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https://www.readbyqxmd.com/read/29230839/prevalence-estimation-when-disease-status-is-verified-only-among-test-positives-applications-in-hiv-screening-programs
#1
Emma G Thomas, Sarah B Peskoe, Donna Spiegelman
The first goal of the United Nations' 90-90-90 HIV/AIDS elimination strategy is to ensure that, by 2020, 90% of HIV-positive people know their HIV status. Estimating the prevalence of HIV among people eligible for screening allows assessment of the number of additional cases that might be diagnosed through continued screening efforts in this group. Here, we present methods for estimating prevalence when HIV status is verified by a gold standard only among those who test positive on an initial, imperfect screening test with known sensitivity and specificity...
December 11, 2017: Statistics in Medicine
https://www.readbyqxmd.com/read/29194469/biobakery-a-meta-omic-analysis-environment
#2
Lauren J McIver, Galeb Abu-Ali, Eric A Franzosa, Randall Schwager, Xochitl C Morgan, Levi Waldron, Nicola Segata, Curtis Huttenhower
Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility. Availability: bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image...
November 29, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28972376/synthesis-of-au38-sch2ch2ph-24-au36-sph-tbu-24-and-au30-s-tbu-18-nanomolecules-from-a-common-precursor-mixture
#3
Milan Rambukwella, Amala Dass
Phenylethanethiol protected nanomolecules such as Au25, Au38, and Au144 are widely studied by a broad range of scientists in the community, owing primarily to the availability of simple synthetic protocols. However, synthetic methods are not available for other ligands, such as aromatic thiol and bulky ligands, impeding progress. Here we report the facile synthesis of three distinct nanomolecules, Au38(SCH2CH2Ph)24, Au36(SPh-tBu)24, and Au30(S-tBu)18, exclusively, starting from a common Aun(glutathione)m (where n and m are number of gold atoms and glutathiolate ligands) starting material upon reaction with HSCH2CH2Ph, HSPh-tBu, and HStBu, respectively...
October 3, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28715219/synthesis-of-aromatic-thiolate-protected-gold-nanomolecules-by-core-conversion-the-case-of-au36-sph-tbu-24
#4
Shevanuja Theivendran, Amala Dass
Ultrasmall nanomolecules (<2 nm) such as Au25(SCH2CH2Ph)18, Au38(SCH2CH2Ph)24, and Au144(SCH2CH2Ph)60 are well studied and can be prepared using established synthetic procedures. No such synthetic protocols that result in high yield products from commercially available starting materials exist for Au36(SPh-X)24. Here, we report a synthetic procedure for the large-scale synthesis of highly stable Au36(SPh-X)24 with a yield of ∼42%. Au36(SPh-X)24 was conveniently synthesized by using tert-butylbenzenethiol (HSPh-tBu, TBBT) as the ligand, giving a more stable product with better shelf life and higher yield than previously reported for making Au36(SPh)24 from thiophenol (PhSH)...
July 17, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28484369/differential-targeting-of-hsp70-heat-shock-proteins-hspa6-and-hspa1a-with-components-of-a-protein-disaggregation-refolding-machine-in-differentiated-human-neuronal-cells-following-thermal-stress
#5
Catherine A S Deane, Ian R Brown
Heat shock proteins (Hsps) co-operate in multi-protein machines that counter protein misfolding and aggregation and involve DNAJ (Hsp40), HSPA (Hsp70), and HSPH (Hsp105α). The HSPA family is a multigene family composed of inducible and constitutively expressed members. Inducible HSPA6 (Hsp70B') is found in the human genome but not in the genomes of mouse and rat. To advance knowledge of this little studied HSPA member, the targeting of HSPA6 to stress-sensitive neuronal sites with components of a disaggregation/refolding machine was investigated following thermal stress...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28323431/au38-sph-24-au38-protected-with-aromatic-thiolate-ligands
#6
Milan Rambukwella, Shayna Burrage, Marie Neubrander, Oscar Baseggio, Edoardo Aprà, Mauro Stener, Alessandro Fortunelli, Amala Dass
Au38(SR)24 is one of the most extensively investigated gold nanomolecules along with Au25(SR)18 and Au144(SR)60. However, so far it has only been prepared using aliphatic-like ligands, where R = -SC6H13, -SC12H25 and -SCH2CH2Ph. Au38(SCH2CH2Ph)24 when reacted with HSPh undergoes core-size conversion to Au36(SPh)24, and existing literature suggests that Au38(SPh)24 cannot be synthesized. Here, contrary to prevailing knowledge, we demonstrate that Au38(SPh)24 can be prepared if the ligand exchanged conditions are optimized, under delicate conditions, without any formation of Au36(SPh)24...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28009867/essential-oils-of-three-cow-parsnips-composition-and-activity-against-nosocomial-and-foodborne-pathogens-and-food-contaminants
#7
Ljuboš Ušjak, Silvana Petrović, Milica Drobac, Marina Soković, Tatjana Stanojković, Ana Ćirić, Marjan Niketić
Although some widespread, native cow parsnips (Heracleum L. spp., Apiaceae) had broad medicinal and culinary applications throughout history, the knowledge about their volatile constituents is insufficient. This work investigates the composition and bioactivities of H. sphondylium L. (HSPH), H. sibiricum L. (HSIB) and H. montanum Schleich. ex Gaudin (HMON) essential oils. The composition was tested by GC and GC-MS. (Z)-β-Ocimene was the most abundant in HSPH (28.9%) and HMON (20.4%) root oils, while in HSIB root oil, β-pinene (26...
December 23, 2016: Food & Function
https://www.readbyqxmd.com/read/27312410/argon-fast-whole-genome-simulation-of-the-discrete-time-wright-fisher-process
#8
Pier Francesco Palamara
MOTIVATION: Simulation under the coalescent model is ubiquitous in the analysis of genetic data. The rapid growth of real data sets from multiple human populations led to increasing interest in simulating very large sample sizes at whole-chromosome scales. When the sample size is large, the coalescent model becomes an increasingly inaccurate approximation of the discrete time Wright-Fisher model (DTWF). Analytical and computational treatment of the DTWF, however, is generally harder. RESULTS: We present a simulator (ARGON) for the DTWF process that scales up to hundreds of thousands of samples and whole-chromosome lengths, with a time/memory performance comparable or superior to currently available methods for coalescent simulation...
October 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26449931/cpgfilter-model-based-cpg-probe-filtering-with-replicates-for-epigenome-wide-association-studies
#9
Jun Chen, Allan C Just, Joel Schwartz, Lifang Hou, Nadereh Jafari, Zhifu Sun, Jean-Pierre A Kocher, Andrea Baccarelli, Xihong Lin
SUMMARY: The development of the Infinium HumanMethylation450 BeadChip enables epigenome-wide association studies at a reduced cost. One observation of the 450K data is that many CpG sites the beadchip interrogates have very large measurement errors. Including these noisy CpGs will decrease the statistical power of detecting relevant associations due to multiple testing correction. We propose to use intra-class correlation coefficient (ICC), which characterizes the relative contribution of the biological variability to the total variability, to filter CpGs when technical replicates are available...
February 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/25706019/public-health-101-nanocourse-a-condensed-educational-tool-for-non-public-health-professionals
#10
Cherie L Ramirez, Zofia K Z Gajdos, Catherine Kreatsoulas, Myriam C Afeiche, Morteza Asgarzadeh, Candace C Nelson, Usheer Kanjee, Alberto J Caban-Martinez
Graduate students and postdoctoral fellows-including those at the Harvard School of Public Health (HSPH)-have somewhat limited opportunities outside of traditional coursework to learn holistically about public health. Because this lack of familiarity could be a barrier to fruitful collaboration across disciplines, HSPH postdocs sought to address this challenge. In response, the Public Health 101 Nanocourse was developed to provide an overview of five core areas of public health (biostatistics, environmental health sciences, epidemiology, health policy and management, and social and behavioral sciences) in a two half-day course format...
March 2015: American Journal of Public Health
https://www.readbyqxmd.com/read/25519381/a-comparative-analysis-of-family-based-and-population-based-association-tests-using-whole-genome-sequence-data
#11
Jin J Zhou, Wai-Ki Yip, Michael H Cho, Dandi Qiao, Merry-Lynn N McDonald, Nan M Laird
The revolution in next-generation sequencing has made obtaining both common and rare high-quality sequence variants across the entire genome feasible. Because researchers are now faced with the analytical challenges of handling a massive amount of genetic variant information from sequencing studies, numerous methods have been developed to assess the impact of both common and rare variants on disease traits. In this report, whole genome sequencing data from Genetic Analysis Workshop 18 was used to compare the power of several methods, considering both family-based and population-based designs, to detect association with variants in the MAP4 gene region and on chromosome 3 with blood pressure...
2014: BMC Proceedings
https://www.readbyqxmd.com/read/25426672/au99-sph-42-nanomolecules-aromatic-thiolate-ligand-induced-conversion-of-au144-sch2ch2ph-60
#12
Praneeth Reddy Nimmala, Amala Dass
A new aromatic thiolate protected gold nanomolecule Au99(SPh)42 has been synthesized by reacting the highly stable Au144(SCH2CH2Ph)60 with thiophenol, HSPh. The ubiquitous Au144(SR)60 is known for its high stability even at elevated temperature and in the presence of excess thiol. This report demonstrates for the first time the reactivity of the Au144(SCH2CH2Ph)60 with thiophenol to form a different 99-Au atom species. The resulting Au99(SPh)42 compound, however, is unreactive and highly stable in the presence of excess aromatic thiol...
December 10, 2014: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/25252224/interlab-comparison-of-elemental-analysis-for-low-ambient-urban-pm2-5-levels
#13
COMPARATIVE STUDY
Choong-Min Kang, Souzana Achilleos, Joy Lawrence, Jack M Wolfson, Petros Koutrakis
There is growing concern about the accuracy of trace elemental analysis of ambient particulate matter (PM) samples. This has become important because ambient PM concentrations have decreased over the years, and the lower filter loadings result in difficulties in accurate analysis. The performance of energy-dispersive X-ray reflectance spectrometry was evaluated at Harvard School of Public Health using several methodologies, including intercomparison between two other laboratories. In reanalysis of standard films as unknown samples following calibration, the HSPH ED XRF measurements represented good performance: 2% errors in precision and 4% errors in accuracy...
October 21, 2014: Environmental Science & Technology
https://www.readbyqxmd.com/read/24990607/fast-and-accurate-imputation-of-summary-statistics-enhances-evidence-of-functional-enrichment
#14
Bogdan Pasaniuc, Noah Zaitlen, Huwenbo Shi, Gaurav Bhatia, Alexander Gusev, Joseph Pickrell, Joel Hirschhorn, David P Strachan, Nick Patterson, Alkes L Price
MOTIVATION: Imputation using external reference panels (e.g. 1000 Genomes) is a widely used approach for increasing power in genome-wide association studies and meta-analysis. Existing hidden Markov models (HMM)-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian imputation from summary association statistics, a type of data that is becoming widely available. RESULTS: In simulations using 1000 Genomes (1000G) data, this method recovers 84% (54%) of the effective sample size for common (>5%) and low-frequency (1-5%) variants [increasing to 87% (60%) when summary linkage disequilibrium information is available from target samples] versus the gold standard of 89% (67%) for HMM-based imputation, which cannot be applied to summary statistics...
October 15, 2014: Bioinformatics
https://www.readbyqxmd.com/read/24596661/hospitals-safety-from-disasters-in-i-r-iran-the-results-from-assessment-of-224-hospitals
#15
Ali Ardalan, Maryam Kandi, Mohammad Taghi Talebian, Hamidreza Khankeh, Gholamreza Masoumi, Reza Mohammadi, Samaneh Maleknia, Jafar Miadfar, Atieh Mobini, Sara Mehranamin
BACKGROUND AND OBJECTIVE: Iran's hospitals have been considerably affected by disasters during last decade. To address this, health system of I.R.Iran has taken an initiative to assess disaster safety of the hospitals using an adopted version of Hospital Safety Index (HSI). This article presents the results of disaster safety assessment in 224 Iran's hospitals. METHODS: A self-assessment approach was applied to assess the disaster safety in 145 items categorized in 3 components including structural, non-structural and functional capacity...
2014: PLoS Currents
https://www.readbyqxmd.com/read/23990415/a-clustering-a-novel-method-for-the-detection-of-co-regulated-methylation-regions-and-regions-associated-with-exposure
#16
Tamar Sofer, Elizabeth D Schifano, Jane A Hoppin, Lifang Hou, Andrea A Baccarelli
MOTIVATION: DNA methylation is a heritable modifiable chemical process that affects gene transcription and is associated with other molecular markers (e.g. gene expression) and biomarkers (e.g. cancer or other diseases). Current technology measures methylation in hundred of thousands, or millions of CpG sites throughout the genome. It is evident that neighboring CpG sites are often highly correlated with each other, and current literature suggests that clusters of adjacent CpG sites are co-regulated...
November 15, 2013: Bioinformatics
https://www.readbyqxmd.com/read/23904097/dnajb6-is-a-peptide-binding-chaperone-which-can-suppress-amyloid-fibrillation-of-polyglutamine-peptides-at-substoichiometric-molar-ratios
#17
Cecilia Månsson, Vaishali Kakkar, Elodie Monsellier, Yannick Sourigues, Johan Härmark, Harm H Kampinga, Ronald Melki, Cecilia Emanuelsson
Expanded polyglutamine (polyQ) stretches lead to protein aggregation and severe neurodegenerative diseases. A highly efficient suppressor of polyQ aggregation was identified, the DNAJB6, when molecular chaperones from the HSPH, HSPA, and DNAJ families were screened for huntingtin exon 1 aggregation in cells (Hageman et al. in Mol Cell 37(3):355-369, 2010). Furthermore, also aggregation of polyQ peptides expressed in cells was recently found to be efficiently suppressed by co-expression of DNAJB6 (Gillis et al...
March 2014: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/23608769/the-chi-linh-health-and-demographic-surveillance-system-chililab-hdss
#18
Bich Huu Tran, Ha Thanh Nguyen, Hien Thi Ho, Cuong Viet Pham, Vui Thi Le, Anh Vu Le
The Chi Linh Health and Demographic Surveillance System (CHILILAB HDSS) is the only health and demographic surveillance system (HDSS) in an urbanizing area of the Chi Linh district of Hai Duong, a northern province of Vietnam. It is one of the few field laboratories in the world that links operational research and health interventions with field training. The CHILILAB HDSS provides longitudinal data on demographic and health indicators for the community of Chi Linh. In 2012, when the CHILILAB HDSS included 57,561 people from 17 993 households in 3 towns and 4 communes, it used structured questionnaires to collect information on population changes (birth, death, migration, marriage, and pregnancy) in the community...
June 2013: International Journal of Epidemiology
https://www.readbyqxmd.com/read/23539302/improved-ancestry-inference-using-weights-from-external-reference-panels
#19
Chia-Yen Chen, Samuela Pollack, David J Hunter, Joel N Hirschhorn, Peter Kraft, Alkes L Price
MOTIVATION: Inference of ancestry using genetic data is motivated by applications in genetic association studies, population genetics and personal genomics. Here, we provide methods and software for improved ancestry inference using genome-wide single nucleotide polymorphism (SNP) weights from external reference panels. This approach makes it possible to leverage the rich ancestry information that is available from large external reference panels, without the administrative and computational complexities of re-analyzing the raw genotype data from the reference panel in subsequent studies...
June 1, 2013: Bioinformatics
https://www.readbyqxmd.com/read/22989357/reactions-of-the-unsaturated-hydroxo-complex-w2cp2-oh-%C3%AE-pph2-2-co-bf4-with-mono-and-bidentate-ligands-having-e-h-bonds-e-o-s-n
#20
Fernanda Cimadevilla, M Esther García, Daniel García-Vivó, Miguel A Ruiz, Claudia Graiff, Antonio Tiripicchio
The title compound reacted with CO at room temperature in the presence of excess HBF(4)·OEt(2) to yield a mixture of the electron-precise complexes [W(2)Cp(2)(μ-PPh(2))(2)(CO)(4)](BF(4))(2) and [W(2)Cp(2)(μ-PPh(2))(2)(CO)(3)(OH(2))](BF(4))(2), with the aquo ligand in the latter complex being easily displaced by simple donors such as acetonitrile. Reaction of the title complex with simple acidic molecules such as HSPh or HBr took place rapidly with elimination of H(2)O to give the 32-electron cations [W(2)Cp(2)(Z)(μ-PPh(2))(2)(CO)](+) [Z = Br, SPh (W-W = 2...
October 1, 2012: Inorganic Chemistry
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