Analysis and Computational Dissection of Molecular Signature Multiplicity

Molecular signatures are computational or mathematical models created to diagnose disease and other phenotypes and to predict clinical outcomes and response to treatment. It is widely recognized that molecular signatures constitute one of the most important translational and basic science developments enabled by recent high-throughput molecular assays. A perplexing phenomenon that characterizes high-throughput data analysis is the ubiquitous multiplicity of molecular signatures. Multiplicity is a special form of data analysis instability in which different analysis methods used on the same data, or different samples from the same population lead to different but apparently maximally predictive signatures. This phenomenon has far-reaching implications for biological discovery and development of next generation patient diagnostics and personalized treatments. Currently the causes and interpretation of signature multiplicity are unknown, and several, often contradictory, conjectures have been made to explain it. We present a formal characterization of signature multiplicity and a new efficient algorithm that offers theoretical guarantees for extracting the set of maximally predictive and non-redundant signatures independent of distribution. The new algorithm identifies exactly the set of optimal signatures in controlled experiments and yields signatures with significantly better predictivity and reproducibility than previous algorithms in human microarray gene expression datasets. Our results shed light on the causes of signature multiplicity, provide computational tools for studying it empirically and introduce a framework for in silico bioequivalence of this important new class of diagnostic and personalized medicine modalities

Utilization of outpatient services in refugee settlement health facilities: a comparison by age, gender, and refugee versus host national status

<p>Abstract</p> <p>Background</p> <p>Comparisons between refugees receiving health care in settlement-based facilities and persons living in host communities have found that refugees have better health outcomes. However, data that compares utilization of health services between refugees and the host population, and across refugee settlements, countries and regions is limited. The paper will address this information gap. The analysis in this paper uses data from the United Nations High Commissioner of Refugees (UNHCR) Health Information System (HIS).</p> <p>Methods</p> <p>Data about settlement populations and the use of outpatient health services were exported from the UNHCR health information system database. Tableau Desktop was used to explore the data. STATA was used for data cleaning and statistical analysis. Differences in various indicators of the use of health services by region, gender, age groups, and status (host national vs. refugee population) were analyzed for statistical significance using generalized estimating equation models that adjusted for correlated data within refugee settlements over time.</p> <p>Results</p> <p>Eighty-one refugee settlements were included in this study and an average population of 1.53 million refugees was receiving outpatient health services between 2008 and 2009. The crude utilization rate among refugees is 2.2 visits per person per year across all settlements. The refugee utilization rate in Asia (3.5) was higher than in Africa on average (1.8). Among refugees, females have a statistically significant higher utilization rate than males (2.4 visits per person per year vs. 2.1). The proportion of new outpatient attributable to refugees is higher than that attributable to host nationals. In the Asian settlements, only 2% outpatient visits, on average, were attributable to host community members. By contrast, in Africa, the proportion of new outpatient (OPD) visits by host nationals was 21% on average; in many Ugandan settlements, the proportion of outpatient visits attributable to host community members was higher than that for refugees. There was no statistically significant difference between the size of the male and female populations across refugee settlements. Across all settlements reporting to the UNHCR database, the percent of the refugee population that was less than five years of age is 16% on average.</p> <p>Conclusions</p> <p>The availability of a centralized database of health information across UNHCR-supported refugee settlements is a rich resource. The SPHERE standard for emergencies of 1-4 visits per person per year appears to be relevant for Asia in the post-emergency phase, but not for Africa. In Africa, a post-emergency standard of 1-2 visits per person per year should be considered. Although it is often assumed that the size of the female population in refugee settlements is higher than males, we found no statistically significant difference between the size of the male and female populations in refugee settlements overall. Another assumption---that the under-fives make up 20% of the settlement population during the emergency phase---does not appear to hold for the post-emergency phase; under-fives made up about 16% of refugee settlement populations.</p

Effect of a Community Popular Opinion Leader HIV/STI Intervention on Stigma in Urban, Coastal Peru

Evaluating interventions that reduce HIV stigma may help to craft effective stigma-reduction programs. This study evaluates the effects of a community popular opinion leader HIV/STI intervention on stigma in urban, coastal Peru. Mixed effects modeling was used to analyze data on 3,049 participants from the Peru site of the NIHM collaborative trial. Analyses looked at differences between the comparison and intervention groups on a stigma index from baseline to 12- and 24-month follow-up. Sub-analyses were conducted on heterosexual-identified men (esquineros), homosexual-identified men (homosexuales), and socially marginalized women (movidas). Compared to participants in the comparison group, intervention participants reported lower levels of stigma at 12- and 24-month follow-up. Similar results were found within esquineros and homosexuales. No significant differences were found within movidas. Findings suggest that interventions designed to normalize HIV prevention behaviors and HIV communication can reduce HIV-related stigma and change community norms

Bonobo personality traits are heritable and associated with vasopressin receptor gene 1a variation

Despite being closely related, bonobos and chimpanzees show remarkable behavioral differences, the proximate origins of which remain unknown. This study examined the link between behavioral variation and variation in the vasopressin 1a receptor gene (Avpr1a) in bonobos. Chimpanzees are polymorphic for a ~360 bp deletion (DupB), which includes a microsatellite (RS3) in the 5′ promoter region of Avpr1a. In chimpanzees, the DupB deletion has been linked to lower sociability, lower social sensitivity, and higher anxiety. Chimpanzees and bonobos differ on these traits, leading some to believe that the absence of the DupB deletion in bonobos may be partly responsible for these differences, and to the prediction that similar associations between Avpr1a genotypes and personality traits should be present in bonobos. We identified bonobo personality dimensions using behavioral measures (Sociability(B), Boldness(B), Openness(B), Activity(B)) and trait ratings (Assertiveness(R), Conscientiousness(R), Openness(R), Agreeableness(R), Attentiveness(R), Extraversion(R)). In the present study we found that all 10 dimensions have nonzero heritabilities, indicating there is a genetic basis to personality, and that bonobos homozygous for shorter RS3 alleles were lower in Attentiveness(R) and higher in Openness(B). These results suggest that variations in Avpr1a genotypes explain both within and between species differences in personality traits of bonobos and chimpanzees

PAD4-Mediated Neutrophil Extracellular Trap Formation Is Not Required for Immunity against Influenza Infection

During an inflammatory response, neutrophils migrate to the site of infection where they can kill invading pathogens by phagocytosis, secretion of anti-microbicidal mediators or the release of neutrophil extracellular traps (NETs). NETs are specialized anti-microbial structures comprised of decondensed chromatin decorated with microbicidal agents. Increased amount of NETs have been found in patients suffering from the chronic lung inflammatory disease cystic fibrosis, correlating with increased severity of pulmonary obstruction. Furthermore, acute lung inflammation during influenza A infection is characterized by a massive influx of neutrophils into the lung. The role of NETs during virus-mediated lung inflammation is unknown. Peptidylarginine deiminase 4 (PAD4)-mediated deimination of histone H3 and H4 is required for NET formation. Therefore, we generated a PAD4-deficient mouse strain that has a striking inability to form NETs. These mice were infected with influenza A/WSN, and the disease was monitored at the level of leukocytic lung infiltration, lung pathology, viral replication, weight loss and mortality. PAD4 KO fared comparable to WT mice in all the parameters tested, but they displayed slight but statistically different weight loss kinetics during infection that was not reflected in enhanced survival. Overall, we conclude that PAD4-mediated NET formation is dispensable in a mouse model of influenza A infection

Excitotoxicity Triggered by Neurobasal Culture Medium

Neurobasal defined culture medium has been optimized for survival of rat embryonic hippocampal neurons and is now widely used for many types of primary neuronal cell culture. Therefore, we were surprised that routine medium exchange with serum- and supplement-free Neurobasal killed as many as 50% of postnatal hippocampal neurons after a 4 h exposure at day in vitro 12–15. Minimal Essential Medium (MEM), in contrast, produced no significant toxicity. Detectable Neurobasal-induced neuronal death occurred with as little as 5 min exposure, measured 24 h later. D-2-Amino-5-phosphonovalerate (D-APV) completely prevented Neurobasal toxicity, implicating direct or indirect N-methyl-D-aspartate (NMDA) receptor-mediated neuronal excitotoxicity. Whole-cell recordings revealed that Neurobasal but not MEM directly activated D-APV-sensitive currents similar in amplitude to those gated by 1 µM glutamate. We hypothesized that L-cysteine likely mediates the excitotoxic effects of Neurobasal incubation. Although the original published formulation of Neurobasal contained only 10 µM L-cysteine, commercial recipes contain 260 µM, a concentration in the range reported to activate NMDA receptors. Consistent with our hypothesis, 260 µM L-cysteine in bicarbonate-buffered saline gated NMDA receptor currents and produced toxicity equivalent to Neurobasal. Although NMDA receptor-mediated depolarization and Ca2+ influx may support survival of young neurons, NMDA receptor agonist effects on development and survival should be considered when employing Neurobasal culture medium

Dynamics of Endoreplication during Drosophila Posterior Scutellar Macrochaete Development

Endoreplication is a variant type of DNA replication, consisting only of alternating G1 and S phases. Many types of Drosophila tissues undergo endoreplication. However, the timing and the extent to which a single endocycling macrochaete undergoes temporally programmed endoreplication during development are unclear. Here, we focused on the dynamics of endoreplication during posterior scutellar (pSC) macrochaete development. Quantitative analyses of C values in shaft cells and socket cells revealed a gradual rise from 8C and 4C at 8 hours after pupal formation (APF) to 72C and 24C at 29 hours APF, respectively. The validity of the values was further confirmed by the measurement of DNA content with a confocal laser microscope. BrdU incorporation assays demonstrated that shaft cells undergo four rounds of endoreplication from 18 to 29.5 hours APF. In contrast, socket cells undergo two rounds of endoreplication during the same period. Statistical analyses showed that the theoretical C values, based on BrdU assays, nearly coincide with the actually measured C values in socket cells, but not in shaft cells after 22 hours APF. These analyses suggest that socket cells undergo two rounds of endoreplication. However, the mechanism of endoreplication in the shaft cells may change from 22 hours APF, suggesting the possibility that shaft cells undergo two or four rounds of endoreplication during the periods. We also found that the timing of endoreplication differs, depending on the type of macrochaete. Moreover, endocycling in shaft cells of both the left and right sides of pSC bristle lineages occurs in the same pattern, indicating that the process is synchronized for specific types of macrochaete. Our findings suggest that endocycling in macrochaete cell lineages can be a model for understanding mechanisms of endoreplication at the single-cell level

Nuclear Factor-Kappa B Inhibition Can Enhance Apoptosis of Differentiated Thyroid Cancer Cells Induced by 131I

Objective: To evaluate changes of nuclear factor-kappa B (NF-kB) during radioiodine 131 ( 131 I) therapy and whether NF-kB inhibition could enhance 131 I-induced apoptosis in differentiated thyroid cancer (DTC) cells in a synergistic manner. Methods: Three human DTC cell lines were used. NF-kB inhibition was achieved by using a NF-kB inhibitor (Bay 11-7082) or by p65 siRNA transfection. Methyl-thiazolyl-tetrazolium assay was performed for cell viability assessment. DNA-binding assay, luciferase reporter assay, and Western blot were adopted to determine function and expression changes of NF-kB. Then NF-kB regulated anti-apoptotic factors XIAP, cIAP1, and Bcl-xL were measured. Apoptosis was analyzed by Western blot for caspase 3 and PARP, and by flow cytometry as well. An iodide uptake assay was performed to determine whether NF-kB inhibition could influence radioactive iodide uptake. Results: The methyl-thiazolyl-tetrazolium assay showed significant decrease of viable cells by combination therapy than by mono-therapies. The DNA-binding assay and luciferase reporter assay showed enhanced NF-kB function and reporter gene activities due to 131 I, yet significant suppression was achieved by NF-kB inhibition. Western blot proved 131 I could increase nuclear NF-kB concentration, while NF-kB inhibition reduced NF-kB concentration. Western blot also demonstrated significant up-regulation of XIAP, cIAP1, and Bcl-xL after 131 I therapy. And inhibition of NF-kB could significantly downregulate these factors. Finally, synergism induced by combined therapy was displayed by significant enhancements o