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https://www.readbyqxmd.com/read/28453677/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#1
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
Summary: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28453306/the-association-of-lung-clearance-index-with-copd-and-fev-1-reduction-in-men-born-in-1914
#2
Suneela Zaigham, Per Wollmer, Gunnar Engström
Lung Clearance Index (LCI) provides an overall measurement of ventilation inhomogeneity. This population-based study examines whether LCI predicts pulmonary obstruction and incidence of chronic obstructive pulmonary disease (COPD) events over a long-term follow-up. Multiple breath nitrogen washout and spirometry were performed in 674 men from the cohort "Men born in 1914" at age 55 years. Subjects were classified into quartiles (Q) of LCI and according to LCI above and below upper limit of normal (ULN). Incidence of COPD events (COPD hospitalisations or COPD-related deaths) were monitored over the remaining life span of the men, by linkage with national hospital registers...
April 28, 2017: COPD
https://www.readbyqxmd.com/read/28453289/identification-of-buctopamine-and-mebuctopamine-a-%C3%AE-2-receptor-agonist-and-its-metabolite-in-swine-hair-and-feed-additives
#3
Ying-Heng Chen, Chia-Ying Yang, Chih Wen Cheng, Yi-Ying Lin, Su Lien Kuo, Ling-Wei Hsin
4-[2-(tert-Butylamino)-1-hydroxyethyl]phenol (buctopamine, 4), a new β2 receptor agonist (β2-agonist), was found to be an adulterant in feed additives for swine in Taiwan, where using β2-agonists in food-production animals is prohibited. Buctopamine and its metabolite, 4-[2-(tert-butylamino)-1-hydroxyethyl]-2-methoxyphenol (mebuctopamine, 2), were detected in swine hair specimens. Authentic compounds 2 and 4 were synthesized with 98.6% and 97.7% purity, respectively, as reference standards for analysis, and both compounds were more hydrophilic than ractopamine and clenbuterol...
April 28, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28449360/biologic-variability-of-cardiac-troponin-i-in-healthy-dogs-and-dogs-with-different-stages-of-myxomatous-mitral-valve-disease-using-standard-and-high-sensitivity-immunoassays
#4
Randolph L Winter, Ashley B Saunders, Sonya G Gordon, Matthew W Miller, Geoffrey T Fosgate, Jan S Suchodolski, Jörg M Steiner
BACKGROUND: Biologic variability (BV) is one aspect of interpreting changes in biomarker concentrations known to be clinically important in people with cardiac disease, but it has not been adequately addressed in dogs so far. OBJECTIVES: The purpose of the study was to determine BV of cardiac troponin I (cTnI) in healthy dogs and dogs with 3 stages of myxomatous mitral valve disease (MMVD). METHODS: Healthy dogs and dogs with 3 stages of MMVD were prospectively assigned to groups based on comprehensive clinical evaluation using current guidelines...
April 27, 2017: Veterinary Clinical Pathology
https://www.readbyqxmd.com/read/28449091/gwab-a-web-server-for-the-network-based-boosting-of-human-genome-wide-association-data
#5
Jung Eun Shim, Changbae Bang, Sunmo Yang, Tak Lee, Sohyun Hwang, Chan Yeong Kim, U Martin Singh-Blom, Edward M Marcotte, Insuk Lee
During the last decade, genome-wide association studies (GWAS) have represented a major approach to dissect complex human genetic diseases. Due in part to limited statistical power, most studies identify only small numbers of candidate genes that pass the conventional significance thresholds (e.g. P ≤ 5 × 10-8). This limitation can be partly overcome by increasing the sample size, but this comes at a higher cost. Alternatively, weak association signals can be boosted by incorporating independent data. Previously, we demonstrated the feasibility of boosting GWAS disease associations using gene networks...
April 26, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448762/bone-turnover-in-osteoporotic-women-during-long-term-oral-bisphosphonates-treatment-implications-for-treatment-failure-and-drug-holiday-in-the-real-world
#6
Yair Liel, Ygal Plakht, Muhammad Abu-Tailakh
OBJECTIVE: Little data exists to support concerns over bone turnover suppression during prolonged oral bisphosphonates treatment and on consequences of the recommended "drug holiday". This study was set to assess bone resorption rates in postmenopausal osteoporotic women on prolonged oral bisphosphonates treatment, and in response to switching to "drug holiday", intravenous bisphosphonate or continuation of oral bisphosphonates. METHODS: Frequency distribution of the bone resorption marker urinary deoxypyridinoline cross-links (uDPD), was obtained retrospectively from 211 osteoporotic women attended at an academic hospital endocrine clinic, treated for >2 years with oral bisphosphonates...
April 27, 2017: Endocrine Practice
https://www.readbyqxmd.com/read/28448754/clinical-evaluation-of-cost-efficacy-of-drugs-for-treatment-of-osteoporosis-a-meta-analysis
#7
Stewart G Albert, Supraja Reddy
OBJECTIVE: To assess the cost efficacy of available regimens for therapy of osteoporosis as defined as the cost time's number need to treat to prevent one fracture. PATIENTS AND METHODS: Existing meta-analyses were supplemented through electronic databases SCOPUS and PubMED between 2013 (a date overlapping the latest meta-analyses) and March 2016. Primary references included all randomized controlled trials of anti-osteoporotic drugs versus comparators using search terms "osteoporosis", "random" and "trial"...
April 27, 2017: Endocrine Practice
https://www.readbyqxmd.com/read/28448581/the-performance-of-bd-facspresto%C3%A2-for-cd4-t-cell-count-cd4-and-hemoglobin-concentration-test-in-ethiopia
#8
Gebremedhin Gebremicael, Yohanes Belay, Fitsum Girma, Yemane Abreha, Atsbeha Gebreegziabxier, Simret Tesfaye, Zelalem Messele, Yibeltal Assefa, Bahrie Bellete, Desta Kassa, Lara Vojnov
INTRODUCTION: In Ethiopia, CD4+ T-cell counting is still required for all patients at baseline before antiretroviral therapy (ART) and to determine eligibility and follow-up of opportunistic infection prophylaxis. However, access to CD4+ T cell count in rural health facilities remains a major challenge in Ethiopia like other resource-limited settings. METHODOLOGY: Both capillary and venous blood was drawn from each of 325 study participant recruited in Addis Ababa and surroundings...
2017: PloS One
https://www.readbyqxmd.com/read/28447766/supervised-dosing-with-a-long-acting-opioid-medication-in-the-management-of-opioid-dependence
#9
REVIEW
Rosella Saulle, Simona Vecchi, Linda Gowing
BACKGROUND: Opioid dependence (OD) is an increasing clinical and public health problem worldwide. International guidelines recommend opioid substitution treatment (OST), such as methadone and buprenorphine, as first-line medication treatment for OD. A negative aspect of OST is that the medication used can be diverted both through sale on the black market, and the unsanctioned use of medications. Daily supervised administration of medications used in OST has the advantage of reducing the risk of diversion, and may promote therapeutic engagement, potentially enhancing the psychosocial aspect of OST, but costs more and is more restrictive on the client than dispensing for off-site consumption...
April 27, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28447416/microfluidics-in-flow-cytometry-and-related-techniques
#10
REVIEW
M C Béné
Technological advances in laboratory automation are now well understood and applied as they considerably improved the speed and robustness of haematological laboratory data, in the companion fields of blood analyzers and flow cytometry. Still rather confidential is the field of microfluidics, mostly confined so far to academic settings and research laboratories. The literature in the field of microfluidics is growing and applications in hematology range from cell counting to flow cytometry, cell sorting, or ex vivo testing...
May 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28447411/establishing-reference-intervals-in-the-coagulation-laboratory
#11
REVIEW
D D Castellone
INTRODUCTION: Obtaining a reference interval (RI) is a challenge for any laboratory and becomes more complicated in the coagulation laboratory due to testing on samples with limited stability on reagents that are poorly standardized. Reference intervals are required to be able to evaluate results in relation to a patients' hemostatic disorder. This becomes one of the most important tasks conducted in the coagulation laboratory. However, many laboratories lack the time, finances and in many cases the expertise to conduct this study...
May 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28447233/total-arsenic-concentrations-in-chinese-children-s-urine-by-different-geographic-locations-ages-and-genders
#12
Xuan Zhang, Beibei Wang, Xiaoyong Cui, Chunye Lin, Xitao Liu, Jin Ma
Little is known about the variation of Chinese children's exposure to arsenic by geography, age, gender, and other potential factors. The main objective of this study was to investigate the total arsenic concentration in Chinese children's urine by geographic locations, ages, and genders. In total, 259 24-h urine samples were collected from 210 2- to 12-year-old children in China and analyzed for total arsenic and creatinine concentrations. The results showed that the upper limit (upper limit of the 90% confidence interval for the 97...
April 26, 2017: Environmental Geochemistry and Health
https://www.readbyqxmd.com/read/28447000/8th-edition-ajcc-uicc-staging-of-cancers-of-the-esophagus-and-esophagogastric-junction-application-to-clinical-practice
#13
Thomas W Rice, Deepa T Patil, Eugene H Blackstone
The 8th edition of the American Joint Committee on Cancer (AJCC) staging of epithelial cancers of the esophagus and esophagogastric junction (EGJ) presents separate classifications for clinical (cTNM), pathologic (pTNM), and postneoadjuvant (ypTNM) stage groups. Histopathologic cell type markedly affects survival of clinically and pathologically staged patients, requiring separate groupings for each cell type, but ypTNM groupings are identical for both cell types. Clinical categories, typically obtained by imaging with minimal histologic information, are limited by resolution of each method...
March 2017: Annals of Cardiothoracic Surgery
https://www.readbyqxmd.com/read/28446793/demonstration-of-shot-noise-limited-swept-source-oct-without-balanced-detection
#14
Vala Fathipour, Tilman Schmoll, Alireza Bonakdar, Skylar Wheaton, Hooman Mohseni
Optical coherence tomography (OCT) has been utilized in a rapidly growing number of clinical and scientific applications. In particular, swept source OCT (SS-OCT) has attracted many attentions due to its excellent performance. So far however, the limitations of existing photon detectors have prevented achieving shot-noise-limited sensitivity without using balanced-detection scheme in SS-OCT, even when superconducting single-photon detectors were used. Unfortunately, balanced-detection increases OCT system size and cost, as it requires many additional components to boost the laser power and maintain near ideal balanced performance across the whole optical bandwidth...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28446741/methodology-to-define-biological-reference-values-in-the-environmental-and-occupational-fields-the-contribution-of-the-italian-society-for-reference-values-sivr
#15
Maria Cristina Aprea, Maria Luisa Scapellato, Maria Carmen Valsania, Andrea Perico, Luigi Perbellini, Maria Cristina Ricossa, Marco Pradella, Sara Negri, Ivo Iavicoli, Piero Lovreglio, Fabiola Salamon, Maurizio Bettinelli, Pietro Apostoli
BACKGROUND: Biological reference values (RVs) explore the relationships between humans and their environment and habits. RVs are fundamental in the environmental field for assessing illnesses possibly associated with environmental pollution, and also in the occupational field, especially in the absence of established biological or environmental limits. OBJECTIVES: The Italian Society for Reference Values (SIVR) determined to test criteria and procedures for the definition of RVs to be used in the environmental and occupational fields...
April 21, 2017: La Medicina del Lavoro
https://www.readbyqxmd.com/read/28446497/best-but-oft-forgotten-practices-mediation-analysis
#16
Amanda J Fairchild, Heather L McDaniel
This contribution in the "Best (but Oft-Forgotten) Practices" series considers mediation analysis. A mediator (sometimes referred to as an intermediate variable, surrogate endpoint, or intermediate endpoint) is a third variable that explains how or why ≥2 other variables relate in a putative causal pathway. The current article discusses mediation analysis with the ultimate intention of helping nutrition researchers to clarify the rationale for examining mediation, avoid common pitfalls when using the model, and conduct well-informed analyses that can contribute to improving causal inference in evaluations of underlying mechanisms of effects on nutrition-related behavioral and health outcomes...
April 26, 2017: American Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28446455/the-economic-burden-of-physical-inactivity-a-systematic-review-and-critical-appraisal
#17
REVIEW
Ding Ding, Tracy Kolbe-Alexander, Binh Nguyen, Peter T Katzmarzyk, Michael Pratt, Kenny D Lawson
OBJECTIVE: To summarise the literature on the economic burden of physical inactivity in populations, with emphases on appraising the methodologies and providing recommendations for future studies. DESIGN: Systematic review following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines (PROSPERO registration number CRD42016047705). DATA SOURCES: Electronic databases for peer-reviewed and grey literature were systematically searched, followed by reference searching and consultation with experts...
April 26, 2017: British Journal of Sports Medicine
https://www.readbyqxmd.com/read/28446169/the-relative-importance-of-large-problems-far-away-versus-small-problems-closer-to-home-insights-into-limiting-the-spread-of-antimicrobial-resistance-in-england
#18
Tjibbe Donker, Katherine L Henderson, Katie L Hopkins, Andrew R Dodgson, Stephanie Thomas, Derrick W Crook, Tim E A Peto, Alan P Johnson, Neil Woodford, A Sarah Walker, Julie V Robotham
BACKGROUND: To combat the spread of antimicrobial resistance (AMR), hospitals are advised to screen high-risk patients for carriage of antibiotic-resistant bacteria on admission. This often includes patients previously admitted to hospitals with a high AMR prevalence. However, the ability of such a strategy to identify introductions (and hence prevent onward transmission) is unclear, as it depends on AMR prevalence in each hospital, the number of patients moving between hospitals, and the number of hospitals considered 'high risk'...
April 27, 2017: BMC Medicine
https://www.readbyqxmd.com/read/28446139/de-novo-assembly-of-highly-polymorphic-metagenomic-data-using-in-situ-generated-reference-sequences-and-a-novel-blast-based-assembly-pipeline
#19
You-Yu Lin, Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen, Hurng-Yi Wang
BACKGROUND: The accuracy of metagenomic assembly is usually compromised by high levels of polymorphism due to divergent reads from the same genomic region recognized as different loci when sequenced and assembled together. A viral quasispecies is a group of abundant and diversified genetically related viruses found in a single carrier. Current mainstream assembly methods, such as Velvet and SOAPdenovo, were not originally intended for the assembly of such metagenomics data, and therefore demands for new methods to provide accurate and informative assembly results for metagenomic data...
April 26, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28445897/adrenal-vein-catecholamine-levels-and-ratios-reference-intervals-derived-from-patients-with-primary-aldosteronism
#20
Candy W C Sze, Samuel Matthew O'Toole, Roger Kent Tirador, Scott A Akker, Matthew Matson, Leslie Perry, Maralyn Rose Druce, Tanja Dekkers, Jaap Deinum, Jacques W M Lenders, Graeme Eisenhofer, William Martyn Drake
Phaeochromocytoma localisation is generally reliably achieved with modern imaging techniques, particularly in sporadic cases. On occasion, however, there can be diagnostic doubt due to the presence of bilateral adrenal abnormalities, particularly in patients with mutations in genes predisposing them to the development of multiple phaeochromocytomas. In such cases, surgical intervention is ideally limited to large or functional lesions due to the long-term consequences associated with hypoadrenalism. Adrenal venous sampling (AVS) for catecholamines has been used in this situation to guide surgery, although there are few data available to support diagnostic thresholds...
April 26, 2017: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
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