Detecting controlling nodes of boolean regulatory networks

Boolean models of regulatory networks are assumed to be tolerant to perturbations. That qualitatively implies that each function can only depend on a few nodes. Biologically motivated constraints further show that functions found in Boolean regulatory networks belong to certain classes of functions, for example, the unate functions. It turns out that these classes have specific properties in the Fourier domain. That motivates us to study the problem of detecting controlling nodes in classes of Boolean networks using spectral techniques. We consider networks with unbalanced functions and functions of an average sensitivity less than 23k, where k is the number of controlling variables for a function. Further, we consider the class of 1-low networks which include unate networks, linear threshold networks, and networks with nested canalyzing functions. We show that the application of spectral learning algorithms leads to both better time and sample complexity for the detection of controlling nodes compared with algorithms based on exhaustive search. For a particular algorithm, we state analytical upper bounds on the number of samples needed to find the controlling nodes of the Boolean functions. Further, improved algorithms for detecting controlling nodes in large-scale unate networks are given and numerically studied

Parkinson’s Disease Subtypes Show a Specific Link between Dopaminergic and Glucose Metabolism in the Striatum

<div><p>Background</p><p>Previous studies have shown different clinical and imaging pattern in tremordominant and akinetic-rigid Parkinson’s disease (PD) subtypes. The association between dopaminergic and glucose metabolism has in contrast not been investigated yet. Therefore, this study compared PD subtypes with respect to clinical and imaging findings with the aim of establishing a relationship between clinical subtypes, dopamine and glucose metabolism.</p><p>Methods</p><p>Two groups of a total of 64 idiopathic PD patients (42 male, 22 female, mean age 56±10.9 years) were analysed: akinetic-rigid (AR, n = 32) and tremor-dominant (TD, n = 32) patients. Both were compared with respect to differential involvement of local striatal dopamine and glucose metabolism using [¹⁸F]-fluoro-L-dopa (F-dopa) and [¹⁸F]-fluorodeoxyglucose (FDG)-PET.</p><p>Results</p><p>The analysis of PD subgroups showed significant differences in the F-dopa uptake in the anterior putamen. Using the results of the local striatal dopamine difference as a volume of interest for the FDG-analysis, analysis of AR patients revealed a significantly lower normalised cerebral metabolic rate of glucose (nCMRGlc) within the ventral striatum.</p><p>Conclusions</p><p>The dual tracer study illlustrates clear differences between TD and AR subtypes in the ventral striatum. In accordance with previous FP-CIT-SPECT studies, it discloses congruent results for the presynaptic dopaminergic system and extends the knowledge about an additional involvement of local metabolic activity in the caudate and anterior putamen. The findings corroborate the specific role of distinct PD subtypes within the cerebello-thalamo-cortical-circuits. Multitracer PET imaging may thus enhance the knowledge about the clinical segregation into subtypes.</p></div

Patients’ characteristics.

<p>Patients’ characteristics.</p

Regional glucose (nCMRGlc) and F-dopa (SOR-1) uptake in a striatal volume of interest identified as subtype-specific for PD patients.

<p>The green regression line demonstrates the correlation of nCMRGlc and F-dopa-uptake for akinetic-rigid patients (<i>r</i> = 0.537, <i>p</i> = 0.032). For methodological considerations see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0096629#pone.0096629.s001" target="_blank">File S1</a>.</p

The Vaginal Microbiota of Pregnant Women Varies with Gestational Age, Maternal Age, and Parity

ABSTRACT The composition of the vaginal microbiota is heavily influenced by pregnancy and may factor into pregnancy complications, including spontaneous preterm birth. However, results among studies have been inconsistent due, in part, to variation in sample sizes and ethnicity. Thus, an association between the vaginal microbiota and preterm labor continues to be debated. Yet, before assessing associations between the composition of the vaginal microbiota and preterm labor, a robust and in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required. Here, we report a large longitudinal study (n = 474 women, 1,862 vaginal samples) of a predominantly African-American cohort—a population that experiences a relatively high rate of pregnancy complications—evaluating associations between individual identity, gestational age, and other maternal characteristics with the composition of the vaginal microbiota throughout gestation resulting in term delivery. The principal factors influencing the composition of the vaginal microbiota in pregnancy are individual identity and gestational age at sampling. Other factors are maternal age, parity, obesity, and self-reported Cannabis use. The general pattern across gestation is for the vaginal microbiota to remain or transition to a state of Lactobacillus dominance. This pattern can be modified by maternal parity and obesity. Regardless, network analyses reveal dynamic associations among specific bacterial taxa within the vaginal ecosystem, which shift throughout the course of pregnancy. This study provides a robust foundational understanding of the vaginal microbiota in pregnancy and sets the stage for further investigation of this microbiota in obstetrical disease. IMPORTANCE There is debate regarding links between the vaginal microbiota and pregnancy complications, especially spontaneous preterm birth. Inconsistencies in results among studies are likely due to differences in sample sizes and cohort ethnicity. Ethnicity is a complicating factor because, although all bacterial taxa commonly inhabiting the vagina are present among all ethnicities, the frequencies of these taxa vary among ethnicities. Therefore, an in-depth characterization of the vaginal microbiota throughout pregnancy in the specific study population under investigation is required prior to evaluating associations between the vaginal microbiota and obstetrical disease. This initial investigation is a large longitudinal study of the vaginal microbiota throughout gestation resulting in a term delivery in a predominantly African-American cohort, a population that experiences disproportionally negative maternal-fetal health outcomes. It establishes the magnitude of associations between maternal characteristics, such as age, parity, body mass index, and self-reported Cannabis use, on the vaginal microbiota in pregnancy

Long access heroin self-administration significantly alters gut microbiome composition and structure

Introduction It is well known that chronic opioid use disorder is associated with alterations in gastrointestinal (GI) function that include constipation, reduced motility, and increased bacterial translocation due to compromised gut barrier function. These signs of disrupted GI function can be associated with alterations in the gut microbiome. However, it is not known if long-access opioid self-administration has effects on the gut microbiome.Methods We used 16S rRNA gene sequencing to investigate the gut microbiome in three independent cohorts (N=40 for each) of NIH heterogeneous stock rats before onset of long-access heroin self-administration (i.e., naive status), at the end of a 15-day period of self-administration, and after post-extinction reinstatement. Measures of microbial alpha- and beta-diversity were evaluated for all phases. High-dimensional class comparisons were carried out with MaAsLin2. PICRUSt2 was used for predicting functional pathways impacted by heroin based on marker gene sequences.Results Community alpha-diversity was not altered by heroin at any of the three phases by comparison to saline-yoked controls. Analyses of beta-diversity showed that the heroin and saline-yoked groups clustered significantly apart from each other using the Bray-Curtis (community structure) index. Heroin caused significant alterations at the ASV level at the self-administration and extinction phases. At the phylum level, the relative abundance of Firmicutes was increased at the self-administration phase. Deferribacteres was decreased in heroin whereas Patescibacteria was increased in heroin at the extinction phase. Potential biomarkers for heroin emerged from the MaAsLin2 analysis. Bacterial metabolomic pathways relating to degradation of carboxylic acids, nucleotides, nucleosides, carbohydrates, and glycogen were increased by heroin while pathways relating to biosynthesis of vitamins, propionic acid, fatty acids, and lipids were decreased.Discussion These findings support the view that long access heroin self-administration significantly alters the structure of the gut microbiome by comparison to saline-yoked controls. Inferred metabolic pathway alterations suggest the development of a microbial imbalance favoring gut inflammation and energy expenditure. Potential microbial biomarkers and related functional pathways likely invoked by heroin self-administration could be targets for therapeutic intervention

Inflammation-induced citrullinated glucose-regulated protein 78 elicits immune responses in human type 1 diabetes

The b-cell has become recognized as a central player in the pathogenesis of type 1 diabetes with the generation of neoantigens as potential triggers for breaking immune tolerance. We report that posttranslationally modified glucose-regulated protein 78 (GRP78) is a novel autoantigen in human type 1 diabetes. When human islets were exposed to inflammatory stress induced by interleukin-1b, tumor necrosis factor-a, and interferon-g, arginine residue R510 within GRP78 was converted into citrulline, as evidenced by liquid chromatography-tandem mass spectrometry. This conversion, known as citrullination, led to the generation of neoepitopes, which effectively could be presented by HLA-DRB1*04:01 molecules. With the use of HLA-DRB1*04:01 tetramers and ELISA techniques, we demonstrate enhanced antigenicity of citrullinated GRP78 with significantly increased CD4+ T-cell responses and autoantibody titers in patients with type 1 diabetes compared with healthy control subjects. Of note, patients with type 1 diabetes had a predominantly higher percentage of central memory cells and a lower percentage of effector memory cells directed against citrullinated GRP78 compared with the native epitope. These results strongly suggest that citrullination of b-cell proteins, exemplified here by the citrullination of GRP78, contributes to loss of self-tolerance toward b-cells in human type 1 diabetes, indicating that b-cells actively participate in their own demise