Registration of retinal images from Public Health by minimising an error between vessels using an affine model with radial distortions

In order to estimate a registration model of eye fundus images made of an affinity and two radial distortions, we introduce an estimation criterion based on an error between the vessels. In [1], we estimated this model by minimising the error between characteristics points. In this paper, the detected vessels are selected using the circle and ellipse equations of the overlap area boundaries deduced from our model. Our method successfully registers 96 % of the 271 pairs in a Public Health dataset acquired mostly with different cameras. This is better than our previous method [1] and better than three other state-of-the-art methods. On a publicly available dataset, ours still better register the images than the reference method

Exponential sums in prime fields for modular forms

The main objective of this article is to study the exponential sums associated to Fourier coefficients of modular forms supported at numbers having a fixed set of prime factors. This is achieved by establishing an improvement on Shparlinski's bound for exponential sums attached to certain recurrence sequences over finite fields

Antitubercular specific activity of ibuprofen and the other 2-arylpropanoic acids using the HT-SPOTi whole-cell phenotypic assay

Objectives: Lead antituberculosis (anti-TB) molecules with novel mechanisms of action are urgently required to fuel the anti-TB drug discovery pipeline. The aim of this study was to validate the use of the high-throughput spot culture growth inhibition (HT-SPOTi) assay for screening libraries of compounds against Mycobacterium tuberculosis and to study the inhibitory effect of ibuprofen (IBP) and the other 2-arylpropanoic acids on the growth inhibition of M tuberculosis and other mycobacterial species. Methods: The HT-SPOTi method was validated not only with known drugs but also with a library of 47 confirmed anti-TB active compounds published in the ChEMBL database. Three over-the-counter non-steroidal anti-inflammatory drugs were also included in the screening. The 2-arylpropanoic acids, including IBP, were comprehensively evaluated against phenotypically and physiologically different strains of mycobacteria, and their cytotoxicity was determined against murine RAW264.7 macrophages. Furthermore, a comparative bioinformatic analysis was employed to propose a potential mycobacterial target. Results: IBP showed antitubercular properties while carprofen was the most potent among the 2-arylpropanoic class. A 3,5-dinitro-IBP derivative was found to be more potent than IBP but equally selective. Other synthetic derivatives of IBP were less active, and the free carboxylic acid of IBP seems to be essential for its anti-TB activity. IBP, carprofen and the 3,5-dinitro-IBP derivative exhibited activity against multidrug-resistant isolates and stationary phase bacilli. On the basis of the human targets of the 2-arylpropanoic analgesics, the protein initiation factor infB (Rv2839c) of M tuberculosis was proposed as a potential molecular target. Conclusions: The HT-SPOTi method can be employed reliably and reproducibly to screen the antimicrobial potency of different compounds. IBP demonstrated specific antitubercular activity, while carprofen was the most selective agent among the 2-arylpropanoic class. Activity against stationary phase bacilli and multidrug-resistant isolates permits us to speculate a novel mechanism of antimycobacterial action. Further medicinal chemistry and target elucidation studies could potentially lead to new therapies against TB

Development of a rapid, reliable and quantitative method: "SPOTi" for testing antifungal efficacy

A reference method for the antimicrobial susceptibility testing of common fungal pathogens such as dermatophytes, is currently lacking. In this study, we report the successful adaptation of solid agar-based spot culture growth inhibition assay (SPOTi) for dermatophytes, currently being used as a gold-standard in the anti-tubercular drug discovery field. The fungal-SPOTi assay correlated with the disc-diffusion method, and is validated using mycelial plugs. We propose the fungal-SPOTi as a high-throughput alternative to the disc-diffusion and broth micro-dilution anti-fungal assays to screen novel anti-fungals

Transcription activator like effector (TALE)-directed piggyBac transposition in human cells.

Insertional therapies have shown great potential for combating genetic disease and safer methods would undoubtedly broaden the variety of possible illness that can be treated. A major challenge that remains is reducing the risk of insertional mutagenesis due to random insertion by both viral and non-viral vectors. Targetable nucleases are capable of inducing double-stranded breaks to enhance homologous recombination for the introduction of transgenes at specific sequences. However, off-target DNA cleavages at unknown sites can lead to mutations that are difficult to detect. Alternatively, the piggyBac transposase is able perform all of the steps required for integration; therefore, cells confirmed to contain a single copy of a targeted transposon, for which its location is known, are likely to be devoid of aberrant genomic modifications. We aimed to retarget transposon insertions by comparing a series of novel hyperactive piggyBac constructs tethered to a custom transcription activator like effector DNA-binding domain designed to bind the first intron of the human CCR5 gene. Multiple targeting strategies were evaluated using combinations of both plasmid-DNA and transposase-protein relocalization to the target sequence. We demonstrated user-defined directed transposition to the CCR5 genomic safe harbor and isolated single-copy clones harboring targeted integrations

Association analysis in Kabuli chickpea (Cicer arietinum L.)

In the millennium of an ever-growing population, feeding the millions ample amount of food with necessarily required nutrition has become a tough challenge. To cater protein requirement, plant-based protein, especially pulses, have always been a better option. Among the pulses, chickpea is one of the choicest crops being extensively cultivated throughout the world. However, the production and productivity of crops are not sufficient to meet consumer demand throughout the world. To aid in the selection process of chickpea breeding, the present study was performed to evaluate fifty-one kabuli chickpea (Cicer arietinum L.) germplasm lines along with four checks for the degree and direction of association of twelve quantitative characters on yield in fifty five kabuli chickpea genotypes. Considerable positive correlation was found between the weight of 100 seeds and the height of the chickpea plant, but the number of pods per plant and seed volume per weight were observed to be in negative association with the former trait. The primary branch depicted a substantial amount of positive correlation with harvest index, seed yield per individual plant, pods produced per plant. Secondly, the current study on association analysis also unveiled positive and highly significant correlations of the number of primary branches, height at the first pod set, pods/plant, and weight of 100 seeds on seed yield, suggesting their further use as selection criteria  in the  process of crop improvement

Mutation studies of the gene encoding YuiC, a stationary phase survival protein in Bacillus subtilis

Aims: YuiC is a stationary phase survival (Sps) protein from the Firmicute Bacillus subtilis that possesses muralytic activity to cleave bacterial cell-wall peptidoglycan. It has a small lytic transglycosylase (MltA) fold analogous to the resuscitation promoting factors (Rpfs) of Actinobacteria which have a hybrid of a mini lysozyme and soluble lytic transglycosylase (Slt35/70) fold. The present study aimed at identifying key residues of YuiC/Sps that are catalytically active and studying the effect of B. subtilis cell growth upon sps/yuiC deletion. Methodology and results: Four forms of mutated yuiC were created through Site-directed, Ligase-Independent Mutagenesis Polymerase Chain Reaction (SLIM PCR) that include the substitutions of D129A, D151A, D162A and K102A. These individual mutated yuiC genes were cloned and expressed in the Escherichia coli BL21 (DE3) expression system and subsequently purified to homogeneity using affinity, cation exchange and size exclusion chromatography. The D129A variant was shown to be insoluble, indicating its role in maintaining the right protein folding of YuiC. The remaining three variants resulted in soluble proteins but were inactive on zymograms indicating that they may be responsible for catalysis. B. subtilis cells harbouring individual sps genes (yuiC, yabE, yocH and yorM) knocked out showed stationary phase defects and altered colony morphologies compared to the wild type. Conclusion, significance and impact of study: This study has identified the key residues involved in catalysis of YuiC, which are the D151, D162 and K102. These are conserved in Sps domains. The catalytic mechanism of YuiC is similar to the mechanism reported for Neisseria gonorrhoeae MltA. sps/yuiC knock outs have implied that each sps/yuiC has a significant role on B. subtilis late growth stage. The B. subtilis YuiC/Sps model has given an insight into Sps functions in the final growth stage of the Firmicutes, which members include etiologic agents of anthrax, botulism and listeriosis. Inhibition of Sps protein may inactivate pathogen replication and facilitate entrance into a non-contagious dormant sporulation stage

Clinical and bacteriological correlates of whole blood interferon gamma (IFN-γ) in newly detected cases of pulmonary TB

AbstractObjectiveTo determine the relationship of the capacity to produce interferon gamma (IFN-γ) in whole blood, bacteriological, hematological, radiographic and clinical presentations in new, HIV seronegative cases of pulmonary tuberculosis (TB).Methods80 cases and 50 control subjects aged 15 years onwards, representative of Kasturba Hospital and Nursing schools of Wardha district of Maharashtra state in India were examined for their health condition with standard methodology.ResultsAmong these TB patients, 73.8% were Quantiferon-TB gold (QFT) positive with IFN-γ concentration as 0.35 IU or more and there was none in healthy controls. The mean IFN-γ concentrations varied between 9.58 IU (50-59 yrs) and 2.58 IU (⩾60 yrs), showing no trend. The differences in positivity and mean IFN-γconcentrations were statistically insignificant. Both the QFT positivity and IFN-γconcentrations were higher in normal lymphocyte percent as compared to below and above normal, but differences were not statistically significant.ConclusionsThe IFN-γconcentrations are not correlated with any of the predictors of disease severity studied, the levels are significantly higher in observation group as compared to healthy group

Dissecting the genetic architecture of coronary artery disease by genome engineering

One of the greatest challenges facing biomedical research since the sequencing of the human genome has been to understand the role of genetic variation in human disease. Many genetic variants have been associated with common diseases. However, determining the functional consequences of these variants has been hard. Several variants are often inherited together in tightly linked blocks, making it difficult to determine the causative variant. People have millions of other genetic differences, making it difficult to correlate cellular phenotypes with a particular variant. Different gene sets are expressed in different cells, but it is difficult to extract disease-relevant cells from large numbers of patients. We describe a method with the potential to revolutionize the functional analysis of genetic variation, using custom nucleases to genetically modify individual variants in induced pluripotent stem cells. This process would provide unprecedented analytical power, present the first general method to determine if a variant is causative, and analyze function disease-relevant cell types. We will focus on variants at the 9p21 region of the genome that have been associated with coronary artery disease (CAD). The methods should provide a new way to unlock the wealth of data from genome-wide association studies, and to probe the genetic architecture of common diseases. We will describe our improved methods for inexpensive and rapid construction of highly active zinc finger and TALE nucleases to examine the functional role of polymorphisms at the 9p21 CAD risk locus