Miracle-dz/UniFAR-FTUs huggingface dataset:
Presence, Behavior, and Resighting Pattern of Transient Bottlenose Dolphins (Tursiops truncatus) in the Humboldt Current System off North-Central Chile1

Abstract: Biotic and abiotic factors determine presence and habitat use pattern of individuals within a population. In this study, presence, behavior, and resighting patterns of transient bottlenose dolphins (Tursiops truncatus) were evaluated in relation to upwelling and downwelling events in a marine reserve in North-Central Chile, between 2005 and 2009. The study period was divided into four phases according to wind direction and intensity: upwelling-favorable (UF), transition I (TI), convergence (Cv) or downwelling, and transition II (TII). Results show that transient bottlenose dolphins are an open population with low resighting rates. Highest occurrence and a largest number of transient dolphins were identified during 2009, probably due to an increase in prey availability. The most frequent behavior observed was traveling, followed by feeding and socializing. Traveling was mainly recorded in individuals seen only once and in years with low productivity. In contrast, feeding was observed in individuals seen two or more times, was similar among phases, and was more frequent in moreproductive years. Social behavior was associated with the highest resighting rates. This study documents how transient bottlenose dolphins use the area based on their resighting patterns and suggests that periods of upwelling and downwelling modulate behavior displayed by these dolphins within the area.
Genetic analysis of yield and heat stress related traits in wheat (Triticum aestivum L. em. Thell) using microsatellite markers

Microsatellite markers were used for genetic analysis of terminal heat tolerance in F2 (PBW373 A— WH1081) population of wheat (Triticum aestivum L. em. Thell). Two parents were evaluated in field under normal sown and late sown conditions. For genotyping DNA from both parents PBW373 and WH1081 was amplified using 200 SSRs. Only 22 SSRs produced polymorphic bands, of size between 100 to 300 bp and an average of 1.45 alleles. The single marker analysis identified 19 markers indicating the putative QTLs for yield, its components and heat stress related physiological traits. The number of markers on these 16 linkage groups varied from one to four. On A genome 13 QTLs on B genome 5 QTLs and on D genome 9 QTLs were identified, respectively. The A, B and D genomes had 1360.3 cM, 272.4 cM and 919.5 cM of linkage coverage with average interval distances of 104.63 cM, 54.48 cM and 102.16 cM/Marker. A total of nine QTLs were resolved following composite interval mapping, one QTL was detected at a LOD score equal to threshold value of 2.5 while eight at LOD scores above the threshold value. All the nine QTLs were shown to be on definitive location on chromosome 3A (QDh.CCSHAU-3A, QDa.CCSHAU-3A and QPm.CCSHAU-3A), chromosome (QBm.CCSHAU-5A, QCtd.CCSHAU-5A and QCl.fl.CCSHAU-5A), chromosome6A (QPh.CCSHAU-6A) and chromosome3B (QTgw.CCSHAU and QMts.CCSHAU-3B). Use of these markers save times, resources and energy that are needed not only for raising large segregating populations for sveral generations, but also for estimating the parameters used for selection.
Changes in seed quality of chickpea cultivars under salinity stress

A factorial experiment on the basis of RCB design with three replications was conducted in 2007 to evaluate the effects of salt stress (S 1 , S 2 and S 3 : control, 5 and 10 dS/m NaCl, respectively) on seed quality of three chickpea cultivars (ILC and Jam from kabuli type and Pirooz from desi type) at different stages of pod filling. Seed viability and germination rate of chickpea cultivars increased with enhancing seed weight on the mother plant under both saline and non-saline conditions. However, seed weight and consequently viability percentage and germination rate decreased as salinity increased. Reduction in seed weight due to salinity was closely related with low pod filling rate. Means of maximum seed viability and rate of germination for seeds produced under control and moderate salinity were not significantly differed, but these traits for seeds produced under high salinity were significantly lower than those for control. Seed quality of Pirooz was generally lower than that of ILC and Jam. Variation of seed quality among chickpea cultivars was attributed to differences in genetic constitution. Thus, the quality of chickpea seeds could be influenced by both genotype and salinity stress.
Genome Wide Association and Forward Genetic Studies to Identify Genes Involved in Salt Tolerance

Salinity tolerance varies considerably between natural accessions of rice. In this project, the main aims were to identify well-known genes and novel determinant candidate genes for salinity tolerance using genome wide association study (GWAS) and forward genetic screening. To assess salinity tolerance in rice and Arabidopsis, relative growth rate of plants and cations in roots and shoots were analysed. This research has found that relative growth rate, root K+, and shoot Na+ traits are parameters for salinity tolerance in both species. Moreover, the growth parameter is correlated with the root K+ and shoot Na+. Regarding the identification of determinant genes for saline conditions, the GWAS approach has revealed 120 association signals and several of them were not revealed before using genomic mapping. The association signals contained ~1500 novel candidate genes across the rice genome and 32 well-known published candidate genes that play roles in saline conditions. One of the relevant outcomes was that the genomic region of the well-known qSaltol QTL correlated with a SNP position identified by this approach. The qSaltol has already been introgressed into elite rice cultivars and assessed for its effectiveness in saline field conditions. Concerning forward genetic screening, this approach has identified two candidate genes that have molecular functions which correlate with the candidate genes identified by GWAS. These findings may contribute to our understanding of the complex and dynamic mechanisms of plants and the roles of genes to achieve salinity tolerance in plants.
Selected Properties of Peat Degradation on Different Land Uses and the Sustainable Management

The research aimed to analyze selected properties of peat degradation on different land uses and the sustainable management. The research area is located in the lowland dome peats in the catchment basin of Sibumbung River and Sibotak River in Sub District of East Pedamaran, OKI South Sumatra. The research method used an experimental design of Randomized Completely Block Design with two Blocks and five treatments (Site A: intercropping between oil palm and pineapples; Site B: oil palm plantations, Site C: peat forest; Site D: swamp bush; Site E: swamp grass). The research resulted that drainage and land uses decrease some properties of peats, namely C/N ratio, total pore space, fiber and ash content as well as organic C on cultivated peats and are significantly different at level of 5% compared with uncultivated peats. Bulk density increased due to peat compaction and groundwater table on cultivated peats, which is getting deeper, and significantly different compared with uncultivated peats. All soil series do not show any change because of drainage and different land uses. Sustainable peat management can be implemented through three approaches, namely managements of water, soil and crops.
The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation

Predicting a multicellular organism’s phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits. This work updates the first biorXiv version, February 2017, https://doi.org/10.1101/105437, with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.
Evaluation of cytotoxic and mutagenic effects of two artificial sweeteners by using eukaryotic test systems

Considering the vast use of sweeteners by the Brazilian population and the constant need for toxicological studies of food additives, this study aimed to evaluate the cytotoxic and mutagenic potentials of the sodium saccharin and/or sodium cyclamate sweeteners in plant (Allium cepa) and animal (Mus musculus) test systems based on concentrations permitted by the Brazilian laws. In A. cepa, both the sweeteners individually and their combinations concentration and exposure time (ET: 48, 72 and 168 h) dependently exerted cytotoxic and mutagenic effects. Similarly, an increased in micronuclei formation was also observed by the sweeteners in peripheral blood cells in mice. More toxic effects were observed with the combination doses at 168 ET. There may be a synergistic effect and DNA damage with an increasing concentration and ET. In conclusion, the concentrations considered safe by the Brazilian laws had significant cytotoxic and mutagenic activity on the eukaryotic cells. Key words: Allium cepa, Mus musculus, sweeteners, toxicity.
Integrin αvβ8 on human dendritic cells : a role in intestinal immune homeostasis

THOMAS MCPHERSON FENTON PHD IMMUNOLOGY UNIVERSITY OF MANCHESTER 30/09/2015 Intestinal inflammatory disorders such as Crohn’s disease contribute significantly to human mortality and morbidity. Although the cells and molecules involved in suppression of intestinal inflammation have been extensively documented in mouse models, a full understanding of how these work together in the healthy and diseased gut remains elusive. It is known, however, that tight regulation over TH17 cells and regulatory T cells (Treg) is required to maintain immune homeostasis in the intestine. Activation of the cytokine transforming growth factor-β (TGFβ), which is secreted by immune cells as an inactive complex, plays a crucial role in the induction of both Treg and TH17 cells. Recent work has shown that the αvβ8 integrin is required for activation of TGFβ by murine dendritic cells (DC). Murine integrin αvβ8 is thus of fundamental importance for Treg and TH17 induction and, subsequently, for intestinal immune homeostasis. However, little is known about the signals controlling the expression of integrin αvβ8 on intestinal DC. Furthermore, whether this system is also important for regulation of the human system is entirely unknown. Here, expression of integrin αvβ8 is shown on human intestinal CD1c + CD103 + SIRPα + DC and CD1c + CD103 SIRPα + DC, but not on CD141 + CD103 + SIRPα DC. Expression of integrin αvβ8 is increased on DC from Crohn’s disease patients, and on DC from non-IBD donors treated with LPS. Both LPS and a number of probiotic bacteria were also able to induce integrin αvβ8 expression on human monocyte-derived DC (moDC), which suggested that the microbiota may play a role in the regulation of human integrin αvβ8. Importantly, we have also shown that TGFβ is activated by integrin αvβ8 on human moDC, and that integrin αvβ8 promotes expression of forkhead box P3 (FOXP3) in naïve human T cells in vitro. Together, these data suggest that integrin αvβ8-mediated activation of TGFβ by DC may play an important role in the regulation of human T cell responses in the human intestine, and that this pathway may be perturbed during intestinal inflammation
Effect of exogenous dikegulac on in vitro shoot proliferation of Sideritis raeseri L. - Greek mountain tea species.

In the present study, the effects of 8 dikegulac concentrations (0, 10, 25, 50, 100, 250, 500, 1500 μM) on in vitro shoot proliferation of the Greek mountain tea species “Sideritis raeseri L. ” were investigated. The culture medium used was the MS (Murashige and Skoog) supplemented with 30 g/l sucrose and 3 g/l Phytagel. After 5 weeks of culture in the proliferation medium, shoot number/explant was greatest (5.42) and slightly increased compared to the control (4.09 shoots/explant) with 25 μΜ dikegulac. However, no significant changes were monitored among treatments regarding shoot length (12.48-16.11 mm). The intermediate dikegulac concentrations (50-500 μΜ) substantially enhanced shoot multiplication percentage in relation to the control whereas the marginal ones (10 and 1500 μΜ) inhibited the explants’ ability to proliferate considerably. The shoot multiplication percentage was 100% when 25, 100 or 500 μΜ dikegulac were applied. The percentage of callus formation at the base of the explants was 100% in all treatments except for the highest dikegulac concentration (1500 μΜ) in which a remarkable decrease by 33.33% was recorded. Vitrification was apparent in the majority of the explants including all treatments. In specific, this symptom was less extensive (16.67-18.18%) with low dikegulac concentrations (10 or 25 μΜ) whereas the percentage of explants showing hyperhydration was highest (63.64%) with 50 μΜ dikegulac. An efficient shoot proliferation protocol under in vitro conditions for the Greek mountain tea species – Sideritis raeseri L. was established using the plant growth regulator “dikegulac” as a promoting agent with potential applications in micropropagation.
Detection of bovine rotavirus in diarrheic calves by using rapid test in some Mid-Euphrates provinces

The study was aimed to determine the Rota viral infection rates in diarrheic calves and effectiveness of some epidemiological factors on that rate in some provinces in Mid– Euphrates region in Iraq (Babylon, Al-Najaf, Karbala, Al-Qadisyia provinces). A total of 530 calves aged between 1-60 day were examined and fifty fecal (50) samples were collected from diarrheic calves only within six months period from November-2012 to April -2013. The fecal samples were examined for the presence of rotavirus by rapid rotavirus test (screening test), as well as the clinical examination for these diarrheic calves were done. The rapid test demonstrated that the rotavirus infection rate was 18/50 (36%). A 45.4% of rotavirus infection was found in calves less than 30 days of age which was significantly higher than 28.5% calves (30-60) days old. Male and female (37.5%, 40% respectively) were seen infected without any significant differences. The main clinical signs observed on rotavirus diarrheic calves were include, watery voluminous diarrhea with profound weakness and mild depression, so as temperature, respiration, heart rates could be decreased and appetite was changeable towards loss or anorectic. In Babylon, the highest rotavirus infection rate was recorded 60%, and less rates in Karbala 20% and 40%, 33% in AL-Najaf and AL-Qadisyia provinces respectively. The rotavirus infection rate in diarrheic calves was affected by months significantly, which it was higher at January 75%, so as in November 50%, December 40% and February 33.3%, but not recorded in March and April.
Genome-wide comparison of toxigenic and non-toxigenic Corynebacterium diphtheriae isolates identifies differences in the pan genomes between respiratory and cutaneous strains

Objectives Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species. Methods This study examined genomic diversity among 47 C. diphtheriae isolates collected in Australia over a 10-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis. Results C. diphtheriae sequence type (ST) 32, a non-toxigenic ST with evidence of enhanced virulence that is also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by toxigenic as well as non-toxigenic strains. Conclusions The genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple local and overseas sources of infection and colonisation. Our findings suggest that regular genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae can deliver highly nuanced data in order to inform targeted public health actions and policy for predicting the future impact of this highly successful pathogen.
In vitro immuno-modulatory ability of tryptic caseinate hydrolysate affected by prior caseinate glycation using the Maillard reaction or transglutaminase

ABSTRACT Caseinate was glycated by lactose and oligochitosan via the Maillard reaction and transglutaminase catalysis to yield two glycated caseinates (GC-I and GC-II), followed by trypsin hydrolysis to generate GC-I hydrolysate and GC-II hydrolysate, respectively. In comparison with caseinate hydrolysate, only GC-I hydrolysate showed decreased His, Lys, Tyr, and Val contents. All three hydrolysates in dose-dependent manner exerted in vitro immuno-modulatory abilities via activating three immune cells in terms of lymphocytes, macrophages, and natural killer (NK) cells, enhancing the secretion of seven cytokines in lymphocytes and macrophages, but inhibiting the secretion of one cytokine (interleukine-4) in splenocytes. However, GC-I hydrolysate and GC-II hydrolysate showed respective lower and higher immuno-modulatory abilities than caseinate hydrolysate in the most cases. Amino acid losses of GC-I hydrolysate made partially contribution to its impaired immuno-modulatory ability. It is concluded that lactose glycation and oligochitosan glycation of caseinate could lessen and enhance immuno-modulation of tryptic caseinate hydrolysate, respectively. GRAPHICAL ABSTRACT
Current concepts of Gerbillid phylogeny and classification

Gerbillids constitute a moderately small group of about 20 gênera (Pavlinov et al, 1990; Musser and Carleton, 1993). This group attracted close attention of taxonomists in the 70s and 80s, when several hypothèses about its relations with other muroids and prin¬ cipal phylogenetic divisions were elaborated (Chaline et al, 1977; Pavlinov, 1982; Tong, 1989; Pavlinov et al, 1990). AU thèse stud¬ ies were morphological and considered a very limited data set, mainly dental and bullar morphology. One of the most surprising matters in this respect is that very few biochemical and cytogenetical works hâve been made with gerbillids, when compared with their "neighbors" in the classification (murids, arvicolids, etc.).
Targeting Mitochondrial Respiratory Complex I: A Novel Anticancer Strategy

Tumor cells exhibit profound bioenergetic changes compared to non-transformed cell types. One of the main driving mechanism leading to such a metabolic alteration is triggered by hypoxia. Hypoxia is experienced by cancer cells during tumor progression and leads to a significant enhancement of glycolysis in order to sustain tumor growth and survival. The transcription factor hypoxia-inducible factor-1 (HIF1) is the master regulator of cell adaptation to low oxygen condition, and thus of tumor progression. Our group described the lack of HIF1α in low-proliferative oncocytic tumors, which are characterized by the loss of the mitochondrial respiratory Complex I (CI). Hence, we hypothesized that severe CI dysfunctions prevent HIF1α stabilization and impair tumor adaptation to low oxygen levels. Using the zing finger nucleases technology, we generated NDUFS3-deficient cancer cells that display acute CI deficiency. Engineered CI-defective cancer cells showed a lack of HIF1α stabilization in hypoxic condition, likely due to higher intracellular oxygen concentration and increased levels of the metabolite α-ketoglutarate, which both foster HIF1α proteasomal degradation. In vivo experiments showed that the lack of CI was associated to an impairment in the growth of the xenografts, together with the lack of HIF1 activation and a significant reduction of the expression of HIF1-responsive genes involved in the glycolytic machinery and tumor vascularization. Further analysis showed that CI-deficient xenografts may have developed a tailored structure to compensate the metabolic restriction caused by the lack of CI and HIF1α. Using a Tet-Off expression system, we thus generated NDUFS3-knock out inducible clones, allowing us to target CI during xenografts growth. Removing NDUFS3 from xenografts have successfully recapitulated key oncocytic features. CI loss induced HIF1α destabilization, the accumulation of defective mitochondria and xenografts growth arrest. Overall, these data showed that cancer cells are unable to sustain proliferation when functional CI is lost during tumor progression.
Quantification of the Carbon Content of the Fractions of Humic Substances and Total Organic Carbon in Different Production Systems

Soil organic matter is degraded and easily altered by the type of management. The objective of this work is to determine the total organic carbon and humic substance fractions in the organic matter of the soil with different management types and depths in the western region of Parana, Brazil. The work was carried out in the Experimental Farm “Professor Antonio Carlos dos Santos Pessoa”, belonging to the State University of the West of Parana. Five soil management systems were evaluated: one area with corn cultivation for silage (CS); other area with succession of crops, with soybean in summer and corn in winter (SC); the next area also with succession of crops, with soy in the summer and oat in the winter (SO); the following area with permanent pasture with Tifton (PP); and the last area with crop-livestock integration (ILC). For each management system, four plots were randomly selected, in each plot three simple samples were collected in a diagonal direction to form a composite sample for the depth of 0.00-0.05 m, 0.05-0.10 m and 0.10-0.15 m. Total organic carbon, fractionation of the humic substances and the AH/AF and EA/HUM ratios were calculated. For most of the analyzed variables, it was verified that there were significant differences (P < 0.05) between the systems evaluated in the studied depths. In the evaluated areas, the PP, SO and ILC systems presented the highest carbon content for all attributes analyzed.