bluuebunny/crossref_metadata_2025 huggingface dataset:
Current Recommendations for Cervical Cancer Screening: Do They Render the Annual Pelvic Examination Obsolete?
Authors: Kauffman Robert P. , Griffin Stephen J. , Lund Jon D. , Tullar Paul E.
Published: January 2013

The development of a screening test for cervical dysplasia has been a major force in diminishing the worldwide incidence of invasive cervical cancer. Screening intervals recommended by professional organizations have changed over the past half century. Recognition of the human papillomavirus (HPV) as the causative agent and enhanced understanding of the natural history of HPV and cervical dysplasia in different age groups have prompted the American College of Obstetricians and Gynecologists and other professional societies to defer Pap smear screening to intervals no less than 2 years apart in women 21-29, and every 3 years in women 30 and over assuming no prior history of cervical dysplasia. Screening should start no sooner than age 21. These recommendations more closely resemble those currently practiced in Europe and other parts of the developed world. Those who have undergone hysterectomy no longer need screening unless high-grade dysplasia was present. Although the value of pelvic examination is not debated in women with symptoms referable to the female genital tract, the endorsement by several professional societies of less than annual cervical cancer screening in healthy women also begs the question of whether annual pelvic examination (speculum and/or bimanual examination) benefits asymptomatic women. Some sexually transmitted infections are amenable to self-insertion of a vaginal probe or detectable by voided urine specimen. Bimanual examination is insensitive in detecting early ovarian cancer with a high false-positive rate leading to patient anxiety, excessive diagnostic testing, and unnecessary surgical procedures. Future study should focus on the frequency in which healthy asymptomatic women should undergo pelvic examination.
Calcifying Human Aortic Smooth Muscle Cells Express Different Bone Alkaline Phosphatase Isoforms, Including the Novel B1x Isoform
Authors: Haarhaus Mathias , Arnqvist Hans J. , Magnusson Per
Published: January 2013

Background: Vascular calcification, causing cardiovascular morbidity and mortality, is associated with hyperphosphatemia in chronic kidney disease (CKD). In vitro, phosphate induces transdifferentiation of vascular smooth muscle cells to osteoblast-like cells that express alkaline phosphatase (ALP). In vivo, raised serum ALP activities are associated with increased mortality. A new bone ALP isoform (B1x) has been identified in serum from CKD patients. The present study investigated the different ALP isoforms in calcifying human aortic smooth muscle cells (HAoSMCs). Methods: HAoSMCs were cultured for 30 days in medium containing 5 or 10 mmol/l β-glycerophosphate in the presence or absence of the ALP-specific inhibitor tetramisole. Results: All known bone-specific ALP (BALP) isoforms (B/I, B1x, B1 and B2) were identified in HAoSMCs. β-Glycerophosphate stimulated calcification of HAoSMCs, which was associated with increased BALP isoforms B/I, B1x and B2. Tetramisole inhibited the β-glycerophosphate-induced HAoSMC calcification, which was paralleled by the inhibition of the B1x and B/I, but not the other isoforms. Conclusions: HAoSMCs express the four known BALP isoforms. B/I, B1x and B2 could be essential for soft tissue calcification. B/I and B1x were more affected by tetramisole than the other isoforms, which suggests different biological functions during calcification of HAoSMCs.
Development of a Chronic Kidney Disease Model in C57BL/6 Mice with Relevance to Human Pathology
Authors: Huang Linghong , Scarpellini Alessandra , Funck Muriel , Verderio Elisabetta A.M. , Johnson Timothy S.
Published: January 2013

Background: Genetically modified mice are used to investigate disease and assess potential interventions. However, research into kidney fibrosis is hampered by a lack of models of chronic kidney disease (CKD) in mice. Recently, aristolochic acid nephropathy (AAN), characterised by severe tubulointerstitial fibrosis, has been identified as a cause of end stage kidney disease and proposed as a model of CKD. Published studies have used various dosing regimens, species and strains, with variable outcomes. Therefore, we aimed to develop a standardised protocol to develop tubulointerstitial fibrosis using pure aristolochic acid I (AAI) in C57BL/6 mice. Methods: AAI dose optimisation was performed by intraperitoneal injection of AAI at varying dose, frequency and duration. Kidney function was assessed by serum creatinine. Fibrosis was quantified by hydroxyproline levels and Masson’s Trichrome staining. Specific collagens were measured by immunofluorescent staining. Results: Single doses of AAI of >10 mg/kg caused acute kidney failure and death. Lower doses of 2.5 mg/kg needed to be administrated more than weekly to cause significant fibrosis. 3 mg/kg once every 3 days for 6 weeks followed by a disease development time of 6 weeks after AAI led to reduced kidney weight and function. Substantial tubulointerstitial fibrosis occurred, with males more severely affected. Increased deposition of collagen I, III and IV contributed to fibrosis, with collagen III and IV higher in males. Conclusions: AAN can be induced in C57BL/6 mice. The regimen of 3 mg/kg every 3 days for 6 weeks followed by 6 weeks of disease development time gives substantial tubulointerstitial fibrosis with lesions similar to those in humans.
Report on a Patient with a 12q24.31 Microdeletion Inherited from an Insulin-Dependent Diabetes Mellitus Father
Authors: Chouery E. , Choucair N. , Abou Ghoch J. , El Sabbagh S. , Corbani S. , Mégarbané A.
Published: January 2013

We report a 2.3-year-old female patient with global developmental delay, infantile spasms, hypotonia, microcephaly, flat face, full cheeks, macroglossia, highly arched palate, retro-gnathia, narrow ear orifices, and café-au-lait spots. Molecular karyotyping revealed approximately a 1-Mb interstitial deletion of the long arm of one chromosome 12, del(12)(q24.31). The same deletion was identified in her father who presents insulin-dependent diabetes mellitus (IDDM) diagnosed at 14 years. Only one other patient with a similar de novo deletion has been reported previously [Mol Syndromol 2010;1:42-45]. A phenotype-genotype correlation is discussed, and the description of a novel rare microdeletion entity is raised.
High Anthocyanin Intake Is Associated With a Reduced Risk of Myocardial Infarction in Young and Middle-Aged Women
Authors: Cassidy Aedín , Mukamal Kenneth J. , Liu Lydia , Franz Mary , Eliassen A. Heather , Rimm Eric B.
Published: January 2013

Background—

Our current knowledge of modifiable risk factors to prevent myocardial infarction (MI) in young and middle-aged women is limited, and the impact of diet is largely unknown. Dietary flavonoids exert potential beneficial effects on endothelial function in short-term trials; however, the relationship between habitual intake and risk of MI in women is unknown.

Methods and Results—

We followed up 93 600 women 25 to 42 years of age from the Nurses’ Health Study (NHS) II who were healthy at baseline (1989) to examine the relationship between anthocyanins and other flavonoids and the risk of MI. Intake of flavonoid subclasses was calculated from validated food-frequency questionnaires collected every 4 years using an updated and extended US Department of Agriculture database. During 18 years of follow-up, 405 cases of MI were reported. An inverse association between higher intake of anthocyanins and risk of MI was observed (hazard ratio, 0.68; 95% confidence interval, 0.49–0.96;
P
=0.03, highest versus lowest quintiles) after multivariate adjustment. The addition of intermediate conditions, including history of hypertension, did not significantly attenuate the relationship (hazard ratio, 0.70; 95% confidence interval, 0.50–0.97;
P
=0.03). Combined intake of 2 anthocyanin-rich foods, blueberries and strawberries, tended to be associated with a decreased risk of MI (hazard ratio, 0.66; 95% confidence interval, 0.40–1.08) in a comparison of those consuming >3 servings a week and those with lower intake. Intakes of other flavonoid subclasses were not significantly associated with MI risk.

Conclusions—

A high intake of anthocyanins may reduce MI risk in predominantly young women. Intervention trials are needed to further examine the health impact of increasing intakes of commonly consumed anthocyanin-rich foods.
Precessional Cycles and Their Influence on the North Pacific and North Atlantic Summer Anticyclones
Authors: Mantsis Damianos F. , Clement Amy C. , Kirtman Ben , Broccoli Anthony J. , Erb Michael P.
Published: January 2013

The response of the Northern Hemisphere summer anticyclones to a change in the timing of perihelion is investigated using the GFDL Climate Model version 2.1 (CM2.1). The orbital forcing consists of changes in the seasonal cycle of the top-of-atmosphere insolation as the perihelion shifts from the Northern Hemisphere winter to the Northern Hemisphere summer solstice. The North Pacific summer anticyclone experiences a large strengthening as well as a northward and westward expansion. The North Atlantic subtropical high experiences a smaller change that consists of a slight westward expansion but little change in strength. Experiments with a primitive equation atmospheric model show that these changes represent the circulation response to changes in the diabatic heating, both local and remotely. The remote diabatic forcing is associated with changes in the Southeast Asian and African summer monsoons, and the local forcing is dominated by a combined effect of a change in low clouds and local precipitation.
Projections of a Wetter Sahel in the Twenty-First Century from Global and Regional Models
Authors: Vizy Edward K. , Cook Kerry H. , Crétat Julien , Neupane Naresh
Published: January 2013

Confident regional-scale climate change predictions for the Sahel are needed to support adaptation planning. State-of-the-art regional climate model (RCM) simulations at 90- and 30-km resolutions are run and analyzed along with output from five coupled atmosphere–ocean GCMs (AOGCMs) from phase 5 of the Coupled Model Intercomparison Project (CMIP5) to predict how the Sahel summer surface temperature, precipitation, and surface moisture are likely to change at the mid- and late-twenty-first century due to increased atmospheric CO2 concentrations under the representative concentration pathway 8.5 (RCP8.5) emission scenario and evaluate confidence in such projections. Future lateral boundary conditions are derived from CMIP5 AOGCMs.

It is shown that the regional climate model can realistically simulate the current summer evolution of the West African monsoon climate including the onset and demise of the Sahel wet season, a necessary but not sufficient condition for confident prediction.

RCM and AOGCM projections indicate the likelihood for increased surface air temperatures over this century, with Sahara and Sahel temperature increases of 2–3.5 K by midcentury, and 3–6 K by late century. Summer rainfall and surface moisture are also projected to increase over most of the Sahel. This is primarily associated with an increase in rainfall intensity and not a lengthening of the wet season. Pinpointing exactly when the rainfall and surface moisture increase will first commence and by exactly what magnitude is less certain as these predictions appear to be model dependent. Models that simulate stronger warming over the Sahara are associated with larger and earlier rainfall increases over the Sahel due to an intensification of the low-level West African westerly jet, and vice versa.
Atmospheric Carbon Dioxide Variability in the Community Earth System Model: Evaluation and Transient Dynamics during the Twentieth and Twenty-First Centuries
Authors: Keppel-Aleks Gretchen , Randerson James T. , Lindsay Keith , Stephens Britton B. , Keith Moore J. , Doney Scott C. , Thornton Peter E. , Mahowald Natalie M. , Hoffman Forrest M. , Sweeney Colm , Tans Pieter P. , Wennberg Paul O. , Wofsy Steven C.
Published: January 2013

Changes in atmospheric CO2 variability during the twenty-first century may provide insight about ecosystem responses to climate change and have implications for the design of carbon monitoring programs. This paper describes changes in the three-dimensional structure of atmospheric CO2 for several representative concentration pathways (RCPs 4.5 and 8.5) using the Community Earth System Model–Biogeochemistry (CESM1-BGC). CO2 simulated for the historical period was first compared to surface, aircraft, and column observations. In a second step, the evolution of spatial and temporal gradients during the twenty-first century was examined. The mean annual cycle in atmospheric CO2 was underestimated for the historical period throughout the Northern Hemisphere, suggesting that the growing season net flux in the Community Land Model (the land component of CESM) was too weak. Consistent with weak summer drawdown in Northern Hemisphere high latitudes, simulated CO2 showed correspondingly weak north–south and vertical gradients during the summer. In the simulations of the twenty-first century, CESM predicted increases in the mean annual cycle of atmospheric CO2 and larger horizontal gradients. Not only did the mean north–south gradient increase due to fossil fuel emissions, but east–west contrasts in CO2 also strengthened because of changing patterns in fossil fuel emissions and terrestrial carbon exchange. In the RCP8.5 simulation, where CO2 increased to 1150 ppm by 2100, the CESM predicted increases in interannual variability in the Northern Hemisphere midlatitudes of up to 60% relative to present variability for time series filtered with a 2–10-yr bandpass. Such an increase in variability may impact detection of changing surface fluxes from atmospheric observations.
Comparison between Dual-Doppler and EnKF Storm-Scale Wind Analyses: The 29–30 May 2004 Geary, Oklahoma, Supercell Thunderstorm
Authors: Potvin Corey K. , Wicker Louis J. , Biggerstaff Michael I. , Betten Daniel , Shapiro Alan
Published: January 2013

Kinematical analyses of storm-scale mobile radar observations are critical to advancing our understanding of supercell thunderstorms. Maximizing the accuracy of these analyses, and characterizing the uncertainty in ensuing conclusions about storm structure and processes, requires knowledge of the error characteristics of different retrieval techniques under different observational scenarios. Using storm-scale mobile radar observations of a tornadic supercell, this study examines the impacts on ensemble Kalman filter (EnKF) wind analyses of the number of available radars (one versus two), uncertainty in the model-initialization sounding, the sophistication of the microphysical parameterization scheme (double versus single moment), and assimilating reflectivity observations. The relative accuracy of three-dimensional variational data assimilation (3DVAR) dual-Doppler wind retrievals and single- and dual-radar EnKF wind analyses of the supercell is also explored. The results generally reinforce the findings of a previous study that used observing system simulation experiments to explore the same issues. Both studies suggest that single-radar EnKF wind analyses can be very useful once enough data have been assimilated, but that subsequent analyses that operate on the retrieved wind field gradients should be interpreted with caution. In the present study, severe errors appear to occur in computed Lagrangian circulation time series, imperiling interpretation of the underlying dynamics. This result strongly suggests that dual- and multiple-Doppler radar deployment strategies continue to be used in mobile field campaigns.
Impact of Targeted Winter Storm Reconnaissance Dropwindsonde Data on Midlatitude Numerical Weather Predictions
Authors: Hamill Thomas M. , Yang Fanglin , Cardinali Carla , Majumdar Sharanya J.
Published: January 2013

The impact of assimilating data from the 2011 Winter Storm Reconnaissance (WSR) program on numerical weather forecasts was assessed. Parallel sets of analyses and deterministic 120-h numerical forecasts were generated using the ECMWF four-dimensional variational data assimilation (4D-Var) and Integrated Forecast System. One set of analyses was generated with all of the normally assimilated data plus WSR targeted dropwindsonde data, the other with only the normally assimilated data. Forecasts were then generated from the two analyses. The comparison covered the period from 10 January to 28 March 2011, during which 98 flights and 776 total dropwindsondes were deployed from four different air bases in the Pacific basin and the United States. The dropwindsondes were deployed in situations where guidance indicated the potential for high-impact weather and/or the potential for large subsequent forecast errors. Downstream target verification regions where the high-impact weather was expected were identified for each case. Forecast errors around the target verification regions were evaluated using an approximation to the total-energy norm. Precipitation forecasts were also evaluated over the contiguous United States using the equitable threat score and bias.

Forecast impacts were generally neutral and thus smaller than reported in previous studies, most from over a decade ago, perhaps because of the improved forecast and assimilation system and the somewhat denser observation network. Target areas may also have been undersampled in this study. The neutral results from 2011 suggest that it may be more beneficial to explore other targeted observation concepts for the midlatitudes, such as assimilation of a denser set of cloud-drift winds and radiance data in dynamically sensitive regions.
Objective Limits on Forecasting Skill of Rare Events
Authors: Hitchens Nathan M. , Brooks Harold E. , Kay Michael P.
Published: January 2013

A method for determining baselines of skill for the purpose of the verification of rare-event forecasts is described and examples are presented to illustrate the sensitivity to parameter choices. These “practically perfect” forecasts are designed to resemble a forecast that is consistent with that which a forecaster would make given perfect knowledge of the events beforehand. The Storm Prediction Center’s convective outlook slight risk areas are evaluated over the period from 1973 to 2011 using practically perfect forecasts to define the maximum values of the critical success index that a forecaster could reasonably achieve given the constraints of the forecast, as well as the minimum values of the critical success index that are considered the baseline for skillful forecasts. Based on these upper and lower bounds, the relative skill of convective outlook areas shows little to no skill until the mid-1990s, after which this value increases steadily. The annual frequency of skillful daily forecasts continues to increase from the beginning of the period of study, and the annual cycle shows maxima of the frequency of skillful daily forecasts occurring in May and June.
Reexamining El Niño and Cholera in Peru: A Climate Affairs Approach
Authors: Ramírez Iván J. , Grady Sue C. , Glantz Michael H.
Published: January 2013

In the 1990s Peru experienced the first cholera epidemic after almost a century. The source of emergence was initially attributed to a cargo ship, but later there was evidence of an El Niño association. It was hypothesized that marine ecosystem changes associated with El Niño led to the propagation of V. cholerae along the coast of Peru, which in turn initiated the onset of the epidemic in 1991. Earlier studies supported this explanation by demonstrating a relationship between elevated temperatures and increased cholera incidence in Peru; however, other aspects of El Niño–Southern Oscillation (ENSO) and their potential impacts on cholera were not investigated. Therefore, this study examines the relationship between El Niño and cholera in Peru from a holistic view of the ENSO cycle. A “climate affairs” approach is employed as a conceptual framework to incorporate ENSO’s multidimensional nature and to generate new hypotheses about the ENSO and cholera association in Peru. The findings reveal that ENSO may have been linked to the cholera epidemic through multiple pathways, including rainfall extremes, La Niña, and social vulnerability, with impacts depending on the geography of teleconnections within Peru. When the definition of an ENSO event is examined, cholera appears to have emerged either during ENSO neutral or La Niña conditions. Furthermore, the analysis herein suggests that the impact of El Niño arrived much later, possibly resulting in heightened transmission in the austral summer of 1992. In conclusion, a modified hypothesis with these new insights on cholera emergence and transmission in Peru is presented.
Plasma Fatty Acids in Premature Infants With Hyperbilirubinemia
Authors: Klein Catherine J. , Havranek Thomas G. , Revenis Mary E. , Hassanali Zahra , Scavo Louis M.
Published: January 2013

Infants who are dependent on parenteral nutrition (PN) sometimes develop PN‐associated cholestasis (PNAC). A compassionate use protocol, approved by the U.S. Food and Drug Administration and the institutional review board, guided enrollment of hospitalized infants with PNAC (<1 year of age, PN dependence for >3 weeks). Plasma concentrations of essential fatty acids were monitored before and after a soybean‐based PN lipid, infused at 3 g/kg body weight/d, was replaced by an experimental fish oil–based intravenous fat emulsion (FO‐IVFE) at 1.0 g/kg/d. All participants were born premature (n = 10; 20% male). At enrollment, infants were (mean ± SD) 86.5 ± 53.5 days of life and weighed 2.24 ± 0.87 kg; direct bilirubin was 5.5 ± 1.3 mg/dL. After treatment, blood concentrations significantly increased from baseline (P < .017) for circulating eicosapentaenoic acid (6.3 ± 3.0 to 147.8 ± 53.1 µg/mL), docosahexaenoic acid (20.7 ± 6.5 to 163.7 ± 43.4 µg/mL), pristanic acid (0.01 ± 0.01 to 0.17 ± 0.03 µg/mL), and phytanic acid (0.06 ± 0.03 to 0.64 ± 0.15 µg/mL). In contrast, total plasma ω‐6 fatty acids (including linoleic acid) decreased (P < .017). The triene/tetraene ratio remained below the threshold value of 0.2 that defines ω‐6 deficiency. No adverse effects were observed attributable to FO‐IVFE. Discontinuation of FO‐IVFE was typically due to infants (body weight 3.76 ± 1.68 kg) transitioning to enteral feeding rather than for resolution of hyperbilirubinemia (direct bilirubin 7.9 ± 4.8 mg/dL). These exploratory results suggest that FO‐IVFE raises circulating ω‐3 fatty acids in premature infants without development of ω‐6 deficiency in the 8.3 ± 5.8–week time frame of this study.
Identifying Red Flags
Authors: Frigaard Martin , Goto Keiko , Wolff Cindy , Bianco-Simeral Stephanie , Fahey Thomas
Published: January 2013

Childhood obesity is predictive of adulthood obesity, hypertension, and cardiovascular disease risk. The purpose of this study was to examine BMI for age as an independent risk factor for elevated blood pressure (EBP) and pre-EBP in children, controlling for sex, race/ethnicity, and age. The secondary objective was to identify associations among BMI, BP, race/ethnicity, and sex. EBP was defined as having a BP ≥95th percentile for age, gender, and height; measurements ≥90th percentile were considered indicative of pre-EBP. The study sample included 166 fifth-grade students from 5 low-income elementary schools in northern California. It was found that 32% of students were either overweight ( ≥85th percentile BMI for age) or obese ( ≥95th percentile BMI for age), with significantly higher rates (55%) among Hispanic children (P < .01). Also, 22% of students presented with pre-EBP/EBP. Obese students were more likely than normal-weight students to present with a systolic pre-EBP reading (P < .05). Overweight and obese students were more likely than normal-weight students to present with a diastolic pre-EBP reading (P < .05). BMI is independently predictive of EBP. Fitness testing with anthropometric measurements should incorporate BP screenings for students with a BMI ≥85th percentile.
Mid-Upper-Arm Circumference (MUAC) as a Simple Measure to Assess the Nutritional Status of Adolescent Girls as Compared With BMI
Authors: Jeyakumar Angeline , Ghugre Padmini , Gadhave Swapnil
Published: January 2013

Background. The use of mid-upper-arm circumference (MUAC) as a screening measure for assessing undernutrition has the following advantages: makes use of simple equipment, is easy to carry to field sites, and requires minimal training. MUAC cutoffs for undernutrition are available for children and adults but not for adolescents. Objective. To compare MUAC with BMI in assessing undernutrition among adolescent girls and to evaluate the sensitivity and specificity of MUAC as a tool in assessing their nutritional status. Methodology. A total of 565 unmarried adolescent girls of both school-going and non-school-going age (16-18 years old) from the urban slums of Pune city Maharashtra, India, were recruited for the cross-sectional study. Anthropometric measurements, including height, weight, and MUAC were recorded. Results. The percentage of adolescents who were malnourished was 4.8% according to BMI and 5.0% for MUAC. BMI highly correlated with MUAC (r = 0.593), and MUAC as a screening tool showed 28.57% sensitivity and 96.46% specificity. Further studies among different age groups need to be carried out to arrive at standard cutoffs for MUAC.
Improving acute promyelocytic leukemia (APL) outcome in developing countries through networking, results of the International Consortium on APL
Authors: Rego Eduardo M. , Kim Haesook T. , Ruiz-Argüelles Guillermo J. , Undurraga Maria Soledad , Uriarte Maria del Rosario , Jacomo Rafael H. , Gutiérrez-Aguirre Homero , Melo Raul A. M. , Bittencourt Rosane , Pasquini Ricardo , Pagnano Katia , Fagundes Evandro M. , Chauffaille Maria de Lourdes , Chiattone Carlos S. , Martinez Lem , Meillón Luis A. , Gómez-Almaguer David , Kwaan Hau C. , Garcés-Eisele Javier , Gallagher Robert , Niemeyer Charlotte M. , Schrier Stanley L. , Tallman Martin , Grimwade David , Ganser Arnold , Berliner Nancy , Ribeiro Raul C. , Lo-Coco Francesco , Löwenberg Bob , Sanz Miguel A.
Published: January 2013

Key Points

For patients in developing countries with APL, a clinical network of institutions made it possible to reduce significantly the early mortality and improve the OS.
Accurate prediction of protein enzymatic class by N-to-1 Neural Networks
Authors: Volpato Viola , Adelfio Alessandro , Pollastri Gianluca
Published: January 2013

We present a novel ab initio predictor of protein enzymatic class. The predictor can classify proteins, solely based on their sequences, into one of six classes extracted from the enzyme commission (EC) classification scheme and is trained on a large, curated database of over 6,000 non-redundant proteins which we have assembled in this work. The predictor is powered by an ensemble of N-to-1 Neural Network, a novel architecture which we have recently developed. N-to-1 Neural Networks operate on the full sequence and not on predefined features. All motifs of a predefined length (31 residues in this work) are considered and are compressed by an N-to-1 Neural Network into a feature vector which is automatically determined during training. We test our predictor in 10-fold cross-validation and obtain state of the art results, with a 96% correct classification and 86% generalized correlation. All six classes are predicted with a specificity of at least 80% and false positive rates never exceeding 7%. We are currently investigating enhanced input encoding schemes which include structural information, and are analyzing trained networks to mine motifs that are most informative for the prediction, hence, likely, functionally relevant.
Expression dynamics and genome distribution of osmoprotectants in soybean: identifying important components to face abiotic stress
Authors: Kido Ederson A , Ferreira Neto José RC , Silva Roberta LO , Belarmino Luis C , Bezerra Neto João P , Soares-Cavalcanti Nina M , Pandolfi Valesca , Silva Manassés D , Nepomuceno Alexandre L , Benko-Iseppon Ana M
Published: January 2013

Background

Despite the importance of osmoprotectants, no previous in silico evaluation of high throughput data is available for higher plants. The present approach aimed at the identification and annotation of osmoprotectant-related sequences applied to short transcripts from a soybean HT-SuperSAGE (High Throughput Super Serial Analysis of Gene Expression; 26-bp tags) database, and also its comparison with other transcriptomic and genomic data available from different sources.

Methods

A curated set of osmoprotectants related sequences was generated using text mining and selected seed sequences for identification of the respective transcripts and proteins in higher plants. To test the efficiency of the seed sequences, these were aligned against four HT-SuperSAGE contrasting libraries generated by our group using soybean tolerant and sensible plants against water deficit, considering only differentially expressed transcripts (p ≤ 0.05). Identified transcripts from soybean and their respective tags were aligned and anchored against the soybean virtual genome.

Results

The workflow applied resulted in a set including 1,996 seed sequences that allowed the identification of 36 differentially expressed genes related to the biosynthesis of osmoprotectants [Proline (P5CS: 4, P5CR: 2), Trehalose (TPS1: 9, TPPB: 1), Glycine betaine (BADH: 4) and Myo- inositol (MIPS: 7, INPS1: 8)], also mapped in silico in the soybean genome (25 loci). Another approach considered matches using Arabidopsis full length sequences as seed sequences, and allowed the identification of 124 osmoprotectant-related sequences, matching ~10.500 tags anchored in the soybean virtual chromosomes. Osmoprotectant-related genes appeared clustered in all soybean chromosomes, with higher density in some subterminal regions and synteny among some chromosome pairs.

Conclusions

Soybean presents all searched osmoprotectant categories with some important members differentially expressed among the comparisons considered (drought tolerant or sensible vs. control; tolerant vs. sensible), allowing the identification of interesting candidates for biotechnological inferences. The identified tags aligned to corresponding genes that matched 19 soybean chromosomes. Osmoprotectant-related genes are not regularly distributed in the soybean genome, but clustered in some regions near the chromosome terminals, with some redundant clusters in different chromosomes indicating their involvement in previous duplication and rearrangements events. The seed sequences, transcripts and map represent the first transversal evaluation for osmoprotectant-related genes and may be easily applied to other plants of interest.
Finding reproducible cluster partitions for the k-means algorithm
Authors: Lisboa Paulo JG , Etchells Terence A , Jarman Ian H , Chambers Simon J
Published: January 2013

K-means clustering is widely used for exploratory data analysis. While its dependence on initialisation is well-known, it is common practice to assume that the partition with lowest sum-of-squares (SSQ) total i.e. within cluster variance, is both reproducible under repeated initialisations and also the closest that k-means can provide to true structure, when applied to synthetic data. We show that this is generally the case for small numbers of clusters, but for values of k that are still of theoretical and practical interest, similar values of SSQ can correspond to markedly different cluster partitions.

This paper extends stability measures previously presented in the context of finding optimal values of cluster number, into a component of a 2-d map of the local minima found by the k-means algorithm, from which not only can values of k be identified for further analysis but, more importantly, it is made clear whether the best SSQ is a suitable solution or whether obtaining a consistently good partition requires further application of the stability index. The proposed method is illustrated by application to five synthetic datasets replicating a real world breast cancer dataset with varying data density, and a large bioinformatics dataset.
Young aboriginals are less likely to receive a renal transplant: a Canadian national study
Authors: Promislow Steven , Hemmelgarn Brenda , Rigatto Claudio , Tangri Navdeep , Komenda Paul , Storsley Leroy , Yeates Karen , Mojica Julie , Sood Manish M
Published: January 2013

Background

Previous studies have demonstrated Aboriginals are less likely to receive a renal transplant in comparison to Caucasians however whether this applies to the entire population or specific subsets remains unclear. We examined the effect of age on renal transplantation in Aboriginals.

Methods

Data on 30,688 dialysis (Aboriginal 2,361, Caucasian 28, 327) patients obtained between Jan. 2000 and Dec. 2009 were included in the final analysis. Racial status was self-reported. Cox proportional hazards, the Fine and Grey sub-distribution method and Poisson regression were used to determine the association between race, age and transplantation.

Results

In comparison to Caucasians, Aboriginals were less likely to receive a renal transplant (Adjusted HR 0.66 95% CI 0.57-0.77, P < 0.0001) however after stratification by age and treating death as a competing outcome, the effect was more predominant in younger Aboriginals (Age 18–40: 20.6% aboriginals vs. 48.3% Caucasians transplanted; aHR 0.50(0.39-0.61), p < 0.0001, Age 41–50: 10.2% aboriginals vs. 33.9% Caucasians transplanted; aHR 0.46(0.32-0.64), p = 0.005, Age 51–60: 8.2% aboriginals vs. 19.5% Caucasians transplanted; aHR0.65(0.49-0.88), p = 0.01, Age >60: 2.7% aboriginals vs. 2.6% Caucasians transplanted; aHR 1.21(0.76-1.91), P = 0.4, Age X race interaction p < 0.0001). Both living and deceased donor transplants were lower in Aboriginals under the age of 60 compared to Caucasians.

Conclusion

Younger Aboriginals are less likely to receive a renal transplant compared to their Caucasian counterparts, even after adjustment for comorbidity. Determination of the reasons behind these discrepancies and interventions specifically targeting the Aboriginal population are warranted.
Selecting renal replacement therapies: what do African American and non-African American patients and their families think others should know? A mixed methods study
Authors: DePasquale Nicole , Ephraim Patti L , Ameling Jessica , Lewis-Boyér Lapricia , Crews Deidra C , Greer Raquel C , Rabb Hamid , Powe Neil R , Jaar Bernard G , Gimenez Luis , Auguste Priscilla , Jenckes Mollie , Boulware L Ebony
Published: January 2013

Background

Little is known regarding the types of information African American and non-African American patients with chronic kidney disease (CKD) and their families need to inform renal replacement therapy (RRT) decisions.

Methods

In 20 structured group interviews, we elicited views of African American and non-African American patients with CKD and their families about factors that should be addressed in educational materials informing patients’ RRT selection decisions. We asked participants to select factors from a list and obtained their open-ended feedback.

Results

Ten groups of patients (5 African American, 5 non-African American; total 68 individuals) and ten groups of family members (5 African American, 5 non-African American; total 62 individuals) participated. Patients and families had a range (none to extensive) of experiences with various RRTs. Patients identified morbidity or mortality, autonomy, treatment delivery, and symptoms as important factors to address. Family members identified similar factors but also cited the effects of RRT decisions on patients’ psychological well-being and finances. Views of African American and non-African American participants were largely similar.

Conclusions

Educational resources addressing the influence of RRT selection on patients’ morbidity and mortality, autonomy, treatment delivery, and symptoms could help patients and their families select RRT options closely aligned with their values. Including information about the influence of RRT selection on patients’ personal relationships and finances could enhance resources’ cultural relevance for African Americans.
Gender difference in the characteristics of and high-risk behaviours among non-injecting heterosexual methamphetamine users in Qingdao, Shandong Province, China
Authors: Liu Dianchang , Wang Zhenhong , Chu Tongsheng , Chen Shumin
Published: January 2013

Background

Despite the increasing risk of HIV infections, few studies concerning the characteristics of non-injecting heterosexual methamphetamine (MA) users and related risk behaviours have been conducted in China.

Methods

Gender differences in socio-demographic characteristics, perception of MA and STD/HIV, MA use practices, and sexual behaviours related to MA use were examined among 398 non-injecting heterosexual MA users (288 males, 110 females).

Results

Male MA users were more likely to be married, local, and self-employed; female MA users were more likely to be young, single, engaged in commercial service or unemployed. Female MA users usually start MA use at an earlier age than males (24.3 vs. 31.3 years old), with shorter abuse durations (2.6 vs. 2.9 years), higher frequency of MA use (3.6 vs. 2.4 times per week), and higher likelihood of using MA with heterosexual partners (100% vs. 78.1%). More male MA users have had multiple sex partners (96.9% vs. 77.3%) and sex exchanges (72.9% vs. 46.4%). Among 277 males who had had sex with commercial sex workers (CSW), 69.4% never used condoms, and among 77 males who had had sex with multiple partners who are commercial sex workers and always or usually used condoms, 87.0% never changed condoms when changing partners.

Conclusion

There may be gender difference in the characteristics of high-risk behaviours among non-injecting heterosexual MA users. The findings suggest the integration of specific risk reduction strategies into intervention programs for non-injecting heterosexual MA user populations may significantly improve program goals.
Gamified physical activation of young men – a Multidisciplinary Population-Based Randomized Controlled Trial (MOPO study)
Authors: Ahola Riikka , Pyky Riitta , Jämsä Timo , Mäntysaari Matti , Koskimäki Heli , Ikäheimo Tiina M , Huotari Maija-Leena , Röning Juha , Heikkinen Hannu I , Korpelainen Raija
Published: January 2013

Background

Inactive and unhealthy lifestyles are common among adolescent men. The planned intervention examines the effectiveness of an interactive, gamified activation method, based on tailored health information, peer networks and participation, on physical activity, health and wellbeing in young men. We hypothesize that following the intervention the physical activation group will have an improved physical activity, as well as self-determined and measured health compared with the controls.

Methods/design

Conscription-aged men (18 years) attending compulsory annual call-ups for military service in the city of Oulu in Finland (n = 1500) will be randomized to a 6-months intervention (n = 640) or a control group (n = 640) during the fall 2013. A questionnaire on health, health behaviour, diet and wellbeing is administered in the beginning and end of the intervention. In addition, anthropometric measures (height, weight and waist circumference), body composition, grip strength, heart rate variability and aerobic fitness will be measured. The activation group utilizes an online gamified activation method in combination with communal youth services, objective physical activity measurement, social networking, tailored health information and exercise programs according to baseline activity level and the readiness of changes of each individual. Daily physical activity of the participants is monitored in both the activation and control groups. The activation service rewards improvements in physical activity or reductions in sedentary behaviour. The performance and completion of the military service of the participants will also be followed.

Discussion

The study will provide new information of physical activity, health and health behaviour of young men. Furthermore, a novel model including methods for increasing physical activity among young people is developed and its effects tested through an intervention. This unique gamified service for activating young men can provide a translational model for community use. It can also be utilized as such or tailored to other selected populations or age groups.

Trial registration

ClinicalTrials.gov Identifier: NCT01376986
Vitamin D deficiency among healthy adolescents in Al Ain, United Arab Emirates
Authors: Muhairi Shamma J , Mehairi Aaesha E , Khouri Aysha A , Naqbi Muna M , Maskari Fatima A , Kaabi Juma Al , Dhaheri Ayesha S Al , Nagelkerke Nico , Shah Syed M
Published: January 2013

Background

Although vitamin D deficiency has been studied in various adult populations, there are few data on the prevalence of this nutritional deficiency among healthy adolescents in the United Arab Emirates (UAE). This study was conducted to determine the prevalence of vitamin D deficiency and to examine its correlates in adolescents aged 15 to 18 years.

Methods

This was a cross-sectional study in urban schools. Healthy adolescents (N=315) from a sample of 8 schools were randomly selected from the 142 schools in Al Ain, Abu Dhabi Emirate. Outcomes measured included serum concentrations of 25-hydroxy vitamin D (25OHD), plasma lipids, blood sugar, blood pressure and anthropometric data, nutrition and lifestyle variables.

Results

Fourty-one participants (19.7%) were vitamin D deficient (serum 25OHD level ≤15 ng/mL [≤37.5 nmol/L]. Using a cutoff level of 25(OH) D of ≤20 ng/ml [≤50 nmol/l] 143 participants (45.4%) were vitamin D insufficient. Overall 65.1% of study participants were either vitamin D deficient or insufficient. The prevalence of vitamin D deficiency varied between boys (10%) and girls (28%). In a final multivariate model, serum 25(OH) D concentrations were inversely correlated with female gender, consumption of fast food per week, and body mass index and positively correlated with physical activity scores after adjustment for age.

Conclusions

Vitamin D deficiency and insufficiency were highly prevalent in adolescents, and more common in girls.
Obesity & hypertension are determinants of poor hemodynamic control during total joint arthroplasty: a retrospective review
Authors: Nwachukwu Benedict U , Collins Jamie E , Nelson Emily P , Concepcion Mercedes , Thornhill Thomas S , Katz Jeffrey N
Published: January 2013

Background

Proper blood pressure control during surgical procedures such as total joint arthroplasty (TJA) is considered critical to good outcome. There is poor understanding of the pre-operative risk factors for poor intra-operative hemodynamic control. The purpose of this study is to identify risk factors for poor hemodynamic control during TJA.

Methods

We performed a retrospective cohort analysis of 118 patients receiving TJA in the Dominican Republic. We collected patient demographic and comorbidity data. We developed an a priori definition for poor hemodynamic control: 1) Mean arterial pressure (MAP) <65% of preoperative MAP or 2) MAP >135% of preoperative MAP. We performed bivariate and multivariate analyses to identify risk factors for poor hemodynamic control during TJA.

Results

Hypertension was relatively common in our study population (76 of 118 patients). Average preoperative mean arterial pressure was 109.0 (corresponding to an average SBP of 149 and DBP of 89). Forty-nine (41.5%) patients had intraoperative blood pressure readings consistent with poor hemodynamic control. Based on multi-variable analysis preoperative hypertension of any type (RR 2.9; 95% CI 1.3-6.3) and an increase in BMI (RR 1.2 per 5 unit increase; 95% CI 1.0-1.5) were significant risk factors for poor hemodynamic control.

Conclusions

Preoperative hypertension and being overweight/obese increase the likelihood of poor blood pressure control during TJA. Hypertensive and/or obese patients warrant further attention and medical optimization prior to TJA. More work is required to elucidate the relationship between these risk factors and overall outcome.
ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format
Authors: Thomas Dennis G , Gaheen Sharon , Harper Stacey L , Fritts Martin , Klaessig Fred , Hahn-Dantona Elizabeth , Paik David , Pan Sue , Stafford Grace A , Freund Elaine T , Klemm Juli D , Baker Nathan A
Published: January 2013

Background and motivation

The high-throughput genomics communities have been successfully using standardized spreadsheet-based formats to capture and share data within labs and among public repositories. The nanomedicine community has yet to adopt similar standards to share the diverse and multi-dimensional types of data (including metadata) pertaining to the description and characterization of nanomaterials. Owing to the lack of standardization in representing and sharing nanomaterial data, most of the data currently shared via publications and data resources are incomplete, poorly-integrated, and not suitable for meaningful interpretation and re-use of the data. Specifically, in its current state, data cannot be effectively utilized for the development of predictive models that will inform the rational design of nanomaterials.

Results

We have developed a specification called ISA-TAB-Nano, which comprises four spreadsheet-based file formats for representing and integrating various types of nanomaterial data. Three file formats (Investigation, Study, and Assay files) have been adapted from the established ISA-TAB specification; while the Material file format was developed de novo to more readily describe the complexity of nanomaterials and associated small molecules. In this paper, we have discussed the main features of each file format and how to use them for sharing nanomaterial descriptions and assay metadata.

Conclusion

The ISA-TAB-Nano file formats provide a general and flexible framework to record and integrate nanomaterial descriptions, assay data (metadata and endpoint measurements) and protocol information. Like ISA-TAB, ISA-TAB-Nano supports the use of ontology terms to promote standardized descriptions and to facilitate search and integration of the data. The ISA-TAB-Nano specification has been submitted as an ASTM work item to obtain community feedback and to provide a nanotechnology data-sharing standard for public development and adoption.