LLukas22/scidocs huggingface dataset:
Comparison of next generation sequencing technologies for transcriptome characterization

We have developed a simulation approach to help determine the optimal mixture of sequencing methods for most complete and cost effective transcriptome sequencing. We compared simulation results for traditional capillary sequencing with "Next Generation" (NG) ultra high-throughput technologies. The simulation model was parameterized using mappings of 130,000 cDNA sequence reads to the Arabidopsis genome (NCBI Accession SRA008180.19). We also generated 454-GS20 sequences and de novo assemblies for the basal eudicot California poppy (Eschscholzia californica) and the magnoliid avocado (Persea americana) using a variety of methods for cDNA synthesis. The Arabidopsis reads tagged more than 15,000 genes, including new splice variants and extended UTR regions. Of the total 134,791 reads (13.8 MB), 119,518 (88.7%) mapped exactly to known exons, while 1,117 (0.8%) mapped to introns, 11,524 (8.6%) spanned annotated intron/exon boundaries, and 3,066 (2.3%) extended beyond the end of annotated UTRs. Sequence-based inference of relative gene expression levels correlated significantly with microarray data. As expected, NG sequencing of normalized libraries tagged more genes than non-normalized libraries, although non-normalized libraries yielded more full-length cDNA sequences. The Arabidopsis data were used to simulate additional rounds of NG and traditional EST sequencing, and various combinations of each. Our simulations suggest a combination of FLX and Solexa sequencing for optimal transcriptome coverage at modest cost. We have also developed ESTcalc http://fgp.huck.psu.edu/NG_Sims/ngsim.pl , an online webtool, which allows users to explore the results of this study by specifying individualized costs and sequencing characteristics. NG sequencing technologies are a highly flexible set of platforms that can be scaled to suit different project goals. In terms of sequence coverage alone, the NG sequencing is a dramatic advance over capillary-based sequencing, but NG sequencing also presents significant challenges in assembly and sequence accuracy due to short read lengths, method-specific sequencing errors, and the absence of physical clones. These problems may be overcome by hybrid sequencing strategies using a mixture of sequencing methodologies, by new assemblers, and by sequencing more deeply. Sequencing and microarray outcomes from multiple experiments suggest that our simulator will be useful for guiding NG transcriptome sequencing projects in a wide range of organisms.
Characterization of new miniSTR loci to aid analysis of degraded DNA.

A number of studies have demonstrated that successful analysis of degraded DNA specimens from mass disasters or forensic evidence improves with smaller sized polymerase chain reaction (PCR) products. We have scanned the literature for new STR loci, unlinked from the CODIS markers, which can generate amplicons less than 125 bp in size and would therefore be helpful in testing degraded DNA samples. New PCR primers were designed and tested for the STR loci D1S1677, D2S441, D4S2364, D10S1248, D14S1434, and D22S1045, arranged into two miniSTR triplexes. All loci show a moderate degree of polymorphism among 474 U.S. population samples tested and were reliable and sensitive to at least 100 pg of DNA template under controlled laboratory conditions and pristine DNA samples. The utility of these new loci were confirmed in comparing the success of the miniSTR assays for typing degraded bone samples while partial profiles were observed with the majority of the samples using a commercial STR kit.
Shared genetic contributions to pathological gambling and major depression in men.

CONTEXT
Although pathological gambling (PG) and major depression (MD) frequently co-occur, little is known regarding the relative contributions of environmental and genetic factors to the codevelopment of the disorders.


OBJECTIVES
To estimate environmental and genetic contributions to PG and MD as defined in DSM-III-R and the lifetime co-occurrence of PG and MD.


DESIGN
Survey data from the Vietnam Era Twin Registry were examined in biometric models.


SETTING
Telephone interview.


PARTICIPANTS
Of 10, 253 eligible participants, 7869 were successfully interviewed.


MAIN OUTCOME MEASURES
Estimated genetic, shared environmental, and unique environmental contributions to PG and MD and their lifetime co-occurrence in bivariate models.


RESULTS
Elevated odds ratios for MD were associated with those of PG (4.06; 95% confidence interval, 2.68-6.13), and the association remained significant following adjustment for sociodemographic and other psychiatric variables (odds ratio = 1.98; 95% confidence interval, 1.14-3.45). The best-fitting bivariate model indicated that 66% of the variance in PG and 41% of the variance in MD were owing to genetic factors, and 34% of the variance in PG and 59% of the variance in MD were owing to unique environmental factors. There was a substantial correlation between the genetic components of PG and MD (r(A) = 0.58), with 34% of the genetic variance for each disorder also contributing to that of the other. The best-fitting model estimated that 100% of the total overlap between PG and MD was genetic.


CONCLUSIONS
The correlation between PG and MD in middle-aged men appears to be largely influenced by overlapping genetic factors. Future research is needed to determine the extent to which these findings extend to other groups (eg, women), identify specific genes, and generate improved prevention and treatment strategies.
“Fat is your fault”. Gatekeepers to health, attributions of responsibility and the portrayal of gender in the Irish media representation of obesity

We investigated the representation of obesity in the Irish media by conducting an inductive thematic analysis on newspaper articles (n=346) published in 2005, 2007 and 2009 sampled from six major publications. The study analysed the media's construction of gender in discussions of obesity and associated attributions of blame. Three dominant themes are discussed: the caricatured portrayal of gender, women as caregivers for others, and emotive parent-blaming for childhood obesity. Men were portrayed as a homogenous group; unaware and unconcerned about weight and health issues. Dieting and engaging in preventative health behaviours were portrayed as activities exclusively within the female domain and women were depicted as responsible for encouraging men to be healthy. Parents, specifically mothers, attracted much blame for childhood obesity and media messages aimed to shame and disgrace parents of obese children through use of emotive and evocative language. This portrayal was broadly consistent across media types and served to reinforce traditional gender roles by positioning women as primarily responsible for health. This analysis offers the first qualitative investigation into the Irish media discourse on obesity and indicates a rather traditional take on gender roles in diet and nutrition.
Applicability assessment of ceramic microbeads coated with hydroxyapatite-binding silver/titanium dioxide ceramic composite earthplus™ to the eradication of Legionella in rainwater storage tanks for household use

Water environments appear to be the habitats of Legionella species. Legionellosis is considered as a preventable illness because bacterial reservoirs can be controlled and removed. Roof-harvested rainwater has attracted significant attention not only as a groundwater recharge but also as a potential alternative source of nonpotable water. We successfully developed ceramic microbeads coated with hydroxyapatite-binding silver/titanium dioxide ceramic composite earthplus™ using the thermal spraying method. The ceramic microbeads were demonstrated to have bactericidal activities against not only Legionella but also coliform and heterotrophic bacteria. Immersing the ceramic microbeads in household rainwater storage tanks was demonstrated to yield the favorable eradication of Legionella organisms. Not only rapid-acting but also long-lasting bactericidal activities of the ceramic microbead were exhibited against Legionella pneumophila. However, time-dependent attenuation of the bactericidal activities against Legionella were also noted in the sustainability appraisal experiment. Therefore, the problems to be overcome surely remain in constantly managing the Legionella-pollution by means of immersing the ceramic microbeads. The results of our investigation apparently indicate that the earthplus™-coated ceramic microbeads would become the favorable tool for Legionella measures in household rainwater storage tanks, which may become the natural reservoir for Legionella species. Our investigation would justify further research and data collection to obtain more reliable procedures to microbiologically regulate the Legionella in rainwater storage tanks.
Measurement of motor recovery after stroke. Outcome assessment and sample size requirements.

BACKGROUND AND PURPOSE
The purpose of this study was to analyze recovery of motor function in a cohort of patients presenting with an acute occlusion in the carotid distribution. Analysis of recovery patterns is important for estimating patient care needs, establishing therapeutic plans, and estimating sample sizes for clinical intervention trials.


METHODS
We prospectively measured the motor deficits of 104 stroke patients over a 6-month period to identify earliest measures that would predict subsequent motor recovery. Motor function was measured with the Fugl-Meyer Assessment. Fifty-four patients were randomly assigned to a training set for model development; 50 patients were assigned to a test set for model validation. In a second analysis, patients were stratified on basis of time and stroke severity. The sample size required to detect a 50% improvement in residual motor function was calculated for each level of impairment and at three points in time.


RESULTS
At baseline the initial Fugl-Meyer motor scores accounted for only half the variance in 6-month motor function (r2 = 0.53, p less than 0.001). After 5 days, both the 5-day motor and sensory scores explained 74% of the variance (p less than 0.001). After 30 days, the 30-day motor score explained 86% of the variance (p less than 0.001). Application of these best models to the test set confirmed the results obtained with the training set. Sample-size calculations revealed that as severity and time since stroke increased, sample sizes required to detect a 50% improvement in residual motor deficits decreased.


CONCLUSIONS
Most of the variability in motor recovery can be explained by 30 days after stroke. These findings have important implications for clinical practice and research.
How does online social networking enhance life satisfaction? The relationships among online supportive interaction, affect, perceived social support, sense of community, and life satisfaction

The purpose of this study is to examine whether supportive interactions on social networking sites mediate the influence of SNS use and the number of SNS friends on perceived social support, affect, sense of community, and life satisfaction. Employing momentary sampling, the current study also looked at the relationship between supportive interaction and immediate affect after the interaction over a period of 5 days. An analysis of 339 adult participants revealed a positive relationship between supportive interaction and positive affect after the interaction. A path model revealed positive associations among the number of SNS friends, supportive interactions, affect, perceived social support, sense of community, and life satisfaction. Implications for the research of online social networking and social support are discussed. 2013 Elsevier Ltd. All rights reserved.
A comparative assessment by optical coherence tomography of the performance of the first and second generation of the everolimus-eluting bioresorbable vascular scaffolds.

AIMS
The first generation of the everolimus-eluting bioresorbable vascular scaffold (BVS 1.0) showed an angiographic late loss higher than the metallic everolimus-eluting stent Xience V due to scaffold shrinkage. The new generation (BVS 1.1) presents a different design and manufacturing process than the BVS 1.0. This study sought to evaluate the differences in late shrinkage, neointimal response, and bioresorption process between these two scaffold generations using optical coherence tomography (OCT).


METHODS AND RESULTS
A total of 12 lesions treated with the BVS 1.0 and 12 selected lesions treated with the revised BVS 1.1 were imaged at baseline and 6-month follow-up with OCT. Late shrinkage and neointimal area (NIA) were derived from OCT area measurements. Neointimal thickness was measured in each strut. Strut appearance has been classified as previously described. Baseline clinical, angiographic, and OCT characteristics were mainly similar in the two groups. At 6 months, absolute and relative shrinkages were significantly larger for the BVS 1.0 than for the BVS 1.1 (0.98 vs. 0.07 mm² and 13.0 vs. 1.0%, respectively; P = 0.01). Neointimal area was significantly higher in the BVS 1.0 than in the BVS 1.1 (in-scaffold area obstruction of 23.6 vs. 12.3%; P < 0.01). Neointimal thickness was also larger in the BVS 1.0 than in the BVS 1.1 (166.0 vs. 76.4 µm; P < 0.01). Consequently, OCT, intravascular ultrasound, and angiographic luminal losses were higher with the BVS 1.0 than with the BVS 1.1. At 6 months, strut appearance was preserved in only 2.9% of the BVS 1.0 struts, but remained unchanged with the BVS 1.1 indicating different state of strut microstucture and/or their reflectivity.


CONCLUSION
The BVS 1.1 has less late shrinkage and less neointimal growth at 6-month follow-up compared with the BVS 1.0. A difference in polymer degradation leading to changes in microstructure and reflectivity is the most plausible explanation for this finding.
Multilevel Algorithms for Multi-Constraint Hypergraph Partitioning

Traditional hypergraph partitioning algorithms compute a bisection a graph such that the number of hyperedges that are cut by the partitioning is minimized and each partit ion has an equal number of vertices. The task of minimizing the cut can be considered as the objectiveand the requirement that the partitions will be of the same si z can be considered as the constraint. In this paper we extend the partitioning problem by incorpo rating an arbitrary number of balancing constraints. In our formulation, a vector of we ights is assigned to each vertex, and the goal is to produce a bisection such that the partitioning satisfies a balancing onstraint associated with each weight, while attempting t o minimize the cut. We present new multi-constraint hypergra ph partitioning algorithms that are based on the multilevel partitioning paradigm. We experimentally evaluate the eff ctiveness of our multi-constraint partitioners on a varie ty of synthetically generated problems. ∗This work was supported by NSF CCR-9972519, by Army Research Office contract DA/DAAG55-98-1-0441, by the DOE ASCI progra m, and by Army High Performance Computing Research Center contrac t number DAAH04-95-C-0008. Access to computing facilities was provided by AHPCRC, Minnesota Supercomputer Institute. Related paper s ar available via WWW at URL: http://www.cs.umn.edu/ ̃karypis
Two-phase flow in high-heat-flux micro-channel heat sink for refrigeration cooling applications: Part II—heat transfer characteristics

This paper is the second of a two-part study concerning two-phase flow and heat transfer characteristics of R134a in a micro-channel heat sink incorporated as an evaporator in a refrigeration cycle. Boiling heat transfer coefficients were measured by controlling heat flux (q00 = 15.9 93.8W/cm) and vapor quality (xe = 0.26 0.87) over a broad range of mass velocity. While prior studies point to either nucleate boiling or annular film evaporation (convective flow boiling) as dominant heat transfer mechanisms in small channels, the present study shows heat transfer is associated with different mechanisms for low, medium and high qualities. Nucleate boiling occurs only at low qualities (xe < 0.05) corresponding to very low heat fluxes, and high fluxes produce medium quality (0.05 < xe < 0.55) or high quality (xe > 0.55) flows dominated by annular film evaporation. Because of the large differences in heat transfer mechanism between the three quality regions, better predictions are possible by dividing the quality range into smaller ranges corresponding to these flow transitions. A new heat transfer coefficient correlation is recommended which shows excellent predictions for both R134a and water. 2004 Elsevier Ltd. All rights reserved.
Human health risk assessment of heavy metal accumulation through fish consumption, from Machilipatnam Coast, Andhra Pradesh, India

*Corresponding Author E mail: drpvkrishna@gmail.com Tel: (+91) 9985206281, Fax: +91.0863-2293378; 2293320 The progress of aquaculture, agriculture and industrial development activities has led to the increased pollutants emission into the coastal ecosystem. Heavy metals are one of the most common pollutants in the coastal area. This observation deals with the human health risk assessment of metal accumulation through the consumption of marine fish Liza macrolepis. The concentration of zinc (Zn), lead (Pb), nickel (Ni), cupper (Cu), mercury (Hg) and cadmium (Cd) were investigated in muscle and liver of the fish in this coast. The study explains the heavy metal concentration in the fish and leads to health risk assessment in the human beings. The average measured concentrations (mg/kg) in the edible organs of fish were follows: Zn concentration was 34.6 and 38.2 that of Pb was 14.2 and 15.5, that of Ni was 10.4 and 11.8; that of Cu was 33.2 and 34.2; that of Hg 2.1 and 2.9 that of Cd were 0.8 and 0.9 in the muscle and liver respectively. The average “Target Hazard Quotient” (THQ) value of Zn goes to 17.9; Pb was 7.3; Ni was 5.3; Cu was 17.2; Hg was 1.08; and Cd was 0.4 recorded in the study area in food fish L. macolepis.
Adaptive Region-Based Image Enhancement Method for Robust Face Recognition Under Variable Illumination Conditions

Variable illumination conditions, especially the side lighting effects in face images, form a main obstacle in face recognition systems. To deal with this problem, this paper presents a novel adaptive region-based image preprocessing scheme that enhances face images and facilitates the illumination invariant face recognition task. The proposed method first segments an image into different regions according to its different local illumination conditions, then both the contrast and the edges are enhanced regionally so as to alleviate the side lighting effect. Different from existing contrast enhancement methods, we apply the proposed adaptive region-based histogram equalization on the low-frequency coefficients to minimize illumination variations under different lighting conditions. Besides contrast enhancement, by observing that under poor illuminations the high-frequency features become more important in recognition, we propose enlarging the high-frequency coefficients to make face images more distinguishable. This procedure is called edge enhancement (EdgeE). The EdgeE is also region-based. Compared with existing image preprocessing methods, our method is shown to be more suitable for dealing with uneven illuminations in face images. Experimental results on the representative databases, the Yale B+Extended Yale B database and the Carnegie Mellon University-Pose, Illumination, and Expression database, show that the proposed method significantly improves the performance of face images with illumination variations. The proposed method does not require any modeling and model fitting steps and can be implemented easily. Moreover, it can be applied directly to any single image without using any lighting assumption, and any prior information on 3-D face geometry.
Proprioceptive Changes Impair Balance Control in Individuals with Chronic Obstructive Pulmonary Disease

INTRODUCTION
Balance deficits are identified as important risk factors for falling in individuals with chronic obstructive pulmonary disease (COPD). However, the specific use of proprioception, which is of primary importance during balance control, has not been studied in individuals with COPD. The objective was to determine the specific proprioceptive control strategy during postural balance in individuals with COPD and healthy controls, and to assess whether this was related to inspiratory muscle weakness.


METHODS
Center of pressure displacement was determined in 20 individuals with COPD and 20 age/gender-matched controls during upright stance on an unstable support surface without vision. Ankle and back muscle vibration were applied to evaluate the relative contribution of different proprioceptive signals used in postural control.


RESULTS
Individuals with COPD showed an increased anterior-posterior body sway during upright stance (p = 0.037). Compared to controls, individuals with COPD showed an increased posterior body sway during ankle muscle vibration (p = 0.047), decreased anterior body sway during back muscle vibration (p = 0.025), and increased posterior body sway during simultaneous ankle-muscle vibration (p = 0.002). Individuals with COPD with the weakest inspiratory muscles showed the greatest reliance on ankle muscle input when compared to the stronger individuals with COPD (p = 0.037).


CONCLUSIONS
Individuals with COPD, especially those with inspiratory muscle weakness, increased their reliance on ankle muscle proprioceptive signals and decreased their reliance on back muscle proprioceptive signals during balance control, resulting in a decreased postural stability compared to healthy controls. These proprioceptive changes may be due to an impaired postural contribution of the inspiratory muscles to trunk stability. Further research is required to determine whether interventions such as proprioceptive training and inspiratory muscle training improve postural balance and reduce the fall risk in individuals with COPD.
Availability of tanning beds on US college campuses.

IMPORTANCE
Indoor tanning is widespread among young adults in the United States despite evidence establishing it as a risk factor for skin cancer. The availability of tanning salons on or near college campuses has not been formally evaluated.


OBJECTIVE
To evaluate the availability of indoor tanning facilities on US college and university campuses (colleges) and in off-campus housing surrounding but not owned by the college.


DESIGN, SETTING, AND PARTICIPANTS
This observational study sampled the top 125 US colleges and universities listed in US News and World Report. Investigators searched websites of the colleges and nearby housing and contacted them by telephone inquiring about tanning services.


MAIN OUTCOMES AND MEASURES
Frequency of indoor tanning facilities on college campus and in off-campus housing facilities, as well as payment options for tanning.


RESULTS
Of the 125 colleges, 48.0% had indoor tanning facilities either on campus or in off-campus housing, and 14.4% of colleges allow campus cash cards to be used to pay for tanning. Indoor tanning was available on campus in 12.0% of colleges and in off-campus housing in 42.4% of colleges. Most off-campus housing facilities with indoor tanning (96%) provide it free to tenants. Midwestern colleges had the highest prevalence of indoor tanning on campus (26.9%), whereas Southern colleges had the highest prevalence of indoor tanning in off-campus housing facilities (67.7%). Presence of on-campus tanning facilities was significantly associated with enrollment (P = .01), region (P = .02), and presence of a school of public health (P = .01) but not private vs public status (P = .18) or presence of a tobacco policy (P = .16). Presence of tanning facilities in off-campus housing was significantly associated with region (P = .002) and private vs public status (P = .01) but not enrollment (P = .38), tobacco policy (P = .80), or presence of a school of public health (P = .69).


CONCLUSIONS AND RELEVANCE
Reducing the availability of indoor tanning on and around college campuses is an important public health target.