Miracle-dz/UniFAR-FTUs huggingface dataset:
Patient specific stem cell models: focus on glioblastoma and neuronal differentiation aspects of chronic granulomatous disease

Pluripotent stem cells can in vitro replicate key pathophysiological aspects of central nervous system. In the first project, we have developed a 3D co-culture system using cancer stem cells isolated from glioblastoma patients and a human stem cell-derived engineered neural tissue, which allowed us to reproduce numerous hallmarks of glioblastoma in vivo, including invasion and formation of secondary foci. Transcriptomic analysis identified that IFN response genes was induced specifically in the co-culture system that was significantly correlating with patient survival. In a second project, we have focused on the role of ROS generating NOX2 enzyme during neural differentiation. Our study demonstrates that during early stages of neurogenesis there is a regulatory role of NOX2, which is conserved from mouse to human. This suggests a contribution of redox mechanisms in the maintenance of neural stem/progenitor. In conclusion, this study exemplifies the potential of stem cells for the study of human pathophysiology.
Chemical Compound Enumeration and Host-Pathogen Protein Interaction Prediction by Graph-Based Approaches

The rapid development of technology and experiment leads to the large amount of data to be analyzed and studied. The representation of data is important because it has an affect on the complexity of data analysis. Because of its versatility and representation power, a graph has been used as a data structure to represent several biological and chemical data such as protein interaction data, cell metabolism data, and a chemical compound in the form of a protein-protein interaction network, a metabolic network, and a molecular graph, respectively. Moreover, representing data by a graph is one method to apply mathematical knowledge, such as graph algorithm, to examine those data. This thesis makes use of a graph representation of biological and chemical data to solve two chemoinformatics and bioinformatics problems, which is the first part and the second part of this thesis, repectively. In the first part of this thesis, we propose two efficient chemical compounds enumeration methods from a chemical formula using a tree structure, an acyclic connected graph, to represent a chemical compound. The enumeration algorithm can be applied to several problems including drug discovery by filtering the unnecessary compounds out and returning only all non-redundant compounds with the desired properties. The first proposed method is the enumeration method for tree-like chemical compounds containing benzene rings and naphthalene rings from a chemical formula. The second enumeration method allows users to input a chemical formula and desired cyclic substructures and generates all non-redundant chemical compounds containing no cycles except for the input substructures. Two proposed algorithms can help the chemists spend less time to discover compounds with the desired number of atoms and substructures. Both of them use a tree structure to represent a chemical compound, where nodes and edges denote atoms and chemical bonds, respectively. One cyclic structure (a benzene ring in the first method and an input substructure in the second method) is compressed into one node with an additional attribute to keep how atoms in the cyclic structure bond with adjacent atoms, while a naphthalene ring in the first method is denoted by two benzene nodes bonding together with a special bond. The results and computational time of proposed methods are compared with those of a commercial general purpose structure generator named MOLGEN. Giving the same number of the enumerated compounds, proposed methods are significantly faster than the existing tool. This result shows both the reliability and the efficiency
Effect of Foliar Application of Micronutrients on Seed Yield, Quality and Storability in Soybean [Glycine Max (L.) Merrill]

The field experiment was carried out to find out the effect of foliar application of micronutrients on seed yield, quality and storability in soybean (Glycine max (L.) Merrill) at Main Agricultural Research Station, Dharwad during kharif 2012. The experiment consisted of eight treatments viz., T0 Control ,T1 ZnSO4 @ 0.3%, T2 Boron @ 0.2%, T3 KNO3 @ 0.5%, T4 ZnSO4 @ 0.3% + Boron @ 0.2%, T5 ZnSO4 @ 0.3 %+ KNO3 @ 0.5%, T6 Boron @ 0.2%+ KNO3 @ 0.5%, T7 ZnSO4 @ 0.3%+ Boron @ 0.2%+ KNO3@ 0.5% and treatments were imposed at 30 and 45 DAS. It was laid out in randomised block design with three replications. Foliar application of ZnSO4 @ 0.3%+ Boron @ 0.2%+ KNO3@ 0.5% at 30 and 45 DAS recorded significantly higher plant height (58.70 cm), more number of leaves per plant (95.67) and leaf area index (5.08), number of pods per plant (39.67), number of seeds per pod (2.51), seed weight per plant (7.89 g), seed yield per plot (1.67 kg), 100 seed weight (14.10 g) and seed yield per hectare (2655 kg) compared to control (52.60 cm, 74.70, 3.98, 34.47, 2.14, 6.32g, 1.42 and 2281 kg, respectively). The storage experiment was conducted in the laboratory of Department of Seed Science and Technology, University of Agricultural Sciences, Dharwad from October 2012 to April 2013. The seeds obtained from foliar application of ZnSO4 @ 0.3%+ Boron @ 0.2%+ KNO3@ 0.5% at 30 and 45 DAS recorded higher germination percentage (92.72 %), root length (9.26 cm), shoot length (7.10 cm), seedling length, seedling vigour index (1529), seedling dry weight (41.95 mg) and oil content (18.1%) as compared to control (85.00 %, 14.4, 13 cm, 2321, 100.47 mg and 16%, respectively) at the end of six months of storage period.
Expression of bacterial glutamine synthetase gene in Arabidopsis thaliana increases the plant biomass and level of nitrogen utilization

Abstract Changes in expression of glutamine synthetase (GS) have effect on plant nitrogen metabolism. In order to improve nitrogen use efficiency, several attempts at over-expressing GS II genes in plants have been previously undertaken, however few GSI and III genes are found such application. In this study, two GS I genes were cloned from bacterial strains and were transformed into Arabidopsis thaliana. Expression of the genes was confirmed under both mRNA and protein levels. Phenotypic studies revealed that all transgenic Arabidopsis lines showed enhanced fresh weight (12%) and dry weight (13%) compared with the wild-type plants at two concentrations of nitrate supplies. Further biochemical characterization confirmed that the transgenic lines had higher total nitrogen content (increased by 5-8%), soluble protein concentration (increased by 7-11%), total amino acid content (increased by 4-8%), leaf GS activity (enhanced by 8-14%) and free NO-3 concentration (increased by 8-16%) compared to wild type Arabidopsis. This work firstly reported that over-expression of bacterial GS I genes in Arabidopsis resulted in improvement of growth phenotype and nitrogen use efficiency (NUE) of plant. The bacterial GS genes could be potentially useful in engineering transgenic plants of high NUE.
Differences in topographic and soil habitat specialization between trees and two understorey plant groups in a Costa Rican lowland rain forest

Abstract: Two core questions in plant community ecology are to what extent the distributions of species are structured by local environmental conditions, and whether taxa differ in this regard. We compared the distributions of trees, Melastomataceae and ferns on soil and topographic gradients in a Costa Rican lowland rain forest (trees and ferns 983 plots, Melastomataceae 277 plots). To test whether these plant groups differed in the prevalence or type of habitat specialization, we calculated species’ environmental optima and tolerances on each gradient. Habitat specialization was defined as a significantly biased optimum, or a narrow tolerance, relative to values obtained under spatially restricted randomizations of species occurrences. Within plant groups, we also asked whether the dispersion of species optima differed from random expectation on each gradient. Fern optima were over-dispersed on multiple gradients, implying considerable interspecific habitat partitioning, and tree optima were over-dispersed in relation to topographic position. Habitat specialization was more prevalent in the two predominantly understorey groups than in trees (75% of Melastomataceae species, 81–87% of ferns, 57–58% of trees). Species optima of Melastomataceae and ferns also tended towards lower landscape positions than did those of trees, perhaps reflecting a higher proportion of drought-sensitive species in these two groups.
Preliminary results of the taxonomic value of Tortula dens a (Velen.) J.-P. Frahm inferred from the Internal Transcribed Spacer (ITS) of the nrDNA

The taxonomic concept of T. ruralis Hedw. , T. calcicolens Kramer and T. dens a (Velen.) J.-P. Frahm varies much among specialists, and hence remains controversial. The species have been merged into a s ingle taxon ( i.e., T. r uralis ), w ere all treated as distinct taxa, or partially lumped with the name T. dens a placed into synonymy with either T. ruralis or T. calcicolens . An analysis of DNA sequences of the Internal Transcribed Spacer 1 and 2 (ITS) of selected Tortul a specimens including specimens referred t o T. ruralis , T. calcicolens and T. dens a from the same locality, revealed that the three morphological entities differ in their nuclear DNA sequences. This result does not support treating the three entities that are morphologically and anatomically distinct are mere phenotypic variants of T. ruralis and T. dens a is a distinct genotype, as indicated by mixed tufts.
Sparse Gaussian graphical mixture model

Abstract. This paper considers the problem of networks reconstruction from heterogeneous data using a Gaussian Graphical Mixture Model (GGMM). It is well known that parameter estimation in this context is challenging due to large numbers of variables coupled with the degenerate nature of the likelihood. We propose as a solution a penalized maximum likelihood technique by imposing an l1 penalty on the precision matrix. Our approach shrinks the parameters thereby resulting in better identiability and variable selection . Resume. Cet article considere le probleme de la reconstruction de reseaux a partir de donnees heterogenes en utilisant le modele graphique gaussien memange (GGMM en Anglais). Il est connu que l'estimation parametrique, dans ce contexte, n'est pas aise a cause du grand nombre de variable et de la nature degeneree de la vraisemblance. Nous proposons comme une solution une methode de penalisation du maximum de vraisemblance en imposant une penalite de type L1 sur la precision de la matrice. Notre methode reduit les parametres et ainsi aboutit a une meilleure identication et a un meilleur choix des variables. Key words : Gaussian graphical mixture model; Expectation maximization algorithm; Graphical LASSO.
Tempests, Poxes, Predators, and People: Stress in Wild Animals and How They Cope

In this age of modern era, the use of internet must be maximized. Yeah, internet will help us very much not only for important thing but also for daily activities. Many people now, from any level can use internet. The sources of internet connection can also be enjoyed in many places. As one of the benefits is to get the on-line tempests poxes predators and people stress in wild animals and how they cope oxford series in behavioral neuroendocrinology book, as the world window, as many people suggest.
Population estimators and adult sex ratio for a population of Bolitoglossa altamazonica (Caudata: Plethodontidae)

Bolitoglossa altamazonica is the species of plethodontid salamander with the widest distribution in the tropics. However, while aspects related to population size, survival rates, recruitment, sex ratios along with other life history traits are well documented for temperate salamanders, such information is relatively scarce for tropical species. We conducted an intensive capture-recapture study on a population of B. altamazonica. We used the Jolly-Seber method to estimate three parameters (size, recruitment and survivorship) for the population as a whole, as well as for males, females and juveniles separately. All these parameters varied monthly for each class and the entire population. Juvenile recruitment occurred between november and july. Survivorship of juveniles increased when there was no recruitment at all. The adult sex ratio during the breeding season was significantly biased towards females (up to 1:3 depending on the month).
Weeds and their control in cassava

Cassava ( Manihot esculenta Crantz) is a major source of carbohydrate for more than 200 million people, mainly in Africa and to some extent in Asia and Latin America. In Africa, cassava is mainly grown in mixtures with other crops by subsistence farmers using unimproved methods of production. Root yields from farmers' fields are generally low, partly due to effects of weed competition. Hoe-weeding is the common practice among cassava farmers. The frequency and timing of weeding depend on such factors as climate, cultural practices, crop growth, soil fertility and weed species. Some common noxious weeds of cassava and their control by chemical, cultural and integrated means are discussed. Appropriate weed control methods for resource-limited cassava farmers, namely, cultural and biological, as well as an integrated system which combines two or more weed control methods at low input levels are suggested as ways of ensuring sustained production of cassava in developing countries. Key Words : Manihot esculenta , noxious weeds Le manioc ( Manihot esculenta Crantz) est la principale source d'hydrates de carbone pour plus de 200 millions d'habitants, essentiellement en Afrique et dans une moindre mesure en Asie et en Amerique Latine. En Afrique, le manioc est surtout cultive en association avec d'autres plantes dans le cadre d'une agriculture de subsistence qui utilise des methodes de production peu elaborees. Les recoltes de tubercules en provenance des champs de paysans sont habituellement faibles ce qui est en partie du aux effets de la competition avec les mauvaises herbes. Le desherbage a la houe est la pratiqde habituelle des agriculteurs traditionnels. La frequence et le calendrier des desherbages dependent de facteurs comme le climat, les pratiques culturales, la croissance des plantes, la fertilite du sol et les especes de mauvaises herbes. Le controle de quelques mauvaises herbes communes, nuisibles en culture du manioc, par des moyens chimiques, culturaux et integres, est discute. Des methodes de controle adaptees aux conditions des planteurs de manioc aux ressources limitees, comme les mesures de type cultural ou biologique, ainsi qu'un systeme integre, qui combine deux ou plus de ces methodes a faible intrant, sont suggerees comme des moyens permettant d'assurer une production satisfaisante de manioc dans les pays en developpement. Mots Cles : Manihot esculenta , mauvaises herbes
ORIGIN OF MICROMORPH FAUNAS IN THE GEOLOGIC RECORD

Stunting, transportation, juvenility and paedomorphosis are the principal causes of mi- cromorph faunas. Stunting may be a result of high or low salinity, low food supply or low oxygen. Transportation can winnow and concentrate smaller members of an assemblage and create a sorted micromorph fauna. Juvenility is the result of large-scale seasonal fluctuations, and paedomorphosis is an evolutionary response to environmental factors such as instability or substrate fluidity. Macrofaunal characteristics potentially diagnostic of these causes are: 1) population dynamics includ- ing growth and mortality rates, age of attainment of sexual maturity, and age and size distributions, 2) diversity, 3) trophic structure, 4) preservational condition and orientation of the individuals in the fossil assemblage, and 5) functional morphological adaptations, behavioral characteristics and en- vironmental tolerances. Other characteristics include trace fossils, microfaunal diversity and composi- tion, sedimentary structures, texture and geochemistry, and stratigraphic evidence of paleogeographic isolation. Models defined by expected conditions for each of these diagnostic criteria are established for each of the principal causes. Although all the above criteria are useful in determining the probable specific cause of micromorphs, population dynamics is the criterion which best permits the distinction between micromorph and normal faunas and the recognition of the principal cause of the micromorph fauna.
The Complete Plastid Genome Sequence of the Wild Rice Zizania latifolia and Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae

Zizania latifolia (Griseb.) Turcz. ex Stapf was once utilized as an important grain in ancient China and has been cultivated as an aquatic vegetable. Here, we report the complete Z. latifolia chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads generated by directly purified chloroplast (cp) DNA genome sequencing. The Z. latifolia cp genome is 136,501 bp in length, comprising a pair of 20,878-bp inverted repeat regions (IR) separated by small and large single copy regions (SSC and LSC) of 12,590 bp and 82,155 bp, respectively. The Z. latifolia cp genome encodes 110 unique genes (77 protein-coding genes, 29 tRNA genes, and 4 rRNA genes), of which 15 encompass introns. Sequence analysis identified a total of 39 direct/inverted repeats and 63 simple sequence repeats (SSR) with an average rate of 0.46 SSRs/kb. Our results revealed that the Z. latifolia cp genome is AT-rich (61.02%) and gene codon usage may be largely affected by a low GC content and codon usage bias for A, T-ending codons. We predicted 33 RNA editing sites in the chloroplast of Z. latifolia, all for C-to-U transitions. Comparative analyses with other available Oryzeae plastid genomes showed that the coding and IR sequences were more conserved than the single-copy and noncoding regions, suggesting that the indels should be cautiously employed in phylogenetic studies. Phylogenetic analysis of 52 complete grass chloroplast genomes including the reported Z. latifolia cp genome in this study yielded an identical tree topology as previous plastid-based trees, providing strong support for a sister relationship between Bambusoideae+Pooideae and Ehrhartoideae in the BEP (Bambusoideae, Ehrhartoideae, Pooideae) clade of the grass family.
Sedimentological and Paleoecological Research Techniques, withApplications to the Environmental History of Loboi Swamp, Kenya

This research involved sedimentological and paleoecological research techniques, with application to the environmental history of Loboi Swamp (Kenya) in the context of water-resource management and wetland conservation. The analyses included non-destructive scanning of sediment cores (magnetic properties, water content, colour spectroscopy, digital photography), determination of bulk sediment composition (organic matter, carbonate, mineral sediments), grain-size analysis, and aquatic invertebrate remains. This was undertaken at Ghent University, department of Biology in the Limnology research unit.
Methodology of virulence screening and race characterization of Plasmopara halstedii, and resistance evaluation in sunflower – a review

Sunflower downy mildew is a disease of high global economic impact as well as a causal agent that is extremely difficult to eradicate. During the past decades, several approaches for the determination of Plasmopara halstedii (Ph) races have been used worldwide and are discussed in this review. Procedures of isolation, cultivation and maintenance of Ph isolates, as well as the screening of sunflower for resistance, are also critically reviewed. The predominant, globally used resistance screening protocol is a ‘whole seedling immersion’ inoculation. ‘Soil drench’ inoculation allows more precise control of the number of Ph zoosporangia applied to a single sunflower seedling. A detached leaf assay has been described, but it has been used mainly for Ph subcultivation and fungicide tests. For race determination, a differential set consisting of nine sunflower genotypes has been used since 1988, coupled with a numerical triplet code for virulence phenotyping of Ph. The increasing variability in global Ph populations has demonstrated the inadequacy of the current set of differentials, and several researchers have proposed additional public lines as new differentials. Furthermore, bulk isolates may show different results in repeated tests, as Ph may contain genetically distinct zoospores within a single zoosporangium. For precise race determination, single zoosporangia or single zoospore isolates are advisable. However, due to low success of isolation, approximately 1–2%, this method cannot be applied in routine Ph race screening. Methods surveyed in this review have a broad spectrum of applications, including taxonomic studies.
A multidirectional d/d damage model for concrete and masonry structures under monotonic and cyclic loading

In the present paper, a new d/d damage model apt for quasi-brittle materials is described and its validation is carried out considering unreinforced concrete, reinforced concrete and masonry elements. Two independent scalar damage variables, d and d, in combination with the split of the reversible strain tensor into its positive and negative counterparts, are adopted in order to simulate the pronounced dissimilar response under tension and compression, typical of these materials. An energy-equivalence framework is considered for representing the orthotropy induced in the material by the degradation process, with the consequence that a thermodynamically consistent constitutive operator, positive definite, symmetric and strain-driven, is derived. In addition to the degradation parameters, the permanent strain tensor is also contemplated by the model and a modification of the exponential softening modulus is proposed in order to treat the evolution of the two causes of dissipation, damage and irreversible deformations, in a coupled way. The damage formulation is integrated with a multidirectional damage procedure, addressed to extend the microcrack closure-reopening (MCR) capabilities of the model to shear cyclic conditions, characterized by orthogonal (or however intersecting) sets of cracks. Maintaining unaltered the dependence of the constitutive law from two scalar variables, d and d, the multidirectional procedure activates or deactivates a tensile (compressive) damage value on the base of the current maximum (minimum) principal strain directions. The adequacy of the proposed constitutive model in reproducing experimental results has been proven for both monotonic and cyclic loading conditions. The two examples of application involving cyclic loads, dominated by shear, constitute a validation of the multidirectional damage approach, showing how the suitable representation of unilateral
BUSINESS ETHICS COURSE ON STUDENT MORAL REASONING

This research aims to identify and measure the effectiveness of business ethics courses on student Moral Reasoning. In-depth interview and a pilot test were conducted to examine the understandability of the experimental instrument. Quasi-experimental methods were conducted on students who join a business ethics course. One hundred twenty-two participants were valid from the manipulation check of pre-test and post-test. Paired T-Test was used to test the score between pre-test and post-test. Moral reasoning was measured using a defining issue test (DIT) to categorise High and Low Moral Reasoning on Participants. The result shows no difference in moral reasoning score between pre-test and post-test on a student who joins the business ethics course. This study finds that student moral reasoning does not improve by joining a business ethics course at university. These results imply that we should evaluate and re-examine the business ethics course syllabus for future research.