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

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

Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells.

Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with increased risk for colorectal cancer (CRC). A molecular understanding of the functional consequences of this genetic variation is complicated because most GWAS SNPs are located in non-coding regions. We used epigenomic information to identify H3K27Ac peaks in HCT116 colon cancer cells that harbor SNPs associated with an increased risk for CRC. Employing CRISPR/Cas9 nucleases, we deleted a CRC risk-associated H3K27Ac peak from HCT116 cells and observed large-scale changes in gene expression, resulting in decreased expression of many nearby genes. As a comparison, we showed that deletion of a robust H3K27Ac peak not associated with CRC had minimal effects on the transcriptome. Interestingly, although there is no H3K27Ac peak in HEK293 cells in the E7 region, deletion of this region in HEK293 cells decreased expression of several of the same genes that were downregulated in HCT116 cells, including the MYC oncogene. Accordingly, deletion of E7 causes changes in cell culture assays in HCT116 and HEK293 cells. In summary, we show that effects on the transcriptome upon deletion of a distal regulatory element cannot be predicted by the size or presence of an H3K27Ac peak

Large Differences in Small RNA Composition Between Human Biofluids.

Extracellular microRNAs (miRNAs) and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. We systematically compared small RNAs in 12 human biofluid types using RNA sequencing (RNA-seq). miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads in all biofluids, but the ratio of miRNA to tDR reads varied from 72 in plasma to 0.004 in bile. miRNA levels were highly correlated across all biofluids, but levels of some miRNAs differed markedly between biofluids. tDR populations differed extensively between biofluids. Y RNA fragments were seen in all biofluids and accounted for >10% of reads in blood plasma, serum, and cerebrospinal fluid (CSF). Reads mapping exclusively to Piwi-interacting RNAs (piRNAs) were very rare, except in seminal plasma. These results demonstrate extensive differences in small RNAs between human biofluids and provide a useful resource for investigating extracellular RNA biology and developing biomarkers

A System in the Wild: Deploying a Two Player Arm Rehabilitation System for Children With Cerebral Palsy in a School Environment

This paper outlines a system for arm rehabilitation for children with upper-limb hemiplegia resulting from cerebral palsy. Our research team designed a two-player, interactive (competitive or collaborative) computer play therapy system that provided powered assistance to children while they played specially designed games that promoted arm exercises. We designed the system for a school environment. To assess the feasibility of deploying the system in a school environment, the research team enlisted the help of teachers and staff in nine schools. Once the system was set up, it was used to deliver therapy without supervision from the research team. Ultimately, the system was found to be suitable for use in schools. However, the overriding need for schools to focus on academic activities meant that children could not use the system enough to achieve the amount of use desired for therapeutic benefit. In this paper, we identify the key challenges encountered during this study. For example, there was a marked reluctance to report system issues (which could have been fixed) that prevented children from using the system. We also discuss future implications of deploying similar studies with this type of system

New Spirometry Indices for Detecting Mild Airflow Obstruction.

The diagnosis of chronic obstructive pulmonary disease (COPD) relies on demonstration of airflow obstruction. Traditional spirometric indices miss a number of subjects with respiratory symptoms or structural lung disease on imaging. We hypothesized that utilizing all data points on the expiratory spirometry curves to assess their shape will improve detection of mild airflow obstruction and structural lung disease. We analyzed spirometry data of 8307 participants enrolled in the COPDGene study, and derived metrics of airflow obstruction based on the shape on the volume-time (Parameter D), and flow-volume curves (Transition Point and Transition Distance). We tested associations of these parameters with CT measures of lung disease, respiratory morbidity, and mortality using regression analyses. There were significant correlations between FEV1/FVC with Parameter D (r = -0.83; p < 0.001), Transition Point (r = 0.69; p < 0.001), and Transition Distance (r = 0.50; p < 0.001). All metrics had significant associations with emphysema, small airway disease, dyspnea, and respiratory-quality of life (p < 0.001). The highest quartile for Parameter D was independently associated with all-cause mortality (adjusted HR 3.22,95% CI 2.42-4.27; p < 0.001) but a substantial number of participants in the highest quartile were categorized as GOLD 0 and 1 by traditional criteria (1.8% and 33.7%). Parameter D identified an additional 9.5% of participants with mild or non-recognized disease as abnormal with greater burden of structural lung disease compared with controls. The data points on the flow-volume and volume-time curves can be used to derive indices of airflow obstruction that identify additional subjects with disease who are deemed to be normal by traditional criteria

Association of Ataxia Telangiectasia Mutated (ATM) Gene Mutation/Deletion with Rhabdomyosarcoma – retraction

<p>Abstract</p> <p>Background</p> <p>Rhabdomyosarcoma is a common malignancy in children. There are two major types of rhabdomyosarcomas, the embryonal and the alveolar, differing in cytogenetic and morphologic features. The alveolar type of rhabdomyosarcoma is frequently associated with chromosome translocation t(2, 13) and poor clinical prognosis. Pathogenesis of rhabdomyosarcoma remains obscure, and especially it occurs in the location where skeletal muscle is absent. We report here that there is a high frequency of association of rhabdomyosarcoma with ataxia telangiectasia mutated (ATM) gene mutation/deletion.</p> <p>Result</p> <p>Totally 17 cases of rhabdomyosarcoma specimens were studied by immunohistochemical or immunofluorescent staining with ATM antibody and revealed that 7 of the 17 cases were negative for ATM expression (41%). Further analyses of rhabdomyosarcoma cell lines with RT-PCR revealed that in Rh30 cells, an alveolar rhabdomyosarcoma cell line, there are three separate deletions/mutations of the ATM mRNA. Western blotting analysis of the Rh30 cellular extract with anti-ATM antibody showed that there is an aberrant form of ATM protein within the Rh30 cells that are smaller than normal control.</p> <p>Conclusion</p> <p>These results suggest a link of ATM gene deletion/mutation with rhabdomyosarcoma, and since ATM kinase is a crucial regulatory protein in DNA damage repair signaling pathway, and ATM deletion/mutation may contribute to pathogenesis of rhabdomyosarcoma.</p