Text Mining for Protein Docking

The rapidly growing amount of publicly available information from biomedical research is readily accessible on the Internet, providing a powerful resource for predictive biomolecular modeling. The accumulated data on experimentally determined structures transformed structure prediction of proteins and protein complexes. Instead of exploring the enormous search space, predictive tools can simply proceed to the solution based on similarity to the existing, previously determined structures. A similar major paradigm shift is emerging due to the rapidly expanding amount of information, other than experimentally determined structures, which still can be used as constraints in biomolecular structure prediction. Automated text mining has been widely used in recreating protein interaction networks, as well as in detecting small ligand binding sites on protein structures. Combining and expanding these two well-developed areas of research, we applied the text mining to structural modeling of protein-protein complexes (protein docking). Protein docking can be significantly improved when constraints on the docking mode are available. We developed a procedure that retrieves published abstracts on a specific protein-protein interaction and extracts information relevant to docking. The procedure was assessed on protein complexes from Dockground (http://dockground.compbio.ku.edu). The results show that correct information on binding residues can be extracted for about half of the complexes. The amount of irrelevant information was reduced by conceptual analysis of a subset of the retrieved abstracts, based on the bag-of-words (features) approach. Support Vector Machine models were trained and validated on the subset. The remaining abstracts were filtered by the best-performing models, which decreased the irrelevant information for ~ 25% complexes in the dataset. The extracted constraints were incorporated in the docking protocol and tested on the Dockground unbound benchmark set, significantly increasing the docking success rate

Wave equation-based reflection tomography of the 1992 Landers earthquake area

In the framework of a recent wave equation-based traveltime seismic tomography, we show that incorporating Moho-reflected phases (PmP and SmS) in addition to the direct P and S phases can significantly increase tomography resolution in the lower crust and this may provide additional evidence to resolve important tectonic issues. To highlight the resolving power of the new strategy, we apply it in the region around the 1992 Landers earthquake (Mw = 7.3) in Southern California using seismic arrivals from local earthquakes, obtaining 3-D high-resolution P and S wave crustal velocity models and Poisson''s ratio structures. In the upper crust, our method confirmed features that had been previously found. However, in the middle-to-lower crust, we found low-velocity anomalies on the southeastern section of the San Jacinto Fault and high Vp and low Vs structures to the west of the Big Bear earthquake, which may be related to upwelling of partial melt from the mantle

Evaluation of the early impacts of the better cotton initiative on smallholder cotton producers in Kurnool District, India: Baseline report

The Better Cotton Standard System is a holistic approach to sustainable cotton production that covers all three pillars of sustainability: environmental, social and economic. The main study research questions is - To what extent has the process of becoming or being certified under BCI sustainability standards had an impact (positive or negative, expected or unexpected) upon smallholders (farmers and households) in Kurnool district? What are the economic (yield, productivity, incomes, food security) and social (child labour, farm workers, no discrimination in wages for women) impacts? In order to be able to measure and attribute impact, but also to understand what has created impact and identify lessons, the study employs a theory based evaluation approach. The baseline and interim performance monitoring rounds of the research have been completed. The end line research is planned in 2018-19

A Comparison of Two Ovine Lumbar Intervertebral Disc Injury Models for the Evaluation and Development of Novel Regenerative Therapies

© The Author(s) 2018. Study Design: Large animal research. Objective: Lumbar discectomy is the most commonly performed spinal surgical procedure. We investigated 2 large animal models of lumbar discectomy in order to study the regenerative capacity of mesenchymal stem cells following disc injury. Methods: Twelve adult ewes underwent baseline 3-T magnetic resonance imaging (MRI) followed by lumbar intervertebral disc injury by either drill bit (n = 6) or annulotomy and partial nucleotomy (APN) (n = 6). Necropsies were performed 6 months later. Lumbar spines underwent 3-T and 9.4-T MRI prior to histological, morphological and biochemical analysis. Results: Drill bit-injured (DBI) and APN-injured discs demonstrated increased Pfirrmann grades relative to uninjured controls (P <.005), with no difference between the 2 models. Disc height index loss was greater in the APN group compared with the DBI group (P <.005). Gross morphology injury scores were higher in APN than DBI discs (P <.05) and both were higher than controls (P <.005). Proteoglycan was reduced in the discs of both injury models relative to controls (P <.005), but lower in the APN group (P <.05). Total collagen of the APN group disc regions was higher than DBI and control discs (P <.05). Histology revealed more matrix degeneration, vascular infiltration, and granulation in the APN model. Conclusion: Although both models produced disc degeneration, the APN model better replicated the pathobiology of human discs postdiscectomy. We therefore concluded that the APN model was a more appropriate model for the investigation of the regenerative capacity of mesenchymal stem cells administered postdiscectomy

Dating of the hominid (Homo neanderthalensis) remains accumulation from El Sidrón Cave (Piloña, Asturias, North Spain): an example of a multi-methodological approach to the dating of Upper Pleistocene sites.

The age of Neanderthal remains and associated sediments from El Sidrón cave has been obtained through different dating methods (14CAMS, U/TH, OSL, ESR and AAR) and samples (charcoal debris, bone, tooth dentine, stalagmitic flowstone, carbonate-rich sediments, sedi- mentary quartz grains, tooth enamel and land snail shells). Detrital Th contamination ren- dered Th/U dating analyses of flowstone unreliable. Recent 14C contamination produced spurious age-values from charcoal samples as well as from inadequately pretreated tooth samples. Most consistent 14C dates are grouped into two series: one between 35 and 40 ka and the other between 48 and 49 ka. Most ESR and AAR samples yielded concordant ages, ranging between 39 and 45 ka; OSL dating results permitted adequate bracketing of the sedimentary layer that contained the human remains. Our results emphasize the value of multi-dating approaches for the establishment of reliable chronologies of human remains

Dating of the hominid (homo neanderthalensis) remains accumulation from el sidrón cave (piloña, asturias, north spain): An example of a multi-methodological approach to the dating of upper pleistocene sites

The age of Neanderthal remains and associated sediments from El Sidrón cave has been obtained through different dating methods (14CAMS, U/TH, OSL, ESR and AAR) and samples (charcoal debris, bone, tooth dentine, stalagmitic flowstone, carbonate-rich sedi