197,353 research outputs found
Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Get PDFThis paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa. The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars. Height and weight were measured following standard techniques. The body mass index (BMI) was computed following standard equation. Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI. We followed the World Health Organization's classification (1995) of the public health problem of low BMI, based on adult populations worldwide. Our results show that, in general, among the tribes studied:
i)Both sexes had very low levels of BMI
ii)There existed high rates of CED indicating a critical nutritional condition 
iii)Women experienced greater nutritional stress
iv)The nutritional situation is similar in both West Bengal as well as Orissa.

Using open access literature to guide full-text query formulation
Get PDF*Background*
Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments.

*Methodology and Results*
We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full-text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. Due to this relatively high precision, the derived query was better suited to the intended application than alternative baseline MeSH queries.

*Significance*
Using open access literature to develop queries for full-text portals is an open, flexible, and effective method for retrieval of biomedical literature articles based on article full-text. We hope our approach will raise awareness of the constraints and opportunities in mainstream full-text information retrieval and provide a useful tool for today’s researchers.

Using open access literature to guide full-text query formulation
Get PDF*Background* 
Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments.
 
*Methodology and Results* 
We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full-text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. Due to this relatively high precision, the derived query was better suited to the intended application than alternative baseline MeSH queries.
 
*Significance* 
Using open access literature to develop queries for full-text portals is an open, flexible, and effective method for retrieval of biomedical literature articles based on article full-text. We hope our approach will raise awareness of the constraints and opportunities in mainstream full-text information retrieval and provide a useful tool for today’s researchers.

Establishment of prophylactic enoxaparin dosing recommendations to achieve targeted anti-factor Xa concentrations in children with CHD
Get PDFBackground
Enoxaparin may be used to prevent central venous catheter-related thrombosis in patients with CHD. We aimed to determine whether current enoxaparin dosing regimens effectively achieve anti-factor Xa concentrations within prophylactic goal ranges in this patient population.
Methods
We implemented a formal protocol aimed at reducing central venous catheter-related thrombosis in children with CHD in January, 2016. Standard empiric prophylactic enoxaparin dosing regimens were used – for example, 0.75 mg/kg/dose every 12 hours for patients <2 months of age and 0.5 mg/kg/dose every 12 hours for patients ⩾2 months of age – with anti-factor Xa goal range of 0.25–0.49 IU/ml. Patients <2 years of age who received enoxaparin and had at least one valid steady-state anti-factor Xa measurement between 25 January, 2016 and 31 August, 2016 were retrospectively reviewed.
Results
During the study period, 47 patients had 186 anti-factor Xa concentrations measured, of which 20 (11%) were above and 112 (60%) were below the prophylactic goal range. Anti-factor Xa concentrations within the goal range were ultimately achieved in 31 patients. Median dose required to achieve anti-factor Xa concentrations within the prophylactic range was 0.89 mg/kg/dose (25, 75%: 0.75, 1.11) for patients <2 months (n=23 patients) and 0.79 mg/kg/dose (25, 75%: 0.62, 1.11) for patients ⩾2 months (n=8 patients).
Conclusions
Enoxaparin doses required to achieve prophylactic anti-factor Xa concentrations in young children with CHD were consistently higher than the currently recommended prophylactic dosing regimens. Further study is needed to determine whether dose titration to achieve prophylactic anti-factor Xa concentrations is effective in preventing central venous catheter-related thrombosis
Objective dysphonia quantification in vocal fold paralysis: comparing nonlinear with classical measures
Get PDFClinical acoustic voice recording analysis is usually performed using classical perturbation measures including jitter, shimmer and noise-to-harmonic ratios. However, restrictive mathematical limitations of these measures prevent analysis for severely dysphonic voices. Previous studies of alternative nonlinear random measures addressed wide varieties of vocal pathologies. Here, we analyze a single vocal pathology cohort, testing the performance of these alternative measures alongside classical measures.

We present voice analysis pre- and post-operatively in unilateral vocal fold paralysis (UVFP) patients and healthy controls, patients undergoing standard medialisation thyroplasty surgery, using jitter, shimmer and noise-to-harmonic ratio (NHR), and nonlinear recurrence period density entropy (RPDE), detrended fluctuation analysis (DFA) and correlation dimension. Systematizing the preparative editing of the recordings, we found that the novel measures were more stable and hence reliable, than the classical measures, on healthy controls.

RPDE and jitter are sensitive to improvements pre- to post-operation. Shimmer, NHR and DFA showed no significant change (p > 0.05). All measures detect statistically significant and clinically important differences between controls and patients, both treated and untreated (p < 0.001, AUC > 0.7). Pre- to post-operation, GRBAS ratings show statistically significant and clinically important improvement in overall dysphonia grade (G) (AUC = 0.946, p < 0.001).

Re-calculating AUCs from other study data, we compare these results in terms of clinical importance. We conclude that, when preparative editing is systematized, nonlinear random measures may be useful UVFP treatment effectiveness monitoring tools, and there may be applications for other forms of dysphonia.

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Get PDFMany advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, "http://tumor.informatics.jax.org":http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.

Although primary source for the data represented in MTB is peer-reviewed scientific literature an increasing amount of data is derived from disparate sources. MTB includes annotated histopathology images and cytogenetic assay images for mouse tumors where these data are available from The Jackson Laboratory’s mouse colonies and from outside contributors. MTB encourages direct submission of mouse tumor data and images from the cancer research community and provides investigators with a web-accessible tool for image submission and annotation. 

Integrated searches of the data in MTB are facilitated by the use of several controlled vocabularies and by adherence to standard nomenclature. MTB also provides links to other related online resources such as the Mouse Genome Database, Mouse Phenome Database, the Biology of the Mammary Gland Web Site, Festing's Listing of Inbred Strains of Mice, the JAX® Mice Web Site, and the Mouse Models of Human Cancers Consortium's Mouse Repository. 

MTB provides access to data on mouse models of cancer via the internet and has been designed to facilitate the selection of experimental models for cancer research, the evaluation of mouse genetic models of human cancer, the review of patterns of mutations in specific cancers, and the identification of genes that are commonly mutated across a spectrum of cancers.

MTB is supported by NCI grant CA089713
Novel developments in SBGN-ED and applications
Get PDFSystems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.
We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps from scratch, to validate these maps for syntactical and semantical correctness, to translate maps from the KEGG database into SBGN, and to export SBGN maps into several file and image formats. SBGN-ED is based on VANTED (Visualization and Analysis of NeTworks containing Experimental Data, http://www.vanted.org) [3].
As applications of SBGN and SBGN-ED we present furthermore MetaCrop (http://metacrop.ipk-gatersleben.de) [4], a database that summarizes diverse information about metabolic pathways in crop plants, and RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development, http://rimas.ipk-gatersleben.de) [5], an information portal that provides a comprehensive overview of regulatory pathways and genetic interactions during Arabidopsis embryo and seed development. 

[1] Le Novère, N. et al. (2009) The Systems Biology Graphical Notation. Nature Biotechnology, 27, 735-741.
[2] Czauderna, T., Klukas, C., Schreiber, F. (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26 (18), 2340-2341.
[3] Junker, B.H., Klukas, C., Schreiber, F. (2006) VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7, 109+.
[4] Grafahrend-Belau, E., Weise, S., Koschützki, D., Scholz, U., Junker, B.H., Schreiber, F. (2008) MetaCrop - A detailed database of crop plant metabolism. Nucleic Acids Research, 36, D954-D958.
[5] Junker, A., Hartmann, A., Schreiber, F., Bäumlein, H. (2010) An engineer's view on regulation of seed development. Trends in Plant Science, 15(6), 303-307.

Biostratigraphic Study of the Gurpi Formation Based on Planktonic Foraminifera In Lar Area (Kuh-e-kurdeh Section)
Get PDFThe study of planktonic foraminifera of the Gurpi formations at Lar area (Kuh-e-kurdeh section) enables me to find the most standard biozones defined in mediterranean regions, especially Tethysian domain. Five biozones were determined. Biozones I (Globotruncanita elevata zone) and II (Globotruncana ventricosa zone) and III (Radotruncana calcarata zone) indicate the Early Campanian and Middle and Late Campanian, respectively. Biozones IV (Globotruncanita stuarti zone) and V (Gansserina gansseri zone) suggest the Early and Middle Maastrichtian, respectively. In the Late Maastrichtian, due to decreasing in water depth at the study area, Abathomphalus mayaroensis zone defined in Tethysian domain was not recognised.


Weight, Length, and Growth in Cutbow Trout (Oncorhynchus mykiss x clarkii)
Get PDFBackground: The cutbow trout (Oncorhynchus mykiss x clarkii) is a fertile hybrid of rainbow and cutthroat trout. Little published length-weight data is available for this hybrid, and a standard weight curve is not established. Eleven Mile Reservoir is a clear mountain reservior in Colorado with a surface area of 13.4 square kilometers, an average depth of 10 m, and a maximum depth of 41 m. 80,000 cutbow trout were stocked through the ice in late winter before samples were taken.
Materials and Methods: Angling provided 171 samples which were weighed and measured (total length and fork length). Dressed weight was also determined with the scales, head, and entrails removed. Estimates of parameters a and b in the model, W(L) = aLb, were obtained by both linear least-squares (LLS) regression (log(W) = log(a) + b log(L)) and non-linear least-squares (NLLS) regression, where W is weight in kg and L is length in cm. Parameter estimates of an improved model, W(L) = (L/L1)b, were also determined by NLLS regression; the parameter L1 is the typical length of a fish weighing 1 kg. The resulting best-fit parameters, parameter standard errors, and covariances are compared between the two models. Average weight and length are considered for each month from June through October to estimate growth rates for fish stocked over the winter. Standard weights (relative to the rainbow trout and cutthroat trout standard weight curves) are also determined, along with the ratio of total length to fork length and typical dressed weight percentage. 
Results: The improved model parameter estimates were b = 2.662 and L1 = 45.32 cm, with correlation coefficient r = 0.969. From June to October, mean relative weight decreased from 101.5% to 93.6% relative to the rainbow trout standard weight and 114.5% to 103.2% relative to the cutthroat trout standard weight as mean total lengths increased from 34.4 cm to 41.9 cm and the mean weights increased from 0.505 kg to 0.830 kg. Typical dressed weight is 71% of the total weight. 
Conclusion: Eleven mile reservoir is an excellent trout fishery, capable of producing large numbers of cutbow trout in good condition. The cutbow trout is well suited to this kind of mountain reservoir and grows fast. As might be expected, the weights of cutbow trout of a given length tend to fall between the standard weights of the rainbow and the cutthroat. For the season, the average relative weight was 97.0% relative to the rainbow trout, and 108.3% relative to cutthroat trout.

Decoding Sequence Classification Models for Acquiring New Biological Insights
Get PDFClassifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.

In this contribution, we propose a new approach to analyzing biological sequences on the basis of support vector machines with sequence kernels. We first extract explicit pattern weights from a given SVM. When classifying a sequence, we then compute a prediction profile by distributing the weight of each pattern to the sequence positions that match the pattern. The final profile not only allows assessing the importance of a position, but also determining for which class it is indicative. Since it is unfeasible to analyze profiles of all sequences in a given data set, we advocate using affinity propagation (AP) clustering to narrow down the analysis to a small set of typical sequences.

The proposed approach is applicable to a wide range of biological sequences and a wide selection of sequence kernels. To illustrate our framework, we present the prediction of oligomerization tendencies of coiled coil proteins as a case study.

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