Miracle-dz/UniFAR-FTUs huggingface dataset:
“Future-Proofing” Blood Processing for Measurement of Circulating miRNAs in Samples from Biobanks and Prospective Clinical Trials

Background: Quantifying circulating nucleic acids is an important new approach to cancer diagnosis/monitoring. Methods: We compared the suitability of serum versus plasma for measuring miRNAs using qRT-PCR and assessed how preanalytic variables that can affect circulating tumor DNA (ctDNA) quantification in plasma also influence miRNA levels. Results: Across 62 blood-derived specimens, plasma samples in EDTA, Streck-DNA, and Streck-RNA tubes showed significantly higher Ct values for multiple housekeeping miRNAs, compared with serum samples. For the EDTA-plasma tubes, this difference was only seen when including the high-speed centrifugation protocol used to optimize ctDNA extraction. In plasma samples derived from blood stored at room temperature for up to 14 days (conditions that typically apply to samples processed for biobanking), levels of endogenous housekeeping miRNAs gradually increased, in parallel with the hemolysis marker hsa-miR-451a, consistent with release from blood cells/platelets. It was necessary to normalize levels of the housekeeping miRNAs to those of hsa-miR-451a, to obtain the stable values needed for referencing test miRNA levels. Conclusions: Our data indicate that plasma samples prepared for ctDNA extraction are suboptimal for miRNA quantification and require the incorporation of multiple data normalization steps. For prospective studies designed to measure both miRNAs and ctDNA, the most suitable approach would be to obtain both serum (for miRNAs) and plasma (for ctDNA). If only plasma can be collected, we recommend an initial low-speed centrifugation step, followed by aliquoting the supernatant into parallel samples, one for direct miRNA quantification, and the other for a further high-speed centrifugation step to optimize ctDNA retrieval. Impact: These recommendations will help “future-proof” clinical studies in which quantification of circulating miRNAs is a component. Cancer Epidemiol Biomarkers Prev; 27(2); 208–18. ©2017 AACR.
Predictors of adherence to a physical activity counseling intervention delivered by exercise physiologists: secondary analysis of the newcOAch trial data

Background: General practitioners (GPs) cite time as a barrier to physical activity counseling. An alternative for time-poor GPs in Australia is the referral of insufficiently active patients to exercise physiologists (EPs). As data on the predictors of adherence to physical activity counseling interventions are limited, this study aimed to identify the sociodemographic, medical, health, and psychological characteristics of insufficiently active primary care patients who adhered to a physical activity counseling intervention delivered by EPs. Methods: This secondary analysis of data from the NewCOACH randomized trial used logistic regression to identify predictors of adherence, defined as patient participation in at least four of the five physical activity counseling sessions. EPs provided information about the number of sessions, while other potential predictors were obtained from the self-administered baseline questionnaire and medical summary sheets provided by the GPs. Results: Of the 132 patients referred to an EP, 102 (77%) were adherent: 91 (69%) and eleven (8.3%) participated in all, or all but one, of the sessions, respectively. Of the remainder, seven (5.3%) patients participated in three sessions, seven (5.3%) participated in two sessions, five (3.8%) participated in one session, and eleven (8.3%) did not participate in any session. The odds of being adherent were 5.84 (95% CI 1.46–23.4, P # 0.05) times higher among retired participants than in those who were not in paid employment. The odds of being adherent 1) increased as the positive outcome expectation score increased (OR 1.89, 95% CI 1.12–3.18, P # 0.05) and 2) decreased as the duration (days) between referral and the initial counseling session increased (OR 0.95, 95% CI 0.92–0.98, P , 0.01). Conclusion: More than three quarters of the patients participated in all, or all but one, of the sessions. Being retired, positive outcome expectations, and having a shorter wait between referral and the initial appointment predicted adherence. Abbreviations: AQol-8D, Assessment of Quality of life-8D Utility instrument; BMi, body mass index; ePs, exercise physiologists; F2F, face-to-face counseling only; F2F Tel, telephone counseling after an initial face-to-face session; n, number of participants; negOe, negative Outcome expectations; PosOe, Positive Outcome expectations.
Predictors of adherence to a physical activity counseling intervention delivered by exercise physiologists: secondary analysis of the newcOAch trial data

Background: General practitioners (GPs) cite time as a barrier to physical activity counseling. An alternative for time-poor GPs in Australia is the referral of insufficiently active patients to exercise physiologists (EPs). As data on the predictors of adherence to physical activity counseling interventions are limited, this study aimed to identify the sociodemographic, medical, health, and psychological characteristics of insufficiently active primary care patients who adhered to a physical activity counseling intervention delivered by EPs. Methods: This secondary analysis of data from the NewCOACH randomized trial used logistic regression to identify predictors of adherence, defined as patient participation in at least four of the five physical activity counseling sessions. EPs provided information about the number of sessions, while other potential predictors were obtained from the self-administered baseline questionnaire and medical summary sheets provided by the GPs. Results: Of the 132 patients referred to an EP, 102 (77%) were adherent: 91 (69%) and eleven (8.3%) participated in all, or all but one, of the sessions, respectively. Of the remainder, seven (5.3%) patients participated in three sessions, seven (5.3%) participated in two sessions, five (3.8%) participated in one session, and eleven (8.3%) did not participate in any session. The odds of being adherent were 5.84 (95% CI 1.46–23.4, P # 0.05) times higher among retired participants than in those who were not in paid employment. The odds of being adherent 1) increased as the positive outcome expectation score increased (OR 1.89, 95% CI 1.12–3.18, P # 0.05) and 2) decreased as the duration (days) between referral and the initial counseling session increased (OR 0.95, 95% CI 0.92–0.98, P , 0.01). Conclusion: More than three quarters of the patients participated in all, or all but one, of the sessions. Being retired, positive outcome expectations, and having a shorter wait between referral and the initial appointment predicted adherence. Abbreviations: AQol-8D, Assessment of Quality of life-8D Utility instrument; BMi, body mass index; ePs, exercise physiologists; face-to-face counseling only; telephone an initial Outcome
BIOINFORMATICS APPLICATIONS NOTE

Summary: NAViGaTOR is a powerful graphing application for the 2D and 3D visualization of biological networks. NAViGaTOR includes a rich suite of visual mark-up tools for manual and automated annotation, fast and scalable layout algorithms and OpenGL hardware acceleration to facilitate the visualization of large graphs. Publication-quality images can be rendered through SVG graphics export. NAViGaTOR supports community-developed data formats (PSI-XML, BioPax and GML), is platform-independent and is extensible through a plug-in architecture. Availability: NAViGaTOR is freely available to the research community from http://ophid.utoronto. ca/navigator/. Installers and documentation are provided for 32-and 64-bit Windows, Mac, Linux and Unix.
Autoestima en estudiantes españoles de secundaria: dimensiones e influencia de variables personales y educativas

El interés de la autoestima durante la adolescencia es fundamental, ya que promover una autoestima positiva y reducir el impacto de la autoestima negativa, posibilita el desarrollo óptimo de gran parte de las experiencias escolares, personales y de bienestar general. El presente estudio tuvo como objetivo evaluar las evidencias de validez y fiabilidad de la Escala de Autoestima (Rosenberg Self-Esteem Scale) en estudiantes españoles y comprobar si el género, la edad, el curso académico y el tipo de centro son determinantes para su desarrollo. Participaron un total de 698 estudiantes de Educación Secundaria Obligatoria (ESO) que se agruparon en dos muestras aleatorias (muestra 1: 364 alumnos, M=12.57; DT= .49 y muestra 2: 334 alumnos, M=14.62; DT= .48). Los resultados identificaron una estructura factorial de dos factores (autoestima positiva y autoestima negativa) (χ2/gl= 2.938; CFI= .948; NNFI= .924; SRMR = .045; RMSEA= .075), con una consistencia interna elevada (α = .853). Asimismo, los análisis de multivarianza mostraron que los adolescentes presentan una mayor autoestima positiva si son de género masculino, cursan primero, segundo o tercero de ESO y estudian en centros concertados, mientras que exhiben una alta autoestima negativa los adolescentes de género masculino que cursan primero de ESO con edades inferiores a los 13 años. La escala Rosenberg ha demostrado tener propiedades psicométricas adecuadas para ser utilizada en estudiantes de educación secundaria de España.
Shape from shading

Understanding how the shape of a three dimensional object may be recovered from shading in a two-dimensional image of the object is one of the most important - and still unresolved - problems in machine vision. Although this important subfield is now in its second decade, this book is the first to provide a comprehensive review of shape from shading. It brings together all of the seminal papers on the subject, shows how recent work relates to more traditional approaches, and provides a comprehensive annotated bibliography.The book's 17 chapters cover: Surface Descriptions from Stereo and Shading. Shape and Source from Shading. The Eikonal Equation: some Results Applicable to Computer Vision. A Method for Enforcing Integrability in Shape from Shading Algorithms. Obtaining Shape from Shading Information. The Variational Approach to Shape from Shading. Calculating the Reflectance Map. Numerical Shape from Shading and Occluding Boundaries. Photometric Invariants Related to Solid Shape. Improved Methods of Estimating Shape from Shading Using the Light Source Coordinate System. A Provably Convergent Algorithm for Shape from Shading. Recovering Three Dimensional Shape from a Single Image of Curved Objects. Perception of Solid Shape from Shading. Local Shading Analysis Pentland. Radarclinometry for the Venus Radar Mapper. Photometric Method for Determining Surface Orientation from Multiple Images.Berthold K. P. Horn is Professor of Electrical Engineering and Computer Science at MIT. He has presided over the field of machine vision for more than a decade and is the author of "Robot Vision. "Michael Brooks is Reader in Computer Science at The Flinders University of South Australia. "Shape from Shading" is included in the Artificial Intelligence series, edited by Michael Brady, Daniel Bobrow, and Randall Davis.
Heat flow evolution, subsidence and erosion in the Rheno-Hercynian orogenic wedge of central Europe

Abstract Numerical, thermal and rheological modelling techniques are applied to unravel the basin-forming processes and the heat flow and burial history of the Rheno-Hercynian fold belt (Rhenish Massif), the adjacent Subvariscan foreland (Ruhr Basin), and the intramontane Saar-Nahe Basin. Thermal history and crustal architecture in the study areas were affected mainly by the Variscan Orogeny during late Palaeozoic times. Calibration of the simulated thermal histories is primarily based on vitrinite reflectance and fission-track data. Mechanical modelling reveals average β values of 1.7, reaching a maximum of 2.4 in the central basin (Mosel Graben) and at the transition to the Giessen Ocean to the south during Early Devonian rifting. This stage was associated with tholeitic magmatism and an elevated heat flow of up to 110 mW m−2, preserved in weakly overprinted syn-rift sediments. Average basal heat flow during maximum burial at the end of the Carboniferous period (i.e. the end of crustal shortening) was between 50 and 70 mW m−2 with a slight decrease from the Subvarian foreland basins towards the Rheno-Hercynian in the south. The values suggest average crustal thicknesses of between 32 and 36 km during late Carboniferous time. For the Saar-Nahe Basin, values between 50 and 75 mW/m2 represent the thermal regime in the upper crust during the late Stephanian and early Permian time. Estimated eroded thicknesses of Palaeozoic sediments vary between 2500 m in the northern and central Ruhr Basin and more than 6000 m in the Osteifel and the Siegen Anticline within the Rheno-Hercynian, and between 1800 and 3600 m in the Saar-Nahe Basin. Fission-track data provide evidence for significant reheating during the Mesozoic era within the entire study area. This phase of heating, probably linked to North Atlantic rifting, coincides with post-Variscan ore formation and with major tectono-magmatic events in central Europe.
Improved Knowledge Retention Among Clinical Pharmacy Students Using an Anthropology Classroom Assessment Technique

Objective. To adapt a classroom assessment technique (CAT) from an anthropology course to a diabetes module in a clinical pharmacy skills laboratory and to determine student knowledge retention from baseline. Design. Diabetes item stems, focused on module objectives, replaced anthropology terms. Answer choices, coded to Bloom’s Taxonomy, were expanded to include higher-order thinking. Students completed the online 5-item probe 4 times: prelaboratory lecture, postlaboratory, and at 6 months and 12 months after laboratory. Statistical analyses utilized a single factor, repeated measures design using rank transformations of means with a Mann-Whitney-Wilcoxon test. Assessment. The CAT revealed a significant increase in knowledge from prelaboratory compared to all postlaboratory measurements (p<0.0001). Significant knowledge retention was maintained with basic terms, but declined with complex terms between 6 and 12 months. Conclusion. The anthropology assessment tool was effectively adapted using Bloom’s Taxonomy as a guide and, when used repeatedly, demonstrated knowledge retention. Minimal time was devoted to application of the probe making it an easily adaptable CAT.
Quality of packaged drinking water produced in Warri Metropolis and potential implications for public health

Five brands of popular packaged water produced in Warri have been screened for coliform, physical and selected chemical characteristics, including cadmium, chromium and lead for the objective of determining potability using appropriate methods. Sachets and bottled water samples were collected from production plants, wholesale outlets and street hawkers. The results were in the following range: pH, 7.1 to 8.2; Total dissolved solids (TDS), 2.26 to 89.6 mg/l; Turbidity, 0.45 to 2.55 NTU; Calcium, 0.11 to 1.21 mg/l; Magnesium, 0.03 to 0.31 mg/l; Sulphate, 0 to 1.21 mg/l; chloride, 0.5 to 3.1 mg/l; nitrate, 0.2 to 0.25 mg/l. Cadmium was detected in three brands in both sachets and bottles and ranged from 0.001 to 0.002 mg/l. Lead detected ranged from 0.001 to 0.003 mg/l and chromium: 0.001 to 0.002 mg/l. While all parameters are well below regulatory guidelines, attention is drawn to the predominantly low Total dissolved solids (TDS) which indicates that the packaged water in Warri is demineralized. Prolonged consumption of demineralized water has been shown from elsewhere to result in micronutrient deficiencies, especially in calcium and magnesium that have been associated with high incidence of ailments including, dieresis, hypertension and coronary heart disease among others. Cohort-epidemiological studies are recommended in Warri and environs where packaged water is the most important drinking water source in order to establish any such health related linkages. Study results would guide water supply policy and regulatory action. Key words: Packaged water, low TDS, heavy metals, public health, Warri, water policy.
Worrying levels of antimicrobial resistance in Gram-negative bacteria isolated from cell phones and uniforms of Peruvian intensive care unit workers.

BACKGROUND Healthcare worker (HCW) uniforms and cell phones are involved in pathogen transmission. This study aimed to characterize pathogenic microorganism isolates from HCW uniforms and cell phones. METHODS Gram-negative microorganisms were recovered from HCW uniforms and cell phones. Antimicrobial susceptibility and the presence of extended-spectrum β-lactamases (ESBL) and carbapenemases were determined. RESULTS Escherichia coli was the most prevalent microorganism. Overall, high levels of resistance to cephalosporins, quinolones, co-trimoxazole and colistin were found. ESBL were mainly related to blaCTX-M-15 and blaSHV- genes. Carbapenem-resistant isolates presented as blaKPC or blaNDM. CONCLUSIONS High levels of antimicrobial resistance, including colistin, were detected. Therefore, strategies are urgently needed to prevent bacterial dissemination.
Pre-emplacement structural history recorded by mantle peridotites: an example from the Lizard Complex, SW England

The Lizard Complex of SW England includes thrusted units of peridotites that were initially exhumed from upper mantle (c. 52 km) to lower crustal (c. 24 km) depths during a period of Early Devonian rifting and break-up. This basin closed during the Late Devonian, when the Lizard Complex was thrust towards the NNW along a major low-angle detachment and became incorporated within a series of Variscan thrust nappes. In the peridotites, a primary high-T and high-P spinel lherzolite mineral assemblage (c. 1119°C and c. 15.7 kbar) was progressively exhumed and re-equilibrated to conditions of lower T and P (c. 991–1010°C and c. 7.5 kbar) during the development of kilometre-scale mylonitic plagioclase- and amphibole-bearing mantle shear zones. These fabrics demonstrably pre-date emplacement related structures. The new structural and geochemical evidence from the peridotites also strongly suggests that the Lizard Complex formed in a rifted, non-volcanic continental margin setting, possibly in a pull-apart basin, rather than at a mid-ocean ridge. The P–T and textural evolution of the Lizard peridotites supports growing evidence that shear zones in the lithospheric upper mantle may to some extent accommodate large-scale displacements associated with crustal extension and continental breakup.
Human-environment interactions during the Holocene: new data and interpretations from the Oban area, Argyll, Scotland

Investigations of the archaeological, geochemical, microscopic charcoal and palynological records from five localities in the Oban area, along an altitudinal transect from coast to upland, have provided new information on human–environment interactions during the Holocene. Some of the results are at variance with previous interpretations of Mesolithic human impacts and the timing of the transition to farming in Atlantic Scotland. High charcoal values and the occurrence of cereal-type pollen grains, which have commonly been used to infer human activity during the Mesolithic, appear in the Oban area at least to be related to climate change. However, the greater frequency of woodland-decline episodes in inland and upland areas prior to 5000 BP is more easily explained in terms of human impact. Archaeological and palynological evidence indicates that the Mesolithic–Neolithic transition in the Oban area occurred atc. 5000 BP and, on evidence from elsewhere in northern Britain, coincided with a marked shift to drier climatic conditions. Up untilc. 1000 BP agricultural communities appear to have had comparatively little impact on the environment. Thereafter, there was rapid and permanent deforestation possibly linked to the development of a distinctive land-use strategy and settlement pattern that survived until the nineteenth century ad.
Associations of maternal birth weight, childhood height, body mass index and change in height and body mass index from childhood to pregnancy with risks of preterm delivery.

BACKGROUND It remains unknown whether maternal early life body size and change in height and BMI from childhood to pregnancy are associated with her risk of having a preterm delivery. OBJECTIVES We investigated whether a woman's birth weight, childhood height, BMI and changes in height and BMI from childhood to pregnancy were associated with preterm delivery. METHODS We studied 47,947 nulliparous women born 1940-1996 from the Copenhagen School Health Records Register with information on birth weight and measured childhood heights and weights at ages 7 and/or 13 y. Gestational age was obtained from the Danish Birth Register as was pre-pregnancy BMI for 13,114 women. Deliveries were classified as very (22- < 32 wk) or moderate (32- < 37 wk) preterm. Risk ratios (RR) and 95% confidence intervals (CI) were estimated using binomial regression. RESULTS A woman's birth weight and childhood height were inversely associated with very and moderate preterm delivery. Childhood BMI had U-shaped associations only with very preterm delivery; at age 7 y, compared to a BMI z score of 0, the RRs were 1.31 (1.11, 1.54) for a z score of -1 and 1.18 (1.01, 1.38) for a z score of +1. Short stature in childhood and adulthood was associated with higher risks of very and moderate preterm delivery. Changing from a BMI at the 85th percentile at 7 y (US CDC reference) to a pre-pregnancy BMI of 22.5 kg/m2 was associated with RRs of 1.12 (0.91, 1.37) and 0.88 (0.78, 0.99) for very and moderate preterm delivery, respectively, compared to a reference woman (50th percentile at 7 y, 22.5 kg/m2 pre-pregnancy BMI). CONCLUSIONS Maternal birth weight, childhood height and BMI are associated with very and moderate preterm delivery, although in different patterns. Consistent short stature is associated with very and moderate preterm delivery, whereas normalizing BMI from childhood to pregnancy may reduce risks of very preterm delivery.