Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT)

Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. We have developed an easy and robust method for tissue-specific RNA-seq by taking advantage of the endogenous trans-splicing process. In this method, transgenic worms are generated in which a spliced leader (SL) RNA gene is fused with a sequence tag and driven by a tissue-specific promoter. Only in the tissue of interest, the tagged SL RNA gene is transcribed and then trans-spliced onto mRNAs. The tag allows enrichment and sequencing of mRNAs from that tissue only. As a proof of principle, we profiled the muscle transcriptome, which showed high coverage and efficient enrichment of muscle specific genes, with low background noise. To demonstrate the robustness of our method, we profiled muscle gene expression in dauer larvae and aging worms, revealing gene expression changes consistent with the physiology of these stages. The resulting muscle transcriptome also revealed 461 novel RNA transcripts, likely muscle-expressed long non-coding RNAs. In summary, the splicing-based RNA tagging (SRT) method provides a convenient and robust tool to profile trans-spliced genes and identify novel transcripts in a tissue-specific manner, with a low false positive rate.
The impact of structural composite materials. Part 2: hypervelocity impact and shock

The combination of high strength and low density has resulted in increasing use of composite materials in structures such as aerospace systems that may be subjected to high-velocity impact during their in-service lives. In this review we focus on recent work surrounding the response of composites, primarily carbon fibre reinforced plastic and glass fibre reinforced plastic-based laminates to very high (hyper)-velocity impacts. To this end, the review is divided into two halves. In the first, hypervelocity impacts (e.g. impacts with velocities greater than ca. 2 km/s) that are likely to be encountered by aerospace systems are considered; while in the second, resultant material behaviour – in the form of shock response – is discussed. This review is designed to (1) build on previous studies which have typically largely focused on high-velocity impacts from the perspective of spacecraft protection against on-orbit impact, and; (2) complement an earlier part which focused on the lower impact velocity regime associated with ballistic-loading (Part 1).
MicroRNA-153/Nrf-2/GPx1 pathway regulates radiosensitivity and stemness of glioma stem cells via reactive oxygen species

Glioma stem cells (GSCs) exhibit stem cell properties and high resistance to radiotherapy. The main aim of our study was to determine the roles of ROS in radioresistance and stemness of GSCs. We found that microRNA (miR)-153 was down-regulated and its target gene nuclear factor-erythroid 2-related factor-2 (Nrf-2) was up-regulated in GSCs compared with that of non-GSCs glioma cells. The enhanced Nrf-2 expression increased glutathione peroxidase 1 (GPx1) transcription and decreased ROS level leading to radioresistance of GSCs. MiR-153 overexpression resulted in increased ROS production and radiosensitization of GSCs. Moreover, miR-153 overexpression led to decreased neurosphere formation capacity and stem cell marker expression, and induced differentiation through ROS-mediated activation of p38 MAPK in GSCs. Nrf-2 overexpression rescued the decreased stemness and radioresistance resulting from miR-153 overexpression in GSCs. In addition, miR-153 overexpression reduced tumorigenic capacity of GSCs and increased survival in mice bearing human GSCs. These findings demonstrated that miR-153 overexpression decreased radioresistance and stemness of GSCs through targeting Nrf-2/GPx1/ROS pathway.
Influence of genotype, floral stage, and water stress on floral nectar yield and composition of mānuka (Leptospermum scoparium)

Abstract Background and Aims Floral nectar can be variable in composition, influencing pollinator behaviour and the composition of honey derived from it. The non-peroxide antibacterial activity of mānuka (Leptospermum scoparium, Myrtaceae) honey results from the chemical conversion of the triose sugar dihydroxyacetone (DHA), after DHA accumulates for an unknown reason in the nectar. This study examined variation in nectar DHA, glucose, fructose and sucrose content with floral stage of development, between mānuka genotypes with differing flower morphology, and in response to water stress. Methods Six mānuka genotypes were grown without nectar-feeding insects. Stages of flower development were defined, nectar was harvested and its composition was compared between stages and genotypes, and with floral morphology. Water stress was imposed and its effect on nectar composition was examined. Key Results Nectar was present from soon after flower opening until the end of petal abscission, with the quantity of accumulated nectar sugars rising, then stabilizing or falling, indicating nectar secretion followed by reabsorption in some genotypes. The quantity of DHA, the ratio of DHA to other nectar sugars and the fructose to glucose ratio also varied with stage of development, indicating differences in rates of production and reabsorption between nectar components. Nectar composition and yield per flower also differed between genotypes, although neither was positively related to nectary area or stomatal density. Drying soil had no effect on nectar composition or yield, but variation in nectar yield was correlated with temperature prior to nectar sampling. Conclusions Mānuka nectar yield and composition are strongly influenced by plant genotype, flower age and the environment. There were clear stoichiometric relationships between glucose, fructose and sucrose per flower, but DHA per flower was only weakly correlated with the amount of other sugars, suggesting that accumulation of the triose sugar is indirectly coupled to secretion of the larger sugars by the nectary parenchyma.
High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins

ABSTRACT Helicobacter pylori infection and high dietary salt intake are risk factors for the development of gastric adenocarcinoma. One possible mechanism by which a high-salt diet could influence gastric cancer risk is by modulating H. pylori gene expression. In this study, we utilized transcriptome sequencing (RNA-seq) methodology to compare the transcriptional profiles of H. pylori grown in media containing different concentrations of sodium chloride. We identified 118 differentially expressed genes (65 upregulated and 53 downregulated in response to high-salt conditions), including multiple members of 14 operons. Twenty-nine of the differentially expressed genes encode proteins previously shown to undergo salt-responsive changes in abundance, based on proteomic analyses. Real-time reverse transcription (RT)-PCR analyses validated differential expression of multiple genes encoding outer membrane proteins, including adhesins (SabA and HopQ) and proteins involved in iron acquisition (FecA2 and FecA3). Transcript levels of sabA, hopA, and hopQ are increased under high-salt conditions, whereas transcript levels of fecA2 and fecA3 are decreased under high-salt conditions. Transcription of sabA, hopA, hopQ, and fecA3 is derepressed in an arsS mutant strain, but salt-responsive transcription of these genes is not mediated by the ArsRS two-component system, and the CrdRS and FlgRS two-component systems do not have any detectable effects on transcription of these genes. In summary, these data provide a comprehensive view of H. pylori transcriptional alterations that occur in response to high-salt environmental conditions.
COMPARATIVE STUDY OF OXIDATIVE STRESS BIOMARKERS TO EVALUATE CELLULAR RESPONSE OF JURKAT T-CELLS EXPOSED TO 1966 MHz ELECTROMAGNETIC FIELDS

The widespread usage of mobile communications has significantly increased human exposure to electromagnetic fields (EMF) causing concerns about potential effects on public health [1-2]. In particular, use of modulated EMF for third-generation (3G) mobile frequencies has raised flags in relation with provoking of significant changes in biological processes [3-4]. Jurkat T-lymphocytes were exposed to Radio Frequency (RF) radiation, at 1966 MHz UMTS (Universal Mobile Telecommunication System) band, to assess EMF-induced oxidative stress. In this study, cells were irradiated in a Gigahertz Transverse Electro-Magnetic chamber by unmodulated-continuous wave (CW), or 3G modulated signal. We determined the levels of a) DNA oxidation (single-/double-strand breaks, 8-hydroxy-2-deoxyguanosine content), b) protein oxidation (carbonyl and S-nitrosylated protein content) and c) lipid peroxidation (8-isoprostanes content) in human Jurkat-T lymphocytes exposed to EMF waves and compared their efficacy to detect EMF-induced oxidative stress. RF exposure did not produce significant changes in cell viability. Among the oxidative biomarkers tested, biomarkers for DNA oxidation appeared to be the most sensitive. Low-intensity levels of CW did not cause significant DNA damage, whereas extreme exposure conditions correlated with a slight increase in DNA damage levels. On the other hand, the UMTS signal caused increased oxidative DNA damage in all examined scenarios.
Does personality influence job acquisition and tenure in people with severe mental illness enrolled in supported employment programs?

Abstract Background: When employment difficulties in people with severe mental illness (SMI) occur, it could be partly linked to issues not specific to SMI, such as personality traits or problems. Despite the fact that personality has a marked influence on almost every aspect of work behavior, it has scarcely been investigated in the context of employment for people with SMI. Aims: We aimed to evaluate if personality was more predictive than clinical variables of different competitive work outcomes, namely acquisition of competitive employment, delay to acquisition and job tenure. Method: A sample of 82 people with a SMI enrolled in supported employment programs (SEP) was recruited and asked to complete various questionnaires and interviews. Statistical analyses included logistic regressions and survival analyses (Cox regressions). Results: Prior employment, personality problems and negative symptoms are significantly related to acquisition of a competitive employment and to delay to acquisition whereas the conscientiousness personality trait was predictive of job tenure. Conclusion: Our results point out the relevance of personality traits and problems as predictors of work outcomes in people with SMI registered in SEP. Future studies should recruit larger samples and also investigate these links with other factors related to work outcomes.
PGE2-mediated cytoprotection in renal epithelial cells: evidence for a pharmacologically distinct receptor.

Although the exact mechanism of prostaglandin E2(PGE2)-mediated cytoprotection has not been elucidated, its ability to induce cytoprotection in cell culture suggests this action occurs at the cellular level. The present studies were conducted to determine whether PGE2 induces protection against 2,3,5-(trisglutathion- S-yl)-hydroquinone [2,3,5-(trisglutathion- S-yl)-HQ]-mediated cytotoxicity in a renal proximal tubule epithelial cell line (LLC-PK1) and to delineate the cellular and molecular mechanisms associated with this response. Pretreatment of LLC-PK1 cells with 0.01-40 μM PGE2 for 24 h fully protects against a moderately toxic concentration of 2,3,5-(trisglutathion- S-yl)-HQ. PGE2-mediated cytoprotection is observed in cells pretreated at pH 7.4 but not at pH 7.8. However, cytoprotection is observed in LLC-PK1 cells pretreated with the PGE2 analog, 11-deoxy-16,16-dimethyl PGE2(DDM-PGE2) but not with the PGE2 receptor [E-prostanoid (EP)] agonists 17-phenyltrinor PGE2(EP1), 11-deoxy PGE1(EP2/EP4), sulprostone (EP1/EP3), PGE1, or PGA2. 12- O-tetradecanoylphorbol-13-acetate (TPA), a potent activator of protein kinase C (PKC), also induces cytoprotection, supporting a role for this pathway in the cytoprotective response. PGE2, DDM-PGE2, and TPA all induce the binding of nuclear proteins to a TPA responsive element (TRE), whereas analogs that did not induce cytoprotection (PGE1, 17-phenyltrinor PGE2, sulprostone) were without effect. DDM-PGE2- and TPA-mediated cytoprotection and TRE binding activity are inhibited by N-(2{[3-(4-bromophenyl)-2-propenyl]-amino}-ethyl)-5-isoquinolinesulfonamide (H-89), a PKC inhibitor. These data suggest that cytoprotection by PGE2 and DDM-PGE2 in LLC-PK1 cells is mediated by a PKC-coupled receptor, which is pharmacologically distinct from the presently classified EP receptor subtypes.
Partner Selection for People with Intellectual Disabilities

BACKGROUND The aim of this research was to understand the characteristics that adults with intellectual disabilities look for in a partner. There have been numerous studies that have explored partner selection for people without intellectual disabilities, but no research that specifically identified the traits valued in a partner by people with intellectual disabilities. METHOD In-depth interviews were conducted with eleven participants across two UK sites. All participants were adults with an intellectual disability who had been in a relationship with a partner for over a year. The narratives were analysed utilizing hermeneutic phenomenology, guided by the theory of Van Manen (1990). RESULTS The findings highlighted that, regardless of age, participant's relationships typically developed within a segregated environment for people with intellectual disabilities over the past 10 years. People with intellectual disabilities expressed a wish to be loved, to be treated kindly and to have companionship. However, they did not place high value on attributes such as financial security, social status or intelligence. CONCLUSIONS The research demonstrated how poorly integrated people with intellectual disabilities are within mainstream society. Desired characteristics and expectations for participant's relationships were rooted in a shared history and culture, which was shaped by their intellectual disability and support needs.
Gestational Alcohol Exposure Altered DNA Methylation Status in the Developing Fetus

Ethanol is well known as a teratogenic factor that is capable of inducing a wide range of developmental abnormalities if the developing fetus is exposed to it. Duration and dose are the critical parameters of exposure that affect teratogenic variation to the developing fetus. It is suggested that ethanol interferes with epigenetic processes especially DNA methylation. We aimed to organize all of the available information on the alteration of DNA methylation by ethanol in utero. Thus, we have summarized all published information regarding alcohol-mediated alterations in DNA methylation during gestation. We tried to arrange information in a way that anyone can easily find the alcohol exposure time, doses, sampling time, and major changes in genomic level. Manuscript texts will also represent the correlation between ethanol metabolites and subsequent changes in methylome patterns. We hope that this review will help future researchers to further examine the issues associated with ethanol exposure.
Le Journal Canadien Des Sciences Neurologiques a Simple and Reproducible Experimental in Vivo Glioma Model

SUMMARY: A simple and reproducible injection technique has been developed for inducing an in vivo experimental astrocy-toma model in rats. Newborn rats were injected with a suspension of astrocytoma C-6 cells in doses ranging from 5 to 1 X 10 i cells. The optimum dose of tumor cells was found to be between 10* and 10 5 cells, with a consistent 100% take rate seen above 1 X 10 4 injected cells. The injection of less than 10* cells resulted in a decreased ability to induce tumors, and a prolonged survival. AUER: Nous avons developpe une technique d'injection reproduisible et simple pour induire in vivo un modele experimental d'astrocytome chez le rat. Des rats nouveau-nes recurent une injection d'une suspension de cellules d'astrocytome C-6 a des doses allant de 5 a 5 X 10 6 cellules. La dose optimale est de 104 cellules tumorales, car le taux de reussile ("prise") approche 100% a cette dose. A des doses infe'rieures a 104, I'habilile a induire des tumeurs est diminuee, et la survie prolongee. La The pathology was consistent with that of a glioblastoma multiforme. The tumor showed a diffuse infiltrating border, necro-sis, and pseudopalisading. Light micro-scopy revealed undifferentiated tumor cells while electron microscopy demonstrated rough endoplasmic reticulum, Golgi complexes , mitochondria, and the occasional cilium and centriole. The nature of the astrocytoma C-6 cell line, and the advantages , disadvantages and possible uses of the model are discussed. pathologie est celle du glioblastome multi-forme. La tumeur montre une bordure infiltrante diffuse, de la necrose et des pseudo-palisades. La microscopie optique montre une tumeur non diffe'renciee et la microscopie electronique un reticulum endoplastique rugueux, des complexes de Golgi, des mitochondries et parfois des cilia et des centrioles. Nous discutons de la nature de la ligne cellulaire astrocytome C-6, des avantages et desavantages et des emplois possibles de ce modele. INTRODUCTION Radiation, viruses and chemical carcinogenesis are the three methods of experimental cerebral tumoroge-nesis commonly employed (Janisch and Schreiber, 1977). These methods do not easily offer the opportunity to create large numbers of animals bearing identical tumors in similar intra-cerebral locations. Carcinogen im-plantation, although resulting in the generation of experimental astrocy-tomas requires a craniotomy with it's attendant morbidity and mortality and results in a host of tumors with unpredictable biological activity only after prolonged and variable latent periods (Janisch and Schreiber, 1977). Serial syngeneic tumor transplanta-tion is also cumbersome requiring repeated craniotomies and …
Reappraisal of the reliability of Doppler echocardiographic estimations for mean pulmonary artery pressure in patients with pulmonary hypertension: a study from a tertiary centre comparing four formulae

Different Doppler echocardiography (DE) models have been proposed for estimation of mean pulmonary arterial pressures (PAMP) from tricuspid regurgitation (TR) jet velocity. We aimed to compare four TR-derived DE models in predicting the PAMP measured by right heart catheterization (RHC) in different groups of precapillary pulmonary hypertension (PH). A total of 287 patients with hemodynamically pre-capillary PH were enrolled (mean age = 51 ± 17.4 years, 59.9% female). All patients underwent DE before RHC (< 3 h) and four formulae (F) were used for TR-derived PAMP estimation (PAMP-DE). These were as follows: F1 = Chemla (0.61 × systolic pulmonary artery pressure [PASP] + 2); F2 = Friedberg (0.69 × PASP − 0.22), F3 = Aduen (0.70 × PASP); and F4 = Bech-Hanssen (0.65 × PASP − 1.2). The PASP and PAMP (mmHg) measured by RHC were 89.1 ± 30.4 and 55.8 ± 20.8, respectively. In the overall PH group, DE estimates for PASP (r = 0.59, P = 0.001) and PAMP (r = 0.56, P = 0.001 for all) showed significant correlations with corresponding RHC measures. Concordance was noted between Chemla and Bech-Hanssen, and Aduen and Bech-Hanssen. The Bland–Altman plot showed that Chemla and Bech-Hanssen overestimated and Friedberg and Aduen underestimated PAMP-RHC measures. Paired-t test showed significant systematic biases for Aduen and Bech-Hanssen while Passing-Bablok non-parametric analysis revealed significant systematic biases all four PAMP-DE estimates. There was poor agreement between PAMP-RHC measures and PAMP-DE deciles (Kappa values were 0.112, 0.097, 0.095, and 0.121, respectively). This study showed a poor agreement between PAMP-DE estimates by four TR-derived formulae and PAMP-RHC in patients with PH, regardless of the etiology. However, these results can not be fully extrapolated to a normal population and did not address the reliability of DE estimates for PH screening procedures.
Evaluation of Undrained Shear Strength of Fine-Grained Soils in Consideration of Soil Plasticity

Undrained shear strength (su) is one of the key geotechnical parameters for both natural and remolded soils. While it is basically a function of water content, it is also related to soil plasticity. There has been a long-lasting debate as to whether the su at the plastic and liquid limits are constant and whether the ratio of the su at the plastic limit to the su at the liquid limit is mostly fixed to 100. While this view is embraced by a great majority of researchers, some proclaim that the range of both the su at the plastic limit (PL) and the su at the liquid limit (LL) is rather wide; therefore, constant values of the su cannot be assigned for either the PL or the LL. Accordingly, the view that there is a constant ratio between the two shear strengths is invalid. The scope of this investigation is to reassess this problem using the laboratory vane shear test (VST) along with a new supplementary tool, the mud-press machine (MPM). Sixty remolded soil samples were employed as the study material. The variation of soil strength at both the plastic and liquid limit is investigated using the VST and MPM methods. While the VST method does not portray a distinctive relationship between the su and the two Atterberg limits, the newly introduced MPM method clearly shows that there is a meaningful relationship between the extrusion force, which is considered akin to the undrained shear strength, at the Atterberg limits and the two consistency limits, particularly the liquid limit. Concerning the constant ratio between the two shear strengths, namely the one at the plastic limit to the one at the liquid limit, it was found that this ratio is a constant, but it increases with the increase in soil plasticity. Keywords: Undrained shear strength, soil plasticity, vane shear test, mud press method, remolded soils.
Effects of High Levels of Deoxynivalenol and Zearalenone on Growth Performance, and Hematological and Immunological Parameters in Pigs

Background: Deoxynivalenol (DON) and zearalenone (ZEN) are common food contaminants produced by Fusarium sp. Mycotoxins are a potential health hazard because of their toxicological effects on both humans and farmed animals. Methods: We analyzed three groups of pigs: a control group (fed a standard diet), and the DON and ZEN groups, fed a diet containing 8 mg/kg DON and 0.8 mg/kg ZEN respectively, for four weeks. Results: DON and ZEN exposure decreased body weight (BW), average daily feed intake (ADFI), food conversion rate (FCR), and the serum levels of immunoglobulin (Ig)G and IgM. The total antioxidant levels significantly decreased in serum and increased in urine samples of both treatment groups. Additionally, DON and ZEN exposure increased serotonin levels in urine. Hematological parameters were not affected by the investigated toxins. Microscopic lesions were evident in sections of kidneys from either treatment group: we found sporadic interstitial nephritis in the DON group and renal glomerulus atrophy in the ZEN group. The expression levels of inflammatory cytokines and chemokine marker genes were reduced in tissues from DON- and ZEN-exposed pigs. Conclusions: chronic ingestion of high doses of DON and ZEN alters the immune response and causes organs damage, and might be associated with various diseases in pigs.