MPJ Express meets YARN:towards Java HPC on Hadoop systems

AbstractMany organizations—including academic, research, commercial institutions—have invested heavily in setting up High Performance Computing (HPC) facilities for running computational science applications. On the other hand, the Apache Hadoop software—after emerging in 2005— has become a popular, reliable, and scalable open-source framework for processing large-scale data (Big Data). Realizing the importance and significance of Big Data, an increasing number of organizations are investing in relatively cheaper Hadoop clusters for executing their mission critical data processing applications. An issue here is that system administrators at these sites might have to maintain two parallel facilities for running HPC and Hadoop computations. This, of course, is not ideal due to redundant maintenance work and poor economics. This paper attempts to bridge this gap by allowing HPC and Hadoop jobs to co-exist on a single hardware facility. We achieve this goal by exploiting YARN—Hadoop v2.0—that de-couples the computational and resource scheduling part of the Hadoop framework from HDFS. In this context, we have developed a YARN-based reference runtime system for the MPJ Express software that allows executing parallel MPI-like Java applications on Hadoop clusters. The main contribution of this paper is provide Big Data community access to MPI-like programming using MPJ Express. As an aside, this work allows parallel Java applications to perform computations on data stored in Hadoop Distributed File System (HDFS)

Kinetic Mechanism of DNA Translocation by the RSC Molecular Motor

ATP-dependent nucleosome repositioning by chromatin remodeling enzymes requires the translocation of these enzymes along the nucleosomal DNA. Using a fluorescence stopped-flow assay we monitored DNA translocation by a minimal RSC motor and through global analysis of these time courses we have determined that this motor has a macroscopic translocation rate of 2.9 bp/s with a step size of 1.24 bp. From the complementary quantitative analysis of the associated time courses of ATP consumption during DNA translocation we have determined that this motor has an efficiency of 3.0 ATP/bp, which is slightly less that the efficiency observed for several genetically related DNA helicases and which likely results from random pausing by the motor during translocation. Nevertheless, this motor is able to exert enough force during translocation to displace streptavidin from biotinylated DNA. Taken together these results are the necessary first step for quantifying both the role of DNA translocation in nucleosome repositioning by RSC and the efficiency at which RSC couples ATP binding and hydrolysis to nucleosome repositioning

Fine needle aspiration cytology in parotid lumps

Over a period of two years, Fine Needle Aspiration Cytology (FNAC) was performed on 33 patients presenting with a parotid lump. Five patients were excluded as they were treated medically after FNAC report. The FNAC results of 28 cases were compared with histopathological diagnoses of surgically resected specimens. There were 8 true positive, 17 true negative, 1 false positive and 2 false negative cases. Sensitivity was 80%, specificity 94.4% and diagnostic accuracy 89.3%. FNAC is a simple quick, accurate and virtually complications free investigative modality. It is also helpful adjunct to assess preoperatively the suitability and extent of the surgical treatment

Impact of Community Orgnizations (CO’S) on Rice Productivity in District Malakand Khyber Pukhtunkhwa, Pakistan

The research study was conducted in selected villages of district Malakand to study the impact of Community Organizations (CO’s) on rice productivity. A total of 70 respondents having different characteristics were interviewed. The main dependent variable was rice productivity which was studied in relation to other variables, inputs and in their application. Contact with various government departments and private sector by (CO’s) to the respondents. The results of the research study show that 7% of the farmers stated the problem of low productivity due to insect/pest attack, reasons were increase cost of the of the insecticides and pesticides. Majority of the respondents as 42.9 % purchased their seed for growing rice crop while the second dominant group was those with their own seed numbered about 32.9 %. Some of the respondents were those who used to grow seed of their own as well they also purchased some of the seed from market, were about 22.9 %. Majority of the sample respondents stated that their source of information regarding various inputs was (CO’s) following by Agri. Extension and fellow farmers. The satisfaction level of the sampled respondents was 81.4 % while 82.9 % sampled respondents stated that their production was increased due to the assistance and credit provided to them by (CO’s). The statistics of the paired T-test shows that the result was highly significant at the rate of 5% sample size and the production was increased by 10.39 % which show the effectiveness of (CO’s) activities in the area. It was concluded from the study that majority of respondents were literate, got proper technical assistance from (CO’s), agricultural extension departments and private companies. On the basis of findings it was recommended that all type of farmers should be involved in such activities and state should encourage the organizations to increase the productivity of various crops, the same techniques of assistance and credit should be adopted for other regions of the country. Keywords: Community Organizations, Rice productivity, variables, statics, technical assistance

Accounting Discretion, Loan Loss Provision in Financial Distress: Evidence from Commercial Banks

This study explores the association between earning management practices and financial distress in commercial banks. Earning management is measured through discretionary loan loss provisions and non-discretionary loan loss provisions. Modified Altman’s Z-score has been used as a proxy for financial distress. Panel regression with fixed and random effect has been employed for empirical analysis. The study finds a significant positive association between DLLP, NDLLP and financial distress in terms of the Altman Z-score. In the case of NDLLP, liquidity reduces the probability of financial distress. Whereas, a bank’s SIZE, LEVG and AQ enhance the likelihood of financial distress. The robustness tests were applied to find the association between NDLLP and FD using logistic regression to validate baseline estimates results of the random effect model. The findings of this study have implications for the policymakers, regulators and internal stakeholders to devise effective regulatory measures for well-informed investment decisions

Allosteric interactions of DNA and nucleotides with S. cerevisiae RSC

RSC, Remodel the Structure of Chromatin, is an essential chromatin remodeler of Saccharomyces cerevisiae that has been shown to have DNA translocase properties. We studied the DNA binding properties of a ‘trimeric minimal RSC’ (RSCt) of the RSC chromatin remodeling complex and the effect of nucleotides on this interaction using fluorescence anisotropy. RSCt binds to 20 bp fluorescein labeled double stranded DNA with a Kd of approximately 100 nM. The affinity of RSCt for DNA is reduced in the presence of AMP-PNP and ADP in a concentration dependent manner with the addition of AMP-PNP having the more pronounced effect. These differences in the magnitude at which the binding of ADP and AMP-PNP affect the affinity of DNA binding by RSCt suggests that the physical movement of the enzyme along DNA begins between the binding of ATP and its subsequent hydrolysis. Furthermore, the fact that the highest affinity for DNA binding by RSCt occurs in the absence of bound nucleotide offers a mechanistic explanation for the low apparent processivity of DNA translocation by the enzyme.This work was supported by National Institutes of Health Grant P20 RR017708 to C.J.F. and NIH GM60415 to B.R.C. Evan Rich was supported, in part, by an Undergraduate Research Award provided by the Kansas University Honors Program

Marketing of selected surplus fruits and vegetables of Dir district

ABSTRACT This study was undertaken in 2005 to enquire into the efficiency of marketing system of selected surplus vegetables and fruits of Dir district. The study reveals that the existing marketing system is, generally speaking, capable of handling the surplus selected products-onion, tomato, okra, citrus, persimmon, peas, walnuts,-in a normal year, and is efficiencies-wise nearly at par with the corresponding system in the province. It has evolved over a long period and is largely compatible with the characteristics of the project area's agricultural sector. The scope for improvement, at every stage in the marketing system is, however, large. The preharvest sale-especially of fruits, the heavy dependence on Beoparies, the heavy post-harvest losses, and occasional scarcity of transport at peak seasons and when especially where there is bumper harvest, the poor physical conditions of wholesale market centers etc, are the major problem areas. Price information of small farmer is not good, and the surplus products is mostly marketed in a far market centers through old connections with Arthi (middleman), wholesalers, etc, which may not necessarily fetch the best possible price. Farmer's net revenue from their selected surplus produce can be improved by 15-20 % by undertaking marketing system improvements through public-private sector cooperation. Farmers Association need to be formed through the existing village organizations in the project area, so as to bring about efficiency in the farming sector, embracing all aspects of production and marketing

Confronting our mistakes: A comprehensive evaluation of radiographic errors in digital chest radiography among adult population in a public sector hospital

Objective: To find out the various types of radiographic errors in digital chest radiography and their effect on image quality leading to image rejection. Material and Methods: This cross-sectional study was carried out in Radiology department of Pakistan Institute of Medical Sciences for a period of One month, September 2019. The study included 1560 digital Chest X-Rays, reaching the Picture Archive and Communication System (PACS), fulfilling the inclusion criteria. All these X-rays were analyzed by two radiology residents for the presence of radiographic errors in them. The various radiographic errors were then classified as: Positioning error, poor collimation, Artifacts, improper exposure, motion blur and mislabeling. The frequency of each radiographic error was measured along with their implication on image quality resulting in three major image categories: ACCEPT, JUST ACCEPTABLE and REJECT. The SPSS was adopted for inferential statistical analysis. Results: The study included 1013 (64.9%) male patients and 547 (35.1%) female patients. The mean age came out to be 36 +/- 15 years. Out of 1560 X-rays, 964 (61.8 %) had radiographic errors in them while 596 (38.2%) were completely devoid of radiographic errors. Positioning error (44.5 percent) was the most frequently encountered error followed by poor collimation (29.8%), artifacts (14.9%), Improper exposure (8%), motion blur (2.2%) and mislabeling (0.5%). The rejection rate came out to be 16.5 %. The major cause of image rejection was anatomy cutoff, especially the cut-off of cardio phrenic (CP) angle. Conclusion: Positioning errors represent the commonest cause of image rejection in chest radiography. The main identified pitfall was lack of radiographer’s education and training in performing an examination and indicates a need to improve their performance. Key words: Digital Radiography, Chest X ray, Radiographic error, Image reject &nbsp