Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

PROFIL WISATAWAN MUSEUM RADYA PUSTAKA SURAKARTA

Anggit Margaret, C9407031 2011. Profil Wisatawan Museum Radya Pustaka Surakarta. Program Studi Diploma III Usaha Perjalanan Wisata Fakultas Sastra Dan Seni Rupa Universitas Sebelas Maret Surakarta. Penelitian tugas akhir ini mengkaji tentang Profil Wisatawan di Museum Radya Pustaka Surakarta. Tujuan dari penelitian ini adalah untuk mengetahui dari daerah mana saja wisatawan yang berkunjung ke Museum Radya Pustaka, bagaimana ciri-ciri wisatawan yang berkunjung ke Museum Radya Pustaka serta harapan-harapan yang diinginkan wisatawan terhadap Museum Radya Pustaka. Penelitian dilakukan dengan metode kualitatif. Pengumpulan data dilakukan melalui wawancara dengan narasumber wisatawan yang berkujung di Museum Radya Pustaka Surakarta tempat penulis melakukan penelitian, serta studi pustaka dan studi dokumen guna menambah sumber data. Hasil penelitian menunjukkan bahwa (1) Sebagian besar wisatawan yang datang berasal dari Semarang sebesar 32%. (2) Mayoritas wisatawan yang berkunjung ke Museum Radya Pustaka berusia antara 17-25 tahun dan kebanyakan dari mereka adalah pelajar atau mahasiswa dengan prosentase 52%. (3) Sebagian besar wisatawan yang datang ke Museum Radya Pustaka adalah bertujuan untuk melakukan penelitian yaitu sebesar 34%. (4) Harapan wisatawan yang berkunjung terhadap kelangsungan Museum Radya Pustaka sebagian besar adalah agar ditingkatkan lagi pengelolaan dan keamanan museum, agar kejadian hilangnya benda-benda koleksi museum tidak terulang lagi dikemudian hari. Kesimpulan dari hasil penelitian ini bahwa wisatawan yang berkujung ke Museum Radya Pustaka Surakarta mayoritas berasal dari Semarang, mayoritas berusia 17-25 tahun dan kebanyakan dari mereka adalah berprofesi sebagai pelajar dan mahasiswa. Kebanyakan wisatawan yang datang bertujuan untuk melakukan penelitian, serta harapan wisatawan terhadap Museum Radya Pustaka adalah supaya lebih ditingkatkan lagi pengelolaan dan keamanan museum

Hypothalamic-pituitary-adrenal axis activity in obese men with and without sleep apnea: Effects of continuous positive airway pressure therapy

Context: Previous studies on the association between the hypothalamic-pituitary-adrenal axis activity and sleep apnea (SA) and obesity are inconsistent and/or limited. Objective: In this study, we evaluated the activity of the hypothalamic-pituitary-adrenal axis in nonpsychologically distressed obese subjects with and without SA and examined the impact of continuous positive airway pressure (CPAP) in SA patients. Design and Participants: In study I, four-night sleep laboratory recordings and serial 24-h plasma measures of cortisol were obtained in 45 obese men with and without apnea and nonobese controls. Sleep apneic patients were reassessed after 3 months of CPAP use. In study II, 38 obese men with and without sleep apnea and nonobese controls were challenged with ovine CRH administration after four nights in the sleep laboratory. Results: The sleep patterns were similar between obese and nonobese controls. Twenty-four-hour plasma cortisol levels were highest in nonobese controls, intermediate in obese apneic patients, and lowest in obese controls (8.8 ± 0.4 vs. 8.1 ± 0.3 vs. 7.5 ± 0.3 μg/dl, P < 0.05). CPAP tended to reduce cortisol levels in the apneic patients (difference -0.7 ± .4 μg/dl, P = 0.1). CRH administration resulted in a higher ACTH response in both obese groups, compared with nonobese controls; the three groups were not different in cortisol response. Conclusions: Nonpsychologically distressed, normally sleeping, obese men had low cortisol secretion. The cortisol secretion was slightly activated by SA and returned to low by CPAP use. The low cortisol secretion in obesity through its inferred hyposecretion of hypothalamic CRH might predispose the obese to sleep apnea. Copyright © 2007 by The Endocrine Society

Activated memory T helper cells in bronchoalveolar lavage fluid from patients with atopic asthma:relation to asthma symptoms, lung function, and bronchial responsiveness

BACKGROUND: Bronchial mucosal inflammation and epithelial damage are characteristic features of asthma. Activation of T helper lymphocytes may contribute to this process by mechanisms including the release of cytokines promoting eosinophil infiltration and activation. METHODS: Bronchial washings and bronchoalveolar lavage fluid were obtained from 29 atopic asthmatic patients (19 with current symptoms and 10 symptom free) and 13 normal volunteers. Flow cytometry was used to assess T cell phenotype and activation status in bronchoalveolar lavage fluid and peripheral blood, and differential cell counts were made on bronchial washings and bronchoalveolar lavage fluid. Findings were related to severity of disease as reflected by symptom scores, baseline lung function, and airway responsiveness. RESULTS: CD4 T lymphocytes in bronchoalveolar lavage fluid and blood from asthmatic patients were activated by comparison with controls (CD4 CD25, median 16.8% v 8.7% for bronchoalveolar lavage fluid, and 15.3% v 8.7% in blood). Bronchoalveolar lavage fluid CD4 T cells from both asthmatic patients and controls were of memory phenotype (95.8% and 96.8% CD45RO and 1.7% and 0.4% CD45RA respectively), whereas both CD45RO and CD45RA T cells were present in blood. Patients with asthma and current symptoms showed increased bronchoalveolar T cell activation compared with patients without symptoms (CD4 CD25 18.7% v 12.3%). Within the asthmatic group there was a significant association between CD4 CD25 lymphocytes and asthma symptom scores (rs = 0.75), airway methacholine responsiveness (log PC20, rs = -0.43) and baseline FEV1 (rs = -0.39). A correlation was also found between CD4 CD25 lymphocytes and eosinophils in bronchoalveolar lavage fluid (rs = 0.48). Eosinophils in bronchoalveolar lavage fluid were increased in asthmatic patients compared with controls and the percentage of eosinophils in bronchoalveolar lavage fluid correlated with asthma symptom score. A relation was found between percentage of epithelial cells in bronchoalveolar lavage fluid and FEV1 and methacholine PC20. CONCLUSION: These results support the hypothesis that selective activation of memory CD4 T cells contributes to eosinophil accumulation, bronchial hyperresponsiveness, and symptoms in asthma