Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Background  

The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words.     

Cognitive Behavioral Therapy and Fluoxetine as Adjuncts to Group Behavioral Therapy for Binge Eating Disorder

Objective: Although binge eating disorder is a common and distressing concomitant of obesity, it has not yet been established whether affected individuals presenting to behavioral weight control programs should receive specialized treatments to supplement standard treatment. This study was designed to examine the added benefit of two adjunctive interventions, individual cognitive behavioral therapy (CBT) and fluoxetine, offered in the context of group behavioral weight control treatment. Research Methods and Procedures: One hundred sixteen overweight/obese women and men with binge eating disorder were all assigned to receive a 16‐session group behavioral weight control treatment over 20 weeks. Simultaneously, subjects were randomly assigned to receive CBT + fluoxetine, CBT + placebo, fluoxetine, or placebo in a two‐by‐two factorial design. Outcome measures, assessed at the end of the 16‐session acute treatment phase, included binge frequency, weight, and measures of eating‐related and general psychopathology. Results: Overall, subjects showed substantial improvement in binge eating and both general and eating‐related psychopathology, but little weight loss. Subjects who received individual CBT improved more in binge frequency than did those not receiving CBT (p < 0.001), and binge abstinence was significantly more common in subjects receiving CBT vs. those who did not (62% vs. 33%, p < 0.001). Fluoxetine treatment was associated with greater reduction in depressive symptoms (p < 0.05). The 54 subjects who achieved binge abstinence improved more on all measures than the 62 subjects who did not. In particular, these subjects lost, on average, 6.2 kg compared with a gain of 0.7 kg among non‐abstainers. Discussion: Adjunctive individual CBT results in significant additional binge reduction in obese binge eaters receiving standard behavioral weight control treatment.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).     

AUTORADIOGRAPHIC LOCALIZATION OF 13N AFTER FIXATION OF 13N-LABELED NITROGEN GAS BY A HETEROCYST-FORMING BLUE-GREEN ALGA

¹³N, generated by proton bombardment of ¹³C powder, is rapidly and easily converted to ¹³N-N₂, 0.01 atm pressure, ca. 10 mCi/ml, by automated Dumas combustion. ¹³N fixed (as ¹³N-N₂) by algal filaments was localized by an autoradiographic technique which permits track autoradiography with isotopes having short half-lives. Our findings show directly that a minimum of about 25% of the N₂ fixation by intact, aerobically grown filaments of Anabaena cylindrica is carried out by the heterocysts. If all of the N₂ fixation takes place in the heterocysts, then the movement of nitrogen along the filaments can be characterized by a constant τ < ca. 5 s (cell^-2).     

Non-native interactions play an effective role in protein folding dynamics

Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well‐defined order. The detailed study of the folding dynamics of protein‐like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non‐native interactions in the folding process), reveals significant differences in the corresponding locking scenarios—the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non‐native contacts. Furthermore, strong evidence for a positive role played by non‐native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non‐native contacts is observed also toward the end of the folding process, suggesting that non‐native contacts may indeed affect the overall folding process. For target models exhibiting clear two‐state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

Effects of mechanical uncouplers, diacetyl monoxime, and cytochalasin-D on the electrophysiology of perfused mouse hearts

Chemical uncouplers diacetyl monoxime (DAM) and cytochalasin D (cyto-D) are used to abolish cardiac contractions in optical studies, yet alter intracellular Ca(2+) concentration ([Ca(2+)](i)) handling and vulnerability to arrhythmias in a species-dependent manner. The effects of uncouplers were investigated in perfused mouse hearts labeled with rhod-2/AM or 4-[beta-[2-(di-n-butylamino)-6-naphthyl]vinyl]pyridinium (di-4-ANEPPS) to map [Ca(2+)](i) transients (emission wavelength = 585 +/- 20 nm) and action potentials (APs) (emission wavelength > 610 nm; excitation wavelength = 530 +/- 20 nm). Confocal images showed that rhod-2 is primarily in the cytosol. DAM (15 mM) and cyto-D (5 microM) increased AP durations (APD(75) = 20.0 +/- 3 to 46.6 +/- 5 ms and 39.9 +/- 8 ms, respectively, n = 4) and refractory periods (45.14 +/- 12.1 to 82.5 +/- 3.5 ms and 78 +/- 4.24 ms, respectively). Cyto-D reduced conduction velocity by 20% within 5 min and DAM by 10% gradually in 1 h (n = 5 each). Uncouplers did not alter the direction and gradient of repolarization, which progressed from apex to base in 15 +/- 3 ms. Peak systolic [Ca(2+)](i) increased with cyto-D from 743 +/- 47 (n = 8) to 944 +/- 17 nM (n = 3, P = 0.01) but decreased with DAM to 398 +/- 44 nM (n = 3, P < 0.01). Diastolic [Ca(2+)](i) was higher with cyto-D (544 +/- 80 nM, n = 3) and lower with DAM (224 +/- 31, n = 3) compared with controls (257 +/- 30 nM, n = 3). DAM prolonged [Ca(2+)](i) transients at 75% recovery (54.3 +/- 5 to 83.6 +/- 1.9 ms), whereas cyto-D had no effect (58.6 +/- 1.2 ms; n = 3). Burst pacing routinely elicited long-lasting ventricular tachycardia but not fibrillation. Uncouplers flattened the slope of AP restitution kinetic curves and blocked ventricular tachycardia induced by burst pacing.     

Multiple mechanisms of reduced major histocompatibility complex class II expression in endotoxin tolerance

Patients after polytrauma, burns, or septic shock frequently develop a life-threatening immunodeficiency. This state is associated with specific functional alterations of monocytic cells. We previously proposed endotoxin tolerance, the monocyte state after acute response to lipopolysaccharide, as a respective model system. One major feature in both the clinical situation and the in vitro model is the dramatic down-regulation of monocyte major histocompatibility complex (MHC) class II surface expression, which is associated with impaired antigen presentation capacity. This study focused on the mechanisms behind reduced MHC class II expression in endotoxin tolerance. Endotoxin priming provoked a decrease of monocyte intracellular MHC class II. It also led to a reduced expression of the chaperonic invariant chain and to an inhibited synthesis of the major lysosomal enzyme for final cleavage of the invariant chain going along with a relative accumulation of p10. The expression of HLA-DM necessary for loading MHC class II with antigenic peptide was also decreased. Additionally, reduced export of MHC class II alphabeta complexes to the cell surface was observed. The down-regulation of HLA-DR, invariant chain, and HLA-DM was regulated at the mRNA level and may be the consequence of reduced class II transactivator expression observed in this study. The simultaneous interference at different regulatory levels may explain the uniquely strong and long lasting MHC class II down-modulating effect of endotoxin priming compared with transforming growth factor-beta and interleukin-10. These results not only contribute to a better understanding of experimental endotoxin tolerance but may also give rise to new therapeutics for temporary immunodeficiency and, conversely, for MHC class II-dependent diseases such as autoimmunity and transplant rejection.