Noise resistant generalized parametric validity index of clustering for gene expression data

This article has been made available through the Brunel Open Access Publishing Fund.Validity indices have been investigated for decades. However, since there is no study of noise-resistance performance of these indices in the literature, there is no guideline for determining the best clustering in noisy data sets, especially microarray data sets. In this paper, we propose a generalized parametric validity (GPV) index which employs two tunable parameters α and β to control the proportions of objects being considered to calculate the dissimilarities. The greatest advantage of the proposed GPV index is its noise-resistance ability, which results from the flexibility of tuning the parameters. Several rules are set to guide the selection of parameter values. To illustrate the noise-resistance performance of the proposed index, we evaluate the GPV index for assessing five clustering algorithms in two gene expression data simulation models with different noise levels and compare the ability of determining the number of clusters with eight existing indices. We also test the GPV in three groups of real gene expression data sets. The experimental results suggest that the proposed GPV index has superior noise-resistance ability and provides fairly accurate judgements

Orbits of Six Late-type Active-Chromosphere Binaries

We present spectroscopic orbits for the active stars HD 82159 (GS Leo), HD 89959, BD +39 2587 (a visual companion to HD 112733), HD 138157 (OX Ser), HD 143705, and HD 160934. This paper is a sequel to one published in this journal in 2006, with similar avowed intention, by Galvez et al.. They showed only graphs, and gave no data, and no orbital elements apart from the periods (only two of which were correct) and in some cases the eccentricities. Here we provide full information and reliable orbital elements for all the stars apart from HD 160934, which has not completed a cycle since it was first observed for radial velocity.Comment: 17 pages, 8 figures. Accepted for publication in Astrophysics & Space Scienc

Accountability in patenting of federally funded research

Bayh-Dole allows academic grantees to patent federally-funded research for purposes of promoting the commercialization of this research. To ensure commercialization goals are achieved, the Act requires grantees to report to funding agencies not only the existence of federally-funded patents but also utilization efforts they and their licensees/assignees are making. Although reporting is a cornerstone of accountability under Bayh-Dole, information about grantee compliance with reporting requirements is incomplete and dated. In fact, the last significant study of the question dates back to the late 1990s and analyzes only 633 patents. Since that time, concerns have emerged that federally-funded university patents are being asserted improperly against independent commercializers or even assigned to so-called “patent trolls.” This article provides fresh evidence indicating substantial under-reporting of the existence of federal funding in over 30,000 academic biomedical patents issued between 1980 to 2007. The article finds substantial under-reporting of federal funding even in the case of patents on FDA-approved drugs, which should presumably receive significant attention from universities. Grantees’ failure to report federal funding suggests similar, or even more significant, noncompliance with requirements to report utilization information. However, compliance with reporting requirements on utilization cannot be assessed because of secrecy associated with relevant government databases. Accordingly, the article makes a fresh argument that the Commerce Department, which has the requisite regulatory authority, work with funding agencies, to improve transparency. Greater transparency would not only motivate grantees to improve reporting but would also allow assessment of whether grantee patent management is actually achieving Bayh-Dole\u27s utilization goals

Dual-layer network representation exploiting information characterization

In this paper, a logical dual-layer representation approach is proposed to facilitate the analysis of directed and weighted complex networks. Unlike the single logical layer structure, which was widely used for the directed and weighted flow graph, the proposed approach replaces the single layer with a dual-layer structure, which introduces a provider layer and a requester layer. The new structure provides the characterization of the nodes by the information, which they provide to and they request from the network. Its features are explained and its implementation and visualization are also detailed. We also design two clustering methods with different strategies respectively, which provide the analysis from different points of view. The effectiveness of the proposed approach is demonstrated using a simplified example. By comparing the graph layout with the conventional directed graph, the new dual-layer representation reveals deeper insight into the complex networks and provides more opportunities for versatile clustering analysis.The National Institute for Health Research (NIHR) under its Programme Grants for Applied Research Programme (Grant Reference Number RP-PG-0310-1004)

Road Rage Menace: A Cross-sectional Study to Assess Driver Anger Level in Public Motor Vehicle Drivers in a City in Central India

Introduction: Road rage and aggressive driving is a prevalent condition in today’s society due to motorists’ frustrations during heavy traffic volumes. Objective: This study was done to assess the level of anger amongst the drivers of public transport vehicles in Indore, using Driving Anger Scale (DAS by Deffenbacher et. al.) and various factors affecting it. Material and Methods: A cross-sectional study was conducted among 135 drivers of Public transport vehicle drivers (Star bus, City-van and star cab drivers) in Indore to assess their anger level using Driving Anger Scale. The participants were required to record the amount of anger they would experience in response to each item in the scale (1=not at all angry, 2=a little angry, 3=some anger, 4=much anger, 5=very much angry). Results: The mean DAS score in Indore was found to be 3.013 and in the three organizations namely Star bus drivers, City van drivers and Star cab drivers was 2.92, 3.08 and 3.04 respectively. The DAS score of drivers with respect to the 6 sub-scales were: hostile gestures (Star bus -3.42,City van -3.67,Star cab -3.38), slow driving (Star bus -2.73,City van driv-2.78,Star cab-3.17), traffic obstructions (Star bus-2.85,City van -3.25,Star cab-3.18), discourtesy (Star bus -3.23,City van-3.33,Star cab -3.25)and police presence (Star bus -2.15,City van -1.99,Star cab -2.78), illegal driving (Star bus -3.04,City van -3.14,Star cab -2.89). The DAS scores of the drivers did not vary significantly with age group, experience, and educational qualification. Conclusion: Though DAS scores did not vary between the three groups of drivers, however average level anger for various given circumstances commonly found in the Indian traffic scenario was on the higher side

Yeast gene CMR1/YDL156W is consistently co-expressed with genes participating in DNA-metabolic processes in a variety of stringent clustering experiments

© 2013 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/3.0/, which permits unrestricted use, provided the original author and source are credited.The binarization of consensus partition matrices (Bi-CoPaM) method has, among its unique features, the ability to perform ensemble clustering over the same set of genes from multiple microarray datasets by using various clustering methods in order to generate tunable tight clusters. Therefore, we have used the Bi-CoPaM method to the most synchronized 500 cell-cycle-regulated yeast genes from different microarray datasets to produce four tight, specific and exclusive clusters of co-expressed genes. We found 19 genes formed the tightest of the four clusters and this included the gene CMR1/YDL156W, which was an uncharacterized gene at the time of our investigations. Two very recent proteomic and biochemical studies have independently revealed many facets of CMR1 protein, although the precise functions of the protein remain to be elucidated. Our computational results complement these biological results and add more evidence to their recent findings of CMR1 as potentially participating in many of the DNA-metabolism processes such as replication, repair and transcription. Interestingly, our results demonstrate the close co-expressions of CMR1 and the replication protein A (RPA), the cohesion complex and the DNA polymerases α, δ and ɛ, as well as suggest functional relationships between CMR1 and the respective proteins. In addition, the analysis provides further substantial evidence that the expression of the CMR1 gene could be regulated by the MBF complex. In summary, the application of a novel analytic technique in large biological datasets has provided supporting evidence for a gene of previously unknown function, further hypotheses to test, and a more general demonstration of the value of sophisticated methods to explore new large datasets now so readily generated in biological experiments.National Institute for Health Researc

On the eclipsing cataclysmic variable star HBHA 4705-03

We present observations and analysis of a new eclipsing binary HBHA 4705-03. Using decomposition of the light curve into accretion disk and hot spot components, we estimated photometrically the mass ratio of the studied system to be q=0.62 +-0.07. Other fundamental parameters was found with modeling. This approach gave: white dwarf mass M_1 = (0.8 +- 0.2) M_sun, secondary mass M_2=(0.497 +- 0.05) M_sun, orbital radius a=1.418 R_sun, orbital inclination i = (81.58 +- 0.5) deg, accretion disk radius r_d/a = 0.366 +- 0.002, and accretion rate dot{M} = (2.5 +- 2) * 10^{18}[g/s], (3*10^{-8} [M_sun/yr]). Power spectrum analysis revealed ambiguous low-period Quasi Periodic Oscillations centered at the frequencies f_{1}=0.00076 Hz, f_2=0.00048 Hz and f_3=0.00036 Hz. The B-V=0.04 [mag] color corresponds to a dwarf novae during an outburst. The examined light curves suggest that HBHA 4705-03 is a nova-like variable star.Comment: 7 figures and 2 tables, accepted for publication in Acta Astronomic

Insular Carcinoma of Thyroid Presenting as a Giant Skull Lesion: A Dilemma in Treatment.

Thyroid surgeons are becoming increasingly more aware of a histologically distinct subset of thyroid carcinoma whose classification falls between well-differentiated and anaplastic carcinomas with respect to both cell differentiation and clinical behavior. This subtype of tumors has been categorized as poorly differentiated or insular carcinoma, based on its characteristic cell groupings. Although the differentiation of insular carcinoma from other thyroid carcinomas has important prognostic and therapeutic significance, relatively little about insular carcinoma has been published in the otolaryngology literature. In this article, we discuss a case of insular carcinoma of thyroid presenting with concurrent distant metastasis to skull, lung, ribs, and inguinal region with review of the literature. We conclude that insular thyroid carcinoma warrants aggressive management with total thyroidectomy and excision of accessible giant lesion followed by radioactive iodine ablation of any remaining thyroid tissue

Critical Appraisal of Baby Friendly Hospital Initiatives among the beneficiaries of Indore Urban - A Comparative Study

Background: Majority of the women in M.P who breastfeed their babies throw away the colostrum before they begin actual feed. Only 14.9% females feed their babies with in 1/2 an hour (National Family Health Survey-3). In Indore 2 hospitals have been given designation of baby friendly hospital (BFH) namely M.Y. hospital (MYH) which is a tertiary care center, attached to Medical College and District hospital (DH). Objectives: (1) To assess the process of implementation of baby friendly hospital initiative programme. (2) Knowledge, Attitude, Practice regarding breast feeding amongst the beneficiaries. Methods: A comparative study was conducted between two BFH and two NBFH (Non Baby Friendly Hospitals) of Indore. The respondents were categorized into health care providers and beneficiaries. A pretested questionnaire was used to interview the respondents which was made taking into consideration the essential 10 Criteria of BFHI Programme. Results: 89% in BFH and 97% in NBFH were having positive attitude towards colostrum feeding. 81% postnatal mothers in BFH and 96% in NBFH were having knowledge about benefits of exclusive breast feeding. 21% postnatal mothers in BFH and 39% in NBFH initiated breast feeding within ½ an hour. 64 % of mothers in BFH and 62 % mothers in NBFH were practicing exclusive breast Feeding. Conclusion: The above findings show that although designated as BFH, the breast feeding practices remained poor as compared to NBFH. There is an utmost need to reinforce training and constant monitoring of health care providers regarding BFHI

Fear expression and return of fear following threat instruction with or without direct contingency experience

Prior research showed that mere instructions about the contingency between a conditioned stimulus (CS) and an unconditioned stimulus (US) can generate fear reactions to the CS. Little is known, however, about the extent to which actual CS US contingency experience adds anything beyond the effect of contingency instructions. Our results extend previous studies on this topic in that it included fear potentiated startle as an additional dependent variable and examined return of fear (ROF) following reinstatement. We observed that CS US pairings can enhance fear reactions beyond the effect of contingency instructions. Moreover, for all measures of fear, instructions elicited immediate fear reactions that could not be completely overridden by subsequent situational safety information. Finally, ROF following reinstatement for instructed CS+s was unaffected by actual experience. In summary, our results demonstrate the power of contingency instructions and reveal the additional impact of actual experience of CS US pairings