Miracle-dz/UniFAR-FTUs huggingface dataset:
Denitrification: From Genes to Ecosystems

Denitrification is a part of the global nitrogen cycle in which fixed nitrogen in the biosphere is returned to the atmosphere, which is mediated by diverse communities of microorganisms. This thesis seeks to gain a greater understanding of the ecology of denitrifying microorganisms by examining the pathway from four different aspects; gene, population, community, and ecosystem. A combination of bioinformatic analysis of denitrification genes in pure cultures and environmental samples as well as experimental work with denitrifying bacterial cultures and soil microcosms was performed to understand the relationship between genes and ecosystems in denitrification. Analysis of the phylogeny of genes involved in key steps in the denitrificaiton pathway revealed a different evolutionary pattern for each gene, as processes such as horizontal gene transfer, duplication/divergence, and lineage sorting have contributed differentially to the evolution of each gene. However, genetic variation is not easily translated into an extended phenotype for a population of denitrifiers, as the denitrification phenotype of a set of closely related denitrifying Bacillus soil isolates was variable depending on pH. Yet, the genetic community structure was shown to be an important factor in determining denitrification rates and end product ratios, as denitrifying communities in soil microcosms showed differential response to altered ratios of organisms with an without the ability to reduce nitrous oxide. Finally, patterns of nirS and nirK sequences suggested that community assembly of both denitrifier types was largely driven by niche-based processes, as community structure varied among habitats with different salinities. However, nirS and nirK denitrifiers were not ecologically equivalent, as patterns of phylogenetic clustering among co-existing nirS and nirK type denitrifying communities along the same environmental gradient were not comparable. In conclusion, denitrification is a complex ecological function that is regulated by the interaction between gene and environmental processes, and evolutionary processes that underlying the diversification and distribution of denitrification genes may have direct consequences on the denitrification unction in ecosystems.
Computer simulation of knee arthrometry to study the effects of partial ACL injury and tibiofemoral contact

We simulated the knee arthrometry test to obtain a deeper understanding of the joint's stability behavior and interpret the arthrometric results more effectively. A 2D sagittal plane finite element model of the lower limb in the standard configuration of knee arthrometry was developed using ANSYS APDL. A detailed model of the knee joint was considered including the femoral articulating contour represented by an ellipse, the tibial plateau represented by a circular arc, and four major knee ligaments and their individual bundles represented by linear and nonlinear tensile springs. A deformable layer of articular cartilage was also considered over the tibial plateau to simulate the bones engagement more precisely. The model was analyzed while the tibia was subjected to an anterior drawer force of up to 150 N with 10 N increments and the tibial anterior translation was obtained. Simulation of the arthrometry test for different curvatures of the tibial plateau revealed that the bones engagement has a considerable effect on the knee joint's laxity. However, a considerable change from the intact knee's data curve was only observed when the ACL total ruptured was simulated. This emphasizes the difficult task involved when trying to distinguish the partial injuries of the ACL using arthrometric data.
The cost-effectiveness of HLA-B*5701 genetic screening to guide initial antiretroviral therapy for HIV

Objective:To evaluate the clinical impact and cost-effectiveness of HLA-B*5701 testing to guide selection of first-line HIV regimens in the United States. Design:Cost-effectiveness analysis using a simulation model of HIV disease. The prevalence of HLA-B*5701 and the probabilities of confirmed and unconfirmed severe systemic hypersensitivity reaction among patients taking abacavir testing HLA-B*5701 positive and negative were from the Prospective Randomized Evaluation of DNA Screening in a Clinical Trial study. The monthly costs of abacavir-based and tenofovir-based regimens were $1135 and $1139, respectively; similar virologic efficacy was assumed and this assumption was varied in sensitivity analysis. Patients:Simulated cohort of patients initiating HIV therapy. Interventions:The interventions are first-line abacavir, lamivudine, and efavirenz without pretreatment HLA-B*5701 testing; the same regimen with HLA-B*5701 testing; and first-line tenofovir, emtricitabine, and efavirenz. Main outcome measures:Quality-adjusted life years and lifetime medical costs discounted at 3% per annum, cost-effectiveness ratios ($/QALY). Results:Abacavir-based treatment without HLA-B*5701 testing resulted in a projected 30.93 years life expectancy, 16.23 discounted quality-adjusted life years, and $472 200 discounted lifetime cost per person. HLA-B*5701 testing added 0.04 quality-adjusted months at an incremental cost of $110, resulting in a cost-effectiveness ratio of $36 700/QALY compared with no testing. Initiating treatment with a tenofovir-based regimen increased costs without improving quality-adjusted life expectancy. HLA-B*5701 testing remained the preferred strategy only if abacavir-based treatment had equal efficacy and cost less per month than tenofovir-based treatment. Results were also sensitive to the cost of HLA-B*5701 testing and the prevalence of HLA-B*5701. Conclusion:Pharmacogenetic testing for HLA-B*5701 is cost-effective only if abacavir-based treatment is as effective and costs less than tenofovir-based treatment.
QUALITY ANALYSIS OF NON-NASAL AND NON-ASPIRATED URDU STOPS , SYNTHESIZED USING HLSYN ( A HIGH LEVEL SYNTHESIZER )

HLSyn is a quasi-articulatory synthesizer (independent of any particular language) with a small set of parameters, which model the complex acoustic consequences of vocal tract. The primary motivation of using HLSyn is to combine the ‘simplicity of control’ of articulatory synthesizers with ‘accuracy and efficiency’ of formant synthesizers. The aim of this paper is to analyze the quality of nonnasal and non-aspirated Urdu Stops, synthesized using HLSyn.
The urge to smoke depends on the expectation of smoking.

AIMS An earlier study (Dols et al. 2000) suggested that cue-induced urge to smoke depends on the expectation of smoking. The present study tried to replicate the findings under stringently controlled conditions. DESIGN A 2 (context) x 2 (cues) x 6 (trial) within-subject design. Each smoker entered two different contexts; one context predicted the future occurrence of smoking (i.e. one puff of a cigarette) and one context predicted the non-occurrence of smoking. In each context smokers were exposed to smoking cues (i.e. cigarettes and lighter) or not. SETTING Laboratory at Maastricht University. PARTICIPANTS Thirty-two daily smokers, smoking at least five cigarettes a day for at least 2 years. MEASUREMENTS Participants reported their urge to smoke in each context in the presence and absence of smoking cues using a computerized visual analogue scale (VAS). FINDINGS The results revealed that the urge to smoke was higher in a context in which smoking was expected relative to a context in which it was not expected. As in the previous study the urge-inducing effect of smoking cues was larger in the smoking context than in the non-smoking context. Moreover, smoking cues did not have a significant effect in the non-smoking context. CONCLUSIONS It was shown that smoking cues elicit craving due mainly to a generated expectation of the occurrence of smoking and less due to salience or long history of associative learning. Theoretical and practical implications of the results are discussed.
A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics

A novel lipid transfer protein, designated as Ag‐LTP, was isolated from aerial parts of the dill Anethum graveolens L. Structural, antimicrobial, and lipid binding properties of the protein were studied. Complete amino acid sequence of Ag‐LTP was determined. The protein has molecular mass of 9524.4 Da, consists of 93 amino acid residues including eight cysteines forming four disulfide bonds. The recombinant Ag‐LTP was overexpressed in Escherichia coli and purified. NMR investigation shows that the Ag‐LTP spatial structure contains four α‐helices, forming the internal hydrophobic cavity, and a long C‐terminal tail. The measured volume of the Ag‐LTP hydrophobic cavity is equal to ~800 A3, which is much larger than those of other plant LTP1s. Ag‐LTP has weak antifungal activity and unpronounced lipid binding specificity but effectively binds plant hormone jasmonic acid. Our results afford further molecular insight into biological functions of LTP in plants. Copyright © 2015 European Peptide Society and John Wiley & Sons, Ltd.
Venlafaxine for the control of hot flashes: results of a longitudinal continuation study.

PURPOSE/OBJECTIVES To evaluate the intermediate term efficacy and toxicity of the use of venlafaxine for the control of hot flashes. DESIGN An open-label continuation phase study following a double-blind, randomized, placebo-controlled clinical trial that tested three doses of venlafaxine for the control of hot flashes. SETTING North Central Cancer Treatment Group institutions. SAMPLE 102 postmenopausal women. METHODS Women could titrate venlafaxine to optimum efficacy while recording daily hot flash counts and weekly toxicity information. MAIN RESEARCH VARIABLES Hot flash frequency, hot flash score. FINDINGS The reduction in hot flashes previously reported in the randomized study phase was maintained during the open-label study. Toxicity did not appear to increase over time. CONCLUSIONS The data from this study provides evidence that venlafaxine has intermediate term efficacy and good tolerability as a treatment for hot flashes. IMPLICATIONS FOR NURSING PRACTICE Nurses can inform symptomatic women that an effective nonhormonal alternative exists to control their hot flashes.
The Value of Mindfulness-Based Methods in Teaching at a Clinical Field Placement

The value of mindfulness-based methods in an undergraduate field placement was investigated in relation to the acquisition of self-care and other basic clinical competencies. The participants were 22 students in an applied behavioral analysis course, which included a mindfulness-based training module, and 20 students enrolled in an experimental psychology course without mindfulness training. The Mindfulness Attention and Awareness Scale, the Freiberg Mindfulness Inventory, and the Kentucky Inventory of Mindfulness Skills were used as measurements before and after intervention. Mindfulness-trained participants kept records and were asked to share their personal experiences during supervision and an exit interview. Results demonstrated that training significantly increased mindfulness. Qualitative data indicated enhanced self-care, attention to well-being, self-awareness, active involvement acquiring skills, and empathy and compassion. The need to expand the utility of mindfulness to the realm of education and the importance of including comparison groups with other self-care modules for future studies were discussed.
Triiodothyronine Reduces Growth Hormone Secretion and Pituitary Growth Hormone mRNA in the Chicken, in Vivo and in Vitro

Abstract The influence of triiodothyronine (T3) on growth hormone (GH) mRNA and GH secretion has been examined in the chicken. Initially T3 treatment in the diet for three days did not alter plasma concentrations of GH. Plasma concentrations of GH were depressed with seven and 14 days of T3 treatment (1 or 5 ppm in the diet). There was a concomitant decline in pituitary GH mRNA with T3 treatment. Pituitary GH content was reduced with 14 but not seven days of T3 treatment. No effect of T3 was observed on the percentage by somatotroph cells in the anterior pituitary gland by fluorescence flow cytometry analysis. While exposure of pituitary cells in vitro from young chickens to GHRF for 2 hr increased GH mRNA, no effect was observed with T3. The presence of T3, for 48 hr in vitro, tended to reduce GH mRNA in adenohypophyseal cells from young chickens and decreased GH mRNA with anterior pituitary cells from adult chicks. It is concluded that T3 chronic administration of T3 depresses circulating concentrations of GH, at least in part, by decreasing GH mRNA and hence GH synthesis.
Stage-specific expression of a developmentally regulated gene in Dirofilaria immitis

ABSTRACT A previously reported cDNA clone encoding 34 kDa antigenic polypeptide of Dirofilaria immitis (λ cD34) was studied to elucidate the mechanism of stage-specific gene expression. The 34 kDa polypeptide was a larva-specific antigen and the mRNA was detectable in microfilariae but not in adult worms and eggs. The λ cD34 gene was not sex linked and was contained in the genome of D. immitis at each stage. The stage-specific expression of the developmentally regulated gene in D. immitis may be controlled primarily at the mRNA level.
Antigenotoxic activity of naturally occurring furanocoumarins

This study was designed to investigate the antigenotoxic effects of a series of naturally occurring furanocoumarins (NOFs) including isoimperatorin, imperatorin, (+)‐oxypeucedanin, (+)‐byakangelicol, and (+)‐byakangelicine on antigenotoxic activities against genotoxicity induced by carcinogens [furylfuramide and N‐methyl‐N′‐nitro‐N‐nitrosoguanidine], and procarcinogens 2‐[2‐(acetylamino)−4‐amino‐5‐methoxyphenyl]−5‐amino‐7‐bromo‐4‐chloro‐2H‐benzotriazole (PBTA‐4) and 2‐amino‐3,4‐dimethyl‐3H‐imidazo‐[4,5‐f] quinoline (MeIQ)] to genotoxic metabolites catalyzed by rat S9 or rat and human recombinant cytochrome P450 (CYP) 1As by using the umu test based on SOS response. Five different NOFs, which were found in the human diets, strongly inhibited the umuC induction by procarcinogens, but did not be affected by carcinogens. Notably, isoimperatorin and (+)‐byakangelicol were found to be potent inhibitors on the metabolic activation of PBTA‐4 and MeIQ to genotoxic metabolites catalyzed by rat and human CYP1A1, or rat and human CYP1A2, respectively. In addition, to elucidate the mechanism of their antigenotoxic effects against procarcinogens, the effects of NOFs on rat and human CYP1A1‐ or rat and human CYP1A2‐related enzyme activities of 7‐ethoxyresorufin‐O‐deethylase (EROD) were also investigated. Reduction of the EROD activities by some of the NOFs with IC50 values of 0.23–20.64 μM was found to be due to strong inhibition of CYP1A1 and CYP1A2 dependent monooxygenases. Furthermore, the mechanism of inhibitions by NOFs on human CYP1A1 and CYP1A2 was analyzed by means of Dixon plots plus Cornish‐Bowden plots. The kinetic studies of inhibition types revealed that these compounds inhibited the human CYP1A1 and CYP1A2 a variety of modes rather than by a uniform one. Moreover, experiments with a two‐stage incubation indicated that NOFs, except for imperatorin, inhibited human CYP1A1 in a mechanism‐based manner, but directly inhibited human CYP1A2. This data suggest that certain NOFs, to which humans are exposed in the diet, may be capable of affecting the metabolic activation of procarcinogens due to inhibitions of CYP1A1 and CYP1A2 enzymes. Environ. Mol. Mutagen. , 2011. © 2011 Wiley‐Liss, Inc.
Characterization of a sialidase (neuraminidase) isolated from Clostridium chauvoei (Jakari strain)

A sialidase from Clostridium chauvoei (Jakari strain), an indigenous bacterial strain that causes blackleg in Nigerian cattle and other ruminants was isolated and partially purified by chromatography on DEAE cellulose, hydroxyapatite and phenyl agarose columns. The enzyme migrated as a 65‐kDa protein after electrophoresis on sodium dodecyl sulphate polyacrylamide gels. It was optimally active at pH 4.5 and 40°C with an activation energy (Ea) of 13.40 kJ mol−1. It had Km and Vmax values of 170 µM and 200 µmole h−1 mg−1 respectively with fetuin as substrate. When sialyllactose (Neu5Ac2,3 lactose) was used as substrate the Km and Vmax values were 8 µM and 5 µmoles min−1 mg−1 respectively. The Clostridium chauvoei sialidase cleaved sialic acids from RBC ghosts of sheep, horse, goat, cattle, pig and mice as well as mouse brain cells, albeit at different rates. The enzyme was activated by Ca2+ and Mg2+ and inhibited by the group‐specific reagents diethylpyrocarbonate (DEP) and N‐ethylmalemide (NEM). The sialidase inhibitors, 2,3 didehydroneuraminic acid (Neu5Ac2,3en) and paranitrophenyl oxamic acid (pNPO) inhibited the enzyme competitively with Ki values of 40 and 30 µM respectively. Copyright © 2005 John Wiley & Sons, Ltd.
Elevation of Serum APE1/Ref-1 in Experimental Murine Myocarditis

Myocarditis is an inflammatory disease of the myocardium that causes cardiogenic shock and death. However, endomyocardial biopsy that is, the gold standard for a diagnosis is limited. Apurinic/apyrimidinic endonuclease 1/redox effector factor-1 (APE1/Ref-1) is a multifunctional protein, which is involved in DNA-based excision repair pathway, and in redox signaling, its changes are observed in various cardiovascular diseases including hypertension and coronary artery disease. We analyzed serum APE1/Ref-1 in experimental murine myocarditis. To induce myocarditis, coxsackievirus B3 was injected intraperitoneally to BALB/c mice. The serum APE1/Ref-1, N-terminal pro-B-type natriuretic peptide (NT-proBNP) and troponin I were measured. The histology and virus titers measurements were performed. The troponin I and inflammation were significantly elevated at day 3, peaked to day 7 and decreased at day 10. The NT-proBNP and virus titers were significantly peaked at day 3, and dropped at day 7 and 10. The serum APE1/Ref-1 was gradually raised and its elevation is still maintained until a later time, namely day 10. Also, its level was positively correlated with myocardial inflammation, reflecting severity of myocardial injury. We suggest that serum APE1/Ref-1 can be used to assess for myocardial injury in viral myocarditis without endomyocardial biopsy.
Role of Environmental Chemicals in Diabetes and Obesity: A National Toxicology Program Workshop Review

Background: There has been increasing interest in the concept that exposures to environmental chemicals may be contributing factors to the epidemics of diabetes and obesity. On 11–13 January 2011, the National Institute of Environmental Health Sciences (NIEHS) Division of the National Toxicology Program (NTP) organized a workshop to evaluate the current state of the science on these topics of increasing public health concern. Objective: The main objective of the workshop was to develop recommendations for a research agenda after completing a critical analysis of the literature for humans and experimental animals exposed to certain environmental chemicals. The environmental exposures considered at the workshop were arsenic, persistent organic pollutants, maternal smoking/nicotine, organotins, phthalates, bisphenol A, and pesticides. High-throughput screening data from Toxicology in the 21st Century (Tox21) were also considered as a way to evaluate potential cellular pathways and generate -hypotheses for testing which and how certain chemicals might perturb biological processes related to diabetes and obesity. Conclusions: Overall, the review of the existing literature identified linkages between several of the environmental exposures and type 2 diabetes. There was also support for the “developmental obesogen” hypothesis, which suggests that chemical exposures may increase the risk of obesity by altering the differentiation of adipocytes or the development of neural circuits that regulate feeding behavior. The effects may be most apparent when the developmental exposure is combined with consumption of a high-calorie, high-carbohydrate, or high-fat diet later in life. Research on environmental chemical exposures and type 1 diabetes was very limited. This lack of research was considered a critical data gap. In this workshop review, we outline the major themes that emerged from the workshop and discuss activities that NIEHS/NTP is undertaking to address research recommendations. This review also serves as an introduction to an upcoming series of articles that review the literature regarding specific exposures and outcomes in more detail.
Screening of bacterial antagonists for biological control of Phytophthora blight of pepper

The aim of this study was to assess the potential of bacterial antagonists to control Phytophthora blight of pepper caused by P. capsici using different screening methods. Among a collection of fluorescent pseudomonas isolated from the rhizosphere of pepper, twelve isolates were initially selected based on dual culture assay on potato dextrose agar and corn meal agar. Further, these twelve isolates were screened for the reduction of disease severity caused by P. capsici using detached leaves and seedling assay. Most of the antagonists showed varying levels of antagonism against P. capsici in both detached leaves and seedlings assay. In addition, few isolates increased shoot and root length of pepper in seedling assays. Among them, isolate PS119 showing highest ability to reduce the disease severity in the in vitro seedling assay was found to be the most efficient antagonists against P. capsici in the in vivo biological control tests. These results indicate that the in vitro seedling assay can be used as a rapid and more accurate technique for the selection of promising biocontrol agents against P. capsici. (© 2005 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A human cell line selected for resistance to adenovirus infection has reduced levels of the virus receptor

To investigate determinants of host cell susceptibility to infection, cells partially resistant to infection were selected from the rare cells which remained adherent after infection of a culture of A549 cells with Ad2RAE, a mutant of adenovirus type 2 whose vertex capsomers lack an Arg-Gly-Asp (RGD) sequence which mediates binding of wild-type virus to integrins. Integrins promote the internalization of attached virions, whereas adsorption itself results from binding of the viral fibers to an unidentified cellular receptor. Following three rounds of selection, a persistently infected culture was established in which virus replication was detected in approximately 5% of the cells. Uninfected cells were readily cloned from the culture, indicating that at any particular time the majority of cells in the culture were uninfected. The resistance of one clone of uninfected cells to infection was correlated with a 10-fold reduction in the concentration of fiber receptors on these cells compared with the parental A549 cell line, indicating that efficiency of virus adsorption depends on the receptor concentration. Surprisingly, the rate at which host cells internalized RGD-negative virus also was strongly dependent on the fiber receptor concentration. While internalization of wild-type virus is promoted by the binding of integrins to the penton base RGD sequence, these results suggest that virus also can enter cells by an alternate pathway which requires binding of virions to multiple fiber receptors.