The Global Burden of Snakebite: A Literature Analysis and Modelling Based on Regional Estimates of Envenoming and Deaths

Janaka de Silva and colleagues estimate that globally at least 421,000 envenomings and 20,000 deaths occur each year due to snakebite

The BigDawg monitoring framework

Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (page 44).In this thesis, I designed and implemented a monitoring framework for the BigDawg federated database system which maintains performance information on benchmark queries. As environmental conditions change, the monitoring framework updates existing performance information to match current conditions. Using this information, the monitoring system can determine the optimal query execution plan for similar incoming queries. A series of test queries were run to assess whether the system correctly determines the optimal plans for such queries.by Peinan Chen.M. Eng

Vfold: a web server for RNA structure and folding thermodynamics prediction.

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies.The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu"

An example of the Vfold3D prediction: the snapshot of Vfold3D web server highlights the input sequence (32 nts for this example) and the 2D structures as defined by the base pairs.

<p>(a) For the most probable 2D structure shown in Fig. 2, Vfold3D predicts 3D structure based on the templates from the known structures. (b) For the predicted alternative structure shown in Fig. 2, Vfold3D cannot predict the 3D structure due to the lack of the available template for the single-stranded chain between the helices.</p

An example of the VfoldThermal prediction: the inputs highlighted in the snapshot of VfoldThermal web server are the sequence (32 nts in this example) with the temperature range of 0°C–100°C, the energy parameters used for base stacks (from MFOLD in this example) and the structure type (non-pseudoknotted in this example).

<p>From the temperature dependence of the partition function Q(<i>T</i>), VfoldThermal gives a list of temperature-dependent heat capacity C(<i>T</i>), with temperature interval of 0.5°C. The <i>eps</i> format of melting curve is generated by Gnuplot.</p

Sporulosol, a New Ketal from the Fungus Paraconiothyrium sporulosum

Sporulosol (1), a new ketal, together with four known compounds, has been isolated from the liquid fermentation cultures of a wetland-soil-derived fungus, Paraconiothyrium sporulosum. Its structure was elucidated primarily by NMR experiments, and was further confirmed by X-ray crystallography. Sporulosol was obtained as a racemic mixture and the resolved two enantiomers racemized immediately after chiral separation. Sporulosol appears to be the first ketal derived from a 6H-benzo[c]chromen-6-one and a benzofuranone unit. The compound showed modest cytotoxicity toward the human tumor cell line T24, with an IC50 value of 18.2 &micro;M

RNA 3D template structure database.

<p>RNA 3D template structure database.</p

An example of Vfold2D prediction: the input information highlighted in the snapshot of the Vfold2D web server are the sequence (32 nts in this example), the temperature (25°C), the energy parameters used for base stacks (from MFOLD in this example) the structural type (non-pseudoknotted in this example).

<p>(1) Vfold2D gives a list of base pair probabilities P<i>_ij</i> (in txt format) between nucleotides <i>i</i> and <i>j</i>. For example, the probability of forming G1-C12 base pair is 0.22. (2) The most probable 2D structure is derived from the base pairs with P<i>_ij</i>>0.5. In this example, the predicted most probable 2D structure (plotted by VARNA in the figure) has the probability of 0.78. (3) Vfold2D also predicts all the possible helices from the predicted base pair probabilities. (4) Possible alternative structures can be found from the helix and base pair probabilities ( in this example).</p