Semantic inference using chemogenomics data for drug discovery

<p>Abstract</p> <p>Background</p> <p>Semantic Web Technology (SWT) makes it possible to integrate and search the large volume of life science datasets in the public domain, as demonstrated by well-known linked data projects such as LODD, Bio2RDF, and Chem2Bio2RDF. Integration of these sets creates large networks of information. We have previously described a tool called WENDI for aggregating information pertaining to new chemical compounds, effectively creating evidence paths relating the compounds to genes, diseases and so on. In this paper we examine the utility of automatically inferring new compound-disease associations (and thus new links in the network) based on semantically marked-up versions of these evidence paths, rule-sets and inference engines.</p> <p>Results</p> <p>Through the implementation of a semantic inference algorithm, rule set, Semantic Web methods (RDF, OWL and SPARQL) and new interfaces, we have created a new tool called Chemogenomic Explorer that uses networks of ontologically annotated RDF statements along with deductive reasoning tools to infer new associations between the query structure and genes and diseases from WENDI results. The tool then permits interactive clustering and filtering of these evidence paths.</p> <p>Conclusions</p> <p>We present a new aggregate approach to inferring links between chemical compounds and diseases using semantic inference. This approach allows multiple evidence paths between compounds and diseases to be identified using a rule-set and semantically annotated data, and for these evidence paths to be clustered to show overall evidence linking the compound to a disease. We believe this is a powerful approach, because it allows compound-disease relationships to be ranked by the amount of evidence supporting them.</p

Controlled Growth of Carbon Spheres Through the Mg-Reduction Route

Hollow spheres, hollow capsules and solid spheres of carbon were selectively synthesized by Mg-reduction of hexachlorobutadiene at appropriate reaction conditions. X-ray powder diffraction and Raman spectra reveal that the as-prepared materials have a well-ordered structure. A possible formation mechanism has been proposed

HIV-Infected Former Plasma Donors in Rural Central China: From Infection to Survival Outcomes, 1985–2008

BACKGROUND: The HIV epidemic among former plasma donors (FPDs) in rural Central China in the early-mid 1990s is likely the largest known HIV-infected cohort in the world related to commercial plasma donation but has never been fully described. The objectives of this study are to estimate the timing and geographic spread of HIV infection in this cohort and to demonstrate the impact of antiretroviral therapy on survival outcomes. METHODOLOGY/PRINCIPAL FINDINGS: HIV-infected FPDs were identified using the national HIV epidemiology and treatment databases. Locations of subjects were mapped. Dates of infection and survival were estimated using the midpoint date between initial-final plasma donation dates from 1985-2008 among those with plasma donation windows ≤2 years. Among 37,084 FPDs in the two databases, 36,110 were included. 95% were located in focal areas of Henan Province and adjacent areas of surrounding provinces. Midpoint year between initial-final plasma donation dates was 1994 among FPDs with known donation dates. Median survival from infection to AIDS was 11.8 years and, among those not treated, 1.6 years from AIDS to death. Among those on treatment, 71% were still alive after five years. Using Cox proportional hazard modeling, untreated AIDS patients were 4.9 times (95% confidence interval 4.6-5.2) more likely to die than those on treatment. CONCLUSIONS/SIGNIFICANCE: The epidemic of HIV-infected FPD in China was not widespread throughout China but rather was centered in Henan Province and the adjacent areas of surrounding provinces. Even in these areas, infections were concentrated in focal locations. Overall, HIV infections in this cohort peaked in 1994, with median survival of 13.4 years from infection to death among those not treated. Among AIDS patients on treatment, 71% were still alive after five years

Multi-Directional Growth of Aligned Carbon Nanotubes Over Catalyst Film Prepared by Atomic Layer Deposition

The structure of vertically aligned carbon nanotubes (CNTs) severely depends on the properties of pre-prepared catalyst films. Aiming for the preparation of precisely controlled catalyst film, atomic layer deposition (ALD) was employed to deposit uniform Fe2O3 film for the growth of CNT arrays on planar substrate surfaces as well as the curved ones. Iron acetylacetonate and ozone were introduced into the reactor alternately as precursors to realize the formation of catalyst films. By varying the deposition cycles, uniform and smooth Fe2O3 catalyst films with different thicknesses were obtained on Si/SiO2 substrate, which supported the growth of highly oriented few-walled CNT arrays. Utilizing the advantage of ALD process in coating non-planar surfaces, uniform catalyst films can also be successfully deposited onto quartz fibers. Aligned few-walled CNTs can be grafted on the quartz fibers, and they self-organized into a leaf-shaped structure due to the curved surface morphology. The growth of aligned CNTs on non-planar surfaces holds promise in constructing hierarchical CNT architectures in future

Electrically driven thermal light emission from individual single-walled carbon nanotubes

Light emission from nanostructures exhibits rich quantum effects and has broad applications. Single-walled carbon nanotubes (SWNTs) are one-dimensional (1D) metals or semiconductors, in which large number of electronic states in a narrow range of energies, known as van Hove singularities, can lead to strong spectral transitions. Photoluminescence and electroluminescence involving interband transitions and excitons have been observed in semiconducting SWNTs, but are not expected in metallic tubes due to non-radiative relaxations. Here, we show that in the negative differential conductance regime, a suspended quasi-metallic SWNT (QM-SWNT) emits light due to joule-heating, displaying strong peaks in the visible and infrared corresponding to interband transitions. This is a result of thermal light emission in 1D, in stark contrast with featureless blackbody-like emission observed in large bundles of SWNTs or multi-walled nanotubes. This allows for probing of the electronic temperature and non-equilibrium hot optical phonons in joule-heated QM-SWNTs

Optimisation of UAVs‐SfM data collection in aeolian landform morphodynamics : a case study from the Gonghe Basin, China

UAVs‐SfM (Unmanned Aerial Vehicles‐ Structure from Motion) systems can generate high‐resolution 3D topographic models of aeolian landforms. To explore the optimisation of UAVs‐SfM for use in aeolian landform morphodynamics, this study tested flight parameters for two contrasting aeolian landform areas (free dune and blowout) to assess the 3D reconstruction accuracy of the UAVs survey compared with field point measurements using differential RTK‐GPS (Real‐time Kinematic‐Global Positioning System). The results reveal the optimum UAVs‐SfM flight set‐up at the free‐dune site was: flying height = 74 m, camera tilt angle = ‐90°, photo overlap ratio = 85%/70% (heading/sideways). The horizontal/vertical location error was around 0.028~0.055 m and 0.053‐0.069 m respectively, and a point cloud density of 463/m3 was found to generate a clear texture using these flying parameters. For the <20m deep blowout the optimum set‐up with highest accuracy and the lowest cliff texture distortion was: flying height = 74 m combined camera tilt angle = ‐90° and ‐60°, photo overlap ratio = 85%/70% (heading/sideways), and an evenly distributed GCPs (Ground Control Points) density of 42/km2 using these flying parameters. When the depth of the blowouts exceeded 40 m, the optimum flight/survey parameters changed slightly to account for more challenging cliff texture generation: flying height = 80 m (with ‐90° and ‐60°combined camera tilt angle), GCPs density = 63/km2 to generate horizontal and vertical location error of 0.024 m and 0.050 m respectively, and point cloud density of 2597.11/m3. The main external factors that affect the successful 3D reconstruction of aeolian landforms using UAVs‐SfM are the weather conditions, manipulation errors, and instrument system errors. The UAVs‐SfM topographic monitoring results demonstrate that UAVs provide a viable and robust means for aeolian landform morphodynamics monitoring. Importantly, the rapid and high precision 3D reconstruction processes were significantly advanced using the optimal flight parameters reported here

Trends in Notifiable Infectious Diseases in China: Implications for Surveillance and Population Health Policy

This study aimed to analyse trends in notifiable infectious diseases in China, in their historical context. Both English and Chinese literature was searched and diseases were categorised according to the type of disease or transmission route. Temporal trends of morbidity and mortality rates were calculated for eight major infectious diseases types. Strong government commitment to public health responses and improvements in quality of life has led to the eradication or containment of a wide range of infectious diseases in China. The overall infectious diseases burden experienced a dramatic drop during 1975–1995, but since then, it reverted and maintained a gradual upward trend to date. Most notifiable diseases are contained at a low endemic level; however, local small-scale outbreaks remain common. Tuberculosis, as a bacterial infection, has re-emerged since the 1990s and has become prevalent in the country. Sexually transmitted infections are in a rapid, exponential growth phase, spreading from core groups to the general population. Together human immunodeficiency virus (HIV), they account for 39% of all death cases due to infectious diseases in China in 2008. Zoonotic infections, such as severe acute respiratory syndrome (SARS), rabies and influenza, pose constant threats to Chinese residents and remain the most deadly disease type among the infected individuals. Therefore, second-generation surveillance of behavioural risks or vectors associated with pathogen transmission should be scaled up. It is necessary to implement public health interventions that target HIV and relevant coinfections, address transmission associated with highly mobile populations, and reduce the risk of cross-species transmission of zoonotic pathogens

Peer-based behavioral health program for drug users in China: a pilot study

<p>Abstract</p> <p>Background</p> <p>Many injection drug users (IDUs) in China have high risk sexual behaviors that contribute to the spread of HIV infection. Although many IDUs in China move through drug rehabilitation centers, this opportunity for sexual health education has largely been overlooked.</p> <p>Methods</p> <p>A convenience sample of 667 drug users from two rehabilitation centers in South China was recruited in the study. Two hundred and forty seven drug users from a single Guangdong Province rehabilitation center received the peer-based education intervention, while 420 drug users from another rehabilitation center received routine HIV/STI education and was used as the control. One hundred and eighty nine (22.1%) individuals refused to participate in the study. HIV/STI behavioral and knowledge domains were assessed at 3 months in rehabilitation centers after the intervention (first follow-up) and at 2-23 months in the community after release (second follow-up).</p> <p>Results</p> <p>Drug users who completed the intervention reported more frequent condom use with casual sex partners (60.0% vs. 12.5% condom use every time, p = 0.011) and less frequent injection (56.7% vs. 26.4% no injection per day, p = 0.008) at the second follow-up compared to those in the routine education group. Loss to follow up was substantial in both control and intervention groups, and was associated with living far from the detention center and having poor HIV knowledge at baseline.</p> <p>Conclusions</p> <p>This study shows that rehabilitation centers may be a useful location for providing behavioral HIV/STI prevention services and referral of individuals to community-based programs upon release. More research is needed on behalf of detained drug users in China who have complex social, medical, and legal needs.</p

Peer-based behavioral health program for drug users in China: a pilot study

<p>Abstract</p> <p>Background</p> <p>Many injection drug users (IDUs) in China have high risk sexual behaviors that contribute to the spread of HIV infection. Although many IDUs in China move through drug rehabilitation centers, this opportunity for sexual health education has largely been overlooked.</p> <p>Methods</p> <p>A convenience sample of 667 drug users from two rehabilitation centers in South China was recruited in the study. Two hundred and forty seven drug users from a single Guangdong Province rehabilitation center received the peer-based education intervention, while 420 drug users from another rehabilitation center received routine HIV/STI education and was used as the control. One hundred and eighty nine (22.1%) individuals refused to participate in the study. HIV/STI behavioral and knowledge domains were assessed at 3 months in rehabilitation centers after the intervention (first follow-up) and at 2-23 months in the community after release (second follow-up).</p> <p>Results</p> <p>Drug users who completed the intervention reported more frequent condom use with casual sex partners (60.0% vs. 12.5% condom use every time, p = 0.011) and less frequent injection (56.7% vs. 26.4% no injection per day, p = 0.008) at the second follow-up compared to those in the routine education group. Loss to follow up was substantial in both control and intervention groups, and was associated with living far from the detention center and having poor HIV knowledge at baseline.</p> <p>Conclusions</p> <p>This study shows that rehabilitation centers may be a useful location for providing behavioral HIV/STI prevention services and referral of individuals to community-based programs upon release. More research is needed on behalf of detained drug users in China who have complex social, medical, and legal needs.</p

Catecholamine up-regulates MMP-7 expression by activating AP-1 and STAT3 in gastric cancer

<p>Abstract</p> <p>Background</p> <p>Stress, anxiety and depression can cause complex physiological and neuroendocrine changes, resulting in increased level of stress related hormone catecholamine, which may constitute a primary mechanism by which physiological factors impact gene expression in tumors. In the present study, we investigated the effects of catecholamine stimulation on MMP-7 expression in gastric cancer cells and elucidated the molecular mechanisms of the up-regulation of MMP-7 level by catecholamine through an adrenergic signaling pathway.</p> <p>Results</p> <p>Increased MMP-7 expression was identified at both mRNA and protein levels in the gastric cancer cells in response to isoproterenol stimulation. β2-AR antigonist effectively abrogated isoproterenol-induced MMP-7 expression. The activation of STAT3 and AP-1 was prominently induced by isoproterenol stimulation and AP-1 displayed a greater efficacy than STAT3 in isoproterenol-induced MMP-7 expression. Mutagenesis of three STAT3 binding sites in MMP-7 promoter failed to repress the transactivation of MMP-7 promoter and silencing STAT3 expression was not effective in preventing isoproterenol-induced MMP-7 expression. However, isoproterenol-induced MMP-7 promoter activities were completely disappeared when the AP-1 site was mutated. STAT3 and c-Jun could physically interact and bind to the AP-1 site, implicating that the interplay of both transcriptional factors on the AP-1 site is responsible for isoproterenol-stimulated MMP-7 expression in gastric cancer cells. The expression of MMP-7 in gastric cancer tissues was found to be at the site where β2-AR was overexpressed and the levels of MMP-7 and β2-AR were the highest in the metastatic locus of gastric cancer.</p> <p>Conclusions</p> <p>Up-regulation of MMP-7 expression through β2-AR-mediated signaling pathway is involved in invasion and metastasis of gastric cancer.</p