Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecogeographic and genetic determinants of kernel weight and colour of wild barley (Hordeum spontaneum) populations in Israel

The aim of this study was to establish associations of kernel weight and colour with ecogeographic factors and molecular markers, based on ten wild barley [Hordeum spontaneum (C. Koch) Thell. ] populations sampled in Israel across a southward transect of increasing aridity. Kernel weight and colour category were scored using barley kernels (naked caryopsis). Small kernel sizes (0.011 g kernel–1) and dark kernels were found in xeric populations. A higher variation of kernel weight was observed in xeric populations. A higher proportion of variation occurred within, rather than among, populations. Water, temperature and soil factors were associated with kernel size variation. Among 18 simple sequence repeats (SSRs) investigated, HVM14, HVM36, HVM43, BMS64 and BMS90 were associated with kernel weight, and HVM68 with kernel colour. The results indicated that high phenotypic variation and genetic diversity are related to ecological stress, and that the association of phenotypic traits with molecular markers, based on natural plant populations, should be interpreted cautiously due to the high chance of spurious associations between traits and molecular markers.
Truly Batch Model-Free Inverse Reinforcement Learning about Multiple Intentions

We consider Inverse Reinforcement Learning (IRL) about multiple intentions, i.e., the problem of estimating the unknown reward functions optimized by a group of experts that demonstrate optimal behaviors. Most of the existing algorithms either require access to a model of the environment or need to repeatedly compute the optimal policies for the hypothesized rewards. However, these requirements are rarely met in real-world applications, in which interacting with the environment can be expensive or even dangerous. In this paper, we address the IRL about multiple intentions in a fully model-free and batch setting. We ﬁrst cast the single IRL problem as a constrained likelihood maximization and then we use this formulation to cluster agents based on the likelihood of the assignment. In this way, we can e ﬃ - ciently solve, without interactions with the environment, both the IRL and the clustering problem. Finally, we evaluate the proposed methodology on simulated domains and on a real-world social-network application.
Structural, physical and genetic interactions of the i-AAA protease Yme1 in Saccharomyces cerevisiae

The i-AAA protease Yme1 is a highly conserved ATP-dependent AAA (ATPase Associated with various cellular Activites) protease anchored to the inner mitochondrial membrane where it mediates protein quality surveillance that is crucial for cell survival. In yeast, deletion of YME1 is associated with pleitropic phenotypes. However, the few known proteolytic substrates and interaction partners of the i-AAA protease cannot explain the molecular basis of these phenotypes. Therefore, different approaches were used to define the function of the i-AAA protease. First, affinity purification of a proteolytic inactive variant of Yme1 working as a substrate trap was employed and led to the identification of eight novel Yme1-interacting proteins that localise to different submitochondrial compartments. Subsequent analysis revealed that two interactors, Mcr1 and Mpm1, represent new proteolytic substrates of the i-AAA protease. Hence, additional functions of the i-AAA protease should be responsible for the other identified interactions. Second, insights into processes that require the function of the i-AAA protease were obtained by a synthetic genetic array (SGA) approach using an assorted library of 96 non-essential mitochondrial gene deletions. 34 identified synthetic lethal interaction potentially link Yme1 to new functions like mitochondrial morphology, protein processing and lipid metabolism. Finally, the synthetic lethal interaction of IMP1 and YME1 was analysed by a high copy suppressor screening. This interaction is of particular interest, as all substrates of the Imp1 catalytic subunit of the IMP processing peptidase could be co-purified with the i-AAA protease. The identified suppressor Pgk1, a key enzyme in glycolysis and gluconeogenesis, suggests a severe impairment of Deltayme1Deltaimp1 cells in energy metabolism. Moreover, in this thesis the substrate recognition by the i-AAA protease was examined by mutational analysis. Recently, two substrate binding regions have been identified within Yme1: the CH-(C-terminal helices) and the NH-(N-terminal helices) region. In contrast to the NH-region, the molecular mechanism of substrate binding to the CH-region has not been studied so far. Here, the CH-region was not only identified to have a role in substrate binding and transfer to the proteolytic cavity, but also for the stabilisation of the i-AAA protease complex. Taken together, novel substrates and interaction partners of the i-AAA protease were identified, pointing to additional functions of Yme1 independent of its proteolytic activity. As only few approaches have addressed the function of the i-AAA protease in higher eukaryotes so far, it will be interesting to examine the relevance of these findings for mammals.
Identification of α1-Antitrypsin Variants in Plasma with the Use of Proteomic Technology

Background: Proteomic technology permits the investigation of genetic metabolic diseases at the level of protein expression. Changes in the expression, polypeptide structure, and posttranslational modification of individual proteins can be detected in complex mixtures of proteins. Methods: We used high-resolution two-dimensional polyacrylamide gel electrophoresis to separate isoforms of plasma proteins and detect abnormalities of mass and/or charge. We confirmed the identity of the separated proteins by in-gel digestion with proteases and N -glycanases and then analyzed the released peptides and glycans by matrix-assisted laser-desorption ionization–time-of-flight mass spectrometry. Results: Complete characterization of the polypeptide sequences and glycosylation of α1-antitrypsin isoforms was achieved in plasma from controls and from patients with three different known α1-antitrypsin deficiencies and congenital disorder of glycosylation type Ia. Conclusions: This study shows that proteomic techniques are a powerful and sensitive means of detecting changes in the amino acid sequence and abnormal posttranslational modifications of specific proteins in a complex biologic matrix.
CANONICAL ANALYSIS OF PRINCIPAL COORDINATES: A USEFUL METHOD OF CONSTRAINED ORDINATION FOR ECOLOGY

A flexible method is needed for constrained ordination on the basis of any distance or dissimilarity measure, which will display a cloud of multivariate points by reference to a specific a priori hypothesis. We suggest the use of principal coordinate analysis (PCO, metric MDS), followed by either a canonical discriminant analysis (CDA, when the hypothesis concerns groups) or a canonical correlation analysis (CCorA, when the hypothesis concerns relationships with environmental or other variables), to provide a flexible and meaningful constrained ordination of ecological species abundance data. Called “CAP” for “Canonical Analysis of Principal coordinates,” this method will allow a constrained ordination to be done on the basis of any distance or dissimilarity measure. We describe CAP in detail, including how it can uncover patterns that are masked in an unconstrained MDS ordination. Canonical tests using permutations are also given, and we show how the method can be used (1) to place a new observation into.
Rice (Oryza sativa) cultivation in Brazil

Rice (Oryza sativa L.) is staple food for the population of South America, including Brazil. In Brazil, it is produced under 2 ecosystems known as upland and lowland. Furthermore, based on farm size, rice is cultivated on small, medium and large farms in Brazil. Small-and medium-farm holdings contribute 26% rice production, while large-scale farms contribute 74% of total rice production in the country. Major part of rice production is totally mechanized in Brazil. During 2012–2013 cropping season, Brazil produced about 12 million tonnes of paddy rice. Area planted under both systems is about 2.62 million ha. Average yield of upland rice is about 1.8 Mg/ha and lowland rice is about 7.0 Mg/ha. Low yield of upland rice compared to lowland rice is due to many biotic and abiotic stresses. These stresses are drought, low soil fertility, diseases, insects and weeds. Lowland rice is mainly grown in 2 southern states known as Santa Catarina and Rio Grande do Sul. Upland rice is mainly grown in the central part of Brazil, locally known as Cerrado region. Upland as well as lowland rice is planted during the rainy season which occurs from October to March. Average rainfall in the Cerrado region is about 1,500 mm and in the southern region where lowland rice is mainly planted is 1,400 mm. Average minimum and maximum air temperature in the Cerrado region during rice-growing season is about 19 and 28°C respectively. Overall, minimum and maximum air temperature during lowland rice growing season in the 2 southern states is 16 and 27°C. Brazil is the fourth largest grain producing country in the world after China, USA and India. However, it is projected that Brazil will be supergrain producing country in the world in the coming decades owing to large land area, water availability, favourable climatic conditions and availability of technology.
GIS-BASED HABITAT MODELS FOR MOUNTAIN GOATS

Abstract We used logistic regression to develop habitat models from observation of mountain goats (Oreamnos americanus) in alpine habitats near Mt. Evans, Colorado. Mountain goats used areas near escape terrain, on moderate slopes, at midelevations, and on southerly exposures more than expected. Habitat models for summer, winter, or all-seasons correctly classified 81–83% of observations and incorrectly classified 12–13% of locations not used by mountain goats. A model based only on distance to escape terrain correctly classified 87% of observations and classified 38% of the study area as suitable habitat. Our models provide a way to use readily available data and simple techniques to quickly identify suitable habitat over large geographical areas.
Biological and Physiological Effects of Some Honey Bee Products and Its Mixtures as Nutritional Additives on Two Strains of The Mulberry Silkworm Bombyx mori

The effect of some honey bee products; royal jelly (RJ 10mg/ml), pollen (P 50mg/100ml), propolis (PR 30mg/100ml), honey (H 1g/100ml) and their mixtures as food additives, on several biological and physiological parameters of the 5 th larval instar of (S1 and S2) of the silkworm Bombyx mori were studied. The above mentioned products, either separately or in combination increased weights of mature larvae, pupae, fresh cocoons and cocoon shells. Larvae fed on mulberry leaves treated with RJ showed a significant increase in weights followed by H and then P in the broad strain. While in the local strain, RJ gave the maximum weights followed by P and then H. The same trend was observed in the total haemolymph protein and the CA surface area in both strains.
Amélioration du taux de multiplication in vitro de Jatropha curcas L.

Dans le but d’améliorer le taux de multiplication in vitro (nombre de tiges/explant/subculture) de Jatropha curcas L. , des noeuds axillaires prélevés sur de jeunes plantes de deux accessions de cette espèce, originaires du Cameroun et du Sénégal, sont cultivés pendant trois semaines sur un milieu MS supplémenté de 8,87 μM de BAP; 4,92 μM d’AIB, ainsi que de 30 g/l de saccharose à pH 5,7 ± 0,1; et solidifié avec 0,7% d’agar. Les tiges obtenues à partir de chaque explant initial sont ensuite transférées sur des milieux de prolifération (MP) constitués du milieu MS complémenté de 2,21 à 8,9 μM de BA ou de 2,21 à 8,9 μM de kinétine en combinaison avec 2,46 μM d’AIB. Chaque combinaison est complétée avec 33,12 μM de sulfate d’adénine; 82,92 μM de glutamine et 30 g/l de saccharose. Les meilleurs taux de multiplication sont obtenus pour le milieu MP contenant 6,65 μM de BA et 2,46 μM d’AIB: 42,72 ± 3,22 et 38,15 ± 4,7 tiges/explants, respectivement pour l’accession camerounaise et sénégalaise après 6 semaines de culture. Les taux de multiplication moyen sont respectivement pour ces deux accessions de 8,27 ± 1,27 et 7,89 ± 1,13 tiges par explant au cours des 7 subcultures suivantes (3 semaines/subculture). Ce milieu est également celui qui permet globalement la meilleure croissance en hauteur des tiges. Les tiges feuillées obtenues peuvent être enracinées sur un milieu contenant la moitié des éléments minéraux majeurs de MS additionné de 5,7 μM d’AIB; 1,5% de saccharose et solidifié avec 0,7% d’agar, puis acclimatées avec un taux de survie de 97%. Ces résultats permettent d’envisager la création d’unités de multiplication industrielle de plants à la fois homogènes et performants issus de clones élites de J. curcas. Amélioration du taux de multiplication in vitro de Jatropha curcas L.
Analysis of the impact of factors affecting survivability of bacteria from the Enterobacteriaceae family during sewage sludge composting

The objective of the performed investigations was to assess the influence of the value of temperature, pH, gas emissions, and doses of BAF microbiological inoculum on the reduction or total elimination of bacteria from the Enterobacteriaceae family. The performed experiment consisted of two stages. In the course of the first trial, sewage sludge was subjected to composting together with straw and sawdust in a cybernetic bioreactor. The experimental design included three treatments, two of which were inoculated twice with BAF inoculum: K1 – control, compost without inoculation; K2 – compost+1500 ml BAF; K3 – compost+750 ml BAF. The BAF (Bacteria-Actinomycetes-Fungi) inoculum was designed at the Department of General and Environmental Microbiology of Poznan University of Life Sciences and was made up of bacterial strains, actinomycetes, and mould fungi isolated from mature compost. The microbiological analyses applied in this experiment involved determination of total counts of bacteria belonging to the Enterobacteriaceae family using, for this purpose, Koch’s plate method followed by biochemical tests confirming species membership of the above-mentioned bacteria. In the second part of the experiment, bacteria from Escherichia, Klebsiella, and Citrobacter genera isolated from mature composts were subjected to the ring method with the aim of examining mutual interactions between the above-mentioned bacterial species and the BAF inoculum. On the basis of the obtained research results, it was found that the recorded reduction in numbers of the discussed microorganisms was caused by physico-chemical factors of the composting process, especially by the inoculation of biowastes by the BAF biopreparation. The performed in vitro analysis of interactions between the Escherichia coli, Citrobacter freundii, and Klebsiella pneumoniae strains and the applied BAF inoculum revealed considerable sensitivity of the above strains to the experimental biopreparation. However, in in vivo conditions, E. coli bacteria exhibited resistance to the action of the above dose of the inoculum. Therefore, continuation of the above investigations appears necessary.
ANTIMICROBIAL POTENTIAL OF BACILLUS MARISMORTUI, A SALT PAN ISOLATE OF CAVELLOSIM, GOA, INDIA

A halotolerant, Gram positive, motile, rod was isolated from the salt pan sediments of Cavellosim, Salcette, Goa, India and screened for its antimicrobial potential. The strain showed an inhibitory effect specifically to Staphylococcus citreus. The isolate showed optimal growth as well as antibiotic production with 4% natural salt and could tolerate up to 6% salt. Dextrose and L-Tryptophan were found to be the best carbon and nitrogen sources for optimum antibiotic production. Based on morphological, biochemical, 16S rDNA sequencing and phylogenetic analysis, the strain was identified as B. marismortui.
Lion's paw scallop (Nodipecten subnodosus, Sowerby 1835) aquaculture in Bahía Magdalena, Mexico: effects of population density and season on juvenile growth and mortality

This study examined the eiects of density and growing season on growth and survival of juvenile lion’s paw scallops (Nodipecten subnodosus )i n Estero San Buto, a mangrove channel in Bah|¤ a Magdalena, Mexico. Scallops were kept in plastic mesh bags in oyster trays at three population densities (500, 1000 and 2000 organisms per tray, or low medium and high density respectively) over a period of 2 months from October to December 2001and from February to April 2002. Growth (shell height increment) was measured every 7^12 days and mortality was evaluated at the end of the experiment (dead shell count). Overall growth was fast (0.24^0.38 mm day 1 ) in comparison with other pectinids. Signi¢cant diierences were found for both, density and season, with faster growth occurring at lower densities and during the fall season when the water temperature was higher. Mortality was low (0.5^3.0% 60 day 1 ) except for the high-density treatment in the fall (44% 60 day 1 ). Crowding together with high water temperatures and increased metabolic oxygen demand of the scallops and possibly competition for food were the probable reasons for this high mortality. Overall, mortality was lower in the spring, when temperatures were lower, O2 values were higher and food was more abundant.
Genetic Polymorphism Detection in Four Genes in Egyptian and Saudi Sheep Breeds

2 Abstract: This work aimed to study the genetic polymorphism in Booroola gene (FecB), Bone morphogenetic protein-15 (BMP-15), Myostatin (MSTN) and Ghrelin genes and its effects on the production. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to detect polymorphisms of three candidate genes in five Egyptian and Saudi sheep breeds (Barki, Ossimi, Rahmani, Najdi and Harri) to detect the genotype of FecB, BMP-15, MSTN genes and their allele frequencies. Genotypes were determined by PCR amplification followed by single nucleotide polymorphism (SNP) anthor method for ghrelin gene (Barki, Rahmani, Saidi, Najdi and Harri). Results showed that the polymorphism frequencies of FecB gene with Avall digestion are significantly imbalanced in five breeds. The Najdi, Harri, Barki, Rahmani and Ossimi sheeps were all homozygous carriers (BB). PCR-RFLP with HinfI digestion was used to investigate the genotyping of FecX loci in exon 2 BMP-15 genes. The genotype frequencies for ++ were: 0.32, 0.30, 0.29 from Barki, Ossimi, G Rahmani, respectively, while +G genotype were 0.68, 0.70 and 0.71 after digestion with HinfI. Frequencies of allele + were 0.66, 0.65 and 0.64 in Barki, Ossimi, Rahmani, breeds in Egypt, while 0.34, 0.35 and 0.36 for allele G in Barki, Ossimi, Rahmani, breeds. BMP-15 gene was found to be monomorphic in Najdi and Harri Saudi sheep breeds. Myostatin gene was found to be monomorphic with HaeIII digestion in all sheep breeds. All Egyptian and Saudi samples in myostatin locus were digested by HaeIII enzyme and showed the mm genotype, all of them were monomorphic. The sequence analysis of ghrelin amplified PCR product indicated three nucleotide substitutions (T to C; A to G and A to C) at nt 38 and nt49, nt 108, nt 60 and nt 71 in Rahmani. The six different detected variables were present in the Saidi sheep breed at different frequencies with a majority of five transversion and one transition (G to T, A to T, A to T, G to C, G to T) at nt 14, nt 56, nt 58, nt 67, nt 60 and 71, respectively. This is one of the first studies on polymorphism of BMP-15, myostatin and ghrelin genes in Egyptian and Saudi sheep breeds.
UNDERSTANDING TRANSCRIPTION FACTOR - DNA RECOGNITION USING IN SILICO, IN VITRO AND IN VIVO APPROACHES: THE CSL CASE

We have investigated whether protein structure-based in silico approaches could be used to provide information about the full repertoire of binding sites. To achieve this, the FOLDX software [1] was used to calculate changes in binding energy when varying the nucleotides within the constraints of the CSL-DNA co-crystal structure. Starting from the X-ray structure in which CSL binds the (current) highest-affinity DNA motif comprised of eight nucleotides CGTGGGAA (PDB code 3BRG,[2]), all 4 8 permutations of an 8-nt motif were tested and the resulting 65536 relative binding energies calculated. A threshold of 3 kcal/mol difference from the top predicted DNA sequence was used as a cut-off, separating 220 putative “bound” motifs from the residual 65316 DNA sequences. These 220 “bound” sequences were used to generate a binding logo and this was compared with the previously used TRANSFAC logo [3].
Versatile, Low-cost Indoor Positioning Combining Bluetooth and Ultra Wideband Technologies

In this paper we present XtremeLoc, a low-cost indoor positioning system designed to work in situations where GPS is not a valid alternative. XtremeLoc relies on the use of portable, low-cost, Bluetooth Low Energy beacons using the iBeacon protocol. Instead of setting these beacons in fixed positions, they are carried by the persons or goods to be tracked. The beacons broadcast a signal that is received by a set of fixed, low-cost antennas. These antennas estimate the distance to the emitter using the perceived intensity of the signal, and transfer this information to a cloud-based server that calculates the position of the emitter, storing it and displaying it through a web-based interface. The use of this technology allows a precision of around two to three meters. To track elements with a higher precision, XtremeLoc allows the concurrent use of custom Ultra Wideband devices, that allow a precision of around 10 cm while using the same interface. In this paper we describe XtremeLoc architecture and main features, how to use it to find persons and goods with the help of Augmented Reality applications, and an example of use of this technology to record the behavior of individual persons during evacuation drills.