Data mining NHANES: Utilizing a Genetic Algorithm to Detect Correlation Between Birth Sex Ratio and Epidemiological Factors

In the past several decades there has been increasing research into factors that may affect the birth sex ratio of parents. These can range from nutrition to hormone levels to psychological factors. The National Health and Nutritional Examination Survey (NHANES) is a broadly encompassing governmental survey that captures some of these aspects making it a rich and easily exploitable data set for these purposes. In this study we utilize custom Perl scripts written to extract such information and attempt to find correlations using a genetic algorithm. Mothers are first identified through inferred relationships within the database. Variables are then analyzed to find any significant difference between groups of women whom have more male or female offspring. Lastly, identified variables are passed on to a genetic algorithm which attempts to find any correlation between the variables and the birth sex ratio. While our analysis did not produce any conclusive results, there were some interesting findings regarding which variables were automatically selected for in the primary analysis. Ultimately the development of the tools used in this project can be helpful in answering other questions about the NHANES data set and they can potentially be applied to other problems outside of NHANES

Properties of Healthcare Teaming Networks as a Function of Network Construction Algorithms

Network models of healthcare systems can be used to examine how providers collaborate, communicate, refer patients to each other. Most healthcare service network models have been constructed from patient claims data, using billing claims to link patients with providers. The data sets can be quite large, making standard methods for network construction computationally challenging and thus requiring the use of alternate construction algorithms. While these alternate methods have seen increasing use in generating healthcare networks, there is little to no literature comparing the differences in the structural properties of the generated networks. To address this issue, we compared the properties of healthcare networks constructed using different algorithms and the 2013 Medicare Part B outpatient claims data. Three different algorithms were compared: binning, sliding frame, and trace-route. Unipartite networks linking either providers or healthcare organizations by shared patients were built using each method. We found that each algorithm produced networks with substantially different topological properties. Provider networks adhered to a power law, and organization networks to a power law with exponential cutoff. Censoring networks to exclude edges with less than 11 shared patients, a common de-identification practice for healthcare network data, markedly reduced edge numbers and greatly altered measures of vertex prominence such as the betweenness centrality. We identified patterns in the distance patients travel between network providers, and most strikingly between providers in the Northeast United States and Florida. We conclude that the choice of network construction algorithm is critical for healthcare network analysis, and discuss the implications for selecting the algorithm best suited to the type of analysis to be performed.Comment: With links to comprehensive, high resolution figures and networks via figshare.co

Humoral Dysregulation Associated with Increased Systemic Inflammation among Injection Heroin Users

Injection drug use is a growing major public health concern. Injection drug users (IDUs) have a higher incidence of co-morbidities including HIV, Hepatitis, and other infections. An effective humoral response is critical for optimal homeostasis and protection from infection; however, the impact of injection heroin use on humoral immunity is poorly understood. We hypothesized that IDUs have altered B cell and antibody profiles.A comprehensive systems biology-based cross-sectional assessment of 130 peripheral blood B cell flow cytometry- and plasma- based features was performed on HIV-/Hepatitis C-, active heroin IDUs who participated in a syringe exchange program (n = 19) and healthy control subjects (n = 19). The IDU group had substantial polydrug use, with 89% reporting cocaine injection within the preceding month. IDUs exhibited a significant, 2-fold increase in total B cells compared to healthy subjects, which was associated with increased activated B cell subsets. Although plasma total IgG titers were similar between groups, IDUs had significantly higher IgG3 and IgG4, suggestive of chronic B cell activation. Total IgM was also increased in IDUs, as well as HIV Envelope-specific IgM, suggestive of increased HIV exposure. IDUs exhibited numerous features suggestive of systemic inflammation, including significantly increased plasma sCD40L, TNF-α, TGF-α, IL-8, and ceramide metabolites. Machine learning multivariate analysis distilled a set of 10 features that classified samples based on group with absolute accuracy.These results demonstrate broad alterations in the steady-state humoral profile of IDUs that are associated with increased systemic inflammation. Such dysregulation may impact the ability of IDUs to generate optimal responses to vaccination and infection, or lead to increased risk for inflammation-related co-morbidities, and should be considered when developing immune-based interventions for this growing population

Expression of the Long Non-Coding RNA HOTAIR Correlates with Disease Progression in Bladder Cancer and Is Contained in Bladder Cancer Patient Urinary Exosomes.

Exosomes are 30-150nM membrane-bound secreted vesicles that are readily isolated from biological fluids such as urine (UEs). Exosomes contain proteins, micro RNA (miRNA), messenger RNA (mRNA), and long non-coding RNA (lncRNA) from their cells of origin. Although miRNA, protein and lncRNA have been isolated from serum as potential biomarkers for benign and malignant disease, it is unknown if lncRNAs in UEs from urothelial bladder cancer (UBC) patients can serve as biomarkers. lncRNAs are > 200 nucleotide long transcripts that do not encode protein and play critical roles in tumor biology. As the number of recognized tumor-associated lncRNAs continues to increase, there is a parallel need to include lncRNAs into biomarker discovery and therapeutic target algorithms. The lncRNA HOX transcript antisense RNA (HOTAIR) has been shown to facilitate tumor initiation and progression and is associated with poor prognosis in several cancers. The importance of HOTAIR in cancer biology has sparked interest in using HOTAIR as a biomarker and potential therapeutic target. Here we show HOTAIR and several tumor-associated lncRNAs are enriched in UEs from UBC patients with high-grade muscle-invasive disease (HGMI pT2-pT4). Knockdown of HOTAIR in UBC cell lines reduces in vitro migration and invasion. Importantly, loss of HOTAIR expression in UBC cell lines alters expression of epithelial-to-mesenchyme transition (EMT) genes including SNAI1, TWIST1, ZEB1, ZO1, MMP1 LAMB3, and LAMC2. Finally, we used RNA-sequencing to identify four additional lncRNAs enriched in UBC patient UEs. These data, suggest that UE-derived lncRNA may potentially serve as biomarkers and therapeutic targets

Broad and Protective Influenza B Virus Neuraminidase Antibodies in Humans after Vaccination and their Clonal Persistence as Plasma Cells

Influenza virus infections continue to cause substantial morbidity and mortality despite the availability of seasonal vaccines. The extensive genetic variability in seasonal and potentially pandemic influenza strains necessitates new vaccine strategies that can induce universal protection by focusing the immune response on generating protective antibodies against conserved targets such as regions within the influenza neuraminidase protein. We have demonstrated that seasonal immunization stimulates neuraminidase-specific antibodies in humans that are broad and potent in their protection from influenza B virus when tested in mice. These antibodies further persist in the bone marrow, where they are expressed by long-lived antibody-producing cells, referred to here as plasma cells. The significance in our research is the demonstration that seasonal influenza immunization can induce a subset of neuraminidase-specific B cells with broad protective potential, a process that if further studied and enhanced could aid in the development of a universal influenza vaccine.Although most seasonal inactivated influenza vaccines (IIV) contain neuraminidase (NA), the extent and mechanisms of action of protective human NA-specific humoral responses induced by vaccination are poorly resolved. Due to the propensity of influenza virus for antigenic drift and shift and its tendency to elicit predominantly strain-specific antibodies, humanity remains susceptible to waves of new strains of seasonal viruses and is at risk from viruses with pandemic potential for which limited or no immunity may exist. Here we demonstrate that the use of IIV results in increased levels of influenza B virus (IBV) NA-specific serum antibodies. Detailed analysis of the IBV NA B cell response indicates concurrent expansion of IBV NA-specific peripheral blood plasmablasts 7 days after IIV immunization which express monoclonal antibodies with broad and potent antiviral activity against both IBV Victoria and Yamagata lineages and prophylactic and therapeutic activity in mice. These IBV NA-specific B cell clonal lineages persisted in CD138+ long-lived bone marrow plasma cells. These results represent the first demonstration that IIV-induced NA human antibodies can protect and treat influenza virus infection in vivo and suggest that IIV can induce a subset of IBV NA-specific B cells with broad protective potential, a feature that warrants further study for universal influenza vaccine development

HGMI (pT2-pT4) UBC patient tumors overexpress several tumor-associated lncRNA and mRNA.

<p>(A) qRT-PCR of tumor-associated mRNAs and lncRNAs in tumors from patients who underwent cystectomy for HG disease (final pathology pT2-pT4). Tumor and distal normal tissue (DNT) mRNA or lncRNA was normalized to 18s and then the ratio of tumor to DNT was calculated. Statistical significance was determined using Student’s t-test to compare tumor to DNT normalized expression, *p<0.05. (n = 10 patients). (B) HOTAIR was not differentially expressed between pT2 tumors and pT4 tumors (Student’s t-test, p>0.05).</p

lncRNAs HYMA1, LINC00477, LOC100506688 and OTX2-AS1 are enriched in UEs of UBC patients with HGMI disease (pT2-pT4).

<p>Confirmatory qRT-PCR of the novel lncRNAs (normalized to 18s) identified by RNA-sequencing in n = 8 UEs from patients with HGMI (pT2-pT4) UBC and UEs from n = 7 HVs. Student’s t-test *p<0.05, **p<0.01, ***p<0.001.</p

Loss of HOTAIR affects EMT factor expression in UBC cell lines.

<p>(A) qRT-PCR of known HOTAIR target genes and classical EMT factors mRNA in shHOTAIR T24 compared to shScramble T24 UBC cells. (B) EMT target gene mRNA expression in shHOTAIR TCC-SUP cells compared to shScramble TCC-SUP cells (in panels A and B EMT mRNA levels were normalized to GAPDH). (C) siRNA targeted against HOTAIR or GFP was used in T24 cells and EMT factors ZEB1 and SNAI1 mRNA expression evaluated by qRT-PCR (mRNA was normalized to 18s). (D) Immunoblot of T24 siGFP and siHOTAIR cells showing reduced protein levels of ZEB1 and SNAI1. GAPDH is a loading control. Beta-actin was used as a loading control. Student’s t-test was used to determine statistical differences between control and HOTAIR knockdown cells in the qRT-PCR experiments presented (A-C) *p<0.1, **p<0.05, ***p<0.01 (n = 3–6 experiments/panel).</p