Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation of microorganisms from infected onions (Allium cepa) popularly consumed by low income earners in Ibadan, Nigeria

Samples of three (3) different varieties of infected onion bulbs were collected from different locations at Ojaoba, Muslim, Oke-ado and Bode markets of Ibadan. Isolation of microorganisms from infected onions (Allium cepa) was carried out. The results revealed that the infected onion bulbs were associated with Escherichia coli, Klebsiella sp. , Salmonella sp. , Proteus sp. , Aspergillus niger, Aspergillus flavus, Rhizopus stolonifer and Aspergillus fumigatus. It was also observed that the market where samples were collected and the variety of onions have no significant effect on the level of bacterial infestation. The mean total bacteria count ranges from 2.2 × 10 to 8.5 × 10. Furthermore, the market where samples were obtained and types of onions had no significant effect on the fungal infestation level. The level of infestation ranges from 1.1 × 10 to 3.1 × 10. E. coli had the lowest bacterial prevalence of 8.3% in the study area when compared to Klebsiella sp. (33.3%), Proteus sp. (30.6%) and Salmonella sp. (27.8%). Aspergillus niger had the highest fungal prevalence of 44.8% while Aspergillus flavus, Aspergillus fumigatus and Rhizopus stolonifer had prevalence of 26.9, 14.9 and 13.4% respectively. It shows that the different varieties of onions purchased at the selected markets in Ibadan, Oyo State contained different pathogenic microorganisms. Adequate care should be taken in processing onions (Allium cepa) to prevent food poisoning.
Long-term effects of chromium and lead upon the activity of soil microbial communities

The inhibitory effects of heavy metals upon microbial populations and the factors limiting microbial activity and growth were determined in soils that had been contaminated with lead (Pb) or chromium (Cr) for more than 40 years. Total Cr and Pb concentrations were 260,000 and 10,000 mg kg −1 soil in Crand Pb-contaminated soils, respectively. The tolerance of bacteria extracted from soil particles to Pb or Cr was assayed by measuring the incorporation of 3H -leucine into macromolecules at a series of CrO42− or Pb2+ concentrations. IC50 (heavy-metal concentration giving 50% reduction of microbial 3H -leucine incorporation compared to the control) for the two metals was similar in the two soils, despite their differences in metal contamination; the IC50values were 4 and 0.02 mM for CrO 42− and Pb2+, respectively. Stimulation of microbial activity and biomass by organic C was measured in microcosms over 56 days. The adverse effects of Cr and Pb were characterized in terms of the ratio of microbial biomass C to soil organic C, basal respiration per unit microbial biomass ( qCO2), and the ratio of substrate-responsive respiration to microbial biomass C (substrate-responsive qCO2). Ratios of microbial biomass C to soil organic C were small: 0.42% in Cr-contaminated soil and 0.36% in Pb-contaminated soil. Values of qCO2 and substrate-responsive qCO2 were significantly higher in Pbthan in Cr-contaminated soils ( P < 0.01). The microcosm results indicate that Cr and Pb decreased microbial activities and led to the accumulation of soil organic C, and that Pb posed greater stress to soil microbes than Cr. © 2002 Elsevier Science B.V. All rights reserved.
Carvacrol and Thymol Modulate the Cross-Talk between TNF-α and IGF-1 Signaling in Radiotherapy-Induced Ovarian Failure

Premature ovarian failure (POF) is a common cause of infertility in premenopausal women who are unavoidably exposed to cytotoxic therapy. Radiotherapy is one of the most effective cytotoxic treatments. However, the radiosensitivity of ovarian tissues limits its therapeutic outcome and results in the depletion of the primordial follicle and loss of fertility. Therefore, the need for an effective radioprotective therapy is evident especially when none of the current clinically used modalities for radioprotection succeeds efficiently. The present study investigated the potential radioprotective effect of carvacrol (CAR) (80 mg) or thymol (80 mg) on gamma- (γ-) irradiation-induced ovarian damage as well as their role in the cross-talk between IGF-1 and TNF-α signaling and antioxidative activity. In immature female Wister rats, a single dose of whole-body irradiation (3.2 Gy, LD20) produced considerable ovarian damage, which was evident by histopathological findings and hormonal changes. Interestingly, pretreatment with CAR or thymol significantly enhanced the follicular development and restored the anti-Mullerian hormone (AMH), E2, and FSH levels. Both essential oils improved the irradiation-mediated oxidative stress and reduction in proliferating cell nuclear antigen (PCNA) expression. Moreover, irradiated rats exhibited an inverse relationship between IGF-1 and TNF-α levels two days post irradiation, which was further inverted by the pretreatment with CAR and thymol and ought to contribute in their radioprotective mechanisms. In conclusion, CAR and thymol showed a radioprotective effect and rescued the ovarian reserve mainly through counteracting oxidative stress and the dysregulated cross-talk between IGF-1 and TNF-α.
Textural Analysis to Assess Heterogeneity in Breast Cancer

1Molecular Imaging Group, IDIS Research Institute, Santiago Compostela, Spain 2Departamento de Psiquiatria, Radioloxia e Saude Publica, Universidade de Santiago de Compostela, Spain 3Servizo Medicina Nuclear, Complexo Hospitalario Universitario de Santiago de Compostela, Spain 4Fundacion Tejerina, Madrid, Spain 5Servizo Radiofisica e Proteccion Radioloxica, Complexo Hospitalario Universitario de Santiago de Compostela, Spain
To Whom should We be Fair? Ethical Issues in Balancing Stakeholder Interests from Banco Compartamos Case Study

In the world of microfinance, interest rate ethics is an important issue, thrown into the limelight by the Initial Public Offering of Compartamos which resulted in millions of dollars of gains, some of which found their way into private pockets. These high gains were based on high interest rates, raising ethical questions. The paper then uses a stakeholder analysis to explain the interests of different stakeholders in this case and present that fairness to one group of stakeholders is often at the expense of another group. We take the position that in this case, specifically, the firm objectives could have been met without such ethical trade-offs. The specifics of the case are then generalised to all NGOs participating in for-profit firms.
Vacuumatics: vacuumatically prestressed (adaptable) structures

Vacuumatics rely on a relatively "new" and therefore yet unproven structural principle of prestressing incoherent (structural) elements by means of atmospheric pressure, by creating a (partial) vacuum inside an enclosing skin (figure 1). This technique leads to rigid – but reconfigurable – load bearing structures (figure 2), quite analogue to vacuum packed coffee. In an attempt to explore the structural potential of vacuumatically prestressed structures the force distribution throughout a simplistic 2-dimensional representation of such a structure is approached by means of an analytical model. A comparable numerical approach of the technique illustrates a remarkable resemblance in prestress derivation, differentiating a so called "direct" and an "indirect" prestressing component, indicating the significance of the elasticity of the applied skin material. This paper sets out to describe the ongoing study on the structural – as well as geometrical – behaviour of vacuumatics, aiming for a fundamental understanding in and control over the underlying design principles.
Home-cage monitoring ascertains signatures of ictal and interictal behavior in mouse models of generalized seizures

Epilepsy is a significant contributor to worldwide disability. In epilepsy, disability has two components: ictal (pertaining to the burden of unpredictable seizures and associated medical complications including death) and interictal (pertaining to more pervasive debilitating changes in cognitive and emotional behavior). In this study, we objectively and noninvasively appraise correlates of ictal and interictal disability in mice using instrumented home-cage chambers designed to assay kinematic and appetitive behavioral measures. We discover that in C57BL/6J mice, intraperitoneal injections of the chemoconvulsant pentylenetetrazole (PTZ) acutely result in complex and dynamic changes in movement and sheltering behavior that evolve (or kindle) with repeated daily injections, and which are separate from the occurrence of convulsions. By closely studying “interictal” periods (between PTZ injections), we identify a syndrome of nocturnal hypoactivity and increased sheltering behavior. We observe elements of this interictal behavioral syndrome in seizure-prone DBA/2J mice and in mice with a pathogenic Scn1a mutation (modeling Dravet syndrome). Through analyzing their responses to PTZ, we illustrate how convulsive severity and “behavioral” severity are distinct and independent aspects of overall seizure severity. Our results illustrate the utility of an ethologically centered automated approach to quantitatively appraise murine expressions of disability in mouse models of seizures and epilepsy. In doing so, this study highlights the very unique psychopharmacological profile of PTZ. Significance Statement Epilepsy is a brain disorder characterized by a pervasively increased risk to develop epileptic seizures. Sadly, patients with epilepsy also experience high rates of anxiety, depression and other psychiatric symptoms that significantly increase overall disability. While many mouse models of seizures and epilepsy exist, we need improved techniques to measure how new treatments impact not only seizure occurrence, but also emotional changes that persist in between seizures. In this study, we apply the technique of home-cage monitoring to clarify precisely how spontaneous mouse behavior is altered in three distinct epilepsy models. Our work illustrates the importance of an ethologically centered appreciation of neuropsychiatric disability in mice and clarifies a new approach to the measurement of “seizure severity”.
Identification of 332G>A Polymorphism in Exon 3 of the Leptin Gene and Partially Effects on Body Size and Tail Dimension in Sanjabi Sheep

The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits. Keywords—Body size, Leptin gene, PCR-RFLP, Sanjabi sheep. Roya Bakhtiar and Hadi Hajarian are with the Campus of Agriculture and Natural Resources, Razi University. Kermanshah, Iran. Alireza Abdolmohammadi is with the Campus of Agriculture and Natural Resources, Razi University. Kermanshah, Iran (corresponding author, e-mail: alirezaam2006@gmail.com). Zahra Nikousefat is with the College of Veterinary Medicine, Razi University, Kermanshah, Iran (e-mail: yaldanikousefat@ gmail.com). Davood Kalantar-Neyestanaki is with the School of Medicine, Kerman University of Medical Sciences, Kerman, Iran (e-mail: davoud1362@gmail.com).
Quantifying expression variability in single-cell RNA sequencing data

Transcriptional noise is an intrinsic feature of cell populations and plays a driving role in mammalian development, tissue homoeostasis and immune function. While expression heterogeneity, a phenotypic readout of transcriptional noise, has been broadly studied in prokaryotic model systems or by profiling individual genes, few whole-transcriptome studies in mammalian systems have been reported. The development of single-cell RNA sequencing technologies introduced powerful tools to investigate transcriptional differences between individual cells, therefore allowing the in-depth characterisation of expression variability. In this thesis, I computationally analysed single-cell RNA sequencing data to understand transcriptional variability and expanded a statistical model to avoid confounding effects when quantifying such variability. First, I profiled individual transcriptomes of CD4+ T cells, identifying a global decrease in transcriptional variability upon immune activation. By extending this analysis across two sub-species of mice, I identified an evolutionarily conserved set of immune response genes for which transcriptional variability increases during ageing. I used a Bayesian modelling framework to quantify mean expression and transcriptional variability but due to a strong confounding effect between these two parameters, variability analysis was restricted to genes that are similarly expressed across the tested conditions. To address this problem, I extended the computational framework allowing the parallel assessment of changes in mean expression and variability. Within this Bayesian framework, I introduced a joint prior linking mean expression and variability parameters, which allowed a residual over-dispersion to be measured for each gene. This measure allowed me to statistically assess changes in variability even for genes with differences in mean expression between conditions. Finally, I applied the model to identify temporal changes in variability over the time-course of spermatogenesis. This unidirectional differentiation process involves several complex steps before mature sperm form from spermatogonial stem cells. When profiling changes in variability across this developmental time-course, peaks in variability are caused by rapid changes in gene expression along the differentiation trajectory. This thesis provides a deeper understanding of technical and biological factors that drive transcriptional variability and offers a basis for future research to characterise its role in health and disease.
Isotope-dilution and its effects on measurements of nitrogen and phosphorus uptake by oceanic microplankton

Nitrogen (NH,+) and phosphorus (pod3-) uptake and recycling were measured in timeseries exper~ments in waters off the coast of Hawaii and in the Sargasso Sea. Patterns of uptake and recycling were similar but regionally distinct. In H a w a ~ i , uptake rates were initially rapid but essentially ceased after only a few hours in lnshore experiments; recycling rates continued for 24 h. Offshore, recycling rates were variable but decreased significantly with incubation time; uptake, on the other hand, continued for 24 h and paralleled photosynthetic carbon uptake. Uptake and recycling fluxes balanced after 24 h. In the Sargasso Sea, both soluble reactive phosphorus (SRP) uptake and recycling rates decreased wlth incubation time but were also in balance Isotope-dilution, resulting from the in vitro production (recycling) of unlabelled substrate was significant and if ignored, could account for 1.5 to 3-fold underestimates in computed uptake rates.
GENETIC VARIABILITY, HERITABILITY AND GENETIC ADVANCE FOR YIELD AND ITS RELATED TRAITS IN WHITE MAIZE (Zea mays L.) INBRED LINES

Maize (Zea mays L.) is the third most important cereal crop after wheat and rice in the world. Field experiments were conducted at Institute for Agricultural Research, Samaru (11°11´N; 07°38’E) in the Northern Guinea Savanna and National Horticultural Research Institute, Bagauda (11°33´N; 8°23´E) in the Sudan Savannah ecological zones of Nigeria between July-October, 2014 rainy season to estimate the heritability and expected genetic advance in the white maize inbred and to evaluate suitable selection criteria for further breeding. The study comprised of 6 parental lines, 15 hybrids and 4 checks which were laid out in partially balanced lattice design with three replications. The study revealed high PCV and GCV values for days to 50% silking (24.49, 22.83), anthesis silking interval (26.26, 27.07), plant height (29.26, 27.07), days to maturity (115.61, 86.56), ear height (72.36, 69.59), ear length (33.63, 22.58), ear diameter (37.58, 29.42), field weight (104.99, 94.58), moisture content at harvest (43.72,35.42) and grain yield (72.34, 69.56. The magnitude of phenotypic coefficient of variation (PCV) estimates in the present study was found to be slightly higher than their respective genotypic coefficient of variations (GCV) for all the studied traits. The result also indicated that days to 50% silking (88%, 75.46), anthesis silking interval (84%, 38.09), plant height (92%, 9.23), ear length (67%, 36.31), ear diameter (81%, 43.84) and yield (92%, 10380.24) had high heritability accompanied with high genetic advance. The significant difference (p≤ 0.05) among the genotypes across locations for most traits evaluated indicates the presence of genetic variability among the genotypes. PCV and GCV values recorded revealed the possibility of improving this traits through selection. The genotypes with high heritability coupled with high genetic advance could be selected and improved at early generation.
Ureide Content of Guar under Influence of Hexaconazole and Triazophos

The important part of regular human diet is vegetable, which supply minerals and nutrients for maintenance of health. India is first rank producer of guar comprise 83% of total world production but these are affected by diseases like leaf spots, leaf blotch and insect pest such as serpentine leaf miners, hairy caterpillars and jassids. The major biotic constraint in vegetable production is pest problem. Application of pesticides has now become a common practice in modern agriculture. Chemicalization of agriculture rescues the crop from pest and diseases but when applied in excessive dose affects on plant health and metabolism. The various stresses alter the plant metabolism including pesticidal stress. The ureide content is reported in this study under pesticidal stress of Hexaconazole and Triazophos in leguminous vegetables guar (Cyamopsis tetragonoloba (L.) Taub. ) after seed treatment and foliar sprays to ensure the nitrogen fixation and metabolism. Changes in the correlation between nitrogen fixation and ureide levels accelerate disturbance in the nitrogen metabolism and nitrogen products in plant. The concentrations of both pesticides for this experiment were 0.05, 0.1, 0.15, 0.2 and 0.3%. The seeds were soaked in these concentrations of pesticides for 12 h. After 12 h seed soaking period, the treated seeds were thoroughly washed with distilled water and sown in earthen pot containing garden soil and manure. The first foliar spray of Hexaconazole and Triazophos were applied with respective concentrations on 10th day while second foliar spray was on 25th day of plant growth. Analysis of ureide was carried out on the 15th and 30th day of growth that is 5 days after each spray. The uriede content in guar was remarkable increased after seed treatment followed by first foliar spray of 0.10, 0.15 and 0.20% hexaconazole however decreased it with dose concentrations of second foliar spray. The ureide content was decreased after both the foliar sprays of Triazophos.
How can you pilot lifelong learning? The experiences of the JISC distributed e-learning regional pilot projects

The fundamental question of lifelong learning concerns the possibility of embedding sustainable practices amongst learners and within institutions which serve the needs of learners as they negotiate formal learning episodes across institutions, informal learning and the demands of everyday life. The identification of efficacious learner and institutional practices can lead to the formation of policy guidelines which can inform both the focus of technological infrastructure and pedagogic and organizational recommendations. One way to identify these practices is to try them out by attempting to embed the technologies that support them. Guided by well-established processes for the adoption of new technology (Rogers, 1962; Moore 1991) the JISC regional Pilot programme was specifically designed to intervene in the adoption cycle of a range of learning technologies in order to establish the long-term efficacy of the learner and institutional practices that evolved around them.
Punchline: Identifying and comparing significant Pfam protein domain differences across draft whole genome sequences

Motivation Short-read draft paired-end Illumina assemblies can be fragmented, contain many contigs and be impacted on by repeat regions, caused by mobile element activity within the genome or inherently repetitive gene structure. Annotating such assemblies for function and analysing gene content can be challenging if predicted genes are fragmented across contigs. Such a case can often occur within specific families of genes such as longer genes with repeating domains, genes specifying several transmembrane domains and of unusual nucleotide content. These genes can often be virulence determinants, therefore losing these specific types of data can seriously impact downstream studies. Results Rather than studying the predicted gene content of draft genomes, we examined predicted protein content using the Pfam domain complements of predicted proteins. We produced a workflow, Punchline, to study the genetic content of draft contig assemblies by looking at the complement of short domains that are unlikely to be affected. We investigated a dataset of Bacteroides ovatus in terms of a grouping involving the vertebrate host from which the organism was isolated and identified potential host restricted functions and host restricted phylogenetic clustering. Availability https://github.com/LCrossman Contact: seq@sequenceanalysis.co.uk