(Un)Structuring for the Next Generation: New Possibilities for Library Data with NoSQL

For many years, libraries have relied upon relational databases (RDBMS) to store, manipulate, and query various types of data, and this database model works extremely well when data are highly structured. As the data become more complex, however, the relational database model strains under the burden of maintaining complex joins, which can decrease a database\u27s performance and limit its functionality. Furthermore, data are not always best represented in the RDBMS\u27s flat, tabular format. Library data often require flexibility and extensibility to accommodate the increasing volume and variety of library resources and metadata. To address these issues, transforming the underlying structure of data will be as important as transforming the data itself. NoSQL offers an alternative model for efficiently managing dynamic data

NADPH Oxidase Limits Innate Immune Responses in the Lungs in Mice

Background: Chronic granulomatous disease (CGD), an inherited disorder of the NADPH oxidase in which phagocytes are defective in generating superoxide anion and downstream reactive oxidant intermediates (ROIs), is characterized by recurrent bacterial and fungal infections and by excessive inflammation (e.g., inflammatory bowel disease). The mechanisms by which NADPH oxidase regulates inflammation are not well understood. Methodology/Principal Findings: We found that NADPH oxidase restrains inflammation by modulating redox-sensitive innate immune pathways. When challenged with either intratracheal zymosan or LPS, NADPH oxidase-deficient p47phox-/- mice and gp91phox-deficient mice developed exaggerated and progressive lung inflammation, augmented NF-kB activation, and elevated downstream pro-inflammatory cytokines (TNF-α, IL-17, and G-CSF) compared to wildtype mice. Replacement of functional NADPH oxidase in bone marrow-derived cells restored the normal lung inflammatory response. Studies in vivo and in isolated macrophages demonstrated that in the absence of functional NADPH oxidase, zymosan failed to activate Nrf2, a key redox-sensitive anti-inflammatory regulator. The triterpenoid, CDDO-Im, activated Nrf2 independently of NADPH oxidase and reduced zymosan-induced lung inflammation in CGD mice. Consistent with these findings, zymosan-treated peripheral blood mononuclear cells from X-linked CGD patients showed impaired Nrf2 activity and increased NF-kB activation. Conclusions/Significance: These studies support a model in which NADPH oxidase-dependent, redox-mediated signaling is critical for termination of lung inflammation and suggest new potential therapeutic targets for CGD

Evaluating the sampling bias in pattern of subterranean species richness: combining approaches

We investigated the pattern of species richness of obligate subterranean (troglobiotic) beetles in caves in the northwestern Balkans, given unequal and biased sampling. On the regional scale, we modeled the relationship between species numbers and sampling intensity using an asymptotic Clench (Michaelis–Menten) function. On the local scale, we calculated Chao 2 species richness estimates for 20 × 20 km grid cells, and investigated the distribution of uniques, species found in only one cave within the grid cell. Cells having high positive residuals, those with above average species richness than expected according to the Clench function, can be considered true hotspots. They were nearly identical to the observed areas of highest species richness. As sampling intensity in a grid cell increases the expected number of uniques decreases for any fixed number of species in the grid cell. High positive residuals show above average species richness for a certain level of sampling intensity within a cell, so further sampling has the most potential for additional species. In some cells this was supported by high numbers of uniques, also indicating insufficient sampling. Cells with low negative residuals have fewer species than would be expected, and some of them also had a low number of uniques, both indicating sufficient sampling. By combining different analyses in a novel way we were able to evaluate observed species richness pattern as well as identify, where further sampling would be most beneficial. Approach we demonstrate is of broad interest to study of biota with high levels of endemism, small distribution ranges and low catchability

[(99m)Tc]Tilmanocept Accurately Detects Sentinel Lymph Nodes and Predicts Node Pathology Status in Patients with Oral Squamous Cell Carcinoma of the Head and Neck: Results of a Phase III Multi-institutional Trial

[(99m)Tc]Tilmanocept, a novel CD206 receptor-targeted radiopharmaceutical, was evaluated in an open-label, phase III trial to determine the false negative rate (FNR) of sentinel lymph node biopsy (SLNB) relative to the pathologic nodal status in patients with intraoral or cutaneous head and neck squamous cell carcinoma (HNSCC) undergoing tumor resection, SLNB, and planned elective neck dissection (END). Negative predictive value (NPV), overall accuracy of SLNB, and the impact of radiopharmaceutical injection timing relative to surgery were assessed. This multicenter, non-randomized, single-arm trial (ClinicalTrials.gov identifier NCT00911326) enrolled 101 patients with T1-T4, N0, and M0 HNSCC. Patients received 50 µg [(99m)Tc]tilmanocept radiolabeled with either 0.5 mCi (same day) or 2.0 mCi (next day), followed by lymphoscintigraphy, SLNB, and END. All excised tissues were evaluated for tissue type and tumor presence. [(99m)Tc]Tilmanocept identified one or more SLNs in 81 of 83 patients (97.6 %). Of 39 patients identified with any tumor-positive nodes (SLN or non-SLN), one patient had a single tumor-positive non-SLN in whom all SLNs were tumor-negative, yielding an FNR of 2.56 %; NPV was 97.8 % and overall accuracy was 98.8 %. No significant differences were observed between same-day and next-day procedures. Use of receptor-targeted [(99m)Tc]tilmanocept for lymphatic mapping allows for a high rate of SLN identification in patients with intraoral and cutaneous HNSCC. SLNB employing [(99m)Tc]tilmanocept accurately predicts the pathologic nodal status of intraoral HNSCC patients with low FNR, high NPV, and high overall accuracy. The use of [(99m)Tc]tilmanocept for SLNB in select patients may be appropriate and may obviate the need to perform more extensive procedures such as END

NADPH oxidase limits innate immune responses in the lungs in mice.

BackgroundChronic granulomatous disease (CGD), an inherited disorder of the NADPH oxidase in which phagocytes are defective in generating superoxide anion and downstream reactive oxidant intermediates (ROIs), is characterized by recurrent bacterial and fungal infections and by excessive inflammation (e.g., inflammatory bowel disease). The mechanisms by which NADPH oxidase regulates inflammation are not well understood.Methodology/principal findingsWe found that NADPH oxidase restrains inflammation by modulating redox-sensitive innate immune pathways. When challenged with either intratracheal zymosan or LPS, NADPH oxidase-deficient p47(phox-/-) mice and gp91(phox)-deficient mice developed exaggerated and progressive lung inflammation, augmented NF-kappaB activation, and elevated downstream pro-inflammatory cytokines (TNF-alpha, IL-17, and G-CSF) compared to wildtype mice. Replacement of functional NADPH oxidase in bone marrow-derived cells restored the normal lung inflammatory response. Studies in vivo and in isolated macrophages demonstrated that in the absence of functional NADPH oxidase, zymosan failed to activate Nrf2, a key redox-sensitive anti-inflammatory regulator. The triterpenoid, CDDO-Im, activated Nrf2 independently of NADPH oxidase and reduced zymosan-induced lung inflammation in CGD mice. Consistent with these findings, zymosan-treated peripheral blood mononuclear cells from X-linked CGD patients showed impaired Nrf2 activity and increased NF-kappaB activation.Conclusions/significanceThese studies support a model in which NADPH oxidase-dependent, redox-mediated signaling is critical for termination of lung inflammation and suggest new potential therapeutic targets for CGD

Myc represses transcription through recruitment of DNA methyltransferase corepressor

The Myc transcription factor is an essential mediator of cell growth and proliferation through its ability to both positively and negatively regulate transcription. The mechanisms by which Myc silences gene expression are not well understood. The current model is that Myc represses transcription through functional interference with transcriptional activators. Here we show that Myc binds the corepressor Dnmt3a and associates with DNA methyltransferase activity in vivo. In cells with reduced Dnmt3a levels, we observe specific reactivation of the Myc-repressed p21Cip1 gene, whereas the expression of Myc-activated E-boxes genes is unchanged. In addition, we find that Myc can target Dnmt3a selectively to the promoter of p21Cip1. Myc is known to be recruited to the p21Cip1 promoter by the DNA-binding factor Miz-1. Consistent with this, we observe that Myc and Dnmt3a form a ternary complex with Miz-1 and that this complex can corepress the p21Cip1 promoter. Finally, we show that DNA methylation is required for Myc-mediated repression of p21Cip1. Our data identify a new mechanism by which Myc can silence gene expression not only by passive functional interference but also by active recruitment of corepressor proteins. Furthermore, these findings suggest that targeting of DNA methyltransferases by transcription factors is a wide and general mechanism for the generation of specific DNA methylation patterns within a cell

NADPH oxidase augments Nrf2 activation and restrains NF-κB activation in human PBMCs.

<p>PBMCs from normal donors (n = 8) and X-linked CGD patients (n = 5) were stimulated with zymosan (20 µg/ml). A) Nrf2 activation. B) NF-κB activation. *, p<0.05 comparing normal donor and CGD PBMCs.</p

p47<i>^phox−/−</i> mice develop increased zymosan-induced lung inflammation compared to wildtype (WT) mice.

<p>Representative lung histology of WT (A) and p47<i>^phox−/−</i> (CGD) mice (B) at days 3, 7, 14, 25 after i.t. zymosan. All slides are H&E stained, 20x, and are representative of at least 3 mice per genotype per time point. C) Percent of lung parenchyma with consolidation or granulomatous inflammation. Bronchoalveolar lavage fluid (BALF) neutrophil (D) and macrophage (E) concentrations. 2-way ANOVA showed a significant difference between genotypes in % lung inflammation (p<0.0001) and BALF neutrophil concentration (p<0.0001), with significant differences at the indicated time points by Boneferroni post-test. *, p<0.01; **, p<0.001).</p