Stochastic Weighted Graphs: Flexible Model Specification and Simulation

In most domains of network analysis researchers consider networks that arise in nature with weighted edges. Such networks are routinely dichotomized in the interest of using available methods for statistical inference with networks. The generalized exponential random graph model (GERGM) is a recently proposed method used to simulate and model the edges of a weighted graph. The GERGM specifies a joint distribution for an exponential family of graphs with continuous-valued edge weights. However, current estimation algorithms for the GERGM only allow inference on a restricted family of model specifications. To address this issue, we develop a Metropolis--Hastings method that can be used to estimate any GERGM specification, thereby significantly extending the family of weighted graphs that can be modeled with the GERGM. We show that new flexible model specifications are capable of avoiding likelihood degeneracy and efficiently capturing network structure in applications where such models were not previously available. We demonstrate the utility of this new class of GERGMs through application to two real network data sets, and we further assess the effectiveness of our proposed methodology by simulating non-degenerate model specifications from the well-studied two-stars model. A working R version of the GERGM code is available in the supplement and will be incorporated in the gergm CRAN package.Comment: 33 pages, 6 figures. To appear in Social Network

AAV-mediated delivery of optogenetic constructs to the macaque brain triggers humoral immune responses

Gene delivery to the primate central nervous system via recombinant adeno-associated viral vectors (AAV) allows neurophysiologists to control and observe neural activity precisely. A current limitation of this approach is variability in vector transduction efficiency. Low levels of transduction can foil experimental manipulations, prompting vector readministration. The ability to make multiple vector injections into the same animal, even in cases where successful vector transduction has already been achieved, is also desirable. However, vector readministration has consequences for humoral immunity and gene delivery that depend on vector dosage and route of administration in complex ways. As part of optogenetic experiments in rhesus monkeys, we analyzed blood sera collected before and after AAV injections into the brain and quantified neutralizing antibodies to AAV using an in vitro assay. We found that injections of AAV1 and AAV9 vectors elevated neutralizing antibody titers consistently. These immune responses were specific to the serotype injected and were long lasting. These results demonstrate that optogenetic manipulations in monkeys trigger immune responses to AAV capsids, suggesting that vector readministration may have a higher likelihood of success by avoiding serotypes injected previously

Determinants of gene targeting and regulation by response regulators in Clostridioides difficile

Bacteria use two-component signal transduction systems to sense the conditions of the environment and adapt their behavior to ensure survival. The separate roles of signal perception and response output are carried out by histidine kinase and response regulator proteins, respectively. Most response regulators alter gene transcription, but it is not yet possible to predict which genes they regulate. The precise prediction of these gene regulatory outputs could enable researchers to predict, and doctors and patients to mitigate, various bacterial behaviors. This dissertation presents the elucidation of the genes and biological functions regulated by two response regulators, RR_1586 and RR_1677, from the hypervirulent human pathogen Clostridioides difficile R20291. The data presented herein supports the conclusion that RR_1586 regulates genes involved in phosphate transport, and further characterization of its activity suggests several mechanisms it uses to regulate those genes. The bacterial one-hybrid assay used in this study to elucidate the gene regulatory targets of RR_1586 could potentially be used to find a generalizable solution to predicting gene targets of all response regulators from genome sequences alone. In the process of optimizing the bacterial one-hybrid assay for such a broadly impactful endeavor, it was found that RR_1677 appears to regulate the processes of protein synthesis and cell wall synthesis. A bioinformatics pipeline was also constructed by combining several existing utilities to analyze and interpret the experimental results. Two additional lines of research are also presented. The first is the adaptation of Fourier-transform infrared spectroscopy to observe response regulator phosphorylation. This method offers an alternative from the more labor-intensive methods currently available. The second is an analysis of the biophysical interactions between a response regulator from Saccharomyces cerevisiae and its binding partner, a histidine-containing phosphotransfer protein. Characterization of this interaction elucidates the physical impetus behind the evolutionary conservation of a specific glycine residue near the active site whose role was previously unknown

The misuse and abuse of statistics in biomedical research

Statistics are the primary tools for assessing relationships and evaluating study questions. Unfortunately, these tools are often misused, either inadvertently because of ignorance or lack of planning, or conspicuously to achieve a specified result. Data abuses include the incorrect application of statistical tests, lack of transparency and disclosure about decisions that are made, incomplete or incorrect multivariate model building, or exclusion of outliers. Individually, each of these actions may completely invalidate a study, and often studies are victim to more than one offense. Increasingly there are tools and guidance for researchers to look to, including the development of an analysis plan and a series of study specific checklists, in order to prevent or mitigate these offenses

Amplitude Modulation and Relaxation-Oscillation of Counterpropagating Rolls within a Broken-Symmetry Laser-Induced Electroconvection Strip

We report a liquid-crystal pattern-formation experiment in which we break the lateral (translational) symmetry of a nematic medium with a laser-induced thermal gradient. The work is motivated by an improved measurement (reported here) of the temperature dependence of the electroconvection threshold voltage in planar-nematic 4-methoxybenzylidene-4-butylaniline (MBBA). In contrast with other broken-symmetry-pattern studies that report a uniform drift, we observe a strip of counterpropagating rolls that collide at a sink point, and a strong temporally periodic amplitude modulation within a width of 3-4 rolls about the sink point. The time dependence of the amplitude at a fixed position is periodic but displays a nonsinusoidal relaxation-oscillation profile. After reporting experimental results based on spacetime contours and wavenumber profiles, along with a measurement of the change in the drift frequency with applied voltage at a fixed control parameter, we propose some potential guidelines for a theoretical model based on saddle-point solutions for Eckhaus-unstable states and coupled complex Ginzburg-Landau equations. Published in PRE 73, 036317 (2006).Comment: Published in Physical Review E in March 200

AAV-mediated delivery of optogenetic constructs to the macaque brain triggers humoral immune responses

Gene delivery to the primate central nervous system via recombinant adeno-associated viral vectors (AAV) allows neurophysiologists to control and observe neural activity precisely. A current limitation of this approach is variability in vector transduction efficiency. Low levels of transduction can foil experimental manipulations, prompting vector readministration. The ability to make multiple vector injections into the same animal, even in cases where successful vector transduction has already been achieved, is also desirable. However, vector readministration has consequences for humoral immunity and gene delivery that depend on vector dosage and route of administration in complex ways. As part of optogenetic experiments in rhesus monkeys, we analyzed blood sera collected before and after AAV injections into the brain and quantified neutralizing antibodies to AAV using an in vitro assay. We found that injections of AAV1 and AAV9 vectors elevated neutralizing antibody titers consistently. These immune responses were specific to the serotype injected and were long lasting. These results demonstrate that optogenetic manipulations in monkeys trigger immune responses to AAV capsids, suggesting that vector readministration may have a higher likelihood of success by avoiding serotypes injected previously

Phytoplankton Plastid Proteomics: Cracking Open Diatoms to Understand Plastid Biochemistry Under Iron Limitation

Diatoms, such as Thalassiosira pseudonana, are important oceanic primary producers, as they sequester carbon dioxide (CO₂) out of the atmosphere, die, and precipitate to the ocean floor. In many areas of the world’s oceans, phytoplankton, such as diatoms, are limited in growth by the availability of iron (Fe). Fe is an essential nutrient for phytoplankton, as it is central in the electron transport chain component of photosynthesis. Through this study, we examined if Fe-limitation makes a significant difference in the proteins expressed within the chloroplast, the power source for diatoms. Here, we utilized a new plastid isolation technique specific to diatoms and completed 14 mass spectrometry experiments to determine how many proteins transit the plastid membrane, if there are any differences in the expressed proteomes within the plastid grown under Fe-replete and Fe-limited conditions, and what those differences are. Over 900 unique proteins were identified from the isolated plastids, and cluster analyses of the data verified that statistical differences are present between the Fe-replete and Fe-limited growth conditions. Furthermore, our plastid proteome is in agreement with many of the recognized proteins previously discovered in land plant plastids, suggesting the isolation method followed by proteomic mass spectrometry is valid and sensitive. Through the isolation and analysis of plastid proteins, as shown here, scientists can now better identify which nutrients and/or trace metals directly affect diatom photosynthetic capacity so they can design better experiments to increase CO₂ fixation rates

Sample Size Requirements for Studies of Treatment Effects on Beta-Cell Function in Newly Diagnosed Type 1 Diabetes

Preservation of -cell function as measured by stimulated C-peptide has recently been accepted as a therapeutic target for subjects with newly diagnosed type 1 diabetes. In recently completed studies conducted by the Type 1 Diabetes Trial Network (TrialNet), repeated 2-hour Mixed Meal Tolerance Tests (MMTT) were obtained for up to 24 months from 156 subjects with up to 3 months duration of type 1 diabetes at the time of study enrollment. These data provide the information needed to more accurately determine the sample size needed for future studies of the effects of new agents on the 2-hour area under the curve (AUC) of the C-peptide values. The natural log(), log(+1) and square-root transformations of the AUC were assessed. In general, a transformation of the data is needed to better satisfy the normality assumptions for commonly used statistical tests. Statistical analysis of the raw and transformed data are provided to estimate the mean levels over time and the residual variation in untreated subjects that allow sample size calculations for future studies at either 12 or 24 months of follow-up and among children 8–12 years of age, adolescents (13–17 years) and adults (18+ years). The sample size needed to detect a given relative (percentage) difference with treatment versus control is greater at 24 months than at 12 months of follow-up, and differs among age categories. Owing to greater residual variation among those 13–17 years of age, a larger sample size is required for this age group. Methods are also described for assessment of sample size for mixtures of subjects among the age categories. Statistical expressions are presented for the presentation of analyses of log(+1) and transformed values in terms of the original units of measurement (pmol/ml). Analyses using different transformations are described for the TrialNet study of masked anti-CD20 (rituximab) versus masked placebo. These results provide the information needed to accurately evaluate the sample size for studies of new agents to preserve C-peptide levels in newly diagnosed type 1 diabetes