Toll-like receptor 9 agonist enhances anti-tumor immunity and inhibits tumor-associated immunosuppressive cells numbers in a mouse cervical cancer model following recombinant lipoprotein therapy

BACKGROUND: Although cytotoxic T lymphocytes (CTLs) play a major role in eradicating cancer cells during immunotherapy, the cancer-associated immunosuppressive microenvironment often limits the success of such therapies. Therefore, the simultaneous induction of cancer-specific CTLs and reversal of the immunosuppressive tumor microenvironment may be more effectively achieved through a single therapeutic vaccine. A recombinant lipoprotein with intrinsic Toll-like receptor 2 (TLR2) agonist activity containing a mutant form of E7 (E7m) and a bacterial lipid moiety (rlipo-E7m) has been demonstrated to induce robust CTL responses against small tumors. This treatment in combination with other TLR agonists is able to eliminate large tumors. METHODS: Mouse bone marrow-derived dendritic cells (DCs) were employed to determine the synergistic production of pro-inflammatory cytokines upon combination of rlipo-E7m and other TLR agonists. Antigen-specific CTL responses were investigated using immunospots or in vivo cytolytic assays after immunization in mice. Mice bearing various tumor sizes were used to evaluate the anti-tumor effects of the formulation. Specific subpopulations of immunosuppressive cells in the tumor infiltrate were quantitatively determined by flow cytometry. RESULTS: We demonstrate that a TLR9 agonist (unmethylated CpG oligodeoxynucleotide, CpG ODN) enhances CTL responses and eradicates large tumors when combined with rlipo-E7m. Moreover, combined treatment with rlipo-E7m and CpG ODN effectively increases tumor infiltration by CTLs and reduces the numbers of myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs) and regulatory T cells (Tregs) in the tumor microenvironment. CONCLUSION: These findings suggest that the dramatic anti-tumor effects of the recombinant lipoprotein together with CpG ODN may reflect the amplification of CTL responses and the repression of the immunosuppressive environment. This promising approach could be applied for the development of additional therapeutic cancer vaccines

Genome-wide association study for subclinical atherosclerosis in major arterial territories in the NHLBI's Framingham Heart Study

Introduction: Subclinical atherosclerosis (SCA) measures in multiple arterial beds are heritable phenotypes that are associated with increased incidence of cardiovascular disease. We conducted a genome-wide association study (GWAS) for SCA measurements in the community-based Framingham Heart Study. Methods: Over 100,000 single nucleotide polymorphisms (SNPs) were genotyped (Human 100K GeneChip, Affymetrix) in 1345 subjects from 310 families. We calculated sex-specific age-adjusted and multivariable-adjusted residuals in subjects tested for quantitative SCA phenotypes, including ankle-brachial index, coronary artery calcification and abdominal aortic calcification using multi-detector computed tomography, and carotid intimal medial thickness (IMT) using carotid ultrasonography. We evaluated associations of these phenotypes with 70,987 autosomal SNPs with minor allele frequency $\geq 0.10$, call rate $\geq 80\%$, and Hardy-Weinberg p-value $\geq 0.001$ in samples ranging from 673 to 984 subjects, using linear regression with generalized estimating equations (GEE) methodology and family-based association testing (FBAT). Variance components LOD scores were also calculated. Results: There was no association result meeting criteria for genome-wide significance, but our methods identified 11 SNPs with $p < 10^{-5}$ by GEE and five SNPs with $p < 10^{-5}$ by FBAT for multivariable-adjusted phenotypes. Among the associated variants were SNPs in or near genes that may be considered candidates for further study, such as $rs1376877 (GEE p < 0.000001, located in ABI2)$ for maximum internal carotid artery IMT and rs4814615 (FBAT p = 0.000003, located in PCSK2) for maximum common carotid artery IMT. Modest significant associations were noted with various SCA phenotypes for variants in previously reported atherosclerosis candidate genes, including NOS3 and ESR1. Associations were also noted of a region on chromosome 9p21 with CAC phenotypes that confirm associations with coronary heart disease and CAC in two recently reported genome-wide association studies. In linkage analyses, several regions of genome-wide linkage were noted, confirming previously reported linkage of internal carotid artery IMT on chromosome 12. All GEE, FBAT and linkage results are provided as an open-access results resource at http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin\study.cgi?id=phs000007. Conclusion: The results from this GWAS generate hypotheses regarding several SNPs that may be associated with SCA phenotypes in multiple arterial beds. Given the number of tests conducted, subsequent independent replication in a staged approach is essential to identify genetic variants that may be implicated in atherosclerosis

Data abstractions for decision tree induction

AbstractWhen descriptions of data values in a database are too concrete or too detailed, the computational complexity needed to discover useful knowledge from the database will be generally increased. Furthermore, discovered knowledge tends to become complicated. A notion of data abstraction seems useful to resolve this kind of problems, as we obtain a smaller and more general database after the abstraction, from which we can quickly extract more abstract knowledge that is expected to be easier to understand. In general, however, since there exist several possible abstractions, we have to carefully select one according to which the original database is generalized. An inadequate selection would make the accuracy of extracted knowledge worse.From this point of view, we propose in this paper a method of selecting an appropriate abstraction from possible ones, assuming that our task is to construct a decision tree from a relational database. Suppose that, for each attribute in a relational database, we have a class of possible abstractions for the attribute values. As an appropriate abstraction for each attribute, we prefer an abstraction such that, even after the abstraction, the distribution of target classes necessary to perform our classification task can be preserved within an acceptable error range given by user.By the selected abstractions, the original database can be transformed into a small generalized database written in abstract values. Therefore, it would be expected that, from the generalized database, we can construct a decision tree whose size is much smaller than one constructed from the original database. Furthermore, such a size reduction can be justified under some theoretical assumptions. The appropriateness of abstraction is precisely defined in terms of the standard information theory. Therefore, we call our abstraction framework Information Theoretical Abstraction.We show some experimental results obtained by a system ITA that is an implementation of our abstraction method. From those results, it is verified that our method is very effective in reducing the size of detected decision tree without making classification errors so worse

Waterproofed Photomultiplier Tube Assemblies for the Daya Bay Reactor Neutrino Experiment

In the Daya Bay Reactor Neutrino Experiment 960 20-cm-diameter waterproof photomultiplier tubes are used to instrument three water pools as Cherenkov detectors for detecting cosmic-ray muons. Of these 960 photomultiplier tubes, 341 are recycled from the MACRO experiment. A systematic program was undertaken to refurbish them as waterproof assemblies. In the context of passing the water leakage check, a success rate better than 97% was achieved. Details of the design, fabrication, testing, operation, and performance of these waterproofed photomultiplier-tube assemblies are presented.Comment: 16 pages, 11 figures. Submitted to Nucl. Instr. Met

Tidal Effects on Circulation in and near the East China Sea

We incorporate tidal currents into a previously validated, three-dimensional, subtidal circulation model to assess tidal effects on the circulation in and around the East China Sea. Of particular interest is the tide-enhanced Changjiang plume dispersal and circulation in the southern East China Sea. The modeling results show that without tides, the Changjiang plume in summer presents itself as a stagnant, expansive pool in regions bordering the northern East China Sea and Yellow Sea, too far north and too accumulating relative to observations. The winter plume dispersal pushed by the north-northeast monsoon follows the China coastline southeastward as a coastal current that matches more closely with observations with or without tides. Incorporating the effect of tides brings the model closer to observation, especially in summer. During summer the Taiwan Warm Current shifts to lower latitudes, enhances upwelling off southeast China and induces a southward tidal residual coastal flow off southeast China. Tides also induce the observed seaward detachment of the summer plume. In winter, the prevailing north-northeast monsoon suppresses the Taiwan Warm Current to the minimum. However, if the winter monsoon is weakened for a few weeks, the Taiwan Warm Current reappears and these three mechanisms begin to operate as in summer. CTD surveys and satellite observations south of the Changjiang River estuary contribute to a better understanding of the tidal effects on regional ocean currents

Medial reward and lateral non-reward orbitofrontal cortex circuits change in opposite directions in depression

The first brain-wide voxel-level resting state functional-connectivity neuroimaging analysis of depression is reported, with 421 patients with major depressive disorder and 488 controls. Resting state functional connectivity between different voxels reflects correlations of activity between those voxels and is a fundamental tool in helping to understand the brain regions with altered connectivity and function in depression. One major circuit with altered functional connectivity involved the medial orbitofrontal cortex BA 13, which is implicated in reward, and which had reduced functional connectivity in depression with memory systems in the parahippocampal gyrus and medial temporal lobe, especially involving the perirhinal cortex BA 36 and entorhinal cortex BA 28. The Hamilton Depression Rating Scale scores were correlated with weakened functional connectivity of the medial orbitofrontal cortex BA 13. Thus in depression there is decreased reward-related and memory system functional connectivity, and this is related to the depressed symptoms. The lateral orbitofrontal cortex BA 47/12, involved in non-reward and punishing events, did not have this reduced functional connectivity with memory systems. Second, the lateral orbitofrontal cortex BA 47/12 had increased functional connectivity with the precuneus, the angular gyrus, and the temporal visual cortex BA 21. This enhanced functional connectivity of the non-reward/punishment system (BA 47/12) with the precuneus (involved in the sense of self and agency), and the angular gyrus (involved in language) is thus related to the explicit affectively negative sense of the self, and of self-esteem, in depression. A comparison of the functional connectivity in 185 depressed patients not receiving medication and 182 patients receiving medication showed that the functional connectivity of the lateral orbitofrontal cortex BA 47/12 with these three brain areas was lower in the medicated than the unmedicated patients. This is consistent with the hypothesis that the increased functional connectivity of the lateral orbitofrontal cortex BA 47/12 is related to depression. Relating the changes in cortical connectivity to our understanding of the functions of different parts of the orbitofrontal cortex in emotion helps to provide new insight into the brain changes related to depression, which are considered in the Discussion

Critical quality attributes (CQAs) of a therapeutic antibody produced from integrated continuous bioprocessing

The integrated continuous bioprocess provides an innovative way to produce protein drugs with flexibility and efficiency. However, during the long-term cultivation and complicated production, how to ensure the process stability and product quality is critically important. In this study, the monoclonal antibody (mAb) was produced in a bioreactor operated in a perfusion mode utilizing the ATF cell retention system for up to 32 days. The 2L harvest per day starting at day 10 was continuously purified using the 3-column periodic counter-current (PCC) chromatography system. The first protein A capture purification was performed with the dynamic binding capacity of 50% breakthrough around 60 mg mAb/mL of resin (vs 20 mg/mL resin for batch purification) for 120 cycles or 360 column operations followed by a polishing step of mixed mode chromatography for 20 cycles. The process and quality attributes were monitored daily. The results demonstrate consistency in both the purification process and the mAb qualities (in the aspects of product integrity, aggregates, and glycan profile) between PCC and batch purifications. Culture-related charge heterogeneity was observed accompanied by an increase of bioreactor harvest time using both batch and PCC purification processes. In addition, the impurities such as endotoxin and HCP were also monitored while under this high capacity utilization of chromatography resins. By sharing the insights of process and quality attributes, we hope to provide better understanding on the process-related heterogeneity between batch and continuous production and/or purification

Genome-Wide Gene-Environment Interaction Analysis Using Set-Based Association Tests

The identification of gene-environment interactions (G × E) may eventually guide health-related choices and medical interventions for complex diseases. More powerful methods must be developed to identify G × E. The “adaptive combination of Bayes factors method” (ADABF) has been proposed as a powerful genome-wide polygenic approach to detect G × E. In this work, we evaluate its performance when serving as a gene-based G × E test. We compare ADABF with six tests including the “Set-Based gene-EnviRonment InterAction test” (SBERIA), “gene-environment set association test” (GESAT), etc. With extensive simulations, SBERIA and ADABF are found to be more powerful than other G × E tests. However, SBERIA suffers from a power loss when 50% SNP main effects are in the same direction with the SNP × E interaction effects while 50% are in the opposite direction. We further applied these seven G × E methods to the Taiwan Biobank data to explore gene× alcohol interactions on blood pressure levels. The ADAMTS7P1 gene at chromosome 15q25.2 was detected to interact with alcohol consumption on diastolic blood pressure (p = 9.5 × 10−7, according to the GESAT test). At this gene, the P-values provided by other six tests all reached the suggestive significance level (p &lt; 5 × 10−5). Regarding the computation time required for a genome-wide G × E analysis, SBERIA is the fastest method, followed by ADABF. Considering the validity, power performance, robustness, and computation time, ADABF is recommended for genome-wide G × E analyses

EXAFS Peaks and TPR Characterizing Bimetallic Interactions: Effects of Impregnation Methods on the Structure of Pt-Ru/C Catalysts

To investigate bimetallic interactions, Pt-Ru/C catalysts were prepared by coimpregnation (Pt-Ruco/C) and successive impregnation (Ru-Ptse/C), while Pt/C, Ru/C, and reduced Pt-Rublack were used as reference. Those samples were characterized by XAS and TPR. When Pt(absorber)-Ru(backscatter) phase-and-amplitude correction is applied to Fourier transformed (FT) EXAFS of Pt-Rublack at Pt edge, the characteristic peak of Pt-Ru interactions appears at 2.70 Å´, whereas, when Pt-Pt correction is applied, the peak appears at about 2.5 Å´. Detailed EXAFS analysis for Pt-Ruco/C and Pt-Ruse/C confirms the nature of the characteristic peak and further indicates that the interactions can semiquantitatively be determined by the relative intensity between Pt-Ru and Pt-Pt characteristic peaks. This simple method in determining bimetallic interaction can be extended to characterize Pt-Pd/γ-Al2O3. However, for Pt-Re/γ-Al2O3, Pt-Re interactions cannot be determined by the method because of the overlap of Pt-Pt and Pt-Re characteristic peaks due to similar phase functions