Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a life cycle bioassay with Chironomus tentans in artificial streams

The objective of the work described in this thesis was to develop a novel life cycle bioassay for evaluating metal mine effluent effects using the midge Chironomus tentans in artificial streams. The bioassay was tested in situ using an environmentally relevant concentration (45%) of effluent from the Copper Cliff Wastewater Treatment Plant at INCO Ltd. in Sudbury, ON, Canada. There was reduced survival {p=O.OOl), reduced total emergence {p<O.OOl), increased time to emergence {p<O.OOl), and reduced hatching success {p=O.OOl) of C. tentans exposed to 45% Copper Cliff effluent relative to a reference water treatment. This research showed that the life cycle bioassay in artificial streams could be used in situ to assess metal mine effluent effects on life cycle endpoints in a benthic invertebrate. The artificial stream bioassay was also evaluated in the laboratory where sensitivity of the bioassay was compared to an existing beaker life cycle bioassay in a side-by-side exposure. Response patterns were consistent between the two bioassays for hatching success and time to emergence. However, effluent effects were observed for growth, survival, numbers emerged, and number of eggs per egg case in the artificial stream bioassay, but not in the beaker bioassay. Conversely, significant responses in sex ratios and number of egg cases per female were observed in the beaker bioassay, but not in the artificial stream bioassay. The inconsistencies in response between the two bioassays may be explained by the larger number of organisms per replicate in the artificial stream bioassay which may have resulted in decreased variability in endpoint measurement and smaller effect sizes. Results were compared between the laboratory
Sequence Analysis of Redundant Usage of DNA Fragments in Complete Genomes

DNA is a polymer of four kinds of nucleotides, and genetic information is described in their order. If the sequence of DNA is completely random, the expected frequency of observing oligonucleotides of certain lengths becomes one or less when 4windowsize ≥ Genomesize. However, there is actually functional and evolutionary constraints to the genome. Here we counted the oligonucleotides of lengths from 3 to 15 appearing in the genome.
Diversidade e potencial biotecnológico da comunidade bacteriana endofítica de sementes de soja

Abstract – The objectives of this work were to isolate, characterize and identify the endophytic bacterial community of soybean seeds, and to test the biotechnological potential of this community. Seeds from 12 soybean cultivars were used. The endophytic bacterial isolates were evaluated for in vitro antagonism against phytopathogenic fungi, synthesis of indoleacetic acid (IAA), and capacity to solubilize phosphate. Isolation techniques, ampliﬁ ed ribosomal DNA restriction analysis (ARDRA) grouping, and identiﬁ cation by means of partially sequencing the 16S rDNA were used in community characterization. The isolates with best biotechnological potential were inoculated in seeds to evaluate their ability to promote plant growth. Twelve ribotypes were identify by means of ARDRA and classiﬁ ed as: Acinetobacter , Bacillus , Brevibacterium , Chryseobacterium , Citrobacter , Curtobacterium , Enterobacter , Methylobacterium , Microbacterium , Micromonospora , Pantoea , Paenibacillus , Pseudomonas
The Metabolism of Anammox

Anaerobic ammonium-oxidizing (anammox) bacteria derive their energy for growth from the conversion of ammonium and nitrite into dinitrogen gas. The bacteria are the latest addition to the biogeochemical nitrogen cycle. The slowly growing micro-organisms that belong to the Planctomycetes are characterized by a compartmentalized cell architecture featuring a central cell organelle, the ‘anammoxosome’. Membrane systems surrounding the different cellular compartments are composed of unique ‘ladderane’ lipid molecules. Although the metabolism has not been completely resolved, nitrogen formation seems to involve the intermediary formation of hydrazine, a most reactive and toxic compound. Anammox bacteria have been detected in many oxygen-limited freshwater and marine ecosystems investigated. In the marine environment, over 50% of the nitrogen gas released is made by anammox bacteria. Application of the anammox process offers an attractive alternative to current wastewater treatment systems for the removal of fixed nitrogen. Key concepts Ammonium is converted under anaerobic conditions into dinitrogen gas by a newly discovered and specialized group of micro-organisms, the anammox bacteria. Anammox bacteria are chemolithoautotrophic organisms that gain their energy for growth from the conversion of the inorganic substrates ammonium and nitrite. Cell carbon is derived from carbon dioxide. Anammox bacteria are characterised by a unique cell plan featuring a central cell organelle, the anammoxosome. The lipids from anammox bacteria are composed of highly unusual ‘ladderane’ molecules. The conversion of ammonium and nitrite into dinitrogen gas proceeds through the intermediary formation of the toxic and highly reactive hydrazine. Anammox bacteria synthesize adenosine triphosphate (ATP) by an electrochemical proton gradient most likely established across the anammoxosome membrane. In nature approximately 50% of the dinitrogen gas released into the atmosphere is made by anammox bacteria. Anammox bacteria offer an economically attractive and environmentally friendly alternative to current wastewater treatment processes for the removal of fixed nitrogen. Keywords: anammox; anammoxosome; ladderane lipids; hydrazine
Mécanismes de la protéolyse dans le lait lors de l'inflammation de la glande mammaire chez la vache laitière : activité des protéases leucocytaires et des protéases bactériennes (cas d'Escherichia coli)

La mammite est la pathologie la plus frequente chez la vache laitiere, affectant toute la filiere laitiere du producteur jusqu'au transformateur. L'objectif de ce travail est l'etude de l'incidence des facteurs endogenes (cellules somatiques, systeme plasmine-plasminogene) et des facteurs exogenes (bacteries) sur la caseinolyse. Ceci a ete rendu possible grâce a des modeles experimentaux de mammite in vivo a E. coli ou a LPS, et au modele in vitro d'inoculation d'E. coli dans du lait cru. La proteolyse dans le modele in vivo a E. coli a permis d'etablir une sequentialite de proteolyse ou les cellules somatiques et les bacteries interviendraient entre 3 et 216 h PI, et une phase entre 15 et 33 h PI ou la plasmine serait predominante. Plusieurs fractions peptidiques appartenant a la fraction proteose peptones, sont presentes pendant la phase aigue de l'inflammation, dont deux peptides d'origine cellulaire. Dans ce modele le role bacterien dans les mecanismes de la proteolyse est difficilement apprehendable. L'etude in vitro de la proteolyse d'origine bacterienne avec le modele E. coli/lait a montre une interaction entre les bacteries, les proteases bacteriennes et le systeme plasmine-plasminogene. Le second modele in vitro proteases d'E. coli/caseines a quant a lui permis d'etablir un ordre preferentiel de degradation des caseines. Le modele in vivo a LPS a montre que l'activite de la gelatinase dans la fraction constituee de cellules matures est plus importante que dans la fraction constituee de cellules immatures
Insect transgenesis: methods and applications.

Preface Introduction An Introduction to the History and Methodology of Insect Gene Transfer - A.M. Handler Gene Targeting Targeted Transformation of the Insect Genome - P. Eggleston and Y. Zhao Site-specific Recombination for the Genetic Manipulation of Transgenic Insects - Y.S. Rong and K.G. Golic Transgenic Selection Eye Color Genes for Selection of Transgenic Insects - A. Sarkar and F.H. Collins Green Fluorecent Protein (GFP) as a Marker for Transgenic Insects - S. Higgs and D. Lewis Resistance Genes as Candidates for Insect Transgenesis - R. ffrench-Constant and M. Benedict Viral Vectors Pantropic Retroviral Vectors for Insect Gene Transfer - J.C. Burns Densonucleosis Virus as Transducing Vectors for Insects - J.C. Carlson, B. Afanasiev, and E. Suchman Sindbis Virus Expression Systems in Mosquitoes: Background, Methods and Applications - K.E. Olson Retrotransposons and Retroviruses in Insect Genomes - C. Terzian, A. Pelisson, and A. Bucheton Polydnaviruses and Insect Transgenic Research - B.A. Webb Transposable Element Vectors Hermes and Other hAT Elements as Gene Vectors in Insects - P.W. Atkinson and D.A. O'Brochta Genetic Engineering of Insects with mariner Transposons - D.J. Lampe, K.K. O. Walden, J.M. Sherwood, and H.M. Robertson The TTAA-specific Family of Transposable Elements: Identification, Functional Characterization, and Utility for Transformation of Insects - M.J. Fraser Symbiont Vectors Wolbachia as a Vehicle to Modify Insect Populations - S.P. Sinkins and S.L. O'Neill Bacterial Symbiont Transformation in Chagas Disease Vectors - C.B. Beard, R.V. Durvasula and F.F. Richards Strategies, Risk Assessment and Regulation The Application of Transgenic Insect Technology in the Sterile Insect Technique - A.S. Robinson and G. Franz Control of Disease Transmission Through Genetic Modification of Mosquitoes - A.A. James Deploying Transgenic Arthropods in Pest Management Programs: Risks and Realities - M.A. Hoy Regulation of Transgenic Arthropods and other Invertebrates in the United States - O.P. Young, S.P. Ingebritsen and A.S. Foudin
Chromatographic Methods for the Determination of Carbohydrates and Organic Acids in Foods of Animal Origin

Carbohydrates are ubiquitous and range from simple monosaccharides to large complex polysaccharides. Organic acids are compounds with acidic properties. Both occur naturally in many foods and in fermented products. Organic acids are usually derived from the hydrolysis of carbohydrates by microorganisms such as lactic acid bacteria. These bacteria convert carbohydrates into energy required for growth, since they are not equipped with the enzymes necessary for respiration and are unable to perform oxidative phosphorylation. Determination of carbohydrates and organic acids in foods of animal origin is important, since they contribute to flavor and texture. Their presence and proportions can affect the chemical and sensory characteristics of a food matrix and they can provide information on nutritional properties of food and the means to optimize selected technological processes. Furthermore, the levels of carbohydrate and organic acid are important to monitor bacterial growth and activity. Actually, these compounds can be quantified by several methods including high-performance liquid chromatography (HPLC) and gas chromatography (GC). High-performance liquid chromatography has been widely used to analyze carbohydrates and nonvolatile organic acids, while gas chromatography has been used to determine the volatile organic acids in complex matrices. This contribution provides an overview of chromatographic methods (HPLC and GC) used to analyze carbohydrates and organic acids in foods of animal origin.
Cellulose synthesis during endocarp hardening of peach fruit

Summary Changes in cellulose content and the accumulation of PpCesA1 mRNA, putatively encoding the catalytic subunit of cellulose synthase (CesA), were analysed in endocarp and mesocarp during endocarp hardening in peach fruit. The cellulose content of the endocarp was undetectable or very low [< 0.1 mg g–1 fresh weight (FW) of endocarp] until 48 d after full bloom (DAFB), but began to increase rapidly at 55 DAFB, when the endocarp had attained its maximum size, and reached 4.4 mg g–1 FW of endocarp at 85 DAFB. In contrast, the cellulose content of the mesocarp reached a detectable level (1.5 mg g–1 FW of mesocarp) at 34 DAFB, stayed at this level until 85 DAFB, but then was lower at 107 DAFB. PpCesA1 mRNA was detected in the endocarp throughout the hardening, but was undetectable in the mesocarp. It is suggested that PpCesA1 has a role in the rapid synthesis of cellulose in the secondary cell walls of endocarp tissue during hardening.
GP CaKe: Effective brain connectivity with causal kernels

A fundamental goal in network neuroscience is to understand how activity in one brain region drives activity elsewhere, a process referred to as effective connectivity. Here we propose to model this causal interaction using integro-differential equations and causal kernels that allow for a rich analysis of effective connectivity. The approach combines the tractability and flexibility of autoregressive modeling with the biophysical interpretability of dynamic causal modeling. The causal kernels are learned nonparametrically using Gaussian process regression, yielding an efficient framework for causal inference. We construct a novel class of causal covariance functions that enforce the desired properties of the causal kernels, an approach which we call GP CaKe. By construction, the model and its hyperparameters have biophysical meaning and are therefore easily interpretable. We demonstrate the efficacy of GP CaKe on a number of simulations and give an example of a realistic application on magnetoencephalography (MEG) data.
In vitro antioxidant activity and preliminary phytochemical analysis of medicinal legumes.

The methanolic exts. of leaves of Humbolditia brunonis, Caesalpinia mimosoides, Derris scandens traditionally used in traditional medicines were screened for antioxidant and free radical scavenging activities using ascorbic acid and butylated hydroxyl toluene (BHT) as stds. The antioxidant potential was evaluated by using di-Ph picryl hydrazyl free radical (DPPH), phospho molybdenum total antioxidant assay, reducing power assay and hydrogen peroxide assay. Preliminary phytochem. anal. of methanolic exts. of these plants indicated the presence of tannins, saponins, steroids, terpenoids, anthraquinones and phlobatonins. All these legumes showed antioxidant properties with greater activity being found in Humbolditia brunonis. The present result suggest that leaves ext. of these legumes could be the potential sources of natural antioxidant that could be of great importance for the treatment of radical related and age assocd. diseases. [on SciFinder(R)]
Effect of mercuric chloride on terrestrial slug Semperula maculata and histopathology of reproductive organs: a comprehensive study

Since the last few decades, terrestrial diversity is found to be under stress due to the contamination by various chemicals and gases of aquatic and agricultural media. The bioaccumulation of these compounds at certain concentrations in different tissues produces histopathological changes leading to behavioral changes in target animals. This study focused on terrestrial molluscan slug, Semperula maculata, against lethal concentrations of mercury chloride (HgCl2). Bioaccumulation of Hg was highest in ovotestis, while lowest in the molluscan penis. Histopathological changes were observed in the cellular arrangement of reproductive organs. Alterations in the penis and the dart gland included dilated unicellular, multicellular glands, and muscular dystrophy, dilated peripheral glandular cells, respectively; dilation being maximal in the prostate gland. Ovotestis showed depleted number of gametocytes. Vacoulized pre-vitellogenic oocytes with early vitellogenic oocytes were noted under light microscopy. Mercury produced toxicity on secretory functions and lowered the rate of reproduction in animals. Evidence indicates that Hg produced gamete degeneration, impacted reproductive capacity and survival of this species in the ecosystem.
Vaginal Colonization by Escherichia coli in Pregnant Women at King Abdulaziz University Hospital, Jeddah, Saudi Arabia

Citation Jamal TY, Younus HA, Abduljabbar HS, Fatani AA, Makled AF. Vaginal colonization by Escherichia coli in pregnant women at King Abdulaziz University Hospital, Jeddah, Saudi Arabia. JKAU Med Sci 2017; 24 (3): 39-49. DOI: 10.4197/Med. 24.3. 4 Abstract Maternal and neonatal infections by Escherichia coli remain a challenging problem for obstetricians and pediatricians. This study aims to determine the prevalence of vaginal colonization by Escherichia coli among pregnant women attending the Antenatal Clinics at King Abdulaziz University Hospital in JeddahSaudi Arabia, and to investigate the susceptibility of isolated Escherichia coli to the most commonly used antimicrobials. In this study, 100 pregnant women in the last trimester and 25 non-pregnant women were screened for vaginal colonization of Escherichia coli. The suspected colonies were identifi ed by conventional methods and were confi rmed by automated technology "Vitek 2 System". Also, antimicrobial susceptibility tests were done by the same methods". Escherichia coli isolates were serotyped to detect the presence of K1 antigen. Out of 100 pregnant women in the last trimester; twenty-one (21%) were Escherichia coli positive. Also, out of 25 non-pregnant women; four (16%) were Escherichia coli-positive. All of the isolated Escherichia coli were susceptible to most antimicrobial agents. The percentage of vaginal Escherichia coli resistance to trimethoprim/sulfamethoxazole, ampicillin and piperacillin ranged from 38.1% to 42.9%. The virulence factor K1 antigen was demonstrated in 42.9% of Escherichia coli -positive pregnant women.
cag, the Pathogenicity Island of Helicobacter pylori, Triggers Host Responses

Helicobacter pylori was isolated by accidental extended incubation. It is a spiral-shaped, gram-negative, microaerophilic microorganism that colonizes and survives in the hostile environment of the human stomach, in an equilibrium that permanently links the parasite to the host. Strains isolated from patients with peptic ulcer disease (PUD) contain the cagA gene (cytotoxin-associated gene A) and express the immunodominant CagA antigen. CagA and VacA are frequently coexpressed; however, their genes are 300 kb apart and VacA expression does not require the presence of the cagA gene, since null cagA mutants still produce the VacA protein. In most industrialized countries, 70 to 80% of the clinical isolates express CagA. Clinical isolates have been grouped into two broad families, type I and type II, in which type I strains possess the cag pathogenicity island (PAI). As with the related Cag proteins of H. pylori, the Icm/Dot proteins act as an exporters for the virulence factor(s) targeted to the intracellular environment to enhance survival and to kill host macrophages. The existence of 30 different proteins all encoded within cag underscores the functional importance of specialized chaperones in macromolecular export. Recent data suggest that VirB4, VirB7, VirB9, VirBlO, and VirB 11 assemble as a complex and form the core of the transporter. The diffusion of H. pylori entails the spread of a population's culture. This was influenced by the history of parasitic association of the bacterium with the human species and the migratory expansion.
Clinical features of mitochondrial disease in a family

Abstract Mitochondrial disorders, once thought to be relatively rare, are now thought to be the most prevalent metabolic disease. They represent a challenge to clinicians, especially in children, in whom clinical presentation and course show enormous variation. We report a respiratory chain enzyme activity disorder (complex I, III and IV) in a girl, with a severe presentation since the perinatal period. An older female sibling had died at the age of 11 months from an encephalopathy, with a similar clinical presentation. Enzyme activity disorders could not been disclosed. This association has been described only rarely. Mitochondrial disorders associated with defects in the respiratory chain can be attributable to mutations in the mitochondrial genome (mitochondrial DNA) or the nuclear genome (nuclear DNA). The diagnosis is based on the presence of clusters of abnormal mitochondria in muscle cells and a biochemically defined defect in the respiratory chain enzymes or, more recently, also on mutations in the mitochondrial DNA. In our case muscular biopsy to assess enzymatic activity of the respiratory chain complexes disclosed defects in respiratory chain complexes I, III and IV (cytochrome c oxidase). The patients, as our case, usually present early in life and are more severely affected than patients with isolated complex deficiencies. Therapy remains largely ineffective.
Late Fermentation Expression of FLO1 in Saccharomyces Cerevisiae1

A strategy to alter the flocculation properties of nonflocculent yeast in such a way that flocculation occurred toward the end of fermentation was developed. In a double cross-over event, the wild-type FLO1 promoter of the haploid, nonflocculent S. cerevisiae FY23 strain was replaced by a construct consisting of the SMRI-410 marker gene and the HSP30 promoter. In this way, the genomic copy of the wild-type FLO1 open reading frame was brought under transcriptional control of the HSP30 promoter. The transformants showed strong flocculation toward the end of fermentation, resulting in a distinctly clearer beer than the beer obtained with wild-type cells. The other properties of the wild-type strain were conserved. Moreover, it was shown that the transformants were extremely stable and that flocculation could be induced earlier during fermentation by a heat-shock treatment or the addition of ethanol to the medium. These results suggest that the flocculation properties of weakly flocculent brewer's yeast strains can be improved using controlled expression of the FLO1 gene.
SOCIAL CAPITAL AND INNOVATION CAPITAL: ACCOUNTABILITY TOWARDS SMALL MEDIUM ENTERPRISES’ (SMEs) SUSTAINABLE PERFORMANCE

SMEs have the potential role to substantially contribute to the current and future economy. In today’s complex business environment, SMEs arefacing various challenges in surviving and sustaining their operations. The sudden economic changes and globalization have seen many smallenterprises failed in managing their business. In this innovation capital and social capital are two main intangible resources in the organization,which are vital for sustainable performance in any organization. Hence, in discharging their accountability towards the relevant stakeholders,SMEs should deploy their intangible resources. In this regard, the main aim of this study is to investigate the relationship between innovationcapital and social capital with SMEs performance. Data were captured via questionnaires, which were distributed to eighty SMEs companiesin four states in Malaysia. The results of the study provide evidence that innovation capital and social capital influence the performanceof SMEs. In addition, all the dimensions under innovation capital and social capital which are innovation capabilities, innovation culture,structural and relational are significantly positive related with SMEs performance. This reflects that intangible resources in SMEs beingcapability, culture in working environment, social interaction within organization, network, and the strength of ties among the employeeare crucial to influence the efficiency of SMEs organization. Thus, the results of this study offer guidelines and evidences for SMEs in managing their intangible resources in order to be competitive and sustainable in business. Keywords: Innovation capital, social capital, SMEs, SMEs performance, sustainable performance