Classification of Mammogramsusing Support Vector Machine

Dharmesh Singh,Mandeep Singh 보안공학연구지원센터 2016 International Journal of Signal Processing, Image Vol.9 No.5

In the present work, a computer aided classification system has been proposed for classification of mammogram images into normal, benign and cancer classes. The work has been carried out on thirty Digital Database for Screeningmammography(DDSM) cases consisting of 10 normal, 10 benign and 10 cancer images. The regions of interest (ROI) have been extracted from the right Medio Lateral Oblique (RMLO) part of the mammogram. We extracted 256×256 pixel size ROI from each case. Texture descriptors based on gray level co-occurrence method by varying the value of inter pixel distance ‘d’ from 1 to 8 have been used. The SVM classifier has been used for the classification task. The result of the study indicates that GLCM mean and range features computed at d=1 yield the maximum overall classification accuracy of 75% and 65 % respectively.

Similarities and Contrasts in the Archaeal Community of Two Japanese Mountains: Mt. Norikura Compared to Mt. Fuji

Singh, Dharmesh,Takahashi, Koichi,Park, Jungok,Adams, Jonathan M. Springer-Verlag 2016 Microbial ecology Vol.71 No.2

<P>The community ecology, abundance, and diversity patterns of soil archaea are poorly understood-despite the fact that they are a major branch of life that is ubiquitous and important in nitrogen cycling in terrestrial ecosystems. We set out to investigate the elevational patterns of archaeal ecology, and how these compare with other groups of organisms. Many studies of different groups of organisms (plants, birds, etc.) have shown a series of distinct communities with elevation, and often a diversity maximum in mid-elevations. We investigated the soil archaeal communities on Mt. Norikura, Japan, using 454 pyrosequencing of the 16S ribosomal RNA (rRNA) gene. There was a strong mid-elevation maximum in diversity, and a mid-elevation maximum in abundance of soil archaea 16S rRNA and amoA genes. These diversity and abundance maximums could not be correlated with any identifiable soil parameter, nor plant diversity. Discrete, predictable communities of archaea occurred at each elevational level, also not explicable in terms of pH or major nutrients. When we compared the archaeal community and diversity patterns with those found in an earlier study of Mt Fuji, both mountains showed mid-elevation maximums in diversity and abundance of archaea, possibly a result of some common environmental factor such as soil disturbance frequency. However, they showed distinct sets of archaeal communities at similar elevational sampling points. Presumably, the difference reflects their distinct geology (Norikura being andesitic, while Fuji is basaltic) and the resulting combinations of soil chemistry and environmental conditions, although no explanatory variable was found. Clearly, many soil archaea have strongly defined niches and will only occur in a narrow subset of the range of possible climate and soil conditions. The findings of a mid-elevation diversity maximum on Norikura provides a further instance of how widespread this unexplained pattern is in nature, in a wide variety of groups of organisms.</P>

A hump-backed trend in bacterial diversity with elevation on Mount Fuji, Japan.

Singh, Dharmesh,Takahashi, Koichi,Kim, Mincheol,Chun, Jongsik,Adams, Jonathan M Springer-Verlag 2012 Microbial ecology Vol.63 No.2

<P>Little is known of how bacterial diversity in soils varies with elevation. One previous study found a decline with elevation, whereas another found no trend. We chose Mount Fuji of Japan as a geologically and topographically simple mountain system. Samples were taken at elevational intervals, between the base of the mountain at 1,000 m and its summit at 3,700 m. Polymerase chain reaction-amplified soil DNA for the bacterial 16S gene targeting V1-V3 region was pyrosequenced using the 454 Roche machine, and taxonomically classified with reference to a bioinformatic database. There was a significant 'peak' in total bacterial diversity at around 2,500 m above the tree line with a decline towards the highest elevations around 3,700 m near the summit. Individual bacterial phyla show distinct trends-increase, decrease, or a mid-elevational 'bulge' in diversity. Bacterial diversity does not parallel woody plant or herbaceous plant diversity. We suggest that beyond the tree and vegetation line, the more extreme temperature fluctuations, stronger UV, lack of nutrients, and more frequent disturbance of the loose substrate of these slopes allows less competition and greater bacterial species diversity due to 'lottery' recruitment. However, at the highest elevations, the physiological challenges are so extreme that fewer bacterial species are capable of surviving.</P>

Bacterial Diversity in the Mountains of South-West China: Climate Dominates Over Soil Parameters

Dharmesh Singh,Lingling Shi,Jonathan Miles Adams 한국미생물학회 2013 The journal of microbiology Vol.51 No.4

Certain patterns in soil bacterial diversity and community composition have become evident from metagenomics studies on a range of scales, from various parts of the world. For example, soil pH has generally been seen as dominating variation in bacterial diversity, above all other soil and climate parameters. It is important however to test the generality of these relationships by studying previously unsampled areas. We compared soil bacterial diversity and community composition under a wide range of climatic and edaphic conditions in mountainous Yunnan Province, SW China. Soil samples were taken from a range of primary forest types and altitudes, reflecting the great variation of forest environments in this region. From each soil sample, DNA was extracted and pyrosequenced for bacterial 16S rRNA gene identification. In contrast to other recent studies from other parts of the world, pH was a weaker predictor of bacterial community composition and diversity than exchangeable Ca2+ concentration, and also the more poorly defined environmental parameter of elevation. Samples from within each forest type clustered strongly, showing the distinctive pattern of their microbial communities on a regional scale. It is clear that on a regional scale in a very heterogeneous environment, additional factors beyond pH can emerge as more important in determining bacterial diversity.

Clinical Profile of Children with Primary Headache at a Tertiary Care Center in North India: A Retrospective Study

Rahul Sinha,Dharmesh Soneji,Gautam Kamila,Sonali Singh,Ashish Upadhyay 대한소아신경학회 2023 대한소아신경학회지 Vol.31 No.3

Purpose: The present study investigated the clinical profile of children with primary headache at a tertiary care center in North India. Methods: A retrospective observational study was conducted between January 2021 and October 2022. In total, 100 children 5 to 18 years of age who attended the pediatric outpatient department or the emergency department with primary headache were included. Children with secondary causes of headache were excluded. Results: This study included 100 children (40 boys, 60 girls), and the female-to-male ratio was 1.5:1. The patients ranged in age from 5 to 18 years (mean±standard deviation, 10.1±2.8). Migraine headaches were most commonly reported (60%) followed by tension-type headache (28%) and others (12%). The throbbing type of pain was most common (43%), followed by the tightening type in 32%. The pain location was bilateral frontal in 47% of patients, followed by bitemporal in 20% and occipital in 17%. Most of the children (87%) had a headache duration of 2 to 4 hours. The common precipitating factors were skipped meals (25%), bright light (18%), lack of sleep (16%), and schoolwork (15%). A family history was present in around 62%. Around 70% of children required prophylactic medications (flunarizine and propranolol). Long screen time (2 to 4 hours/day) and a family history of headache were significantly associated with primary headache (P<0.05). Conclusion: The present study highlights that migraine is most common cause of primary headache in children, and every effort should be made for the early detection and management of headaches among children.

Distinctive phyllosphere bacterial communities in tropical trees.

Kim, Mincheol,Singh, Dharmesh,Lai-Hoe, Ang,Go, Rusea,Abdul Rahim, Raha,Ainuddin, A N,Chun, Jongsik,Adams, Jonathan M Springer-Verlag 2012 Microbial ecology Vol.63 No.3

<P>Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.</P>

Tropical Soil Bacterial Communities in Malaysia: pH Dominates in the Equatorial Tropics Too

Tripathi, Binu M.,Kim, Mincheol,Singh, Dharmesh,Lee-Cruz, Larisa,Lai-Hoe, Ang,Ainuddin, A. N.,Go, Rusea,Rahim, Raha Abdul,Husni, M. H. A.,Chun, Jongsik,Adams, Jonathan M. Springer-Verlag 2012 Microbial ecology Vol.64 No.2

Spatial Scaling Effects on Soil Bacterial Communities in Malaysian Tropical Forests

Tripathi, Binu M.,Lee-Cruz, Larisa,Kim, Mincheol,Singh, Dharmesh,Go, Rusea,Shukor, Noraini A. A.,Husni, M. H. A.,Chun, Jongsik,Adams, Jonathan M. Springer-Verlag 2014 Microbial ecology Vol.68 No.2