ParaKMeans: Implementation of a parallelized K-means algorithm suitable for general laboratory use

<p>Abstract</p> <p>Background</p> <p>During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data is to perform cluster analysis. While many clustering algorithms have been developed, they all suffer a significant decrease in computational performance as the size of the dataset being analyzed becomes very large. For example, clustering 10000 genes from an experiment containing 200 microarrays can be quite time consuming and challenging on a desktop PC. One solution to the scalability problem of clustering algorithms is to distribute or parallelize the algorithm across multiple computers.</p> <p>Results</p> <p>The software described in this paper is a high performance multithreaded application that implements a parallelized version of the K-means Clustering algorithm. Most parallel processing applications are not accessible to the general public and require specialized software libraries (e.g. MPI) and specialized hardware configurations. The parallel nature of the application comes from the use of a web service to perform the distance calculations and cluster assignments. Here we show our parallel implementation provides significant performance gains over a wide range of datasets using as little as seven nodes. The software was written in C# and was designed in a modular fashion to provide both deployment flexibility as well as flexibility in the user interface.</p> <p>Conclusion</p> <p>ParaKMeans was designed to provide the general scientific community with an easy and manageable client-server application that can be installed on a wide variety of Windows operating systems.</p

Estimation of uncertainty of effective area of a pneumatic pressure reference standard using Monte Carlo method

The current paper presents a comparative investigation of the experimental as well as simulated evaluation of effective area and the associated uncertainties, of a pneumatic pressure reference standard (NPLI-4) of CSIR-National Physical Laboratory, India, (NPLI). The experimental evaluation has been compared to the simulated estimation of the effective area obtained through Monte Carlo method (MCM). The Monte Carlo method has been applied by taking fixed number of trials (FMCM) and also by trials chosen adaptively (AMCM). The measurement uncertainties have been calculated using the conventional method, i.e., law of propagation of uncertainty (LPU) as well as MCM. Experimentally, the NPLI-4 has cross-floated against our newly established pneumatic primary pressure standard (NPLI-P10), which is a large diameter piston gauge. An excellent agreement in effective area and measurement uncertainty has been observed between these approaches

Perspectives of chalcopyrite-based CIGSe thin-film solar cell: a review

Solar photovoltaic (PV) is empowering, reliable, and ecofriendly technology for harvesting energy which can be assessed from the fact that PV panels with total electricity generation capacity of 505 GW have been installed by the end of 2018. Thin-film solar cells based on copper indium gallium selenide (CIGSe) are promising photovoltaic absorber material owing to an alternative to crystalline silicon (c-Si)-based solar cells because of the huge potential for low-cost solar electricity production with minimal usage of raw materials. The efficiency record of 23.4% was achieved recently in CIGSe solar cells, which was comparable to c-Si solar cells (27.6%). The manufacturing cost of $0.34/W is expected for 15% efficient CIGSe module. The present review article discusses the perspectives of CISe/CIGSe-based thin-film solar cells with the focus on absorber material. Different vacuum and non-vacuum techniques for fabricating these materials are discussed along with the operation of solar cells and their manufacturability. The working mechanism of CIGSe solar cells with the characteristic features of the open-circuit voltage and current density as well as the factors influencing the efficiency in different fabrication techniques are reviewed. Moreover, some strategies toward the improvement of solar cells performance contemplating modified deposition are reviewed. Furthermore, how these strategies can be executed in order to make it cost effective methods is also discussed in detail. Prevailing constrictions for the commercial maturity are deliberated, and future perspectives for improvement at lab as well as industrial scalabilities are outlined

Rekonstrukcija velike ventrolateralne kile u bivola s acelularnim dermalnim matriksom: metoda liječenja velike kile u životinja - prikaz slučaja.

A buffalo, 4 years of age presented with a history of a large swelling in the ventral abdominal region. The case was diagnosed as ventro-lateral hernia. Since the size of the hernial ring was about 15 cm in diameter, hernioplasty was performed using an acellular rabbit dermal matrix. The animal made an uneventful recovery.Bivol u dobi od četiri godine bio je primljen sa znakovima velike otekline u ventralnom abdominalnom području. Postavljena je dijagnoza ventrolateralne kile. Budući da je veličina hernijalnog prstena bila promjera oko 15 cm, provedena je hernioplastika primjenom kunićjeg acelularnog dermalnog matriksa. Životinja se oporavila bez komplikacija

Rekonstrukcija velike ventrolateralne kile u bivola s acelularnim dermalnim matriksom: metoda liječenja velike kile u životinja - prikaz slučaja.

A buffalo, 4 years of age presented with a history of a large swelling in the ventral abdominal region. The case was diagnosed as ventro-lateral hernia. Since the size of the hernial ring was about 15 cm in diameter, hernioplasty was performed using an acellular rabbit dermal matrix. The animal made an uneventful recovery.Bivol u dobi od četiri godine bio je primljen sa znakovima velike otekline u ventralnom abdominalnom području. Postavljena je dijagnoza ventrolateralne kile. Budući da je veličina hernijalnog prstena bila promjera oko 15 cm, provedena je hernioplastika primjenom kunićjeg acelularnog dermalnog matriksa. Životinja se oporavila bez komplikacija

Heterosis in white-grained grain mold resistant sorghum hybrids

Sorghum (Sorghum bicolor) is an important food and feed crop grown in more than 90 countries. Globally it is grown on over 40 million ha predominantly in tropical Africa and India for food and in temperate areas (Americas, Europe and Australia) as a feed crop (Reddy et al. 2011). India has largest area (7.5 million ha) under sorghum and 40% of this area is in rainy season while postrainy season sorghum accounts for the remaining area. Grain mold, a highly destructive disease of sorghum cultivated in the rainy season, is widely distributed in the semi-arid tropics of Africa, Americas and Asia including India (Stenhouse et al. 1997)..

Hydrogen Bond Symmetrization in Glycinium Oxalate under Pressure

We report here the evidences of hydrogen bond symmetrization in the simplest amino acid- carboxylic acid complex, glycinium oxalate, at moderate pressures of 8 GPa using in-situ infrared and Raman spectroscopic investigations combined with first-principles simulations. The protonation of the semioxalate units through dynamic proton movement results in infinite oxalate chains. At pressures above 12 GPa, the glycine units systematically reorient with pressure to form hydrogen bonded supramolecular assemblies held together by these chains

Understanding genetic control of biotic stress resistance in sorghum for applied breeding

Sorghum yield and production stabillity are constrained by various biotic stresses such as different insects and diseaes. The biotic stresses not only reduce the yield but results in poor grain quality thus hampering its marketability and utiilization leading to severe economic losses. Development of host plant resistance is one of the cheapest and sustainable methodss for managing the insect pests and diseases. Improvement in stress resistance will increase ecological fitness, reduce pesticide use, and facilitate creation of a sustainable production system with increased efficiency, profitability and to enhance grain quality/end use traits. An integrated synergistic system involving plant breeding and genomics research using advanced molecular tools could increase the efficiency and precision of crop improvement. This chapter deals with recent development with regard to sorghum adaptation to different production systems, major biotic stresses affecting sorghum production, understanding genetic control of biotic stress resistance, screening techniques developed, QTLs identified for various stresses and the program made in cultivar development using this knowledge