scholarly journals CoeViz 2: Protein Graphs Derived From Amino Acid Covariance

2021 ◽  
Vol 1 ◽  
Author(s):  
Daniel Corcoran ◽  
Nicholas Maltbie ◽  
Shivchander Sudalairaj ◽  
Frazier N. Baker ◽  
Joseph Hirschfeld ◽  
...  
Keyword(s):  
Metal Binding ◽  
Large Scale ◽  
Pearson Correlation ◽  
3D Structure ◽  
Covariance Analysis ◽  
Web Based ◽  
Functional Sites ◽  
3D Space ◽  
Chi Squared ◽  
Molecular Functions

Proteins by and large carry out their molecular functions in a folded state when residues, distant in sequence, assemble together in 3D space to bind a ligand, catalyze a reaction, form a channel, or exert another concerted macromolecular interaction. It has been long recognized that covariance of amino acids between distant positions within a protein sequence allows for the inference of long range contacts to facilitate 3D structure modeling. In this work, we investigated whether covariance analysis may reveal residues involved in the same molecular function. Building upon our previous work, CoeViz, we have conducted a large scale covariance analysis among 7,595 non-redundant proteins with resolved 3D structures to assess 1) whether the residues with the same function coevolve, 2) which covariance metric captures such couplings better, and 3) how different molecular functions compare in this context. We found that the chi-squared metric is the most informative for the identification of coevolving functional sites, followed by the Pearson correlation-based, whereas mutual information is the least informative. Of the seven categories of the most common natural ligands, including coenzyme A, dinucleotide, DNA/RNA, heme, metal, nucleoside, and sugar, the trace metal binding residues display the most prominent coupling, followed by the sugar binding sites. We also developed a web-based tool, CoeViz 2, that enables the interactive visualization of covarying residues as cliques from a larger protein graph. CoeViz 2 is publicly available at https://research.cchmc.org/CoevLab/.

scholarly journals Comparison between an interactive web-based self-administered 24 h dietary record and an interview by a dietitian for large-scale epidemiological studies

2010 ◽  
Vol 105 (7) ◽  
pp. 1055-1064 ◽  
Author(s):  
Mathilde Touvier ◽  
Emmanuelle Kesse-Guyot ◽  
Caroline Méjean ◽  
Clothilde Pollet ◽  
Aurélie Malon ◽  
...  
Keyword(s):  
Large Scale ◽  
Pearson Correlation ◽  
Large Population ◽  
Intraclass Correlation ◽  
Data Entry ◽  
Epidemiological Studies ◽  
Web Based ◽  
Dietary Record ◽  
The Mean ◽  
The Web

Online self-administered data collection, by reducing the logistic burden and cost, could advantageously replace classical methods based on dietitian's interviews when assessing dietary intake in large epidemiological studies. Studies comparing such new instruments with traditional methods are necessary. Our objective was to compare one NutriNet-Santé web-based self-administered 24 h dietary record with one 24 h recall carried out by a dietitian. Subjects completed the web-based record, which was followed the next day by a dietitian-conducted 24 h recall by telephone (corresponding to the same day and using the same computerised interface for data entry). The subjects were 147 volunteers aged 48–75 years (women 59·2 %). The study was conducted in February 2009 in France. Agreement was assessed by intraclass correlation coefficients (ICC) for foods and energy-adjusted Pearson's correlations for nutrients. Agreement between the two methods was high, although it may have been overestimated because the two assessments were consecutive to one another. Among consumers only, the median of ICC for foods was 0·8 in men and 0·7 in women (range 0·5–0·9). The median of energy-adjusted Pearson's correlations for nutrients was 0·8 in both sexes (range 0·6–0·9). The mean Pearson correlation was higher in subjects ≤ 60 years (P = 0·02) and in those who declared being ‘experienced/expert’ with computers (P = 0·0003), but no difference was observed according to educational level (P = 0·12). The mean completion time was similar between the two methods (median for both methods: 25 min). The web-based method was preferred by 66·1 % of users. Our web-based dietary assessment, permitting considerable logistic simplification and cost savings, may be highly advantageous for large population-based surveys.

Using Web-based Testing for Large-Scale Assessment

2013 ◽  
Author(s):  
Laura S. Hamilton ◽  
Stephen P. Klein ◽  
William Lorie
Keyword(s):  
Large Scale ◽  
Web Based ◽  
Large Scale Assessment ◽  
Scale Assessment

Impact of COVID-19 on Nuclear Medicine in Germany, Austria and Switzerland: An International Survey in April 2020

2020 ◽  
Vol 59 (04) ◽  
pp. 294-299 ◽  
Author(s):  
Lutz S. Freudenberg ◽  
Ulf Dittmer ◽  
Ken Herrmann
Keyword(s):  
Nuclear Medicine ◽  
Health Systems ◽  
Personal Protective Equipment ◽  
Large Scale ◽  
Diagnostic Procedures ◽  
Protective Equipment ◽  
Current Crisis ◽  
Web Based ◽  
Public Versus Private ◽  
The Impact

Abstract Introduction Preparations of health systems to accommodate large number of severely ill COVID-19 patients in March/April 2020 has a significant impact on nuclear medicine departments. Materials and Methods A web-based questionnaire was designed to differentiate the impact of the pandemic on inpatient and outpatient nuclear medicine operations and on public versus private health systems, respectively. Questions were addressing the following issues: impact on nuclear medicine diagnostics and therapy, use of recommendations, personal protective equipment, and organizational adaptations. The survey was available for 6 days and closed on April 20, 2020. Results 113 complete responses were recorded. Nearly all participants (97 %) report a decline of nuclear medicine diagnostic procedures. The mean reduction in the last three weeks for PET/CT, scintigraphies of bone, myocardium, lung thyroid, sentinel lymph-node are –14.4 %, –47.2 %, –47.5 %, –40.7 %, –58.4 %, and –25.2 % respectively. Furthermore, 76 % of the participants report a reduction in therapies especially for benign thyroid disease (-41.8 %) and radiosynoviorthesis (–53.8 %) while tumor therapies remained mainly stable. 48 % of the participants report a shortage of personal protective equipment. Conclusions Nuclear medicine services are notably reduced 3 weeks after the SARS-CoV-2 pandemic reached Germany, Austria and Switzerland on a large scale. We must be aware that the current crisis will also have a significant economic impact on the healthcare system. As the survey cannot adapt to daily dynamic changes in priorities, it serves as a first snapshot requiring follow-up studies and comparisons with other countries and regions.

Ethnopharmacological Survey of Medicinal Plants Used in Traditional Treatment of Kidney Diseases in Fez–Meknes Region, Morocco

2019 ◽  
Vol 18 (2) ◽  
pp. 99-114
Author(s):  
M. Chebaibi ◽  
D. Bousta ◽  
I. Iken ◽  
H. Hoummani ◽  
A. Ech-Choayeby ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Medicinal Plants ◽  
Kidney Diseases ◽  
Rank Order ◽  
Pearson Correlation ◽  
Use Value ◽  
Traditional Treatment ◽  
Toxic Plants ◽  
A Value ◽  
Chi Squared

The purpose of this study was to inventory and collect information on plants and mixtures commonly used by herbalists to treat kidney disease in the Fez–Meknes region. We also aimed to compare the results obtained with the results of the other studies and exploit the correlations between different factors. An ethnopharmacological survey was conducted from 289 local herbalists in eight different areas of Fez–Meknes region. Ethnomedicinal uses and ethnobotanical indices were analyzed using quantitative tools, i.e., the total number of citation (TNC), use value (UV), family use value (FUV), fidelity level (FL), and rank order priority (ROP). Statistical analyses such as Pearson correlation and chi-squared test were performed to delineate any correlation. Two hundred and eighty-nine herbalists were questioned. Sixty-nine plant species belonging to 38 families were cited by herbalists for traditional treatment of kidney disease. The highest value of UV was obtained for Herniaria glabra L. (UV = 0.79), and Caryophyllaceae was the family frequently cited (FUV = 0.795). Ammodaucus leucotrichus Coss. & Dur. had the highest value of FL with a value of 100%, and the highest value of ROP was recorded for Herniaria glabra L. (ROP = 91%). Sociodemographic characteristics had a significant impact on the knowledge of toxic plants. Our study has revealed a cultural heritage linked to herbalism and a great wealth of medicinal plants, whose valorization and protection are necessary. Several studies are needed to sensitize herbalists and population on the danger of toxic plants, to extract chemical compounds from the main plants used, and to evaluate their toxicity.

scholarly journals Age impairs mnemonic discrimination of objects more than scenes: A web-based, large-scale approach across the lifespan

Cortex ◽  
2021 ◽  
Vol 137 ◽  
pp. 138-148
Author(s):  
Jeremie Güsten ◽  
Gabriel Ziegler ◽  
Emrah Düzel ◽  
David Berron
Keyword(s):  
Large Scale ◽  
Web Based

scholarly journals Evaluation of dietary intake assessed by the Dutch self-administered web-based dietary 24-h recall tool (Compl-eat™) against interviewer-administered telephone-based 24-h recalls

2017 ◽  
Vol 6 ◽  
Author(s):  
Saskia Meijboom ◽  
Martinette T. van Houts-Streppel ◽  
Corine Perenboom ◽  
Els Siebelink ◽  
Anne M. van de Wiel ◽  
...  
Keyword(s):  
Dietary Intake ◽  
Large Scale ◽  
Alcohol Intake ◽  
Lower Number ◽  
Vitamin B ◽  
Food Groups ◽  
Web Based ◽  
The Web

AbstractSelf-administered web-based 24-h dietary recalls (24 hR) may save a lot of time and money as compared with interviewer-administered telephone-based 24 hR interviews and may therefore be useful in large-scale studies. Within the Nutrition Questionnaires plus (NQplus) study, the web-based 24 hR tool Compl-eat™ was developed to assess Dutch participants’ dietary intake. The aim of the present study was to evaluate the performance of this tool against the interviewer-administered telephone-based 24 hR method. A subgroup of participants of the NQplus study (20–70 years, n 514) completed three self-administered web-based 24 hR and three telephone 24 hR interviews administered by a dietitian over a 1-year period. Compl-eat™ as well as the dietitians guided the participants to report all foods consumed the previous day. Compl-eat™ on average underestimated the intake of energy by 8 %, of macronutrients by 10 % and of micronutrients by 13 % as compared with telephone recalls. The agreement between both methods, estimated using Lin's concordance coefficients (LCC), ranged from 0·15 for vitamin B1 to 0·70 for alcohol intake (mean LCC 0·38). The lower estimations by Compl-eat™ can be explained by a lower number of total reported foods and lower estimated intakes of the food groups, fats, oils and savoury sauces, sugar and confectionery, dairy and cheese. The performance of the tool may be improved by, for example, adding an option to automatically select frequently used foods and including more recall cues. We conclude that Compl-eat™ may be a useful tool in large-scale Dutch studies after suggested improvements have been implemented and evaluated.

scholarly journals Metalearning approach for leukemia informative genes prioritization

2020 ◽  
Vol 17 (1) ◽  
Author(s):  
Vânia Rodrigues ◽  
Sérgio Deusdado
Keyword(s):  
High Performance ◽  
Information Gain ◽  
Pearson Correlation ◽  
Microarray Gene Expression Data ◽  
Microarray Gene Expression ◽  
The Public ◽  
Leukemia Diagnosis ◽  
Chi Squared ◽  
Logistic Regression Method ◽  
Single Attribute

AbstractThe discovery of diagnostic or prognostic biomarkers is fundamental to optimize therapeutics for patients. By enhancing the interpretability of the prediction model, this work is aimed to optimize Leukemia diagnosis while retaining a high-performance evaluation in the identification of informative genes. For this purpose, we used an optimal parameterization of Kernel Logistic Regression method on Leukemia microarray gene expression data classification, applying metalearners to select attributes, reducing the data dimensionality before passing it to the classifier. Pearson correlation and chi-squared statistic were the attribute evaluators applied on metalearners, having information gain as single-attribute evaluator. The implemented models relied on 10-fold cross-validation. The metalearners approach identified 12 common genes, with highest average merit of 0.999. The practical work was developed using the public datamining software WEKA.

scholarly journals Comparison of a web-based food record tool and a food-frequency questionnaire and objective validation using the doubly labelled water technique in a Swedish middle-aged population

2016 ◽  
Vol 5 ◽  
Author(s):  
Sanna Nybacka ◽  
Heléne Bertéus Forslund ◽  
Elisabet Wirfält ◽  
Ingrid Larsson ◽  
Ulrika Ericson ◽  
...  
Keyword(s):  
Energy Intake ◽  
Large Scale ◽  
Dietary Assessment ◽  
Assessment Tools ◽  
Future Research ◽  
Food Record ◽  
Frequency Method ◽  
Doubly Labelled Water ◽  
Web Based ◽  
Food Frequency

AbstractTwo web-based dietary assessment tools have been developed for use in large-scale studies: the Riksmaten method (4-d food record) and MiniMeal-Q (food-frequency method). The aim of the present study was to examine the ability of these methods to capture energy intake against objectively measured total energy expenditure (TEE) with the doubly labelled water technique (TEEDLW), and to compare reported energy and macronutrient intake. This study was conducted within the pilot study of the Swedish CArdioPulmonary bioImage Study (SCAPIS), which included 1111 randomly selected men and women aged 50–64 years from the Gothenburg general population. Of these, 200 were enrolled in the SCAPIS diet substudy. TEEDLW was measured in a subsample (n 40). Compared with TEEDLW, both methods underestimated energy intake: −2·5 (sd  2·9) MJ with the Riksmaten method; −2·3 (sd 3·6) MJ with MiniMeal-Q. Mean reporting accuracy was 80 and 82 %, respectively. The correlation between reported energy intake and TEEDLW was r 0·4 for the Riksmaten method (P < 0·05) and r 0·28 (non-significant) for MiniMeal-Q. Women reported similar average intake of energy and macronutrients in both methods whereas men reported higher intakes with the Riksmaten method. Energy-adjusted correlations ranged from 0·14 (polyunsaturated fat) to 0·77 (alcohol). Bland–Altman plots showed acceptable agreement for energy and energy-adjusted protein and carbohydrate intake, whereas the agreement for fat intake was poorer. According to energy intake data, both methods displayed similar precision on energy intake reporting. However, MiniMeal-Q was less successful in ranking individuals than the Riksmaten method. The development of methods to achieve limited under-reporting is a major challenge for future research.

Sign in / Sign up

Export Citation Format

Share Document