CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Systemic analysis of available large-scale biological/biomedical data is critical for studying biological mechanisms, and developing novel and effective treatment approaches against diseases. However, different layers of the available data are produced using different technologies and scattered across individual computational resources without any explicit connections to each other, which hinders extensive and integrative multi-omics-based analysis. We aimed to address this issue by developing a new data integration/representation methodology and its application by constructing a biological data resource. CROssBAR is a comprehensive system that integrates large-scale biological/biomedical data from various resources and stores them in a NoSQL database. CROssBAR is enriched with the deep-learning-based prediction of relationships between numerous data entries, which is followed by the rigorous analysis of the enriched data to obtain biologically meaningful modules. These complex sets of entities and relationships are displayed to users via easy-to-interpret, interactive knowledge graphs within an open-access service. CROssBAR knowledge graphs incorporate relevant genes-proteins, molecular interactions, pathways, phenotypes, diseases, as well as known/predicted drugs and bioactive compounds, and they are constructed on-the-fly based on simple non-programmatic user queries. These intensely processed heterogeneous networks are expected to aid systems-level research, especially to infer biological mechanisms in relation to genes, proteins, their ligands, and diseases.     

Réduction des effets de la respiration en imagerie TEP pulmonaire par une acquisition synchronisée à la respiration associée à une TDM en apnée

Respiratory motion causes a spread of lesion uptake over a larger area in Positron Emission Tomography (PET) images for moving structures. When CT images are used for attenuation correction of emission data, this motion may alter the quantization of PET images. We present the clinical results of a respiratory-gated PET processing “CT-based” method, which aims to improve PET-CT coregistration by using an additional breath-hold CT (BH-CT). The CT-based protocol consisted in a 10-min List Mode respiratory-gated PET acquisition, followed by an end-expiration BH-CT acquisition. During these two examinations, the respiratory signal was recorded continuously. Eleven pulmonary lesions were studied. Patients underwent both a standard clinical PET protocol (free breathing) and the CT-based protocol. The respective performances of the CT-based and clinical PET methods were evaluated by comparing the distances between the lesions’ centroids on PET and CT images. SUV_MAX (Standardized Uptake Value) and volume variations were also investigated. The CT-based method showed a significant reduction (p = 0.049) of centroid distances (mean relative change versus standard method: 49%). We also noted a higher SUV_MAX (mean change: 39%). Lesion volumes were significantly lower (p = 0.026) in CT-based PET volumes (mean change: 43%) compared with standard ones. The CT-based method improves PET-CT coregistration of pulmonary lesions. This protocol should lead to more accurate attenuation correction and thus improve SUV measurement.     

Microwave-assisted synthesis of dihydropyrimidin-2(1H)-ones using graphite supported lanthanum chloride as a mild and efficient catalyst

Graphite supported lanthanum chloride efficiently catalyzes the three-component coupling of beta-ketoesters, aldehydes and urea/thiourea to afford corresponding dihydropyrimidinones in good yields under microwave irradiation.     

Opsonization of HIV with complement enhances infection of dendritic cells and viral transfer to CD4 T cells in a CR3 and DC-SIGN-dependent manner

In the present study, we demonstrated that opsonization of primary HIV-1 with human complement enhances infection of immature monocyte-derived dendritic cells (iDC) and transmission in trans of HIV to autologous CD4(+) T lymphocytes. Infection of iDC by opsonized primary R5- and X4-tropic HIV was increased 3- to 5-fold as compared with infection by the corresponding unopsonized HIV. Enhancement of infection was dependent on CR3 as demonstrated by inhibition induced by blocking Abs. The interaction of HIV with CCR5 and CXCR4 on iDC was affected by opsonization. Indeed, stromal-derived factor-1 was more efficient in inhibiting infection of iDC with opsonized R5-tropic HIV-1(BaL) (45%) than with heat-inactivated complement opsonized virus and similarly RANTES inhibited more efficiently infection of iDC with opsonized X4-tropic HIV-1(NDK) (42%) than with heat-inactivated complement opsonized virus. We also showed that attachment of complement-opsonized virus to DC-specific ICAM-grabbing nonintegrin (DC-SIGN) molecule on iDC and HeLa DC-SIGN(+) CR3(-) cells was 46% and 50% higher compared with heat-inactivated complement opsonized virus, respectively. Hence, Abs to DC-SIGN suppressed up to 80% and 60% the binding of opsonized virus to HeLa cells and iDC, respectively. Furthermore, Abs to DC-SIGN inhibited up to 70% of the infection of iDC and up to 65% of infection in trans of autologous lymphocytes with opsonized virus. These results further demonstrated the role of DC-SIGN in complement opsonized virus uptake and infection. Thus, the virus uses complement to its advantage to facilitate early steps leading to infection following mucosal transmission of HIV.     

Evaluating the Probiotic Potential of Lactobacillus plantarum Strains from Algerian Infant Feces: Towards the Design of Probiotic Starter Cultures Tailored for Developing Countries

Probiotics and Antimicrobial Proteins - Lactobacilli naturally present in the neonatal gut are believed to be beneficial for the human hosts and are investigated as potential probiotics. In this...     

Epidemiology of Drug Use and HIV-Related Risk Behaviors among People Who Inject Drugs in Mwanza,Tanzania

Heroin trafficking and consumption has increased steadily over the past decade in Tanzania, but limited information regarding HIV and drug use exists for the city of Mwanza. Our study investigates the epidemiology of drug use, and HIV risk behaviors among drug users in the northwestern city of Mwanza. Using a combination of targeted sampling and participant referral, we recruited 480 participants in Mwanza between June and August 2014. The sample was 92% male. Seventy-nine (16.4%) participants reported injecting heroin, while 434 (90.4%) reported smoking heroin. Unstable housing and cohabitation status were the only socioeconomic characteristics significantly associated with heroin injection. More than half of heroin injectors left syringes in common locations, and half reported sharing needles and syringes. Other risk behaviors such as lack of condom use during sex, and the use of illicit drugs during sex was widely reported as well. Among the study sample, there was poor awareness of health risks posed by needle/syringe sharing and drug use. Our results show that heroin use and HIV risk related behaviors are pressing problems that should not be ignored in Mwanza. Harm reduction programs are urgently needed in this population.