Miracle-dz/UniFAR-FTUs huggingface dataset:
Extracellular matrix-induced signaling pathways and pancreatic beta cell survival

Le but majeur de ce travail de these a ete de mieux comprendre l'impact de la matrice extracellulaire sur la signalisation intracellulaire des cellules beta, menant a une meilleure survies. D'autre part, nous avons montre que la matrice extracellulaire favorise la survie de la cellule beta et que son impact sur l'activite de Akt/PKB et de ERK/MAPK est implique dans son effet anti-apoptotique. D'autre part, nous avons montre que cette matrice extracellulaire active le facteur de transcription NF-kB. NF-kB n'est pas implique dans l'effet anti-apoptotique de la matrice extracellulaire, mais est implique dans l'etalement des cellules et la reorganisation du cytosquelette d'actine induites par la matrice extracellulaire, ainsi que dans la secretion de l'insuline. Dans l'ensemble, ce travail de these a permis la caracterisaiton des voies de signalisation activees par la matrice extracellulaire et responsables d'une meilleures regulation de la secretion et survie des cellules beta.
On the memory properties of recurrent neural models

In this paper, we investigate the memory properties of two popular gated units: long short term memory (LSTM) and gated recurrent units (GRU), which have been used in recurrent neural networks (RNN) to achieve state-of-the-art performance on several machine learning tasks. We propose five basic tasks for isolating and examining specific capabilities relating to the implementation of memory. Results show that (i) both types of gated unit perform less reliably than standard RNN units on tasks testing fixed delay recall, (ii) the reliability of stochastic gradient descent decreases as network complexity increases, and (iii) gated units are found to perform better than standard RNNs on tasks that require values to be stored in memory and updated conditionally upon input to the network. Task performance is found to be surprisingly independent of network depth (number of layers) and connection architecture. Finally, visualisations of the solutions found by these networks are presented and explored, exposing for the first time how logic operations are implemented by individual gated cells and small groups of these cells.
Role of the CDC25 Homology Domain of Phospholipase Cε in Amplification of Rap1-dependent Signaling*

Phospholipase Cε (PLCε) is a novel class of phosphoinositide-specific PLC characterized by possession of CDC25 homology and Ras/Rap1-associating domains. We and others have shown that human PLCε is translocated from the cytoplasm to the plasma membrane and activated by direct association with Ras at its Ras/Rap1-associating domain. In addition, translocation to the perinuclear region was induced upon association with Rap1·GTP. However, the function of the CDC25 homology domain remains to be clarified. Here we show that the CDC25 homology domain of PLCε functions as a guanine nucleotide exchange factor for Rap1 but not for any other Ras family GTPases examined including Rap2 and Ha-Ras. Consistent with this, coexpression of full-length PLCε or its N-terminal fragment carrying the CDC25 homology domain causes an increase of the intracellular level of Rap1·GTP. Concurrently, stimulation of the downstream kinases B-Raf and extracellular signal-regulated kinase is observed, whereas the intracellular level of Ras·GTP and Raf-1 kinase activity are unaffected. In wild-type Rap1-overexpressing cells, epidermal growth factor induces translocation of PLCε to the perinuclear compartments such as the Golgi apparatus, which is sustained for at least 20 min. In contrast, PLCε lacking the CDC25 domain translocates to the perinuclear compartments only transiently. Further, the formation of Rap1·GTP upon epidermal growth factor stimulation exhibits a prolonged time course in cells expressing full-length PLCε compared with those expressing PLCε lacking the CDC25 homology domain. These results suggest a pivotal role of the CDC25 homology domain in amplifying Rap1-dependent signal transduction, including the activation of PLCε itself, at specific subcellular locations such as the Golgi apparatus.
Liver structural alterations accompanying chronic toxicity in fishes: Potential biomarkers of exposure

Hepatic neoplasms in fish involve hepatocytes, biliary epithelial cells and possibly perisinusoidal and endothelial cells. The application of this spectrum of hepatic alterations as biomarkers for field investigations will be proposed. Alternations in livers of sea pen cultured salmonids will be reviewed as an in situ verification of the validity of liver responses. Observations in livers of mature, moribund striped bass from the Carquinez Strait die-off will be reviewed as an example of hepatotoxicity in lethally injured feral fish. Confounding alterations associated with infectious disease including parasites will be compared using results obtained from recent survey of fishes of the Kanawha River, a heavily industrialized stream in West Virginia. Practical morphometric approaches designed to evaluate stress-related alterations in livers and their relation to assay of feral fishes will be presented. Histologic, progressive responses in a carcinogen resistant and a carcinogen responsive species will be presented and discussed as one means to determine toxic, but not necessarily neoplastic, alternations in livers of impacted organisms.
Challenges and Opportunities Facing the Community College President in the 21st Century

The significant problems we face cannot be solved at the same level of thinking we were at when we created them” Albert Einstein. The quote by Albert Einstein indicates where community college presidents are in solving the issues facing their institutions. The 21st Century has brought new challenges and opportunities to college presidents. A college leader is no longer just concerned about academic matters. While there are significant challenges facing community college leaders, opportunities are available for them to make changes to adapt to the changing landscape of higher education. “The significant problems we face cannot be solved at the same level of thinking we were at when we created them” Albert Einstein. The quote by Albert Einstein indicates where community college presidents are in solving the issues facing their institutions. The 21st Century has brought new challenges and opportunities to college presidents. A college leader is no longer just concerned about academic matters. Community college presidents have tried to respect the traditions, history and characteristics of the community college. They have experienced challenges in many areas especially financially (Cohen & Brawer, 2008). Community college presidents have had to learn how to accomplish more with less resources, compete with four-year institutions, and raise persistence, retention, and graduation rates (Cohen & Brawer, 2008). While there are significant challenges facing community college leaders, opportunities are available for them to make changes to adapt to the changing landscape of higher education. The leadership of the nation's community colleges has experienced unprecedented change in the last 20 years. According to Williams (1989) community college leader’s success will be determined by their ability to complete the following tasks:  successfully market their strengths;  increase their enrollment bases;  function in a fiscally responsible manner;  and maintain strong leadership and a devoted faculty. Expectations of community college presidents are increasing in regards to knowledge required to run a successful institution. A community college has become a complex organization with several constituents that it serve. The mission has had to change based on external factors affecting it. According to Bogart (1994) the community college’s mission has been wide-ranging in nature which includes many areas:  open access admission,  a comprehensive curriculum, 1 Morris: Challenges and Opportunities Facing the Community College Preside Published by ScholarWorks@UARK, 2017
The Spatial and Temporal Dynamics of Host-Parasitoid Interactions

1. Introduction 2. A Simple Framework 3. Parasitism and Host Density Dependence 4. Heterogeneity in Host-Parasitoid Interactions 5. Continuous Time and Age-Structure 6. Multispecies Host-Parasitoid Systems 7. Metapopulations of Hosts and Parasitoids 8. Epilogue Indexes and Bibliography
Effect of antimalarial drugs and malaria pigment ( *-haematin) on monocyte phagocytosis and GTP-cyclohydrolase 1 gene expression.

During the erythrocytic stage, the malaria parasite digests host cell haemoglobin into amino acids. Toxic haeme is released and is incorporated into an insoluble non-toxic crystal called haemozoin. Haemozoin is released into the blood stream along with the merozoites when the erythrocyte bursts and is phagocytosed by circulating monocytes and macrophages resident in tissues. Phagocytosed haemozoin impairs many functions of the monocytes, including antigen presentation and adhesion to T cells, differentiation and maturation to dendritic cells, erythropoiesis and thrombopoiesis, but stimulates the release of proinflammatory cytokines and activation of metalloproteinase 9 expression. In response to interferon-γ secretion by T-helper cells subtype 1, monocytes secrete neopterin, which is used as a marker of a cell mediated immune response. Neopterin is an oxidation product of 7,8-dihydroneopterin, produced by the dephosphorylation of 7,8dihydroneopterin triphosphate which results from the conversion of guanosine triphosphate that is catalysed by GTP-cyclohydrolase 1. Elevated plasma and urine neopterin levels have been detected in malaria infections and are associated with severe anaemia, respiratory distress, peak temperatures as well as feverand parasite-clearance times. It has also been reported that monocytic U937 cells treated with P. falciparum-infected red blood cell lysate secrete elevated levels of neopterin. Antimalarial drugs are known to modulate the functions of monocytes, including inhibition of cytokine release, changes in phospholipid metabolism, decrease in expression of cytoadherance receptors as well as TNF receptors and MHC Class I and II molecules, changes in the production of reactive oxygen and nitrogen intermediates, and decreased phagocytosis. However, the effects of antimalarial drugs on haemozoin phagocytosis and GTP-cyclohydrolase 1 mRNA expression by monocytes are unknown. This study aimed to determine the effects of seven antimalarial drugs, amodiaquine, artemisinin, chloroquine, doxycycline, primaquine, pyrimethamine and quinine, on the phagocytosis of latex beads and β-haematin, a synthetic equivalent of haemozoin. Phagocytosis of β-haematin and latex beads by two monocytic cell lines, J774A.1 and U937, as well as peripheral blood mononuclear cells were monitored by enumeration and a novel
Variation in photosynthesis, transpiration and instantaneous water use efficiency in the clones of sandalwood (Santalum album L.).

Variability in single leaf photosynthesis and related gas exchange parameters were studied on 37 clones of sandalwood (Santalum album L.). One-year-old grafts of each clone were grown under controlled conditions and gas exchange measurements were recorded using portable photosynthesis system under saturated light intensities and ambient CO2 concentrations. Significant variations in single leaf photosynthesis (Pn), stomatal conductance (gs), intercellular CO2 concentration (Ci), transpiration rate (Tr) has been observed among the clones studied. Instantaneous water use efficiency (WUE) calculated as Pn/gs and carboxylation efficiency (CE) estimated by Pn/Ci also showed significant variation. Biochemical parameters such as total chlorophyll and buffer soluble protein differed significantly. Correlation studies showed linear positive relationship between Pn and gs (r=0.80) suggesting that photosynthesis is controlled more by stomatal factors. Cluster analysis revealed that the clones did not cluster on the basis of their geographic locations.
Computational discovery and analysis of rDNA sequence heterogeneity in yeast

Ribosomal RNA genes, known as ribosomal DNA or rDNA, are commonly found in tandem arrays of hundreds of repeating units. The sequences of each unit in an array were thought to be near-identical but it is now known that frequent mutations may occur, causing heterogeneity amongst units. Opposing these divergent mutational processes, unit sequences are homogenised through concerted evolutionary processes such as unequal sister chromatid exchange (USCE) and gene conversion (GC). In this study Perl software has been used to uncover rDNA sequence variation in the yeast Saccharomyces paradoxus, using data derived from the Saccharomyces Genome Resequencing Project. This analysis, in conjunction with a reanalysis of the Saccharomyces cerevisiae data from the same project, has provided detailed information regarding rDNA sequence heterogeneity in two contrasting, yet closelyrelated yeast species. Additionally, the rDNA flanking sequences of four yeast strains have been characterised via an analysis of new next generation sequencing reads, adding to our knowledge of concerted evolutionary processes in these genomic regions. Partial Single Nucleotide Polymorphisms (pSNPs) within these datasets are shown to reflect genome mosaicism within a population, and to identify strains with signs of genome hybridisation undetectable by other means. This information provides further insights into the dynamics of the rDNA region in the two yeast species. In particular, examination of the percentage occupancies of pSNPs reveals U-shaped distributions which differ between the two species. Further investigations of rDNA evolutionary dynamics through the development of two Java simulation tools (SIMPLEX and CONCERTINA), which model USCE and GC events, follow the fate of both single and multiple pSNPs in one or more rDNA arrays. Initial simulations show the distribution of pSNPs varies depending upon the balance between mutations and concerted evolutionary events, and provide a framework to investigate the mechanisms involved in altered rDNA dynamics in various cellular processes.
Jaderná architektura a genová exprese u Caenorhabditis elegans

3 1. LITERÁRNÍ PŘEHLED . 5 1.1. Jaderná architektura a mobilita chromatinu . 5 1.2. Jaderná architektura parentálních genomů . 5 1.3. Genová exprese v meióze . 7 1.4. Hlístice Caenorhabditis elegans . 7 1.5. Gametogeneze u C. elegans . 8 1.6. Genová exprese v meióze C. elegans . 9 1.7. Oplození a časná embryogeneze C. elegans . 9 1.8. Nukleo-cytoplazmatický poměr . 10 1.9. Nukleo-cytoplazmatický poměr u C. elegans . 10 2. CÍLE PRÁCE . 11 3. MATERÁL A METODY . 11 4. VÝSLEDKY . 12 4.1. Dynamika parentálního chromatinu v časném embryonálním vývoji C. elegans . 12 4.2. Transkripční aktivita v gonádě C. elegans . 13 4.3. Nukleo-cytoplazmatický poměr C. elegans . 14 5. DISKUSE . 15 5.1. Separace parentálních genomů v časném embryu C. elegans . 15 5.2. Transkripční aktivita v gonádě C. elegans . 16 5.3. Nukleo-cytoplazmatický poměr u C. elegans . 17 6. SHRNUTÍ . 18 7. POUŽITÁ LITERATURA. 19 8. SEZNAM PUBLIKACÍ DOKTORANDA . 22
Production potentials and the physicochemical composition of selected duck strains: a mini review.

Physicochemical composition of meat is an important factor in human nutrition and contributes to the choice of food by mankind. In recent times humans are much conscious of the health benefits of what they consume. Emphasize on the consumption of balance diets have been given much attention. The consumption of organic foods, vegetables, fruits, foods high in fibre, foods of animal origin with less fat and cholesterol are among the food stuffs being upheld. Poultry meat, eggs and products are widely consumed worldwide without much religious restrictions. The high consumption of poultry meat is partly due to it ease for preparing different dishes and the development of a wide range of processed ready-to-eat meals incorporated with chicken as a major protein source. Poultry meat (white meat) is known to be healthier than red meat probably due to its low calorie and lipid contents. Duck meat is comparable to that of chicken despite being red meat and it is a close alternative source of protein and other nutrients for humans. Duck meat is high in protein, iron, selenium and niacin; and lower in calories compared to many cuts of beef. This minireview reports on the production potentials of ducks and the physicochemical composition of selected duck strains. It also reports on world duck population.
Plant proteins : applications, biological effects, and chemistry

Examines the major role plant proteins play in both human and animal diets. Discusses the use of plant proteins in both Western and traditional foods of developing countries; plant and meat protein blended foods; effects on skeletal integrity, trace mineral utilization, atherosclerosis, and cancer incidence; effects of processing on proteins; and novel, lesser known proteins. Of interest to nutritionists, food scientists, and clinicians concerned about nutritional aspects of plant proteins for humans. Also helpful to food chemists and biochemists, dieticians, and medicinal chemists concerned with nutrition.
Molecular Analysis of Cytokines and Cytokine Receptors

During the last decades, analysis of cytokines and cytokine receptor research have gathered much interest. Numerous methods have been developed for the detection and quantification of cytokines and cytokine receptors, which may be detected at either the protein or the mRNA level. This chapter focuses on improvements of the recently developed real-time quantitative PCR that has been used in our laboratory for a couple of years in comparison to other available techniques. The methods described allow quantification of minute amounts of mRNA in small samples due to the exponential amplification of the target sequence and the generation of fluorescent molecules that are detected during the amplification reaction. The performance of amplification reactions is affected to a large extent by the concentrations of magnesium ions and oligonucleotide primers. Usually, specificity of primer annealing increases with decreasing magnesium ion concentration. With real-time PCR, specificity in terms of amplification of only the correct sequence is not the major goal, since hybridization and cleavage of the internal probe guarantee specificity of target quantification. A major advantage of the real-time PCR is its application as a high-throughput analytical system in routine diagnostics and research, as, in contrast to other conventional PCR-based techniques, no post-PCR processing of the reaction products is required.
Genetic Linkage and Association Studies for Bone Geometry and Bone Mineral Density

Osteoporosis is a common skeletal disease becoming one of the biggest public health menaces with the consequence of millions of fractures annually around the world. Osteoporosis is mainly characterized by compromised bone strength that is determined by many skeletal factors such as bone mineral density (BMD), bone geometry, bone microarchitecture, and intrinsic material properties. The BMD and bone geometry all have strong genetic determinations. Identifying their genetic determinants has both biological and clinical importance. I first performed a remarkably large-scale whole genome linkage scan involving 3,998 individuals from 434 pedigrees for four FNCS (femoral neck cross-sectional) geometry parameters, namely buckling ratio (BR), cross-sectional area (CSA), cortical thickness (CT), and section modulus (Z). Significant linkage evidence (Threshold LOD = 3.72 after correction for tests of multiple phenotypes) was found in the regions of 20ql2 and Xq25 for CT (LOD = 4.28 and 3.90, respectively). I also identified 8 suggestive linkage signals (Threshold LOD = 2.31 after correction for multiple tests) for the respective geometry traits. Particularly, 20ql2 was of prime interest because it was linked to multiple FNCS geometry traits and significantly interacted with 5 other genomic loci to influence CSA variation. The effects of 20ql2 on FNCS geometry were present in both male and female subgroups. There are also sex-specific QTLs for FNCS traits in the regions such as 2pl4, 3q26, 7q21 and 15q21. Second, I conducted a large-scale family-based association study by screening 20 important and novel osteoporosis candidate genes with 277 SNPs (single nucleotide polymorphisms) for the quantitative trait - BMD (bone mineral density) variation and the qualitative trait - osteoporosis (OP) at three clinically important skeletal sites - spine, hip and ultradistal radius (UD). 1873 subjects from 405 Caucasian nuclear families were genotyped and analyzed with an average density of 1 SNP per 4 kb across the 20 genes. I detected four genes (DBP, LRP5, CYP17 and RANK) that showed 'highly suggestive' association (10,000-permutation derived empirical global P values < .01) with spine BMD/OP; four genes (CYP19, RANK, RANKL and CYP17) highly suggestive for hip BMD/OP; and four genes (CYP19, BMP2, RANK, TNFR2) highly suggestive for UD BMD/OP. Some of these findings supported previous results while the others were novel discoveries. The associations between BMP2 with UD BMD, and those between RANK with OP at spine, hip and UD also met the experimentwide stringent criterion (empirical global P values <.0007). In addition, I identified and validated a two-locus gene-gene interaction model involving GCR and ESR2, for which prior biological evidence exists. My results suggested the prioritization of osteoporosis candidate genes from among the many proposed in recent years and revealed the significant gene-gene interaction effects influencing osteoporosis risk. Taken together, my linkage and association studies for bone geometry and bone mass…
Foreign Direct Investment (FDI) and Economic Growth in East African Countries

This paper investigates the Impact of Foreign Direct Investment (FDI) on Economic Growth of East African Countries. We apply Fully Modified Ordinary Least Square (FMOLS) technique for the data from 4 East African Community Member Countries (Kenya, Rwanda, Uganda and United Republic of Tanzania) covering the period 1990 to 2015 to examine the long term coefficients after confirmation the existence of panel cointegration. We find foreign direct investment (FDI) accelerates positive impact on economic growth in most of east African countries with significant results at 10 percent level of significance. We suggest that the East African countries region should remain their economies open to attract more potential investors to invest in sectors that promote the economy in order to achieve the desired objectives. Keywords: Foreign Direct Investment, Economic growth, FMOLS, East African countries.