Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Spirulina Supplementation Protects Visual Function From Photostress by Suppressing Retinal Neurodegeneration in Mice

Purpose We investigated whether daily consumption of Spirulina, an antioxidant generating cyanobacterial nutritional supplement, would suppress photostress-induced retinal damage and prevent vision loss in mice. Methods Six-week-old male BALB/cAJcl mice were allowed constant access to either a standard or Spirulina-supplemented diet (20% Spirulina) that included the antioxidants, β-carotene and zeaxanthin, and proteins for 4 weeks. Following dark adaptation, mice were exposed to 3000-lux white light for 1 hour and returned to their cages. Visual function was analyzed by electroretinogram, and retinal histology by hematoxylin and eosin staining, terminal deoxynucleotidyl transferase-mediated, deoxyuridine triphosphate nick-end labeling (TUNEL) assay, and immunohistochemistry. Retinal expression of proteins, reactive oxygen species (ROS), and mRNAs were measured using immunoblot analysis, enzyme-linked immunosorbent assay (ELISA), 2′,7′-dichlorofluorescein-diacetate, or ROS Brite 700 Dyes, and real-time reverse-transcription polymerase chain reaction, respectively. Results Light-induced visual function impairment was suppressed by constant Spirulina intake. Thinning of the photoreceptor layer and outer segments, photoreceptor cell death, decreased rhodopsin protein, and induction of glial fibrillary acidic protein were ameliorated in the Spirulina-intake group. Increased retinal ROS levels after light exposure were reduced by Spirulina supplementation. Light-induced superoxide dismutase 2 and heme oxygenase-1 mRNAs in the retina, and Nrf2 activation in the photoreceptor cells, were preserved with Spirulina supplementation, despite reduced ROS levels, suggesting two pathways for suppressing ROS, scavenging and induction of endogenous antioxidative enzymes. Light-induced MCP-1 retinal mRNA and proteins were also suppressed by Spirulina. Conclusions Spirulina ingestion protected retinal photoreceptors from photostress in the retina. Translational Relevance Spirulina has potential as a nutrient supplement to prevent vision loss related to oxidative damage in the future.
Molecular docking enabled updated screening of the matrix protein VP40 from Ebola virus with millions of compounds in the MCULE database for potential inhibitors

Ebola virus is known for several outbreaks of hemorrhagic fever in West Africa. This RNA virus is linked to high fatality and easy transmission. Recently, an effective vaccine and a monoclonal antibody cocktail have been introduced to combat Ebola virus infection. The matrix protein VP40 of Ebola virus is a known drug target and it is essential for viral life cycle through participation in RNA transcription as well as for the budding of the mature virus. It is known that residues phenylalanine 125 and arginine 134 of VP40 are involved in the interaction with RNA. Therefore, it is of interest to screen VP40 with millions of compounds at the mcule.com database for potential inhibitors. The output hits were ranked according to their minimum binding energy to matrix protein VP40. We further calculated the pharmacokinetics and toxicology properties for the best five hits using several predictive ADME analysis web tools. We report a candidate lead (compound #5: ((10R)-10-(4-hydroxyphenyl)-11,12,14,16-tetraazatetracyclo[7.7. 0.02,7.011,15] hexadeca-1(16), 2(7),3,5,8,12,14-heptaen-8-ol)) with high drug-likeness score, promising lead-likeness behaviour and high median lethal dose. The candidate lead compound #5 engages in hydrogen bonding and hydrophobic interactions with VP40 active site residues. Thus, the lead compound #5 is recommended for further in vitro and in vivo validations for further consideration.
Bone Healing in the Presence of a Biodegradable PBS-DLA Copolyester and Its Composite Containing Hydroxyapatite

The healing process of the fractured bone in a presence of poly(butylene succinate-butylene dilinoleate) (PBS-DLA) copolymer containing nanosized hydroxyapatite (HAP) particles has been investigated. The PBS-DLA material containing PBS hard segments and DLA soft segments (50:50 wt %) was used to prepare a polymer/ceramic composite with 30 wt % HAP. A new PBS-DLA copolymer showed a high elasticity of 500% and 15 MPa tensile strength. Addition of HAP improved tensile strength up to 25 MPa while high elasticity has been preserved going down only to 300% of elongation at break. A polymer nanocomposite was fabricated into small elastic polymer rods 15 mm long and 1 × 2 mm in cross section and used for tibia bone fixation in rats. Mallory trichrome staining indicated that new biodegradable copolymers and its composite containing HAP have triggered the most advanced bone healing of all tested materials, thus indicating their high potential for bone tissue engineering and repair.
Genome-wide identification of C2H2 zinc-finger genes and their expression patterns under heat stress in tomato (Solanum lycopersicum L.)

The C2H2 zinc finger protein (C2H2-ZFP) transcription factor family regulates the expression of a wide variety of genes in response to various developmental processes or abiotic stresses; however, these proteins have not yet been comprehensively analyzed in tomato (Solanum lycopersicum). In this study, a total of 104 C2H2-ZFs were identified in an uneven distribution across the entire tomato genome, and include seven segmental duplication events. Based on their phylogenetic relationships, these genes were clustered into nine distinct categories analogous to those in Arabidopsis thaliana. High similarities were found between the exon–intron structures and conserved motifs of the genes within each group. Correspondingly, the expression patterns of the C2H2-ZF genes indicated that they function in different tissues and at different developmental stages. Additionally, quantitative real-time PCR (qRT-PCR) results demonstrated that the expression levels of 34 selected C2H2-ZFs are changed dramatically among the roots, stems, and leaves at different time points of a heat stress treatment, suggesting that the C2H2-ZFPs are extensively involved in the heat stress response but have potentially varying roles. These results form the basis for the further molecular and functional analysis of the C2H2-ZFPs, especially for those members that significantly varied under heat treatment, which may be targeted to improve the heat tolerance of tomato and other Solanaceae species.
Characteristics of the complete mitochondrial genome of the monotypic genus Arctictis (Family: Viverridae) and its phylogenetic implications

The binturong (Arctictis binturong) is classified as a member of the subfamily Paradoxurinae within the family Viverridae (Carnivora: Mammalia) and comprises nine subspecies spread across Southern and Southeast Asia. Here, we describe the complete mitochondrial genome of the Indian subspecies A. b. albifrons using next-generation sequencing methods. The total length of the A. b. albifrons mitogenome was 16,642 bp. Phylogenetic analyses based on 13 mitochondrial protein-coding genes placed the binturong as a sister taxon to Paguma larvata within the Paradoxurinae and supported the clustering of Genettinae and Viverrinae and the monophyly of Viverridae and six other families of feliforms, consistent with previous studies. Divergence time estimates suggest that the Viverridae diversified during the Miocene (22.62 Mya: 95% CI [20.78–24.54] Mya) and that Arctictis and Paguma split 12.57 Mya (95% CI [8.66–15.67] Mya). Further molecular studies are required to test the distinctiveness and diversity of the nine putative subspecies of binturong.
Pharmacokinetic/pharmacodynamic modeling and simulation of dotinurad, a novel uricosuric agent, in healthy volunteers

This study aimed to investigate the pharmacokinetic and pharmacodynamic (PK/PD) profiles of dotinurad, a novel uricosuric agent, and to construct a PK/PD model to predict serum urate (SUA) levels after dotinurad administration in healthy men. PK/PD model was constructed using single‐dose study data considering the physiological features of urate handling. Model validation was performed by comparing the predicted SUA levels with the SUA levels in a multiple‐dose study. Dotinurad was absorbed rapidly, and its exposure increased proportionally in the tested dose ranges (0.5–20 mg) after a single‐dose administration. The PK model after oral administration was described using a one‐compartment model with first‐order absorption. Effects on SUA and renal urate excretion of dotinurad increased with dose escalation but were apparently saturable at a dose >5 mg. The simple maximal effect (Emax) model was selected as the PD model of dotinurad on renal urate reabsorption, resulting in an estimated Emax of 0.51. The plasma concentration at the half‐maximal effect of dotinurad was 196 ng/mL. Other PD parameters were calculated from the change in SUA level or urinary excretion of urate before and after dotinurad administration. The predicted SUA levels, using the PK/PD model, were well‐fitted with the observed values. The constructed PK/PD model of dotinurad appropriately described the profiles of dotinurad plasma concentrations and SUA level in multiple administration study.
Using co‐occurrence network topology in assessing ecological stress in benthic macroinvertebrate communities

Abstract Ecological monitoring of streams has often focused on assessing the biotic integrity of individual benthic macroinvertebrate (BMI) communities through local measures of diversity, such as taxonomic or functional richness. However, as individual BMI communities are frequently linked by a variety of ecological processes at a regional scale, there is a need to assess biotic integrity of groups of communities at the scale of watersheds. Using 4,619 sampled communities of streambed BMIs, we investigate this question using co‐occurrence networks generated from groups of communities selected within California watersheds under different levels of stress due to upstream land use. Building on a number of arguments in theoretical ecology and network theory, we propose a framework for the assessment of the biotic integrity of watershed‐scale groupings of BMI communities using measures of their co‐occurrence network topology. We found significant correlations between stress, as described by a mean measure of upstream land use within a watershed, and topological measures of co‐occurrence networks such as network size (r = −.81, p < 10–4), connectance (r = .31, p < 10–4), mean co‐occurrence strength (r = .25, p < 10–4), degree heterogeneity (r = −.10, p < 10–4), and modularity (r = .11, p < 10–4). Using these five topological measures, we constructed a linear model of biotic integrity, here a composite of taxonomic and functional diversity known as the California Stream Condition Index, of groups of BMI communities within a watershed. This model can account for 66% of among‐watershed variation in the mean biotic integrity of communities. These observations imply a role for co‐occurrence networks in assessing the current status of biotic integrity for BMI communities, as well as their potential use in assessing other ecological communities.
Effects of size‐ and sex‐selective harvesting: An integral projection model approach

Abstract Harvesting is often size‐selective, and in species with sexual size dimorphism, it may also be sex‐selective. A powerful approach to investigate potential consequences of size‐ and/or sex‐selective harvesting is to simulate it in a demographic population model. We developed a population‐based integral projection model for a size‐ and sex‐structured species, the commonly exploited pike (Esox lucius). The model allows reproductive success to be proportional to body size and potentially limited by both sexes. We ran all harvest simulations with both lower size limits and slot limits, and to quantify the effects of selective harvesting, we calculated sex ratios and the long‐term population growth rate (λ). In addition, we quantified to what degree purely size‐selective harvesting was sex‐selective, and determined when λ shifted from being female to male limited under size‐ and sex‐selective harvesting. We found that purely size‐selective harvest can be sex‐selective, and that it depends on the harvest limits and the size distributions of the sexes. For the size‐ and sex‐selective harvest simulations, λ increased with harvest intensity up to a threshold as females limited reproduction. Beyond this threshold, males became the limiting sex, and λ decreased as more males were harvested. The peak in λ, and the corresponding sex ratio in harvest, varied with both the selectivity and the intensity of the harvest simulation. Our model represents a useful extension of size‐structured population models as it includes both sexes, relaxes the assumption of female dominance, and accounts for size‐dependent fecundity. The consequences of selective harvesting presented here are especially relevant for size‐ and sex‐structured exploited species, such as commercial fisheries. Thus, our model provides a useful contribution toward the development of more sustainable harvesting regimes.
Effect of pasture availability on the fatty acid profile and oxidative status of rabbit meat

To verify the effect of organic rearing system on fatty acid profile of meat, 20 Leprino di Viterbo rabbits were assigned to two homogeneous groups: control group reared in double standard cages and organic group in pen provided of a grass pasture area. Acidic composition and tocopherol content of feed and pasture were assessed; acidic profile, tocopherol content and oxidative stability of two retail cuts were carried out. A higher content of n-3 long chain polyunsaturated fatty acid (P<0.001) was found in both biceps femoris and longissimus dorsi of rabbits reared in organic system with respect to control group, whereas no significant differences was found between groups regarding the oxidative stability. These results demonstrate that organic rearing system and in particular grass ingestion and exercise could useful in improving rabbit meat quality.
Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers.
Elevation of Survivin correlated with APC mutation in Iraqi Patients with Colorectal Adenocarcinoma

Objective: To investigate expression and elevation of Survivin protein and expression of mutation in APC gene in colorectal cancer, and analyze the correlation between these two parameters. Method : Immunohistochemistry was employed to detect expression of Survivin protein and PCR technique for detection of mutation in APC gene in 50 patients with CRC lesions. All patients were admitted to Gastroenterology and Hepatology Diseases hospital, and Baghdad Teaching Hospital, between periods from March 2013-November2013 Results: Positive rates of Survivin expression were detected in 21(42%). Positive frequency of survivin were detected in 4(19%), 9(42.9%) and 8(38.1%) in well, moderate and poorly differentiated tumour respectively. No significant differences in scoring between the three grade of tumour. High positive rates of the expression of APC gene mutation detected in 33 (66%) for in CRC also the high percentage of mutation appeared in well 14 (42.5% ), 17 (51.5%) in moderate differentiated and low 2(6.1%) in poorly differentiated tumour p value < 0.05. The results showed high percentage 18(85.7%) of patients have mutation in APC gene with expression of Survivin protein with P value 0.012. Conclusion: The expression rates of survivin higher and increased with progression of tumour suggesting decrease the chance of apoptosis in cancer cells. The rate of mutation in APC gene was higher in sporadic colon cancer suggesting that the expression of this mutation in tumour suppresser gene (APC) play an important role in tumourgenesis and malignant transformation.
Objective Measurement of Local Rod and Cone Function Using Gaze-Controlled Chromatic Pupil Campimetry in Healthy Subjects

Purpose We introduce a new approach for functional mapping of rod and cone activity by measuring pupillary responses to local stimulation via gaze-controlled chromatic pupil campimetry (CPC). Methods Pupillary constriction amplitude and latency to constriction onset to local photopic and scotopic light stimuli at different locations within the 30° central visual field were analyzed in 14 healthy subjects (4 males, 34 ± 11 years, mean ± standard deviation [SD]). All subjects were measured twice for evaluating the test–retest variability and reproducibility of the method. Results For the cone-favoring protocol (ConeProt), the relative maximal constriction amplitude was most pronounced in the center (26.8% ± 6.3%) with a hill-shaped decrease from the fovea to the periphery. For the rod-favoring protocol (RodProt), it was smaller (center, 13.5% ± 4.5%) with a profile lacking the central peak. Mean latency to constriction onset was faster for cones (277 ± 25 ms) than for rods (372 ± 13 ms). Mean intraclass correlation at the different stimulus locations was 0.84 ± 0.08 for RodProt and 0.75 ± 0.11 for ConeProt; mean coefficients of repeatability value of all stimulus locations was 5.9% ± 1.2% and 8.6% ± 1.7%, respectively. Conclusions CPC provides an objective evaluation of local rod and cone function within the central 30° visual field. It shows a photoreceptor-specific profile in healthy subjects. Due to its easy, noncontact, gaze-controlled character, it is a clinically applicable method and may fill the gap of functional diagnostics of rods and cones of the human retina. Translational Relevance Chromatic pupil campimetry provides information about the local rod and cone function of the human retina with distinct pattern of distributions in an objective manner.
Expression Profile of the Digestive Enzymes of Manis javanica Reveals Its Adaptation to Diet Specialization

The expression of animal digestive enzymes reflects important dietary adaptations. The pangolin, also known as scaly anteater, is a specialized myrmecophage that consumes mainly ants and termites, but its digestive enzymes have not been fully investigated. Therefore, in this study, we used shotgun proteomic analysis to examine the protein components of the saliva and intestinal juice of a Sunda pangolin (Manis javanica) that died shortly after being rescued. The intestinal juice contained greater variety of digestive enzymes, including α-amylase, maltase-glucoamylase, α,α-trehalase, sucrase-isomaltase, pepsin A, trypsin, pancreatic endopeptidase E, carboxypeptidase A1, carboxypeptidase B, dipeptidyl-peptidase 4, and pancreatic triacylglycerol lipase. The digestive enzymes identified in the saliva were maltase-glucoamylase and trypsin, and chitinase which was also found in the intestinal juice. Compared with other animals, the Sunda pangolin has less intestinal protease diversity and lacks key digestive enzymes, such as chymotrypsin and pancreatic elastase. The expression profile of the digestive enzymes of the Sunda pangolin reveals animal’s adaptation to a diet consisting mainly of ants and termites. Our results will facilitate the preparation of artificial food for rescued pangolins and for those in captivity for conservation breeding efforts.
Experiences of romantic relationships and desires to marry and have children among youth in a low-fertility society

Introduction: This study aims to explore experiences of romantic relationships and to examine determinants of desires to marry and have children in the future among Japanese university students. Methods: A cross-sectional study was conducted among undergraduate students of A University, located in the capital city of a Japanese prefecture, using an anonymous self-administered and structured questionnaire developed by an online survey software. Results: A total of 815 respondents with complete data were analyzed by logistic regression analysis. Over 80% of males and females expressed the desire to marry and have children in the future. It was found that for both female and male respondents, the “desire to marry” was associated with currently being in a romantic relationship or having experience of sexual intercourse. On the contrary, the “desire to have children” was associated with currently being in a romantic relationship or having experience of sexual intercourse only among male respondents, and no significant association was observed among female respondents. Conclusion: “Currently being in a romantic relationship” and “having experience of sexual intercourse” were associated with wanting to marry and have children in the future among male university students. This suggests that these may be important factors in providing a positive perception regarding having children when they attain childbearing age.