Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex differences in gene expression in response to ischemia in the human myocardium

Background Sex differences exist in the prevalence, presentation, and outcomes of ischemic heart disease. Females have higher risk of heart failure post myocardial infarction relative to males and the female sex is an independent risk factor for hospital and operative mortality after cardiac surgery. However, the mechanisms underlying this sexual dimorphism remain unclear. We examined sex differences in human myocardial gene expression in response to ischemia. Methods Left ventricular biopsies from 68 male and 46 female patients undergoing aortic valve replacement surgery were obtained at baseline and after a median 74 minutes of cold cardioplegic arrest/ischemia and respective transcriptomes were quantified by RNA-Seq. Sex-specific responses to ischemia were quantified by differential gene expression, expression quantitative trait loci (eQTL) and pathway and functional analysis. Cell-type enrichment analysis. was used to obtain an estimate of the identity and relative proportions of different cell types present in each sample. Results A sex-specific response to ischemia was observed for 271 genes. Functional annotation analysis revealed sex-specific modulation of the oxytocin signaling pathway and common pathway of fibrin clot formation. The eQTL analysis identified variant-by-sex interaction eQTLs at baseline and post-ischemia, indicative of sex differences in the genotypic effects on gene expression, and cell-type enrichment analysis showed sex-bias in proportion of specific cell types. Conclusion In response to myocardial ischemia, the human left ventricle demonstrates changes in gene expression that differ between the sexes. These differences provide insight into the sexual dimorphism of ischemic heart disease and may aid in the development of sex-specific therapies that reduce myocardial injury.
Effects of Media Cultures and Benzyladenine ( BA ) Concentrations in Micropropagation of Three Types of Cherry Rootstock ( Establishment and Multiplication )

This expereament was carried out in plant tissue culture laboratory of the Horticulture Department, Faculty of Agriculture, University of Duhok, Iraq, during 2014, using two types of explants (Shoot tips and nod segments) in the establishment stage. The highest percentage of shoot /explant (100%) was obtained from Stockton Morello rootstock on both media, while 96.88% was recorded with WPM (Woody plant medium) from nodal segment in F12/1 Mazzard and (87.5%) was observed from shoot tip in Mohaleb. While the highest shoot number with three rootstocks (24.50, 24.38 and 22.25 shoot /explant) with Stockton Morello, F12/1 Mazzard and Mahaleb respectively, were recorded from nodal segment with WPM. While the lowest number of shoots (19.63 shoots /explant) was formed when the shoot tips were cultured on MS medium. At the multiplication stage, the maximum number of shoot per explant (9.50 and 9.17 shoots /explant) in Stockton Morello rootstock was recorded with WPM and MS medium provided with 3mg l -1 BA. The interaction of Stockton Morello with WPM and MS medium having 1.5 mg l -1 BA produced an average of shoot length (3.58 and 3.52 cm) and the increased of shoot length was significantly compared with all treatment without the treatment in combination of Stockton Morello rootstock in WPM medium supplemented with 3 mg l -1 BA. Also the highest length of shoot per explant with three rootstocks 3.58 and 2.98 cm in Stockton Morello and F12/1 Maazard were recorded in WPM having 1.5mg l -1 BA and in Mahaleb rootstock (2.92 cm) was recorded on MS medium containing 1.5mg l -1 BA.
The genetic architecture of neuropsychiatric traits: mechanism, polygenicity, and genome function

Recent progress in genome science has enabled advances in our understanding of the molecular basis underlying susceptibility to a broad spectrum of complex traits, including neuropsychiatric disorders. Methodologically, genome-wide association studies have been remarkably successful in identifying trait-associated variation, but the ever-increasing repository of reproducible genetic associations has highlighted an important gap, namely crucial insight into the underlying mechanisms for most of the identified genetic loci. Here we develop analytic methods that improve on existing approaches and present molecular data that may serve as intermediate phenotypes to higher-order clinical traits with the goal of helping to dissect, more precisely, the functional consequences of the discovered variants. We explore the challenges (methodological and translational) that emerge from the recognition of the polygenicity of neuropsychiatric disease predisposition and the implications on the types of analyses that can advance our understanding of the genetic architecture of neuropsychiatric disorders. Finally, we present research aimed at leveraging our current understanding of regulatory variation in the genome and developing an integrative approach to systematize this knowledge into elucidating the cellular and biological consequences of trait-associated variation.
Some Aspects of Glyphosate Action in Purple Nutsedge (Cyperus rotundus)

Research was conducted to determine effects of glyphosate [N-(phosphonomethyl)glycine] on the chlorophyll and carotenoid and on the catalase specific activity in purple nutsedge (Cyperus rotundus L.). The isopropylamine salt of glyphosate caused chlorosis to appear on the center leaves of plants maintained under lighted conditions after treatment. Glyphosate-induced chlorosis was delayed by darkness but occurred when treated plants were placed in the light. Glyphosate caused significant reducations in the chlorophyll and carotenoids content of purple nutsedge leaves. Based on levels in untreated plants, carotenoid content was reduced more rapidly than chlorophyll in glyphosate-treated plants. The catalase specific activity was reduced by glyphosate to about 70% of the level in untreated plants. Interrelationships among the effects of glyphosate on the carotenoid and chlorophyll content and catalase activity were not determined but possible interactions are discussed.
Determinants of cyanobacterial species composition in the splash zone of two Croatian islands

ABSTRACT Cyanobacterial communities of the splash zone of two Croatian islands, Veruda and Ugljan, were surveyed. At each island, we studied eight localities with different aspects. From all 336 samples, a total of 42 cyanobacterial species, one green alga, and one red alga were found. In both islands Hyella spp. and Gloeocapsopsis crepidinum dominated and Entophysalis deusta, Solentia spp. , Kyrtuthrix dalmatica and Mastigocoleus testarum were found frequently. Multivariate statistical analysis of species composition shows that the vertical gradient is the strongest determinant of species composition and that there are statistically significant but not very pronounced differences in species composition between the two islands. Species composition among individual sites within islands differed slightly, and between localities decreased rather slowly with the distance of individual samples (i.e. the similarity distance decay was very slow), showing that even close samples can have quite different species composition. The species accumulation curves do not reach their asymptote, indicating that many samples are needed to reasonably cover the species richness of a site. This study highlights the importance of in-depth species counts and high density sampling along vertical gradients for satisfactory cyanobacterial community assessments in marine coastal splash zones.
The volatile leaf oils of Juniperus flaccida Schltdl., J. martinezii Perez de la Rosa and J. poblana (Mart.) R. P. Adams, re-examined

The volatile leaf oils of J. flaccida, J. martinezii and J. poblana are re-examined and the composition is published using FID quantitation. The leaf oil of J. flaccida is dominated by α-pinene (65.0%) with moderate amounts of β-pinene (4.8%), myrcene (4.3%), limonene (3.5%), β-phellandrene (3.4%), linalool (2.9%) and manool oxide (3.5%). The oil of J. poblana is somewhat similar as it is dominated by α-pinene (52.9%) with moderate amounts of β-pinene (4.2%), myrcene (4.3%), limonene (2.2%), β-phellandrene (3.5%) and linalool (1.9%), but contains several unique compounds: δ-2-carene (1.8%), δ-3-carene (1.4%), trans-verbenol (2.7%), methyl chavicol (0.7%), and (E)-nerolidol (2.5%). The oil of J. martinezii was quite distinct with major components being α-pinene (16.6%), sabinene (10.4%) and camphor (11.1%) and moderate amounts of β-pinene (1.4%), myrcene (3.6%), limonene (1.8%), βphellandrene (5.3%),linalool (2.8%), γ-terpinene (1.8%) and terpinen-4-ol (6.1%). It also contain several unique compounds: p-cymenene (0.7%), karahanaenone (1.3%), trans-dehydrocarvone (0.6%), transchrysanthenyl acetate (0.5%), linalool acetate (0.4%), noe0iso-3-thyjanyl acetate (0.8%), an aromatic phenol (KI 1320, 0.5%), trans-muurola-4(14), 5-diene (0.7%), epi-cubebol (0.5%), cubebol (1.1%), 1-epicubebol (1.0%), and an unknown diterpene (KI 1978, 0.6%). Published on-line www.phytologia. org Phytologia 97(2): 145-151 (April 1, 2015). ISSN 030319430.
Characterisation of some Scutellonema species (Tylenchida: Hoplolaimidae) occurring in Botswana, South Africa, Costa Rica and the USA, with description of S. clavicaudatum sp. n. and a molecular phylogeny of the genus

The genus Scutellonema contains more than 40 species of spiral nematodes with enlarged phasmids called scutella. In this study, we provide morphological and molecular characterisation of S. clavicaudatum sp. n. , S. brachyurus , S. bradys , S. cavenessi , S. transvaalense , S. truncatum and Scutellonema sp. A. from North and Central America, and Africa. The new species, S. clavicaudatum sp. n. , was found on sugarcane in South Africa and is characterised by a lack of lip annuli as in S. africanum , S. siamense and S. truncatum . The lip region, in both males and females, is conical and marked by six large rectangular blocks separated or fused with the submedian and lateral lip sectors, which surround a round and distinct labial disc. Females of this new species also have large vaginal glands, a functional spermatheca, the lateral field posterior to the scutellum ending in a bluntly pointed shape and a clavate tail. Morphological descriptions, measurements, light and scanning electron microscopic photos and drawings are also given for S. bradys , S. cavenessi , S. transvaalense and S. truncatum . The study of spiral nematode samples from Florida, USA, confirmed the presence of a morphologically and genetically atypical populations of S. bradys . The morphology of the S. bradys population from Bermuda grass in pasture land from central Florida fits that of type specimens of this species, but differs in having a truncate tail terminus rather than round and also a prominent spermatheca filled with flagellate spermatozoa. Other Florida Scutellonema samples analysed in this study belonged to S. cavenessi , a species native to West Africa. This is the first report of S. cavenessi in Florida, where it parasitises the ornamental plant Sansevieria trifasciata . Our study showed a high level of intraspecific variation for Scutellonema rRNA and mtDNA genes, which can reach 5.6% for the D2-D3 of 28S rRNA, 12.9% for the ITS rRNA genes and 14.4% for the COI gene. Phylogenetic relationships within Scutellonema are given as inferred from the analyses of the D2-D3 of 28S rRNA, ITS rRNA and the COI mtDNA gene sequences.
Mitochondrial Instability, Lack of Erk1/2 Activation and High Expression of P75NTR in Engrailed-Deficient Mesencephalic Dopaminergic Neurons

Progressive loss of mesencephalic dopaminergic (mesDA) neurons is the main pathological feature of Prakinson’s Disease. The homeobox transcription factors, Engrailed-1 and Engrailed-2, are essential for survival and long-term maintenance of this neuronal population. In mutant embryos, null for both genes, the mesDA neurons are generated and start to express their neurotransmitter phenotype, but fail to differentiate and die during midgestation. The mice, heterozygous for Engrailed-1 and homozygous null for Engrailed-2, suffer a Parkinson’s Disease-like postnatal degeneration of their nigral DA neurons. Prior studies had shown that the Engrailed-deficient mesDA neurons die by apoptosis, evident from activation of caspase-3 and presence of pyknotic nuclei. The subject of this study was to elaborate more on the molecular pathway of death and to find out the mechanisms of survival by interfering with this process. In this work, I demonstrate that reduction in expression of Engrailed in mesDA neurons results in a higher sensitivity to mitochondrial apoptotic insult. The increased vulnerability to treatment with MPTP or specific inhibitors of Bcl-2 and Bcl-XL causes release of cytochrome C from the mitochondrial inter-membrane space into the cytosol and subsequent activation of caspases. I also show that the Engrailed deficiency results in increased expression of P75 neurotrophin receptor, which is causal to death of the neurons. The death of Engrailed double mutant mesDA neurons, as a direct result of high expression of P75, can be inhibited by application of TrkB/C-specific neurotrophins, BDNF, NT4 or NT3, by siRNA knockdown (of P75) or by addition of an inhibiting antibody for P75. The rescue effect of these survival factors is diminished by concurrent treatment of the primary cell cultures with an inhibitor of the extracellular signal regulated kinase1/2 (Erk1/2) pathway. Additionally, there is an inverse correlation between expression of P75 and phosphorylation of Erk1/2, suggesting that Erk1/2 deactivation is critical to the death signaling of P75. This study shows a connection between the etiology of PD, exemplified by mitochondrial instability, and the dose dependent survival effect of the Engrailed genes. In addition to causing mitochondrial vulnerability, the absence of engrailed genes activates a death pathway, instigated by the high expression of P75 and inhibition of activation of Erk1/2 pathway.
Wild cacao trees (Theobroma cacao L.) in French Guiana

Spontaneous cacao trees ( Theobroma cacao L.) found in south-eastern French Guiana form a particular genetic group, the “Guiana” group, which could be used in cacao breeding. Since 1987, CIRAD* has set itself the objective of collecting and characterizing those cacao trees, carrying out agronomic and sensory assessments, and studying the ir diversity. The main results acquired are presented. Four surveys took place from 1987 to 201 2 in the upper reaches of the Oyapok and Tanpok rivers. The plant material collected, from 226 moth er-trees, has been planted in a collection at CIRAD 's Sinnamary station, as open-pollinated progenies or clones. The trees are observed individually for ten years for various agronomic descriptors: juvenile growth, adult vigour, early yielding, yields, “cropping efficiency”, percentage of rotten pods and average pod weight. Various morphological, biochemical and molecular de scriptors have been used to study the diversity of the “Guiana” group. Resistance to black pod rot caused by stramenopiles of the genus Phytophthora (P. palmivora and P. capsici) was assessed in early tests and many resistant clo nes have been identified. Sensory studies have revealed a cocoa f lavour that is statistically better than that of the industrial reference (“West African Amelonado”). As this germplasm seems very promising in cacao breeding, it is therefore important to continue sur veys in French Guiana (some zones have yet to be surveyed) and maybe in the Guiana Shield, and to as sess all clones for their performance in relation to other pests and diseases. (Resume d'auteur)
Photolysis of propyne at 1470 A

The photolysis of propyne (methylacetylene) has been examined at the 1470‐A Xe resonance line and at low pressures (0.2 torr) in order to minimize polymerization. The major products observed in decreasing order of importance are H2, C2H2, C2H6, and CH4. Evidence is presented for the occurrence of primary processes forming atomic and molecular hydrogen. The following are energetically possible at 1470 A: CH3C≡CH+hΛ→C3H3+H →C3H2+H2 →C3H+H2+H →C3+2H2. The dominant process is atomic hydrogen formation via A. The formation of acetylene and ethane is attributed to the reaction sequence H+CH3C≡CH→CH3+C2H2, 2CH3→C2H6. This is consistent with the observation that the ratio of C2H2 to C2H6 is close to two and that, in the photolysis of CD3C≡CH, the acetylene is 75% C2H2 and the ethane is 95% C2D6.
The need for large‐scale distribution data to estimate regional changes in species richness under future climate change

Species distribution models built with geographically restricted data often fail to capture the full range of conditions experienced by species across their entire distribution area. Using such models to predict distribution shifts under future environmental change may, therefore, produce biased projections. However, restricted‐scale models have the potential to include a larger sample of taxa for which distribution data are available and to provide finer‐resolution projections that are better applied to conservation planning than the forecasts of broad‐scale models. We examine the circumstances under which the projected shifts in species richness patterns derived from restricted‐scale and broad‐scale models are most likely to be similar.
Gifted and non-gifted students’ diurnal preference and the relationship between personality, sleep, and sleep quality

Abstract The current study had two main objectives. First, we examined gifted and non-gifted students’ diurnal preferences. Secondly, we examined the relationships among age, gender, personality, sleep quality, and chronotype of gifted students. Data were gathered from 276 gifted students and 1921 non-gifted students whose ages range between 7 and 17 years old, in same three cities in Turkey using the Composite Scale of Morningness (CSM) to assess diurnal preference, the Big Five Inventory (BIG-5) to assess personality and the Pittsburgh Sleep Quality Index (PSQI) to measure sleep quality. The first result indicated that gifted students were more morning-oriented compared to non-gifted students. The other main result was that the conscientiousness was the best predictor of CSM scores in gifted students. Additionally, conscientiousness, age, and global PSQI predicted CSM scores, respectively. Moreover agreeableness, conscientiousness, and emotional stability were positively related to morning orientation, while age, sleep quality, sleep latency, daytime dysfunction, and global PSQI were negatively related with chronotype in gifted students.
Cloning and Characterization of Lipase Gene from A Local Isolate of Pseudoxanthomonas Sp.

Lipase gene from Pseudoxanthomonas sp. was cloned through in vitro amplification from total chromosomal DNA. The gene was sequenced and characterized, coding for 312 amino acid residues. Homological analysis showed that the gene has 98% similarity to lipolytic gene from Uncultured Pseudomonas sp (GenBank No. AKA58891.1). Further analysis appeared that the sequences showed similar unique motifs of lipase sub-family I.1, such as pentapeptide (GHSHG) motif, tetrapeptide (GMLG) motif, and catalytic triad. In additional, 3D structure analysis based on crystal structure of Pseudomonas aeruginose (PDB ID 1ex9) showed that both structure of lipases are similar except on the conformation of catalytic residue of His277 showing to shift more far away compared to that the control.
Identification and characterization of candidate genes influencing salinity tolerance in Macrobrachium australiense : a model for the molecular basis of colonization of low ionic environments

Climate change models suggest increased sea levels will alter salinity gradients within coastal freshwater systems. This project aimed to identify candidate genes involved with osmoregulation in an endemic Australian freshwater prawn, Macrobrachium australiense, to understand the molecular basis of adaptation to low ionic environments. Next generation sequencing was used to identify important genes and functional mutations that underpin osmoregulation. These genes were tested by maintaining prawns under different salinity conditions to validate their osmoregulatory roles. Results indicate this species is able to tolerate a range of salinities and will be able to cope in salinity levels under climate change scenarios.
The Role of Glycogen Synthase Kinase in Glioblastoma Multiforme Migration and Invasion

ii Dedication . v Acknowledgments. vi Vita.viii List of Tables. x List of Figures . xi Chapter 1: Introduction . 1 Chapter 2: Review of Literature. 13 Chapter 3: Characterization of GSK-3 Inhibitors in vitro. 46 Chapter 4: Indirubins Inhibit Glioma Migration in vivo. 94 Chapter 5 STAT3 and Glioma Migration . 136 Chapter 6 Final Discussion and Future Directions.162 References . 168
Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium‐chain‐specific thioesterase and acyl carrier protein

Biofuel from fatty acids with chain lengths of 8–15 (C8–C15) have properties similar to those of conventional diesel and jet fuels, thus, can save time and reduce costs for the refurbishment of engines and maintenance of oiling facilities. Most oil‐producing algae yield C16–C18 fatty acids; however, the manipulation of algae using genetic engineering is a promising approach to obtain C8–C15 fatty acids. The introduction of a medium‐chain‐specific thioesterase (TE) is expected to effectively alter algae to produce medium‐chain fatty acids (MCFAs). TE is the main determinant of fatty acid chain length as it releases fatty acids from the acyl carrier protein (ACP) in the fatty acid elongation cycle. In a previous study, the introduction of heterologous C8–C12‐specific TEs into Chlamydomonas reinhardtii did not increase the yield of MCFAs. This effect was attributed to a low affinity of the heterologous TEs to C. reinhardtii ACP. Therefore, we introduced both the C10–C14‐specific TE gene and the ACP gene from the land plant Cuphea lanceolata into C. reinhardtii. We measured free fatty acids (FFAs) and triacylglycerols (TAGs) in the transformants using liquid chromatography–mass spectrometry. The production of C12:0 and C14:0, chain length 12 and 14 without unsaturation, FFAs was not significantly increased in any of the tested strains. However, we found a slight but significant increase in TAG‐containing MCFAs in both TE only and TE–ACP transformants. The increased production rate of C14:0‐containing TAGs ranged from 1.25‐ to 1.58‐fold, indicating the ability of medium‐chain‐specific TE to increase MCFAs. These results suggest that the selection of specific TEs is important when modifying eukaryotic algae to produce MCFAs.
Individual tradable permit market and traffic congestion: An experimental study

This paper investigates the potential of an individual tradable permit system in an experimental two-sided repeated double auction market to overcome over-consumption through road demand management. The evaluation of this system shows that traders exhibit strong dependence on reservation price and there are significant transfers of permit from low value users to high value users. During peak hours, the permit price increases owing to high demand, so the cost of using the road is high during congestion. This creates incentive for low value drivers to postpone their trips and resell permits in the peak hours to gain profit. The results show the delayer pays principle, in which drivers who value highly have to pay drivers who are willing to stay off the road during peak hours.