Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of arbuscular mycorrhizal fungi in Brazil's Caatinga and experimental agroecosystems

Cowpea (Vigna unguiculata) is a nutritious legume crop for both its grain and leaves and comprises an important component in both human and animal nutrition. In Brazil, the use of mulch, such as coconut fiber, and organic fertilizers to maximize cowpea production offers an alternative to conventional mineral fertilizer strategies. Farming practices affect the diversity and activity of soil microorganisms, including arbuscular mycorrhizal fungi (AMF), important plant growth promoters for legumes. Our objective was to determine the effect of mulching with coconut fiber and manure on AMF diversity in cowpea. Soil samples were collected from an Experimental Station in Petrolina, NE Brazil: one Caatinga (natural dry‐forest vegetation), one fallow, and one experimental site established in the fallow area and cultivated with cowpea receiving cattle manure and four doses (0, 12, 24, 48 t/ha) of coconut fiber. AMF species richness, abundance, and diversity were evaluated. Sixty‐four AMF species were recorded, with predominance of Glomeraceae and Acaulosporaceae. Highest species richness (47) was recovered from the Caatinga but AMF diversity was also high in the cultivated sites, demonstrating the importance of mycotrophic plants, such as cowpea, in crop production systems for the maintenance of AMF species richness. Although several species, such as Claroideoglomus etunicatum, Acaulospora scrobiculata, Glomus trufemii, and Paraglomus pernambucanum, revealed pronounced sporulation patterns, even high doses of coconut fiber did not affect AMF richness and diversity, compared to fallow. Consequently, cultivation of mycotrophic plants and use of organic manures are able to maintain high AMF species richness in tropical agroecosystems.
The influence of disturbance on driving carbon stocks and tree dynamics of riparian forests in Cerrado

Aims Riparian forests in the Brazilian Cerrado, also known as gallery forests, are very heterogeneous in structure, species composition and ecological features due to strong and abrupt variations of soil, hydrological and topographic properties. However, what are the variables driving forest carbon stock and productivity, mortality and recruitment in disturbed gallery forests? Methods We used 36 permanent plots data from a gallery forest in the Brazilian Cerrado. We investigated how tree community dynamics vary in a gallery forest on two contrasting disturbance levels—logged and non‐logged—across a topographic gradient intrinsically related to differences in moisture conditions, edge effects, as well as soil fertility and texture. Important Findings Soil variables were reduced into principal components and we used structural equation modelling to disentangle covarying variables. We also included carbon stocks as a determinant variable of dynamics rates. Logged forest had 50% higher productivity than non‐logged forest and streamside forest had aboveground carbon stocks 70% higher than the forest edge. Both logging and natural disturbance drove variation in the carbon stocks which contributed to shaping productivity and recruitment rates. Distance from the river also drove mortality and carbon stock rates. Areas with high‐carbon stocks favoured higher competition and lessened productivity and recruitment rates. Although soil fertility and texture are considered crucial components shaping forest dynamics, there was no clear influence of those variables on the present forest, probably because the strong effects of soil moisture, forest edge and disturbance disrupted the correlation between soil and forest dynamics.
Effect of berberine on endoplasmic reticulum stress PERK apoptosis pathway in HK-2 cells by high fructose

Objective To investigate the effect of berberine on endoplasmic reticulum stress PERK apoptosis pathway in HK-2 cells by high fructose. Methods HK-2 cells were grown in DMEM/F12, containing 10% fetal bovine serum (FBS) and divided randomly into four groups: normal control group (Group C); Fructose group (Group F): it contains 25mmol/L fructose culture; Berberine group (Group B): 25mmol/L fructose + 10μmol/L berberine treatment group; TUDCA group (Group T): 25mmol/L fructose +2μmol/L TUDCA culture group; Cells were collected after culturing 24h. The expression of glucose-regulated protein 78 (GRP78), CHOP protein and the phosphorylation levels of PERK, eIF2α were tested by Western blotting. The cell cycles were detected by flow cytometry and the apoptosis of cells were detected by TUNEL staining. Results Western blotting showed that the expression of GRP78 and CHOP protein in group F was significantly higher than that in group C, and the levels of p-PERK and p-eIF2α in group F were significantly higher than those in group F. Compared with group F, GRP78, CHOP, p-PERK and p-eIF2α in group B and T were significantly lower (P 0.05). Conclusion Persistent high fructose can activate the intracellular PERK pathway in HK-2 cells, causing endoplasmic reticulum stress. Berberine can inhibit the fructose-induced PERK and eIF2α phosphorylation, down-regulated the expression of GRP78, CHOP protein, thus by regulating PERK Pathways to alleviate cell cycle arrest and reduce cell apoptosis. DOI: 10.11855/j.issn. 0577-7402.2017. 01.02
Influence of dietary composition on coccidiosis vaccination efficacy in broilers

Influence of Dietary Composition on Coccidiosis Vaccination Efficacy in Broilers. (December 2006) Jason Thomas Lee, B.S., Texas A&M University; M.S. Texas A&M University Chair of Advisory Committee: Dr. David J. Caldwell This research program included a series of experiments to investigate the effect of starter diet protein level on the performance of broilers vaccinated with Coccivac®-B and subsequently challenged with a mixed species Eimeria challenge compared to nonvaccinated broilers. Pre-challenge performance data indicates that vaccination may decrease body weights and increase feed conversion ratio (FCR) with vaccination. The time period associated with the observed effects is between 13 to 17 d of age. This reduction in performance of vaccinated broilers versus non-vaccinated broilers was eliminated by the conclusion of the experiments (27 d) in the higher protein diets. Vaccination was effective at generating protective immunity against the Eimeria challenge evidenced by significantly increased body weight gains, improved feed conversions, reduced post-challenge mortality, and reduced lesion development in vaccinated broilers compared to non-vaccinated. The final experiment included the comparison of Coccivac®-B to Bio-Cox® (salinomycin) for controlling field strain Eimeria in broilers reared on two different
Grid Based Distributed Data Mining–A Review

-Grid computing is modern and well defined structure for implementing distributed computing. Grid computing enables coordinated resource sharing and problem solving in dynamic, multi-institutional virtual organizations. Distributed data mining intends to get the global knowledge from the local data at distributed sites. Distributed data mining addresses the impact of distribution of users, software and computational resources. Grid technologies, combined with distributed data mining techniques, obtain best results over heterogeneous data and jointly these approaches called as Grid based distributed data mining. Grid based distributed data miners are the software architectures for geographically distributed high-performance knowledge discovery applications such as Knowledge Grid, Data Mining Grid etc. These miners are designed on crest of different grid environments such as Globus, GridBus. This paper reviews different grid computing architectures, types of grids, distributed data mining and grid based distributed data miners.
Thumbnail Evaluation of drought tolerance mechanisms in Mesoamerican dry bean genotypes

xiv CHAPTER ONE: INTRODUCTION . 1 1.1. Dry bean production and distribution. 1 1.2. Problem statement and justification . 2 1.3. Objectives . 4 1.4. Hypotheses . 5 CHAPTER TWO: LITERATURE REVIEW . 6 2.1. Mesoamerican gene pool . 6 2.2. Constraints to dry bean production . 6 2.3. Effects of drought on dry beans . 9 2.4. Adaptation mechanisms of dry bean to drought stress . 10 CHAPTER THREE . 13 FARMER PARTICIPATORY DRY BEAN VARIETAL SELECTION FOR DROUGHT TOLERANCE . 13 3.1. Abstract . 13 3.2. Introduction . 14 3.3. Materials and Methods . 16 3.4. Results . 20 3.5. Discussion . 32 CHAPTER FOUR . 35 AGRONOMIC PERFORMANCE OF MESOAMERICAN DRY BEAN GENOTYPES UNDER DROUGHT STRESS AND NON STRESS CONDITIONS . 35 4.1. Abstract . 35 4.2. Introduction . 36 4.3. Materials and Methods . 37
CHARACTERIZATION, IN SILICO AND IN VITRO DETERMINATION OF ANTIDIABETIC AND ANTI-INFLAMMATORY POTENTIAL OF ETHANOLIC EXTRACT OF SARGASSUM WIGHTII

Objective: This study was intended to investigate and characterize the phytoconstituents of Sargassum wightii, evaluate its antidiabetic and antiinflammatory potential under in silico and in vitro conditions. Methods: The marine algae S. wightii was extracted with ethanol. The ethanolic extract was screened for various phytoconstituents, quantified for total flavonoid, and polyphenol content. Fourier transform infrared (FT-IR) and mass spectrometry were used for characterizing the ethanolic extract. The antidiabetic potential of the phytoconstituents was analyzed by molecular docking and enzyme inhibition assays. The anti-inflammatory potential was evaluated by albumin denaturation assay. Results: The phytochemical screening revealed the presence of flavonoids, polyphenols, alkaloids, tannins, carbohydrates, proteins, oils, and fat present in the ethanol extract. The FT-IR analysis showed the presence of α,b unsaturated ketone, alcohol, and ether groups in the extract. MS analysis identified l (+) ascorbic acid 2, 6 dihexadeconoate and dotriacontyl isopropyl ether in the ethanolic extract. The molecular docking studies revealed that l (+) ascorbic acid 2, 6 dihexadeconoate interacted with both α-amylase and α-glucosidase with a consensus score of 5. The results of in vitro analysis showed that the ethanolic extract exhibited strong inhibitory activity on α-amylase (inhibitory concentration [IC50] 8 mg/ml) and α-glucosidase (IC50 6 mg/ml), respectively. The ethanolic extract also inhibited the formation of advanced glycation end products (IC50 10 mg/ml). Further, the ethanolic extract inhibited the denaturation of albumin (IC50 2.5 mg/ml) thereby revealing the anti-inflammatory potential of S. wightii. Conclusion: Hence, it can be concluded that S. wightii possesses antidiabetic and anti-inflammatory potential which may be due to the presence of l (+) ascorbic acid 2, 6 dihexadeconoate and flavonoids, polyphenols, alkaloids, tannins, carbohydrates, proteins, oils, and fat present in the extract.
A transcriptional-microRNA network for β-catenin-driven stemness in hepatocellular carcinoma

Wnt/β-catenin pathway is important in maintaining stemness of embryonic, adult and cancer stem cells (CSCs) in various organs including liver. However, the mechanisms underlying its deregulation in liver CSCs are poorly understood. Ma and colleagues have recently demonstrated that Oct4/microRNA-1246 signaling axis activates Wnt/β-catenin signaling in a subset of liver CSCs, providing a mechanistic basis for future diagnostic, prognostic and therapeutic developments.
Correction: Photodynamic antimicrobial chemotherapy with cationic phthalocyanines against Escherichia coli planktonic and biofilm cultures

Correction for ‘Photodynamic antimicrobial chemotherapy with cationic phthalocyanines against Escherichia coli planktonic and biofilm cultures’ by Min Li et al., RSC Adv. , 2017, 7, 40734–40744, https://doi.org/10.1039/C7RA06073D.
Effects of habitat fragmentation on a tri-trophic system: Silene latifolia, Hadena bicruris and its parasitoids

Hadena bicruris is the most important predispersal seed predator of Silene latifolia. Parasitoids attacking the larvae of this specialist noctuid can potentially decrease the amount of damage to the plant. However, the parasitoid complex associated with H. bicruris has not yet been described nor quantified in detail. This paper describes and quantifies the parasitoid complex associated with H. bicruris along the river Waal in the Netherlands, and gives information about life history characters of the individual parasitoid species. From a total of 1773 collected caterpillars, 44 % were parasitised by at least 14 species of parasitoids. The most important parasitoids were the braconids Microplitis tristis (22.9%) and Bracon variator (4.9%) and the ichneumonids Eurylabus tristis (11.7%) and Ophion pteridis (3.4%). Other species occurring sporadically were: the ichneumonids Scambus brevicornis, S. buolianae, S. annulatus, Erigorgus cerinops, and Hyposoter sp. ; the tachinids Phryxe vulgaris, P. nemea, Blondelia nigripes and Siphona geniculata; and a Mermithidae sp. On M. tristis the ichneumonid true hyperparasitoid Mesochorus lanceolatus was occasionally found. The ichneumonid pseudohyperparasitoids Gelis agilis, G. hortensis and the chalcids Baryscapus endemus, Pteromalus chrysos and P. vibulenus were found on cocoons of both M. tristis and B. variator. Only M. tristis, E. tristis and M. lanceolatus are specialists on their hosts. All others are generalists attacking many other species. The effect of the parasitoids on herbivory by their host is probably small because most of the parasitoid species are koinobionts that attack large hosts. Only B. variator, which is an ectoparasitoid, stops host development immediately upon parasitism, but like the other parasitoids, it attacks mainly large L4 or L5 hosts. The gregarious M. tristis and B. variator produce clutches with a female biased sex ratio, in contrast to the solitary E. tristis where the sex ratio approaches equality. The ectoparasitoid B. variator produces mostly single-sex clutches, probably avoiding deleterious effects of inbreeding. Large clutches of M. tristis and B. variator are probably caused by superparasitism. THE PARASITOID COMPLEX OF HADENA BICRURIS
A Statistical Framework for GeneSet Enrichement Analysis based on DNA Methylation and Gene Expression

DNA methylation and gene expression are important regulatory processes in cell proliferation, differentiation and many disease traits. Aberrant changes in methylation can alter gene expression and even be fatal in fetus development. Gene expression regulation has been extensively used in deciphering numerous phenotype traits and uncovering potential targeted therapy for complex diseases. The association between observed molecular changes and phenotypes can be better detected if the analysis of gene expression can be combined with other genetic and epigenetic features. We propose a new statistical framework to integrate gene expression and DNA methylation based on a variety of scoring schemes devised for evaluation of association strength. Our method utilizes a gene set enrichment approach to uncover relevant pathways. The method was applied to two datasets, the breast cancer invasive carcinoma disease and the lymphatic/blood endothelial cells. Our statistical framework detected several previously identified disregulated pathways including Wnt and hedghog signaling pathways and DNA damage response in breast cancer. In addition, potential novel pathways have been suggested by our model.
Engineering Ashbya Gossypii for the Production of Ricinoleic and Linoleic Acid

Ashbya gossypii is a natural overproducer of riboflavin or vitamin B2, and it is used nowadays in industrial scale for its production. This filamentous fungus is suitable for metabolic engineering approaches due to the development of a large number of molecular biology techniques, its fully sequenced genome and its high similarity to the model organism Saccharomyces cerevisiae. Additionally, it has been recently proposed as a paradigm in biolipid production, because of its highly active lipid metabolism and its ability to accumulate triacylglycerol. We here propose the use of A. gossypii for the production of ricinoleic acid and linoleic acid, two high value lipids with different industrial applications. The first is widely used as a building block for biopolymers and the second is essential for human health. Interestingly, A. gossypii mainly accumulates oleic acid, which is the common substrate for the synthesis of ricinoleic and linoleic acid. With this purpose, we manipulated A. gossypii by the heterologous expression of a gene from Claviceps purpurea, CpFAH12, an enzyme than inserts either a hydroxyl group or a double bond in the twelfth carbon of oleic acid. In our conditions, ricinoleic acid is only synthesized in modest amounts in an engineered strain that achieves high lipid production. However, linoleic acid accumulation is produced up to 20 % with respect to total fatty acids in one of the engineered strains, 15-fold the wild type amount. The genetic background of this strain consists on the simultaneous overexpression of the two ∆9 desaturases identified in A. gossypii, which catalyse the insertion of the first double bond in palmitic and stearic acid, producing palmitoleic and oleic acid respectively. This strain presents an increased lipid accumulation with respect to wild type as this desaturation step is one of the rate limiting steps in lipid synthesis. Therefore, CpFAH12 major contribution in A. gossypii lipid synthesis is related to its ∆12 desaturase function, enhancing linoleic acid synthesis and representing a great starting point for metabolic engineering of this fungus for producing omega-6 and omega-3 fatty acids.
A taxonomic revision of the genus Anthriscus (Apiaceae) in Turkey

A taxonomic revision of Anthriscus (Apiaceae, tribe Scandiceae ) in Turkey was carried out. The genus Anthriscus is represented by four sections and eight taxa, including six species with three non-typical infraspecific taxa in that territory, grouped into four sections: i) A. sect. Anthriscus ( A. caucalis var. caucalis and A. tenerrima var. tenerrima ); ii) A. sect. Cerefolium ( A. cerefolium var. trichocarpa ); iii) A. sect. Caroides ( A. kotschyi ); and iv) A. sect. Cacosciadium ( A. lamprocarpa subsp. lamprocarpa , A. lamprocarpa subsp. chelikii , A. sylvestris subsp. sylvestris and A. sylvestris subsp. nemorosa ). A new taxon, A. lamprocarpa subsp. chelikii , was found and published as a preliminary result of the present revisionary study. Some new characters such as length of filament and petal, and the ratio of fruit length to its beak length are used in the identification key for the first time. New localities of some taxa were found and their distribution areas are expanded. According to all morphological findings on Turkish Anthriscus , a new description of the genus was carried out. The taxonomic treatments for all taxa include type, synonyms (when present), morphological descriptions, phenology, and distribution areas (worldwide and local), habitats, phytogeographic region, conservation assessment and specimens examined. A new identification key for the sections and all Turkish species of the genus Anthriscus is reported, and illustrations and distribution maps in Turkey are also given for eight taxa.
Endothelial progenitor cells and associated pathways in multiple myeloma

Multiple myeloma (MM) is characterized by the clonal expansion of plasma cells (PCs) in the bone marrow (BM) that leads to bone destruction, anaemia and renal failure. Although there are several therapeutic options nowadays, there is still no effective cure and the standard survival up to 4 years. The evolution from the asymptomatic stage of monoclonal gammopathy of undetermined significance (MGUS) to MM and the progression of the disease itself are related with cellular and molecular alterations in the BM microenvironment, namely, the development of the vasculature. In postnatal vasculogenesis, there is stimulation of the recruitment of BM progenitors known as endothelial progenitor cells (EPCs) to the tumour vasculature, which will incorporate newly-forming blood vessels and differentiate into endothelial cells. The mobilization of EPCs is tightly controlled by cells and molecules in the BM microenvironment. With this retrospective study, we intended to evaluate the potential of EPCs as biomarkers for MM progression and response to therapy, while assessing their relationship with PCs and the signalling receptors C-X-C motif chemokine receptor (CXCR)4 and platelet-derived growth factor receptor (PDGFR)-β in sequentially collected BM smears from MM patients in different disease stages. Thus, we aimed to: 1) develop a method to quantify EPCs in BM smears from MM patients, 2) establish the temporal evolution of EPCs levels and verify their relationship with PCs, and 3) evaluate the content of CXCR4 and PDGFRβ cells and their connection with EPCs. We examined the percentage of EPCs with multiple immunofluorescence, and with single immunofluorescence the percentage of CXCR4 and PDGFR-β cells, from sequentially collected BM smears from followed MM patients in two main groups: i) patients that evolved from MGUS to MM, and ii) patients with MM that received treatment. Our results show that MM patients with higher BM PCs at diagnosis had significantly higher levels of BM EPCs in MGUS in comparison to the patients with lower MM PCs. On the other hand, MM patients who entered remission after treatment displayed lower initial levels of EPCs than MM patients who did not achieve remission. Both CXCR4 and PDGFR-β cells levels were correlated with EPCs levels throughout the analysed stages, which suggests that these receptors may be involved in EPC-related molecular processes such as recruitment to the tumour location and proliferation in MM. Taken together, our findings highlight for the first time in sequential archived BM samples that EPCs can constitute a biomarker for an aggravated progression from MGUS to MM and a worse response to therapy. Moreover, we also underline the need to study the mechanisms related to EPC-mediated vasculogenesis in MM.
Patofyziologie zásobování organismu a jeho tkání kyslíkem se zaměřením na hypoxii.

Prace se zabýva fyziologickými a patofyziologickými mechanismy procesu dýchani. Je zaměřena na hypoxii, ktera je jednim ze siroke skaly patofyziologických jevů spojených s timto procesem. Buňky bezobratlých i obratlovců vykazuji celou řadu adaptacnich mechanismů na kyslikovou nedostatecnost. Tyto mechanismy jsou uplatňovany na systemove, buněcne i molekularni urovni a jsou zcasti řizeny hypoxii indukovanými transkripcnimi faktory, ktere postupně moduluji expresi hypoxicky regulovaných genů. V hypoxických podminkach dochazi uvnitř buňky k tvorbě reaktivnich metabolitů kysliku. Ty jsou považovany za významne signalni molekuly ovlivňujici mnohe buněcne pochody. Jednim z podnětů pro zpracovani teto prace je výskyt neobvyklých adaptacnich strategii při nadechovem potapěni, při kterem dosud neni objasněn jeho vliv na centralni nervový system, zejmena u hloubkových disciplin.
Semi-supervised algorithm with knowledge-based features for learner's profiles interoperability

Nowadays, the user can have several profiles found in different adaptive systems relative to various fields. In particular, adaptive e-learning systems respond to a strong need to adapt to each learner their proposed activities based on the data stored in his/her profile (learning-style, interest, etc.). However, each system can have incomplete data as far as the learner is concerned. Hence, the exchange of the learner's profile data is extremely important in order to enhance his/her learning experience. The exchange requires a matching process so as to resolve the large number of a learner's profiles differences whether in syntax, structure or semantics. In this context, we propose a matching process to automatically detect the similarity between the profile elements. The originality of this process resides in the fact that it rests on a new semi-supervised Tri-Training algorithm which significantly improves the state of the art approaches.