Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq.

Differences in gene expression were studied after Plum pox virus (PPV, sharka disease) infection in peach GF305 leaves with and without sharka symptoms using RNA-Seq. For each sample, more than 80% of 100-nucleotide paired-end (PE) Illumina reads were aligned on the peach reference genome. In the symptomatic sample, a significant proportion of reads were mapped to PPV reference genomes (1.04% compared with 0.00002% in non-symptomatic leaves), allowing for the ultra-deep assembly of the complete genome of the PPV isolate used (9775 nucleotides, missing only 11 nucleotides at the 5' genome end). In addition, significant alternative splicing events were detected in 359 genes and 12 990 single nucleotide polymorphisms (SNPs) were identified, 425 of which could be annotated. Gene ontology annotation revealed that the high-ranking mRNA target genes associated with the expression of sharka symptoms are mainly related to the response to biotic stimuli, to lipid and carbohydrate metabolism and to the negative regulation of catalytic activity. A greater number of differentially expressed genes were observed in the early asymptomatic phase of PPV infection in comparison with the symptomatic phase. These early infection events were associated with the induction of genes related to pathogen resistance, such as jasmonic acid, chitinases, cytokinin glucosyl transferases and Lys-M proteins. Once the virus had accumulated, the overexpression of Dicer protein 2a genes suggested a gene silencing plant response that was suppressed by the virus HCPro and P1 proteins. These results illustrate the dynamic nature of the peach-PPV interaction at the transcriptome level and confirm that sharka symptom expression is a complex process that can be understood on the basis of changes in plant gene expression.
Induced systemic resistance responses in perennial ryegrass against Magnaporthe oryzae elicited by semi-purified surfactin lipopeptides and live cells of Bacillus amyloliquefaciens.

The suppressive ability of several strains of cyclic lipopeptide-producing Bacillus rhizobacteria to grey leaf spot disease caused by Magnaporthe oryzae has been documented previously; however, the underlying mechanism(s) involved in the induced systemic resistance (ISR) activity in perennial ryegrass (Lolium perenne L.) remains unknown. Root-drench application of solid-phase extraction (SPE)-enriched surfactin and live cells of mutant Bacillus amyloliquefaciens strain FZB42-AK3 (produces surfactin, but not bacillomycin D and fengycin) significantly reduced disease incidence and severity on perennial ryegrass. The application of the treatments revealed a pronounced multilayered ISR defence response activation via timely and enhanced accumulation of hydrogen peroxide (H2O2), elevated cell wall/apoplastic peroxidase activity, and deposition of callose and phenolic/polyphenolic compounds underneath the fungal appressoria in naïve leaves, which was significantly more intense in treated plants than in mock-treated controls. Moreover, a hypersensitive response (HR)-type reaction and enhanced expression of LpPrx (Prx, peroxidase), LpOXO4 (OXO, oxalate oxidase), LpPAL (PAL, phenylalanine ammonia lyase), LpLOXa (LOX, lipoxygenase), LpTHb (putative defensin) and LpDEFa (DEFa, putative defensin) in perennial ryegrass were associated with SPE-enriched surfactin and live AK3 cell treatments, acting as a second layer of defence when pre-invasive defence responses failed. The results indicate that ISR activity following surfactin perception may sensitize H2O2 -mediated defence responses, thereby providing perennial ryegrass with enhanced protection against M. oryzae.
The c-di-GMP phosphodiesterase BifA is involved in the virulence of bacteria from the Pseudomonas syringae complex.

In a recent screen for novel virulence factors involved in the interaction between Pseudomonas savastanoi pv. savastanoi and the olive tree, a mutant was selected that contained a transposon insertion in a putative cyclic diguanylate (c-di-GMP) phosphodiesterase-encoding gene. This gene displayed high similarity to bifA of Pseudomonas aeruginosa and Pseudomonas putida. Here, we examined the role of BifA in free-living and virulence-related phenotypes of two bacterial plant pathogens in the Pseudomonas syringae complex, the tumour-inducing pathogen of woody hosts, P. savastanoi pv. savastanoi NCPPB 3335, and the pathogen of tomato and Arabidopsis, P. syringae pv. tomato DC3000. We showed that deletion of the bifA gene resulted in decreased swimming motility of both bacteria and inhibited swarming motility of DC3000. In contrast, overexpression of BifA in P. savastanoi pv. savastanoi had a positive impact on swimming motility and negatively affected biofilm formation. Deletion of bifA in NCPPB 3335 and DC3000 resulted in reduced fitness and virulence of the microbes in olive (NCPPB 3335) and tomato (DC3000) plants. In addition, real-time monitoring of olive plants infected with green fluorescent protein (GFP)-tagged P. savastanoi cells displayed an altered spatial distribution of mutant ΔbifA cells inside olive knots compared with the wild-type strain. All free-living phenotypes that were altered in both ΔbifA mutants, as well as the virulence of the NCPPB 3335 ΔbifA mutant in olive plants, were fully rescued by complementation with P. aeruginosa BifA, whose phosphodiesterase activity has been demonstrated. Thus, these results suggest that P. syringae and P. savastanoi BifA are also active phosphodiesterases. This first demonstration of the involvement of a putative phosphodiesterase in the virulence of the P. syringae complex provides confirmation of the role of c-di-GMP signalling in the virulence of this group of plant pathogens.
Development and evaluation of a loop-mediated isothermal amplification assay for rapid and simple detection of Campylobacter jejuni and Campylobacter coli.

We developed a loop-mediated isothermal amplification (LAMP) assay for the rapid and simple detection of Campylobacter jejuni and Campylobacter coli. The assay provides a specific LAMP product for each of these two species. The assay correctly identified 65 C. jejuni and 45 C. coli strains, but not 75 non-C. jejuni/coli strains. The sensitivity of the LAMP assay for C. jejuni and C. coli in spiked human stool specimens was 5.6 x 10(3) c.f. u. g(-1) (1.4 c.f.u. per test tube) and 4.8 x 10(3) c.f. u. g(-1) (1.2 c.f.u. per test tube), respectively. When 90 stool specimens from patients with diarrhoea were tested by LAMP and direct plating, the LAMP results showed 81.3 % sensitivity and 96.6 % specificity compared to isolation of C. jejuni and C. coli by direct plating. Further, the LAMP assay required less than 2 h for detection of C. jejuni and C. coli in stool specimens. This LAMP assay is a rapid and simple tool for the detection of C. jejuni and C. coli and will be useful in facilitating the early diagnosis of food poisoning incidents caused by these organisms.
Degradation of the benzoxazolinone class of phytoalexins is important for virulence of Fusarium pseudograminearum towards wheat.

Wheat, maize, rye and certain other agriculturally important species in the Poaceae family produce the benzoxazolinone class of phytoalexins on pest and pathogen attack. Benzoxazolinones can inhibit the growth of pathogens. However, certain fungi can actively detoxify these compounds. Despite this, a clear link between the ability to detoxify benzoxazolinones and pathogen virulence has not been shown. Here, through comparative genome analysis of several Fusarium species, we have identified a conserved genomic region around the FDB2 gene encoding an N-malonyltransferase enzyme known to be involved in benzoxazolinone degradation in the maize pathogen Fusarium verticillioides. Expression analyses demonstrated that a cluster of nine genes was responsive to exogenous benzoxazolinone in the important wheat pathogen Fusarium pseudograminearum. The analysis of independent F. pseudograminearum FDB2 knockouts and complementation of the knockout with FDB2 homologues from F. graminearum and F. verticillioides confirmed that the N-malonyltransferase enzyme encoded by this gene is central to the detoxification of benzoxazolinones, and that Fdb2 contributes quantitatively to virulence towards wheat in head blight inoculation assays. This contrasts with previous observations in F. verticillioides, where no effect of FDB2 mutations on pathogen virulence towards maize was observed. Overall, our results demonstrate that the detoxification of benzoxazolinones is a strategy adopted by wheat-infecting F. pseudograminearum to overcome host-derived chemical defences.
Impact of a Series of Drug Information Interventions on Pharmacy Staff

Purpose A performance-improvement service project consisting of a series of drug information interventions was developed for pharmacy staff to improve the quality and consistency of drug information provided by clinical pharmacists at a university medical center. The impact of interventions was primarily assessed by attendee satisfaction; a secondary measurement was the use of the Stanford Drug Information Center (the center). Methods Five interventions reviewing different electronic drug-information references were presented in September and October 2005. The 1hour presentations consisted of live demonstrations to pharmacy staff. A handout with step-by-step instructions on how to access and search each reference was created and distributed along with a follow-up evaluation. At the end of the interventions, all of the handouts were compiled into a permanent drug-information resource manual. In addition, data regarding inhouse pharmacist call volume to the center and the type of questions asked by inhouse pharmacists were collected for 6 months before and after the interventions. Results Evaluations of the interventions were positive and indicated that the learning objectives for each session had been met. The number of requests from inhouse pharmacists actually increased for the 6-month period after the interventions, as compared to the 6-month period prior to the interventions. Conclusion Feedback from pharmacy staff was positive, and the performance improvement goal was met through the intervention program, as well as the development of a permanent drug-information resource manual. However, further education of pharmacy staff did not translate into decreased requests (lower call volume) to the center.
Direct Measurements of Arterial Blood Pressure During Formal Weightlifting in Cardiac Patients

Intra-arterial pressures and electrocardiographic responses were monitored in eight cardiac patients during progressive weightlifting exercise. Repetitions of single-arm curls, and double- and single-leg presses were performed at 20, 40, 60, and 80 % of maximum. Within a weightlifting activity, the
Characterization of the Sclerotinia sclerotiorum cell wall proteome

Summary We used a proteomic analysis to identify cell wall proteins released from Sclerotinia sclerotiorum hyphal and sclerotial cell walls via a trifluoromethanesulfonic acid (TFMS) digestion. Cell walls from hyphae grown in Vogel's glucose medium (a synthetic medium lacking plant materials), from hyphae grown in potato dextrose broth and from sclerotia produced on potato dextrose agar were used in the analysis. Under the conditions used, TFMS digests the glycosidic linkages in the cell walls to release intact cell wall proteins. The analysis identified 24 glycosylphosphatidylinositol (GPI)‐anchored cell wall proteins and 30 non‐GPI‐anchored cell wall proteins. We found that the cell walls contained an array of cell wall biosynthetic enzymes similar to those found in the cell walls of other fungi. When comparing the proteins in hyphal cell walls grown in potato dextrose broth with those in hyphal cell walls grown in the absence of plant material, it was found that a core group of cell wall biosynthetic proteins and some proteins associated with pathogenicity (secreted cellulases, pectin lyases, glucosidases and proteases) were expressed in both types of hyphae. The hyphae grown in potato dextrose broth contained a number of additional proteins (laccases, oxalate decarboxylase, peroxidase, polysaccharide deacetylase and several proteins unique to Sclerotinia and Botrytis) that might facilitate growth on a plant host. A comparison of the proteins in the sclerotial cell wall with the proteins in the hyphal cell wall demonstrated that sclerotia formation is not marked by a major shift in the composition of cell wall protein. We found that the S. sclerotiorum cell walls contained 11 cell wall proteins that were encoded only in Sclerotinia and Botrytis genomes.
Viral and bacterial pathogens identification in children hospitalised for severe pneumonia and parapneumonic empyema

Pneumonia is caused by respiratory bacteria and/or viruses. Little is known if co-infections are an aggravating factor in hospitalised children with severe pneumonia. We studied the impact of respiratory pathogens on the severity of pneumonia. Between 2007 and 2009, 52 children hospitalised with a well-documented diagnosis of community-acquired pneumonia (CAP), with or without parapneumonic empyema (PPE), were enrolled in the study. The patients were classified into 2 groups: CAP + PPE (n = 28) and CAP (n = 24). The identification of respiratory viruses and bacteria in nasopharyngeal aspirates and pleural effusion samples were performed using conventional bacterial techniques and molecular assays. Using real-time multiplex PCR and antigen detection, Streptococcus pneumoniae was the main agent identified in 76% of the cases by molecular tests and BinaxNOW® in pleural fluid. A total of 8% of pleural fluid samples remained undiagnosed. In nasopharyngeal aspirates, rhinovirus, parainfluenza viruses, human metapneumovirus, and respiratory syncytial virus were detected in both CAP and CAP + PPE populations; however, the percentage of viral co-detection was significantly higher in nasopharyngeal aspirates from CAP + PPE patients (35%) compared with CAP patients (5%). In conclusion, viral co-detection was observed mainly in patients with more severe pneumonia. Molecular biology assays improved the pathogens detection in pneumonia and confirmed the S. pneumoniae detection by BinaxNOW® in pleural effusion samples. Interestingly, the main S. pneumoniae serotypes found in PPE are not the ones targeted by the heptavalent pneumococcal conjugate vaccine.
Sexual behaviour and knowledge regarding sexually transmitted infections among undergraduate students in Durban, South Africa

The objective of this cross-sectional study was to identify the sexual behavior and knowledge of sexually transmitted infections (STIs) amongst 752 undergraduate university students in South Africa, using self-administered questionnaires. More than half (>50%) reported presently being sexually active, the majority used contraceptives and especially used condoms. Almost a third of the sample, had multiple sexual partners, and more than a quarter of them reported to have sex under the influence of alcohol. Students’ knowledge regarding STIs was unsatisfactory, indicating the need to modify social and educational activities, to improve the understanding of the consequences of STIs and HIV and minimizing the associated risks.
The effect of Colocynthis citrullus (Cucurbitaceae) seeds on body weight and haematological parameters in albino rats

This work was designed to evaluate the effects of dried powdered seeds of Colocynthis citrullus (Cucurbitaceae) fed to albino rats on haematological parameters (PCV, Hb, RBC, WBC and Differentials) and weight changes using 12 rats. The rats were separated into 4 groups of 3 rats per group. Animals in group A were fed with the amended diet containing 25%(w/w) Colocynthis citrullus seed powder, group B 50%(w/w) and group C 75%(w/w) for a total of 13 weeks. Group D served as control and fed with standard diets (Feed Master Grower Mash) alone. Blood samples of the animals were collected, from which red blood cell count and white blood cell/differential counts were carried out. At the end of the experiment, it was observed that the faeces of rats fed with 75% formulated diets were loose and the animals showed weight decreases compared with those fed with standard diet. Statistical analysis using analysis of variance (ANOVA) single factor and Dunnett's multiple comparison tests on the haematological data obtained in rats fed with different concentrations of amended diets that contained Colocynthis citrullus powdered seeds showed that there was no significant difference (P
A comparison of the health status of European Roma and Australian Aborigines

Purpose – This paper aims to compare the health status of Roma in Europe and Aborigines in Australia, examining access to health care (both primary and long‐term), administrative and communication problems, environmental risks associated with location of residences, women's health, substance abuse and mental health.Design/methodology/approach – The paper discusses issues generated by cultural practices by both health care providers and the target groups.Findings – Both Roma and Australian Aborigines have significantly poorer health status than the majority of the societies they are embedded in, and are clearly amongst the most disadvantaged members of their respective societies. Nevertheless, affirmative action programs for Aboriginal people over the last 40 years have produced some significant changes, with Aboriginal doctors and nurses, and culturally appropriate service provision being found in many areas.Originality/value – Although there are considerable similarities between the health status and sit.
Cardio-ankle vascular index and ankle pulse wave velocity as a marker of arterial fibrosis in kidney failure treated by hemodialysis.

BACKGROUND Patients with kidney failure treated with hemodialysis have a high incidence of cardiovascular diseases caused by accelerated arteriosclerosis. However, accurate evaluation of the extent of arteriosclerosis is difficult. This study sought to compare the strength of predictions of arterial fibrosis by using a new parameter, the cardio-ankle vascular index (CAVI), versus pulse wave velocity (PWV) in patients with kidney failure treated with hemodialysis. STUDY DESIGN Diagnostic test study. SETTING & PARTICIPANTS 103 patients with kidney failure undergoing surgical construction of an arteriovenous access for hemodialysis therapy. INDEX TEST CAVI and PWV. REFERENCE TEST Arterial fibrosis, evaluated by using Masson trichrome stain on part of the brachial artery obtained during surgery, expressed as percentage of fibrosis of the layer of vascular smooth muscle cells. RESULTS Median percentage of arterial stiffness was 52.85%. Mean PWV and CAVI were 18.3 +/- 5.6 (SD) m/s and 9.9 +/- 2.6, respectively. Multivariate regression analysis showed that arterial fibrosis was significantly associated with older age (0.247%/y; 95% confidence interval, 0.013 to 0.482) and CAVI (6.117%/unit; 95% confidence interval, 4.764 to 4.740), but not with systolic blood pressure (0.039%/mm Hg; 95% confidence interval, -0.076 to 0.153) or PWV (-0.044%/m/s; 95% confidence interval, -0.646 to 0.558). The area under the receiver operating characteristic curve to predict greater than median percentage of arterial stiffness was 0.892 for CAVI and 0.779 for PWV (P = 0.006). LIMITATION It is unclear whether arterial fibrosis of the brachial artery evaluated by using CAVI is applicable for arteriosclerosis of other arterial districts, and clinical outcomes were not evaluated in this study. CONCLUSION CAVI reflects the histological arterial fibrosis of hemodialysis patients and is a useful clinical marker for evaluating arterial stiffness in these patients.
Rapid drug susceptibility testing for Mycobacterium tuberculosis in Thin layer agar media

There is a great need to determine the susceptibility of individual Mycobacterium tuberculosis strains as rapidly as possible because emergence of multidrug-resistant and extensively drug-resistant tuberculosis in developing countries. The study was conducted to evaluate the thin layer agar (TLA) media for rapid detection of resistance of M.tuberculosis to rifampicin (RMP) and isoniazid (INH) in clinical isolates and to determine the sensitivity and time to positivity compared to the proportion method. One hundred clinical isolates of M.tuberculosis were studied. For the TLA method, three compartment Petri plate containing 7H11 agar and 7H11 agar with RMP and INH. Results were compared to the proportion method for RMP and INH. The sensitivity for INH and RMP+INH was 85.7 % and 100%. The use of a TLA plate enables the rapid detection of resistance to the two prime anti-tuberculosis drugs RMP and INH in a median time of 9.60 days. TLA was a rapid method for the detection of resistance of M.tuberculosis in the two drugs studied. This faster method is simple to perform, providing an alternative method when more sophisticated techniques are not available in low-resource settings. DOI: http://dx.doi. org/10.3329/bjmm.v7i1. 19313 Bangladesh J Med Microbiol 2013; 07(01): 2-6
Insecticidal sugar baits for adult biting midges

The mixing of an insecticide with sugar solution creates an oral toxin or insecticidal sugar bait (ISB) useful for reducing adult insect populations. The ability of ISBs to kill the biting midge Culicoides sonorensis Wirth and Jones (Diptera: Ceratopogonidae), a vector of bluetongue virus, epizootic hemorrhagic disease and vesicular stomatitis viruses, was tested. The commercial insecticide formulations (percentage active ingredient) tested included bifenthrin, cyfluthrin, deltamethrin, permethrin, dinotefuran, imidacloprid, thiamethoxam and spinosad. Mortality rates were determined for various concentrations of commercial formulations (0.01, 0.05, 0.1, 1, 2 and 3%) and observed at 1, 4, 10 and 24 h post‐exposure to the ISB. In the first set of assays, laboratory‐reared midges were fed sugar ad libitum and then exposed to insecticide‐treated sugar solutions to measure mortality. The second assay assessed competitive feeding: midges were provided with a control sugar solution (10% sucrose) in one vial, and a sugar and insecticide solution in another. Pyrethroid treatments resulted in the greatest mortality in the first hour at the lowest concentrations and spinosad consumption resulted in the least mortality. Biting midges were not deterred from feeding on the 1% ISB solutions despite the presence of an insecticide‐free alternative source of sugar.
Successful Management of Facebook Addiction in Bangladesh: A Case Report

In the last decade, the use of social networking sites (SNSs) has grown exponentially all over the world. Boyd, Ellison & Nicole described Social networking sites (SNS) as “web-based service” that allow individuals to construct a public or semi-public profile within a bounded system articulate a list of other users with whom they share a connection and view and traverse their list of connections and those made by others within the system. Among the various social networking sites, Facebook is the most the popular one. Statistics provided by Facebook revealed that as of March 2014, there were 1.28 billion active users on the site per month, and at least 802 million of these users logged into Facebook every day. Approximately 81.2% of Facebook active users were outside the United States and Canada. Facebook is the most popular site in Bangladesh.