RNA-Seq optimization with eQTL gold standards.

BackgroundRNA-Sequencing (RNA-Seq) experiments have been optimized for library preparation, mapping, and gene expression estimation. These methods, however, have revealed weaknesses in the next stages of analysis of differential expression, with results sensitive to systematic sample stratification or, in more extreme cases, to outliers. Further, a method to assess normalization and adjustment measures imposed on the data is lacking.ResultsTo address these issues, we utilize previously published eQTLs as a novel gold standard at the center of a framework that integrates DNA genotypes and RNA-Seq data to optimize analysis and aid in the understanding of genetic variation and gene expression. After detecting sample contamination and sequencing outliers in RNA-Seq data, a set of previously published brain eQTLs was used to determine if sample outlier removal was appropriate. Improved replication of known eQTLs supported removal of these samples in downstream analyses. eQTL replication was further employed to assess normalization methods, covariate inclusion, and gene annotation. This method was validated in an independent RNA-Seq blood data set from the GTEx project and a tissue-appropriate set of eQTLs. eQTL replication in both data sets highlights the necessity of accounting for unknown covariates in RNA-Seq data analysis.ConclusionAs each RNA-Seq experiment is unique with its own experiment-specific limitations, we offer an easily-implementable method that uses the replication of known eQTLs to guide each step in one's data analysis pipeline. In the two data sets presented herein, we highlight not only the necessity of careful outlier detection but also the need to account for unknown covariates in RNA-Seq experiments

Studi Pengembangan Ekonomi Kerakyatan di Kawasan Wisata Jawa Timur melalui Penguatan Kelembagaan Sosial Ekonomi Masyarakat Lokal

East Java Province is one of the Indonesia region which high in poverty rate,even higher than national average. One of the effective model to alleviate povertyimplemented in developing countries is the model that able to integrate the poor intothe tourism sector (Ashley, 2000; Cattarinich, 2001). General aim of this study is tobuild a proper institution which able to enlarge an opportunities to the poor to be-come an integral part of the tourism sector. Specific aim of this first year study are:to describe the tourism economic structure in research area of Batu; to describe therelationship intensity between tourism industry and the local economy; to identifythe capacity of economic resources of the poor households in term of education level,skills, and capital accessibility; and to identify the social capital and the existenceand the nature of local institutions. Analysis unit of this study are : the tourism busi-ness unit, the tourists; and the poor household. This study found that : The tourismsector has significance role in the economic structure of Batu. The relationship be-tween tourism industry and local economy is high. Man power, local fruits and veg-etable are the main production input for the tourism businesses. Education level ofthe poor household members is not so low. However, for high level positions in mod-ern tourists industry was mostly filled by people from other area. The role of formaleconomic institutions such as banks and cooperative business unit in study are notsignificant for the poor. In order to gain additional capital, the poor mostly rely onthe traditional capital accumulation revolving system (Arisan). Beside Arisan, socialcapital of the poor is also accumulated trough social and religious gathering

Hubungan Perilaku Anak Remaja Mengenai Permainan Game Online dengan Keluhan Kelelahan Mata di Kelurahan Padang Bulan Medan Tahun 2013

Complaining of eyestrain is one of the health problems in Indonesia, particularly eyes health that the prevalence is still quite high on students. In some areas, it is still a lack of attention on eyes health problems especially on children in Indonesia. This is proven by the presence of school children's health inspection program which is more focused on mouth and teeth's health. Along with the rapid development of technology of internet, the online games makes the gamer or doer especially on students that spend their time in playing online games with no limited time. It is that spark children's eyes health be declining due to the onset of eyestrain complaining and it will affect the quality of human resources in the future. This analysis aims to connect the behavior of students with eyestrain complaining about online games in Padang Bulan area, Medan 2013. The designed of this analysis is cross-sectional. The population in this analysis were all young people by age of 10-18 years in Padang Bulan Area, Medan. Samples are 96 respondents were obtained by accidental sampling. Collecting data through interviews using questionnaires. An analysis of data was done with univariate and bivariate by using chi square test. The results showed that from the 96 respondents, 51 people (53.1%) were often complaints of eyestrain. The symptoms of eyestrain that often be perceived is that the eyes feeling sore and watery were 38 respondents (39.6%). The characteristics of respondents who experienced of eyestrain complaints are men (51%) by age 13-15 years (27.1%) with secondary education (27.1%). From the bivariate data analysis by using chi square test, it was gained a correlation of knowledge (p = 0.016) and the attitude of the respondents (p = 0.030) on the online games that complaints of eyestrain.Based on the results of the analysis, it was suggested that knowledge and attitudes are both to be maintained and further improved, while the poor Juvenile attitude in order to get more attention and the chance to play online games should be reduced in order that the complaints of eyestrain is not often perceived

Rancang Bangun Panel Auto Transfer Switch (ATS) Pada Sistem Hybrid PLN – Panel Surya Berbasis Timer Switch

Penelitian ini bertujuan untuk merancang dan mengimplementasikan panel Auto Transfer Switch (ATS) pada sistem hybrid PLN - panel surya berbasis timer switch. Penelitian ini mengumpulkan data arus listrik dan tegangan dari PLN dan panel surya saat digunakan dengan beban lampu 5, 10, 15, 20, dan 25 watt. Hasil penelitian menunjukkan bahwa arus listrik dari PLN dan panel surya bervariasi dengan beban lampu yang digunakan. Arus listrik dari PLN adalah 0,03 A, 0,06 A, 0,09 A, 0,12 A, dan 0,15 A, dengan tegangan terhitung sebesar 166 Volt. Sementara itu, arus listrik dari panel surya adalah 0,03 A, 0,06 A, 0,09 A, 0,13 A, dan 0,16 A, dengan tegangan terhitung sebesar 166 Volt, 153 Volt, dan 156 Volt. Selain itu, penelitian ini juga memperhitungkan jeda waktu perpindahan dari PLN ke panel surya, yang memiliki nilai sebesar 1,60 detik. Penghematan yang dapat dicapai dengan menggunakan sistem hybrid ini adalah sebesar Rp. 19.468. Dengan menggunakan panel ATS yang dirancang dan diimplementasikan dalam sistem hybrid ini, pengguna dapat secara otomatis beralih antara sumber daya PLN dan panel surya berdasarkan waktu yang telah ditentukan. Hal ini dapat membantu pengguna mengoptimalkan penggunaan energi dan menghemat biaya listrik

Cost estimation alongside a multi-regional, multi-country randomized trial of antenatal ultrasound in five low-and-middle-income countries

Background: Improving maternal health has been a primary goal of international health agencies for many years, with the aim of reducing maternal and child deaths and improving access to antenatal care (ANC) services, particularly in low-and-middle-income countries (LMICs). Health interventions with these aims have received more attention from a clinical effectiveness perspective than for cost impact and economic efficiency.Methods: We collected data on resource use and costs as part of a large, multi-country study assessing the use of routine antenatal screening ultrasound (US) with the aim of considering the implications for economic efficiency. We assessed typical antenatal outpatient and hospital-based (facility) care for pregnant women, in general, with selective complication-related data collection in women participating in a large maternal health registry and clinical trial in five LMICs. We estimated average costs from a facility/health system perspective for outpatient and inpatient services. We converted all country-level currency cost estimates to 2015 United States dollars (USD). We compared average costs across countries for ANC visits, deliveries, higher-risk pregnancies, and complications, and conducted sensitivity analyses.Results: Our study included sites in five countries representing different regions. Overall, the relative cost of individual ANC and delivery-related healthcare use was consistent among countries, generally corresponding to country-specific income levels. ANC outpatient visit cost estimates per patient among countries ranged from 15 to 30 USD, based on average counts for visits with and without US. Estimates for antenatal screening US visits were more costly than non-US visits. Costs associated with higher-risk pregnancies were influenced by rates of hospital delivery by cesarean section (mean per person delivery cost estimate range: 25-65 USD).Conclusions: Despite substantial differences among countries in infrastructures and health system capacity, there were similarities in resource allocation, delivery location, and country-level challenges. Overall, there was no clear suggestion that adding antenatal screening US would result in either major cost savings or major cost increases. However, antenatal screening US would have higher training and maintenance costs. Given the lack of clinical effectiveness evidence and greater resource constraints of LMICs, it is unlikely that introducing antenatal screening US would be economically efficient in these settings--on the demand side (i.e., patients) or supply side (i.e., healthcare providers).Trial registration: Trial number: NCT01990625 (First posted: November 21, 2013 on https://clinicaltrials.gov )

First-generation and continuing-generation college graduates\u27 application, acceptance, and matriculation to U.S. medical schools: A national cohort study

Many U.S. medical schools conduct holistic review of applicants to enhance the socioeconomic and experiential diversity of the physician workforce. The authors examined the role of first-generation college-graduate status on U.S. medical school application, acceptance, and matriculation, hypothesizing that first-generation (vs. continuing-generation) college graduates would be less likely to apply and gain acceptance to medical school.Secondary analysis of de-identified data from a retrospective national-cohort study was conducted for individuals who completed the 2001-2006 Association of American Medical Colleges (AAMC) Pre-Medical College Admission Test Questionnaire (PMQ) and the Medical College Admissions Test (MCAT). AAMC provided medical school application, acceptance, and matriculation data through 06/09/2013. Multivariable logistic regression models identified demographic, academic, and experiential variables independently associated with each outcome and differences between first-generation and continuing-generation students. Of 262,813 PMQ respondents, 211,216 (80.4%) MCAT examinees had complete data for analysis and 24.8% self-identified as first-generation college graduates. Of these, 142,847 (67.6%) applied to U.S. MD-degree-granting medical schools, of whom 86,486 (60.5%) were accepted, including 14,708 (17.0%) first-generation graduates; 84,844 (98.1%) acceptees matriculated. Adjusting for all variables, first-generation (vs. continuing-generation) college graduates were less likely to apply (odds ratio [aOR] 0.84; 95% confidence interval [CI], 0.82-0.86) and be accepted (aOR 0.86; 95% CI, 0.83-0.88) to medical school; accepted first-generation college graduates were as likely as their continuing-generation peers to matriculate. Students with (vs. without) paid work experience outside hospitals/labs/clinics were less likely to apply, be accepted, and matriculate into medical school. Increased efforts to mitigate structural socioeconomic vulnerabilities that may prevent first-generation college students from applying to medical school are needed. Expanded use of holistic review admissions practices may help decision makers value the strengths first-generation college graduates and other underrepresented applicants bring to medical educationand the physician workforce

Community empowerment and involvement of female sex workers in targeted sexual and reproductive health interventions in Africa: A systematic review

Background: Female sex workers (FSWs) experience high levels of sexual and reproductive health (SRH) morbidity, violence and discrimination. Successful SRH interventions for FSWs in India and elsewhere have long prioritised community mobilisation and structural interventions, yet little is known about similar approaches in African settings. We systematically reviewed community empowerment processes within FSW SRH projects in Africa, and assessed them using a framework developed by Ashodaya, an Indian sex worker organisation.Methods: In November 2012 we searched Medline and Web of Science for studies of FSW health services in Africa, and consulted experts and websites of international organisations. Titles and abstracts were screened to identify studies describing relevant services, using a broad definition of empowerment. Data were extracted on service-delivery models and degree of FSW involvement, and analysed with reference to a four-stage framework developed by Ashodaya. This conceptualises community empowerment as progressing from (1) initial engagement with the sex worker community, to (2) community involvement in targeted activities, to (3) ownership, and finally, (4) sustainability of action beyond the community.Results: Of 5413 articles screened, 129 were included, describing 42 projects. Targeted services in FSW 'hotspots' were generally isolated and limited in coverage and scope, mostly offering only free condoms and STI treatment. Many services were provided as part of research activities and offered via a clinic with associated community outreach. Empowerment processes were usually limited to peer-education (stage 2 of framework). Community mobilisation as an activity in its own right was rarely documented and while most projects successfully engaged communities, few progressed to involvement, community ownership or sustainability. Only a few interventions had evolved to facilitate collective action through formal democratic structures (stage 3). These reported improved sexual negotiating power and community solidarity, and positive behavioural and clinical outcomes. Sustainability of many projects was weakened by disunity within transient communities, variable commitment of programmers, low human resource capacity and general resource limitations.Conclusions: Most FSW SRH projects in Africa implemented participatory processes consistent with only the earliest stages of community empowerment, although isolated projects demonstrate proof of concept for successful empowerment interventions in African settings