Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of transhumance on the spread of Rhipicephalus microplus (Canestrini, 1888) in Benin

Objective: Rhipicephalus microplus is a very invasive tick whose control is a current challenge. Its speed of propagation is favored by specific risk factors whose knowledge is an essential prerequisite for a good rather design of strategies to put in place for its control. This study consisted of evaluating the influence of transhumance on the spread of this tick in Benin. Materials and methods: To achieve this objective, two sets of tick sampling were carried out on five animals before and after transhumance in 80 autochthon herds from 8 municipalities in Benin. Results: The abundance of R. microplus varies significantly between breeding type, hosting type, period of ticks collection and between some of their interactions such as: breeding - period, hosting - period and breeding - hosting - period. In addition, the abundance of R. microplus according to each of these factors before transhumance differs significantly from the one observed after transhumance; the parasite load of R. microplus observed before transhumance is much higher than that observed after transhumance. Transhumance contributes to the spread of R. microplus in Benin. Conclusion: It represents a risk factor on which health risk managers could act in terms of surveillance and control of this cattle tick by carrying out the de-parasitage in the health campaign programs of transhumant animals.
An analysis of alternative forms of plant reproduction using Gossypium barbadense and Arabidopsis thaliana

An Analysis of Alternative Forms of Plant Reproduction Using Gossypium barbadense and Arabidopsis thaliana. (December 2006) Kelly Denise Biddle, B.A., Rice University Chair of Advisory Committee: Dr. David Stelly Apomixis holds vast potential for improving agriculture worldwide. It would make plant breeding faster, allow for fixation of hybrid genotypes, and help genetically isolate transgenic crops. However, efforts to introduce apomixis into agriculturally important crops, through either plant breeding or molecular genetics, have failed to produce any new apomictic varieties. This could possibly be remedied if researchers better understood the genetics of apomixis, including the underlying genes, their regulation, and the cellular pathways they control. My work increased our knowledge of these processes by using a mixture of novel methods and underutilized resources. In this study I pursued a two-pronged approach that involved both traditional and reverse molecular genetic techniques. I analyzed the Semigamy mutation from Pima Cotton (Gossypium barbadense), which produces large numbers of haploid and chimeric offspring. Although interesting and potentially useful, little is known about this gene, its expression, regulation, and localization, or the cellular processes in which it is involved. This knowledge advanced our understanding of both this part of apomixis and plant reproduction in general. I was able to determine that the Semigamy mutation is recessive to the wild-type and is incompletely expressed even in the homozygous state.
Molecular characterization of novel isolates of Rhizoctonia solani, Trichoderma atroviride and Fusarium spp. isolated from different plants and cutting woods in Iraq

Three fungal (Fusarium, Rhizoctonia and Trichoderma) species isolated from diseased tomato, maize and wood decayed plants from Iraq were morphologically identified. ITS1 and ITS4 based genetic regions were used for molecular identification and phylogenetic relationship revealed that that Rhizoctonia solani isolates had 99% similarities to Indian, USA and Mexicans isolates. Fusarium solani showed 99% nucleotide identity to Indian, Chinese, Mexicans and Brazilian isolates. Fusarium proliferatum showed >99% nucleotide identity to Asian isolates whereas Trichoderma atroviride showed 99% similarity to Chinese isolates. These identified fungal isolates of F. solani, F. proliferatum and T. atroviride were not previously reported from Iraq and therefore sequences of these fungi were deposited in the GenBank database (NCBI) under the accession numbers KY283953(R. solani), KX000895 (F. solani), KX350051 (F. proliferatum) and KU985151 (T. atroviride) for the first time.
PROTEIN STRUCTURE PREDICTION A STUDY ON DIFFERENT METHODS

-The inference of the three-dimensional structure of a protein from its amino acid sequence is protein structure prediction, that is, the prediction of its folding and its secondary and tertiary structure from its primary structure.Protein structure prediction methods attempt to determine the native, in vivo structure of a given amino acid sequence. In this paper, we have studied various methods like statistical generation, machine learning which included neural networks, case-based reasoning
Phytophagous hoverflies (Diptera: Syrphidae) as indicators of changing landscapes.

Spatial and temporal differences in landscape patterns are of considerable interest for understanding ecological processes. In this study, we assessed habitat quality by using the Syrph The Net database and data on decreasing species richness over a 25-year period for the two largest phytophagous hoverfly genera (Merodon and Cheilosia). Furthermore, within this time frame, we explored congruence between ecological responses (species richness and Biodiversity Maintenance Function for these two genera) and landscape structural changes through correlation analysis. Our results indicate that landscapes have experienced changes in aggregation, isolation/connectivity and landscape diversity, with these parameters being significantly correlated with Cheilosia species richness loss and habitat quality. We conclude that the genus Cheilosia is a good bioindicator that can highlight not only the current quality of an area but also temporal changes in landscape patterns.
Piecewise Logistic Regression: an Application in Credit Scoring

Piecewise regression (also known as “segmented” or “broken-stick” regression) is typically associated with linear regression, and the modelling of a non-linear relationship between a single dependent variable and an independent variable (both continuous). The dependent variable is partitioned into intervals, each of which is introduced as separate variable into a model. It has seldom been used in credit scoring, where the most common approach is use logistic regression to model a binary outcome, with the many predictors (both continuous and categorical) transformed into “weights of evidence” for different ranges/ groups. This paper presents the results of an attempt at using piecewise logistic regression to develop a credit scoring model. The idea came about from an attempt to combine weights of evidence and 0/1 dummy variables in a single regression, as the use of dummies often results in values that do not make sense, necessitating manual and time-consuming adjustments. Weights of evidence were then used for both dummies and non-dummies, and piecewise regression became a logical next step
Les cendres de bois: un nouvel engrais pour l’agriculture suisse

(RS.916.171, 2011) mais une autorisation peut leur être délivrée si elles répondent aux exigences fixées pour les «engrais de recyclage» dans l’annexe 2.6 de l’ORRChim (RS.814.81, 2011). Afin de préserver la qualité des sols et de réduire les risques de transfert de substances indésirables vers la chaine alimentaire, cette annexe définit des teneurs totales maximales à ne pas dépasser pour six éléments traces métalliques (ETM) potentiellement toxiques (Cd, Cu, Hg, Ni, Pb et Zn). Les cendres de bois ne respectent que rarement ces exigences et sont donc généralement mises en décharge, ce qui représente une perte importante d’éléments fertilisants naturels et un coût pour les chaufferies à bois. Or, pour évaluer et prévenir les risques environnementaux, la seule détermination des teneurs totales en ETM n’est pas suffisante, puisque la mobilité, la biodisponibilité et donc la toxicité des ETM dépend avant tout de leur forme chimique (Bruder-Hubscher et al. 2002). D’autre part, c’est la quantité d’ETM épandue à l’hectare qui détermine les risques d’accumulation à long terme d’ETM dans les sols. Les intérêts et risques agro-environnementaux de l’utilisation agricole de ces sous-produits industriels doivent donc être évalués plus précisément. L’équipe de nutrition des plantes d’Agroscope à Changins étudie depuis 2011 les effets agronomiques de l’épandage des cendres sous foyer de la centrale Enerbois. Les objectifs sont (i) la caractérisation de la composition, de la minéralogie et de la forme chimique des macroéléments et des ETM contenus dans les cendres, (ii) l’identification de l’origine de ces ETM et (iii) l’évaluation des effets des cendres sur les propriétés chimiques et biologiques des sols, le rendement et le prélèvement en ETM par les cultures. Le présent article synthétise les résultats d’une étude relative à l’objectif (iii) (Maltas et Sinaj 2013).
The effects of updating ability and knowledge of reading strategies on reading comprehesion Muijselaar,

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Microbial Endophytes that Live within the Seeds of Two Tomato Hybrids Cultivated in Argentina

Tomato (Solanum lycopersicum L.) is probably the most important vegetable consumed around the world, and like other produce is affected by stresses and diseases that reduce the yield and production. The purpose of this work was to study the phytobiome of the tomato seeds of two hybrids in order to understand first of all whether tomato cultivars host similar groups of organisms, as well as their effect on the community structure, particularly of those microbes with the potential to promote growth and/or control plant pathogens. Different cultivars of tomato (genotypes) host significantly different endophytic communities, which is also reflected at the order level. These communities are particularly rich in spore-forming bacteria that have the ability either to promote plant growth or synthetize antimicrobial compounds that deter plant pathogens. We conclude that the seeds of the tomato cultivars Elpida and Silverio are sources of endophytic bacteria capable of synthetizing antifungal substances that could potentially be used for biocontrol against plant-pathogenic fungi.
Characterization of mesenchymal stem cells derived from periodontal ligament

It is well-known that mesenchymal stem cells responsible for periodontal tissue regeneration exist in the periodontal ligament by differentiation into fibroblasts, cementoblasts, and osteoblasts. However, the detailed characteristics of stem cells have not been clarifi ed. Recently, the presence of a novel stem cell called Muse cells has been reported. It was mentioned that Muse cells exist in all mesenchymal tissues, and which can be found in the bone marrow, skin and adipose tissues. Nevertheless, the existence of Muse cells in oral tissues has not yet been reported. This study investigated whether Muse cells are present in the periodontal ligament. Results showed that about 0.83% of Muse cells sorted out from periodontal ligament cells showed the ability for self-renewal as well as the expression of genes present in all three germ layers. When compared to Muse cells derived from the skin for calcifi cation ability, Muse cells derived from periodontal ligament showed higher calcifi cation ability both at gene and tissue levels. Although both cells were considered Muse cells, cells derived from the periodontal ligament have diff erent characteristics compared to the Muse cells derived from the skin. The results suggest that stem cells derived from somatic cells are possible to maintaining the original phenotypes. Therefore, when using stem cells for regenerative medicine, we suggest that the stem cells should be sorted from the same tissue, which expects repair or regeneration of the tissue.
Hard Limits and Performance Tradeoffs in a Class of Sequestration Feedback Systems

Feedback regulation is pervasive in biology at both the organismal and cellular level. In this article, we explore the properties of a particular biomolecular feedback mechanism implemented using the sequestration binding of two molecules. Our work develops an analytic framework for understanding the hard limits, performance tradeoffs, and architectural properties of this simple model of biological feedback control. Using tools from control theory, we show that there are simple parametric relationships that determine both the stability and the performance of these systems in terms of speed, robustness, steady-state error, and leakiness. These findings yield a holistic understanding of the behavior of sequestration feedback and contribute to a more general theory of biological control systems.
Regulation of Neuronal mRNA Localization by Exclusion

Regulation of Neuronal mRNA Localization by Exclusion José C. Martínez Intra-axonal protein synthesis is important for the proper wiring of the nervous system and can have restorative or pathogenic effects in response to nerve injury and neurodegenerative stimuli. The set of axonally translated transcripts, the axonal translatome, is regulated through the control of mRNA localization, stability, and translation. Targeting the axonal translatome could result in the development of novel therapies for the treatment of neurological disorders. Yet, there are gaps in our understanding of the selective mechanism regulating the specific localization of mRNAs into axons. Currently, axonal localization of transcripts is understood to be controlled by the presence of sequence elements that direct axonal transport. In an attempt to identify novel localization motifs, I found that a well-known motif corresponding to the Pumilio Binding Element (PBE) is significantly depleted in axonally enriched mRNAs. Moreover, I found this element to be highly informative of axonal mRNA localization and translation across different neuronal types and developmental stages suggesting that it is a highly conserved regulatory motif. I found Pum2 neuronal expression and subcellular localization to be highly consistent with the way the PBE predicts mRNA regulation. I then demonstrated that interfering with Pum2 function results in increased axonal localization of PBE containing mRNAs. Finally, Pum2 downregulation was associated with gross defects in axonal outgrowth, branching, and regeneration. Altogether, this data suggests that Pum2 regulates axonal mRNA localization through an exclusion mechanism that is important during neuronal development.
Characterizing the role of DNA polymerase gamma in the yeast, Cryptococcus neoformans

The basidiomycetous yeast, Cryptococcus neoformans, is an opportunistic pathogen that is responsible for a common fungal infection of the central nervous system, cryptococcal meningoencephalitis. This is a signal disease of AIDs patients that can also be found in patients of other immune compromising afflictions. This disease can be treated with various antifungal medications, but these drugs must be taken in combination, and are often far too expensive for widespread availability. The current shortcomings of available treatments make it critical that we understand vital systems within this organism that may lead to development of more effective and potentially cheaper medications. DNA polymerase gamma (polG or Mip1p) has been identified as the only polymerase in yeast that is capable of replication and repair of the entire mitochondrial (mt) genome. In S. cerevisiae, deletion of DNA polG leads to the overall lack of mtDNA and the production of petite or wee colonies. C. neoformans is known to be aerobic, and therefore, the integrity of its mitochondrial DNA is hypothesized to be vital to the survival of the yeast. This necessity of mtDNA replication and maintenance makes polG a strong candidate as a potential drug target. Using amino acid sequence homology, a MIP1 homolog has been identified in C. neoformans. This gene, CNAG_06769, has a 45% identity to the MIP1 gene in S. cerevisiae and contains a mitochondrial localization signal (MLS) as well as a DNA polymerase A domain, which is found in all known DNA polG proteins. The polymerase domain identified in C. neoformans polG contains a 62% identity and a 76% similarity to the same domain found in S. cerevisiae polG. There are also regions within the cryptococcal protein that have previously not been seen in other fungal or mammalian polG proteins. This has raised questions regarding what the functions of these domains may be and how these functions may be relevant in DNA polG research. In this project, RNAi has been used to silence the MIP1 gene (MIP1i). Galactose-dependent knock-down of CnMIP1 shows that this gene appears to be essential to C. neoformans survival. Growth curves of the MIP1i strains compared to those of wild type cells show that the strains are unable to proliferate in the absence of this protein. In addition, mitochondrial integrity assays using the vital dye Mitotracker Green indicate that RNAi of MIP1 affects the viability of these cells. Localization of the CnpolG protein with a C-terminal mCherry tag was also attempted. Constructs were created to express this protein from its endogenous promoter, as well as from a copper-repressible promoter. However, the attempts to localize this protein in vivo have been inconclusive to date and require further optimization.
IQD proteins integrate auxin and calcium signaling to regulate microtubule dynamics during Arabidopsis development

Geometry and growth and division direction of individual cells are major contributors to plant organ shape and these processes are dependent on dynamics of microtubules (MT). Different MT structures, like the cortical microtubules, preprophase band and mitotic spindle, are characterized by diverse architectural dynamics (Hashimoto, 2015). While several MT binding proteins have been identified that have various effects on MT stability and architecture, they do not discriminate between the different MT structures. It is therefore likely that specific MT binding proteins exist that differentiate between MT structures in order to allow for the differences in architectural dynamics. Although evidence for the effect of specific cues, such as light and auxin, on MT dynamics has been shown in recent years (Lindeboom et al., 2013; Chen et al., 2014), it remains unknown how such cues are integrated and lead to specific effects. Here we provide evidence for how auxin and calcium signaling can be integrated to modulate MT dynamics, by means of IQD proteins. We show that the Arabidopsis IQD15-18 subclade of this family is regulated by auxin signaling, can bind calmodulins in a calcium-dependent manner and are evolutionarily conserved. Furthermore, AtIQD15-18 directly bind SPIRAL2 protein in vitro and in vivo and modulate its function, likely in a calmodulin-dependent way, thereby providing a missing link between two important regulatory pathways of MT dynamics. One sentence summary IQD proteins integrate auxin and calcium signaling, two major signaling pathways, to control the cytoskeleton dynamics and cell shape of Arabidopsis.
The Potential of Mimosa pudica as a Biopreservative for Food Products: a Bio processing Perspective

The discovery of natural antimicrobials is consistent with the growing demand due to consumer awareness of natural food products and the concern of microbial resistance towards conventional food processing and preservation methods. Generally, bio-preservative can be made from antimicrobial metabolites (e.g., bacteriocin, other metabolites, plant extracts, and enzymes), fermentates, cultures, and bacteriophages [1]. Interestingly, bio-preservative should be used in combination rather than in isolation, as well as together with a physical process like thermal processing to improve its efficacy [2]. Biopreservation allows shelf life of food products to be extended using natural origin. In order to prevent the growth of spoilage microorganisms in foods, the antimicrobials can be applied directly into the food formulation, coated on its surface, or incorporated into packaging materials [3].
Recent Developments in Fiber Genomics of Tetraploid Cotton Species

Cotton ( Gossypium spp.) produces naturally soft, single-celled trichomes as fiber on the seed coat supplying the main source of natural raw material for the textile industry. It is economically considered as one of the most leading cash crops in the world and evolutionarily very important as a model system for detailed scientific investigations. Cotton production is going through a big transition stage such as losing the market share in competition with the synthetic fibers, high popularity of Bt and herbicide resistance genes in cotton cultivars, and the recent shift of fiber demands to meet the standard fiber quality due to change of textile technologies to produce high superior quality of fibers in the global market. Recently, next-generation sequencing technologies through high-throughput sequencing at greatly reduced costs provided opportunities to sequence the diploid and tetraploid cotton genomes. With the availability of large volume of literatures on molecular mapping, new genomic resources, characterization of cotton genomes, dis-coveries of many novel genes, regulatory elements including small and microRNAs and new genetic tools such as gene silencing or gene editing technique for genome manipula-tion, this report attempted to provide the readers a comprehensive review on the recent advances of cotton fiber genomics research.
In silico identification of GPI-anchored proteins in Paracoccidioides

Glycosylphosphatidylinositol-anchored proteins (GPI-proteins) are widely found in eukaryotic organisms. In fungi, GPI-proteins are thought to be involved in diverse cellular mechanisms such as cell wall biosynthesis and cell wall remodeling, adhesion, antigenicity, and virulence. The conserved structural domains of GPI-protein allow the utilization of in silico prediction approach to identify this class of proteins using a genome-wide analysis. We used different previously characterized algorithms to search for genes that encode predicted GPI-proteins in the genome of P. brasiliensis and P. lutzii, thermal dimorphic fungi that causes paracoccidioidomycosis (PCM). By using these methods, 98 GPI-proteins were found in P. brasiliensis with orthologs in P. lutzii. A series of 28 GPI-proteins were classified in functional categories (such as glycoside hydrolases, chitin-processing proteins, and proteins involved in the biogenesis of the cell wall). Furthermore, 70 GPI-proteins exhibited homology with hypothetical conserved proteins of unknown function. These data will be an important resource for the future analysis of GPI-proteins in Paracoccidioides spp.