impregnation method. The resultant composites were characterized by X-ray diffraction (XRD), UV-Vis absorption spectroscopy, transmission electron microscopy (TEM), inductively coupled plasma optical emission spectrometry (ICP-OES) and electrochemical impedance spectroscopy (EIS). It was confirmed that the addition of lanthanum oxide did not much affect the crystallinity, crystal structure and the morphology of P25 TiO2. The catalytic activities of the lanthanum oxide/P25 TiO2 catalysts were tested by using 2,4-dichlorophenoxyacetic acid (2,4-D) as the test pollutant and UV light as the irradiation source. The reaction was caried out for 1 hour at room temperature and the percentage removal was determined using a UV spectrophotometer. The results showed that La loading was an important factor that influenced the photocatalytic activity of the composites. After 1 hour reaction, the best catalyst with 0.1 mol% of La loading showed 24% higher photocatalytic activity than the unmodified P25 TiO2 catalyst. It is shown by EIS that the enhanced photocatalytic activity of the composites was due to the ability of lanthanum oxide in improving the charge separation of the photogenerated electron-hole pairs in TiO2.
Cognate-Corpus-Enhanced Indonesian-Chinese Neural Machine Translation

Low-resource machine translation lacking parallel sentence corpus faces a scientific problem of cross-language semantic paraphrasing. We address the specific low-resource Indonesian-Chinese machine translation issue, explore a language resource extension method based on a cognate corpus, and train a modified neural machine translation (NMT) model by mixing a cognate corpus. This modified model achieved 20.30 BLEU4 score in the experiment of Indonesian-Chinese machine translation. The manual analysis after simple random sampling of experimental results finds that the effect of the modified NMT is comparable to that of the contemporary Google translation. For some sentences, our translation quality is even better. The experimental results prove that the cognate corpus can improve the low-resource NMT effectively, which mainly depends on the morphological similarity and semantic equivalence be-tween the cognate languages.
Selective hydrogenation of phenylacetylene in the presence of styrene

The catalytic performance of a Raney nickel catalyst and eight Pd/Al_2O_3 catalysts in selective hydrogenation of phenylacetylene in the presence of styrene was studied using a high-pressure reactor. The influence of active component loadings, reaction temperature, reaction pressure, reaction time and the stirring velocity on the hydrogenation results,including phenylacetylene conversion and yield of styrene, were investigated. The results showed that Raney nickel catalyst is not suitable for selective hydrogenation of phenylacetylene due to its low activity and selectivity. Low reaction temperature and slightly positive pressure favored Pd/Al_2O_3 catalysts to achieve higher phenylacetylene conversion and styrene yield. Phenylacetylene conversion did not increase with reaction time, while styrene yield declined with reaction time. Increasing stirring velocity is helpful to elimination of the limitation of mass transfer on the reaction. The investigation results also showed that there seemed to be a limitation for phenylacetylene conversion, at which point no improvement on phenylacetylene conversion could be achieved by changing reaction conditions, which may be explained by high active component loadings and large surface area of the catalysts.