Miracle-dz/UniFAR-FTUs huggingface dataset:
Bacterial Community Dynamics during the Production of Ogi from Millet ‘A Nigerian Fermented Food’ Using Culture-Dependent Approach

Analysis of bacterial community dynamics in malted and fermented millet during ogi production was investigated. Malted millet were wet milled using a sterilized blender and kept on conical flasks for 72 hours to allow spontaneous fermentation from which bacterial analysis were performed at 12 hourly interval. Nine bacterial strains were isolated and identified as Lactobacillus sp. Escherichia coli, Streptococcus sp. , Staphylococcus sp. Bacillus sp. , Enterobacter sp. , Leuconostoc sp. , Pediococcus sp. , and Flavobacterium sp. Changes in bacterial community revealed that Lactobacillus sp. , Streptococcus sp. , and Pediococcus sp. predominate in all the days during millet fermentation. Flavobacterium sp. , Escherichia coli were isolated in the first 48 hours of fermentation after which their population declined, while Bacillus sp. was presence in the first, second and third days respectively. The highest aerobic bacterial and lactic acid bacteria count were recorded as 3.9logcfu/g (48h) and 11.2logcfu/g (60h) respectively.
Roles of transcription factor T-bet in memory CD4+ T cell generation, function, homeostasis and tissue targeting

Roles of transcription factor T-bet in memory CD4 T cell generation, function, homeostasis and tissue targeting Jun-Kui Chen Memory T cells are a critical component of immunological memory, which provides long-lasting immunological protection. These cells are characterized by a lower response threshold, rapid effector cytokine production, and prolonged longevity, and thus allow organisms to respond to pathogens more rapidly and effectively. However, the mechanisms that regulate the generation, function, homeostasis and tissue targeting of memory CD4 T cells are not clear. This body of work investigated post-effector requirement for T-bet expression in determining the circulating and tissue resident memory CD4 T cell fate and the implications of early T-bet deletion on lung CD4 TRM development. We used mouse models with conditional expression of T-bet to delete T-bet in CD4 T cells after priming and effector differentiation to analyze the development of resultant memory CD4 T cells. We found that T-bet-ablation following cell priming and Th1 polarization did not impair the ability of Th1 effector cells to produce high levels of IFN-γ production, and moreover, there were dramatic increases in IL-2 production, suggesting post-effector T-bet expression is not required for functional maintenance in effector cells. Memory CD4 T cells that developed from T-bet ablated effector cells after transfer to lymphocyte deficient RAG1/2 hosts or intact congenic hosts had increased persistence, and they maintained lower but substantial levels of IFN-γ and higher IL-2 production. We found elevation of IL-17 production and RORγt expression in T-bet ablated memory CD4 T cells, and transcriptome analysis further showed that these cells upregulated genes expressed by other CD4 T cell subsets, including Foxp3 and GATA3, indicating greater functional plasticity of T-bet-ablated memory CD4 T cells. Increased localization of T-betablated memory CD4 T cells in the lung resident niche was found only in RAG1/2 hosts but not in congenic hosts, indicating the importance of the tissue environment in the development of TRM cells. Using antigen specific T-bet OT-II and T-bet OT-II cells, we found that T-bet OT-II cells had increased persistence while T-bet OT-II cells had decreased persistence compared with the wild type OT-II cells after PR8-OVA influenza virus infection. However, both T-bet and T-bet OT-II cells had normal TRM formation. Collectively, our results reveal the roles of T-bet in regulating the generation, function, maintenance and tissue targeting of memory CD4 T cells.
Detection of heterogeneity in allele sharing of affected relatives

Linkage analyses based on allele sharing of affected relatives are less powerful when genetic heterogeneity exists among sampkd families. To test for heterugweity, we propose using family-specific non-parametric Linkage (NPL) scores and family-level binary covariates that describe varîability in symp toms, prevalence, and/or age of onset of the diseâse. First, we extend the linkage likeli hood of Kong and C m (1997) to include a family indicator covariate and formulate a likelihood ratio test and eEcient score test. Simulation results show that under the nul1 hypothesis of no heterogeneity, the empirical distributions of t hese test statistics do not always follow that specified by standard asymptotic theory. Alternatively, we compare mean XPL scores between two covariate-defined family subgroups using bot h asymptotic and permutation met hods. Applied to simulations, permutation tests have nominal 5% type 1 error. Power decreases when the size of family subgroups is reduced or becomes unbalanced.
Fecha de trasplante, boro, potasio y poda en la producción de frutos de Physalis peruviana L. en hidroponía e invernadero

Physalis peruviana L. is a native shrub to the Andes area, with commercial potential in Mexican markets. Its cultivation depends on the climate, its production system and the technology used to increase its productivity. The objective of this study was to evaluate the effect of transplant date (TD), application of foliar boron (B) and potassium (K) in the nutrient solution, and pruning, during hydroponic fruits production in greenhouse. We carried out the study at the Colegio de Postgraduados, with plants of the “Colombia” variety. The experimental design consisted on divided plots: the large plot was the transplant date, June, July and August 2013; the small plot was the combination of B (0, 1, 3 mg L-1 ), K (3.5 and 7 meq L-1 ) and pruning (maintaining three stems and no pruning). The evaluated variables were fruits fresh weight with calyx (FWC) and without calyx (FWWC), fruit number (FN), fruit average weight (FAW) and number of cracked fruits (CF) during a two-month harvest period. The early transplants (June and July) with high B doses showed the highest fruit yield. However, during the late transplant (August) the plants without B foliar supply achieved the highest yield. B decreased the number of CF in early transplant. The supply of 7 meq L-1 of K reduced the number of FWC and FWWC in the first two dates, and 3.5 meq L-1 of K decreased the number of CF at the second date. Pruning did not change FAW, but reduced the yield on the second transplant date and decreased the number of CF by 50 %.
The Combined Effect of Wheat Germ Oil and Carbamazepine on the Improvement of Learning and Spatial Memory of Epileptic Mice

Accepted: 24 June, 2016 Abstract Background and Objectives: Epilepsy is associated with daily memory loss, learning, and behavioral disorders. Carbamazepine is an anticonvulsant drug, commonly used in the treatment of generalized tonic-clonic seizures. Wheat germ oil has the highest amount of tocopherol (vitamin E) among all vegetable oils. In this study, the combined effect of wheat germ oil and carbamazepine on improvement of learning and spatial memory, was investigated in mouse epilepsy model.
Cupiennius (Araneae, Ctenidae): Biology and sensory ecology of a model spider

Cupiennius is a genus of hunting or wandering spiders typical of Central America including the Golfo Dulce region, which do not live in a silken web or build a web to catch prey. Instead, a prominent feature of their biology is a close association with particular dwelling plants on which they hide during the day and prey and court at night. The complex behavioural patterns of Cupiennius rely on an armament of exquisite sensors tuned to the specific needs in the spiders’ specific environment. After a short introduction to the taxonomy, distribution and habitat, a few examples are given to show how closely spider sensory systems mesh with spider behaviour in the natural habitat. A key for the genus Cupiennius is provided by a companion paper (BARTH & CORDES).
Le rôle des protéines apoptotiques dans la physiophathologie de la sclérose systémique chez l'humain

Sieroderma (systemic scierosis, SSc), an auto-immune disease, is a debilitating connective tissue disease of unknown cause resulting in progressive fibrosis due to fibroblast overgrowth. Since apoptosis or programmed ceil death is implicated in many autoimmune diseases, we hypothesized that prolonged survival of skin fibroblasts could be due to valying expression levels of apoptotic proteins in SSc patients. Biopsies were obtained from 6 diffuse SSc patients, 1 limited and 5 contols. Fibroblasts were isolated and put in primary culture. From diffuse patients, 4 had severe SSc. Proliferation studies, using nocodazole to accumulate cells in G2/M phase and BrdU incorporation, demonstrated lower proliferation rates by SSc fibroblasts than controls. Immunoblot resuits showed an overexpression of alpha-smooth muscle actin (Œ-sma), a specific myofibroblast marker, in 3 severe SSc patients. Myofibroblasts causing fibrosis, differentiated from fibroblasts, are common in SSc. Moreover lesional fibroblasts expressed more a-sma than non-lesional fibroblasts. Bel-2, an anti-apoptotic protein, was underexpressed in all lesional fibroblasts, especially in those of 3 severe SSc patients. Survivin, another anti-apoptotic protein, was under-expressed in both skin types of 3 severe SSc patients. Other results demonstrated under-expression of Mcl1 and c-IAP1, both anti-apoptotic proteins, and pro-apoptotic p53, mainly in lesional fibroblasts. Double staining immunofluorescence showed that survivin expression was inversely correlated with the presence of cells expressing Œ-sma, i.e. myofibroblasts. Survivin underexpression in non-lesional fibroblasts appeared to be an
Characterization of Human T-Bet-Expressing B Lymphocytes and Their Role in the HIV Immune Response

Humoral immunity is critical for the prevention and control of viral infections, yet the specific B cells and mechanisms regulating antiviral responses in humans remain poorly defined. The Th1-associated transcription factor T-bet coordinates intracellular pathogen immune responses, and recent murine studies identified a Tbet-expressing B cell subset that mediates humoral antiviral immunity, but an analogous cell population has not been identified in humans. In this study, we sought to investigate the role of T-bet-expressing B cells during human viral infections. We identified T-bet expression within the memory B cell compartment of healthy individuals and described a relationship between the transcription factor and IgG1 and IgG3, two antiviral antibody isotypes. The T-bet+ B cell population was comprised of two discrete subsets: T-bet low resting memory cells and a highly activated, transcriptionally distinct T-bet high subset displaying an atypical memory phenotype. The T-bet high cell population transiently expanded in blood following vaccination with yellow fever or vaccinia virus; however, these cells were induced and maintained at an elevated frequency by chronic HIV viremia and were associated with increased expression and secretion of IgG1 and IgG3. The HIV gp140-specific response was maintained almost entirely by T-bet+ memory B cells in both viremic and aviremic donors. Together, our findings identify T-bet is a critical regulator of humoral antiviral immunity in humans and suggest T-bet+ B cells specifically mediate the humoral immune responses to live viral vaccines and HIV. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Michael R. Betts
The leukocyte apoptosis assay : a clinical predictor of radiosensitivity

Approximately 6% of patients receiving radiotherapy show signs of late toxicity in normal tissue many months after treatment has been completed. The Leukocyte Apoptosis Assay (LAA) has been developed to predict intrinsic radiosensitivity of normal tissue based on the radiation-induced cytotoxic response of CD4 and CD8 lymphocytes. Apoptosis, or programmed cell death, can be observed after radiation exposure and can be evaluated using flow cytometry. The purpose of this study was to determine the reliability of the LAA assay and to standardise it in South Africa. Briefly, heparinised blood was collected and exposed in vitro to 0Gy (control), 2Gy and 8Gy gamma radiation. One sample was exposed to 0Gy, 2Gy, 4gy and 8gy gamma radiation and compared to 0Gy, 1Gy, 2Gy, 3Gy and 4Gy neutron radiation. After 48 hours, lymphocytes were collected and prepared for flow cytometric analysis using FITC-conjugated anti-CD4 and anti-CD8 monoclonal antibodies. Apoptosis was assessed by measuring internucleosomal DNA degradation using propidium iodide (PI) staining. Percentage radiation-induced apoptosis was determined for each sample. Results showed a clear dose response curve for both gamma and neutron exposure and apoptosis after neutron exposure was higher than at iso-equivalent gamma doses. Although inter donor variation was observed, intra donor variation was low where the mean SD was 1.61 for CD4 and 2.16 for CD8. Results were consistent across cell type and the study therefore yielded enough data to base radiosensitivity measurements on CD4 and CD8 lymphocytes. In the clinical setting, patients showing a low apoptotic response should be considered at risk for developing late effects whereas patients who do not present as radiosensitive may receive increased doses of radiation. The LAA would be able to identify radiosensitive patients, thereby enabling the oncologist to stratify each patient to plan an effective treatment regime.
Factors causing traffic killings of roe deer Capreolus capreolus in Denmark

In Europe, roe deer Capreolus capreolus is one of the biggest mammal species killed in traffic, and the number of accidents seems to increase. The purpose of our paper is to point out the most important factors causing traffic killings and to suggest conservation measures that may reduce the number of roe deer killings in traffic. Our study is based on data including 115 roe deer killed in traffic at the Kalø estate in East Jutland, Denmark, during 1956–1985. No significant correlation was found between the number of traffic killings of roe deer and mean daily traffic, but the number of roe deer killed in traffic varied significantly over the seasons. The distribution pattern of roe deer/car collision sites was clumped. The risk of being killed in traffic was highest for young and old roe deer. Significantly more adult females, adult males and subadult males than expected were killed in traffic, and significantly more individuals were killed in years when most of the fields next to the roads were left unsown in winter. We suggest that the following measures be taken to prevent traffic killings: increasing areas with winter cereal or wintergreen fields, clearing the vegetation adjacent to roads and reducing car speed in high-risk areas.
Characterization of transcriptionally active atwwp1 nuclear bodies that confer partial immunity against begomoviruses

v RESUMO. vii GENERAL INTRODUCTION . 1 References. 6 CHAPTER I PLANT IMMUNITY AGAINST VIRUSES: ANTIVIRAL IMMUNE RECEPTORS IN FOCUS. 8 CHAPTER II ATWWP1, A WW DOMAIN-CONTAINING PROTEIN, FORMS NUCLEAR BODIES THAT COUNTERACT BEGOMOVIRUS INFECTION . 23 Abstract . 24 Introduction . 25 Results . 28 Discussion . 42 Material and methods . 48 References. 58 Supplementary Information. 65 Figures Legends. 69 Figures. 73 CHAPTER III THE IMMUNE ATWWP1NUCLEAR BODIES REPRESENT HOTSPOTS FOR ACTIVE TRANSCRIPTION 89 Abstract . 90 Introduction . 91 Results . 92 Discussion. 99 Material and methodos. 102 References. 109 Supplementary Information. 113 Figure Legends . 115 Figures . 117 GENERAL CONCLUSIONS. 125 ANEXOS . 126
A Review: Anti-microbial, Anti-inflammatory effect and Cardiovascular effects of Garlic: Allium sativum

Allium sativum is a species in the onion genus, Allium. Its close relatives include the onion, shallot, leek, chive, and Allium chinense. With a history of several thousand years of human consumption and use, garlic is native to the region between the Mediterranean and China, and has long been a common seasoning worldwide. Herbs such as garlic with the potential to significantly modulate the activity of drug-metabolizing enzymes (notably cytochrome p450 isozymes) and/or the drug transporter P-glycoprotein participate in potential pharmacokinetic interactions with anticancer drugs. Among the active compounds present in the plant, DTS and DDS are the most active against yeasts and ajoene is the main compound responsible for the antiviral activity of garlic. A great deal of low quality clinical research has been conducted to determine the effect of garlic on preventing cardiovascular diseases and on various biomarkers of cardiovascular health, but as of 2015, the results were contradictory and it was not known if there are any effects. Because garlic might reduce platelet aggregation, people taking anticoagulant medication are cautioned about consuming garlic. Meta-analysis found decreased rates of gastric cancer associated with garlic intake, but cited confounding factors as limitations for interpreting these studies. Further meta-analyses found similar results on the incidence of gastric cancer by consuming allium vegetables including garlic. Garlic is known to cause bad breath (halitosis) and body odor, described as a pungent "garlicky" smell to sweat. This is caused by allyl methyl sulfide (AMS).
Neural plasticity of early sensory pathways in the adult mouse olfactory system

Olfactory sensory deprivation during development has been shown to induce significant alterations in the neurophysiology of olfactory receptor neurons (ORNs), the primary sensory inputs to the brain’s olfactory bulb. Deprivation has also been shown to alter the neurochemistry of the adult olfactory system, but the physiological consequences of these changes are poorly understood. Here we used in vivo synaptopHluorin (spH) imaging to visualize odorant-evoked neurotransmitter release from ORNs in adult transgenic mice that underwent 4 weeks of unilateral olfactory deprivation. Deprivation reduced odorant-evoked spH signals compared to sham-occluded mice. Unexpectedly, this reduction was equivalent between ORNs on the open and plugged sides. Changes in odorant selectivity of glomerular subpopulations of ORNs were also observed, but only in ORNs on the open side of deprived mice. These results suggest that naris occlusion in adult mice produces substantial changes in primary olfactory processing that may reflect not only the decrease in olfactory stimulation on the occluded side but also the alteration of response properties on the intact side. We also observed a modest effect of true sham occlusions that included noseplug insertion and removal, suggesting that conventional noseplug techniques may have physiological effects independent of deprivation per se and thus require more careful controls than has been previously appreciated.
Scab of wheat

The severity of scab infection varies greatly from year to year and is closely associated with the prevailing weather conditions after the heads emerge. In some years, such as 1982, 1990 and 1991, scab infections were widespread and caused losses ranging from 10 to 90 percent. Yet in years that are dry after heading begins, only a trace of scab can be found. Fortunately, latter conditions are more prevalent in Missouri.
Modification of immune defense parameters in the mammary gland and of the estrous cycle by induced energy deficiency in dairy cows

Ovarian cycle activity and the innate immune defense ability of the bovine mammary gland were challenged by a dietary energy deficiency of 49.2% of total energy requirements in mid-lactation. Estrous cycle lengths before, during and after the metabolic challenge due to energetic undersupply were calculated and compared to control fed cows. A cell culture model of milk derived primary bovine mammary epithelial cells was established on the last day of the energetic undersupply and stimulated with mastitis pathogens. Selected gene groups of the innate immune system and lactoferrin, a prominent antimicrobial protein, were analyzed. Finally, no effect of the induced energy deficiency on estrous cycle length was found. The cell culture model confirmed its suitability by transferring metabolic situations in vivo into cell culture conditions in vitro and by displaying immune modulatory effects due to the energetic undersupply.
Investigations on the Microbiology of the Stratosphere and Other Habitats in Relation to the Theory of Panspermia

The theory of Panspermia suggests that life was brought to Earth from an external source in space. The theory can be further divided into a) Neopanspermia, the view that life continues to arrive from space to Earth, b) Pathospermia, the idea that pathogenic organisms arrive from space and c) Cometary Panspermia which specifies that extraterrestrial organisms originate from comets. This main aim of this study was providing evidence in support of Neopanspermia. Six stratospheric balloon launches were carried out in order to sample the stratosphere for microbial cells (biological entities, BE). Analysis of isolates was achieved using Scanning Electron Microscopy (SEM), Energy Dispersive X-Ray Spectroscopy (EDAX), and Molecular techniques, to help determine the biological nature of any isolates and their origin. SEM and EDAX showed that, while most of the isolated material was inorganic cosmic dust, a few were biological in nature, although generally not recognizable as known terrestrial organisms. Some of the BEs were larger than the theoretical 5 micron limit for the transfer of a particle from Earth to the sampling heights, thereby suggesting a non- terrestrial origin. This was confirmed by the lack of similar sized (i.e. exceeding 5 micron) known terrestrial organisms such as pollen, grass shards, and fungal spores. There is clearly no sieve present in the atmosphere that would allow the isolated BEs to be elevated to the stratosphere from Earth while holding back known biological forms. It was therefore concluded that the large biological entities we isolated from the stratosphere are incoming to Earth from space and continually impact the Earth. Single cell amplification and identification also showed the presence of DNA and revealed a diverse population of known microorganisms distinct from the isolated biological entities. The ability of microbes to regain viability from ancient samples was also assessed by the isolation of bacteria from amber and halite rocks, thereby providing evidence that these organisms can survive after an extended period of millions of years, a finding which is of potential relevance to the transfer of microbes in the process of panspermia. Three meteorite types were also examined for biosignatures using SEM and EDAX techniques, two showed microfossil formations which can provide evidence for the theory of cometary panspermia. Evaluation of microbial survivability in the presence of exposure to ultraviolet C when embedded in ice was evaluated, as was the potential shielding by the presence of solid inorganic particles. It was also demonstrated, that the use of visible light generated by UV from fluorescence can provide energy for Cyanobacteria, which might have been the first microbes to inhabit our planet. Showing that life can survive in such conditions without the need of a protective atmosphere made up of oxygen that is necessary to form the protective ozone layer, this may explain how the first microbes were introduced to earth in the panspermia theory.