A temporal switch model for estimating transcriptional activity in gene expression

Motivation: The analysis and mechanistic modelling of time series gene expression data provided by techniques such as microarrays, NanoString, reverse transcription–polymerase chain reaction and advanced sequencing are invaluable for developing an understanding of the variation in key biological processes. We address this by proposing the estimation of a flexible dynamic model, which decouples temporal synthesis and degradation of mRNA and, hence, allows for transcriptional activity to switch between different states. Results: The model is flexible enough to capture a variety of observed transcriptional dynamics, including oscillatory behaviour, in a way that is compatible with the demands imposed by the quality, time-resolution and quantity of the data. We show that the timing and number of switch events in transcriptional activity can be estimated alongside individual gene mRNA stability with the help of a Bayesian reversible jump Markov chain Monte Carlo algorithm. To demonstrate the methodology, we focus on modelling the wild-type behaviour of a selection of 200 circadian genes of the model plant Arabidopsis thaliana. The results support the idea that using a mechanistic model to identify transcriptional switch points is likely to strongly contribute to efforts in elucidating and understanding key biological processes, such as transcription and degradation

Medication treatment perceptions, concerns and expectations among depressed individuals with Type I Bipolar Disorder

BACKGROUND: Subjective experience of illness affects outcomes among populations with bipolar disorder (BD). This cross-sectional study combined qualitative and quantitative approaches to evaluate perceived treatment effects, concerns and expectations among 90 individuals with BD. METHODS: Adults with type I BD, mean age 36.6 years, 51% women, completed a semi-structured interview that was audio taped, transcribed, coded and analyzed along emergent themes. Quantitative scales measured depressive symptoms (Hamilton Depression Scale/HAMD), psychopathology (Clinical Global Impression/CGI), and insight and treatment attitudes (Insight and Treatment Attitudes Questionnaire/ITAQ). RESULTS: Individuals had moderate depression and psychopathology with good insight into need for treatment. Drug treatment was perceived as beneficial, by “stabilizing” or “balancing” mood (42%, N=38), decreasing anxiety/depressive symptoms (19%, N=17) and improving sleep (10%, N=9). While 39%, (N=35) of individuals denied medication concerns, nearly 29%, (N=26) feared possible long-term effects, particularly diabetes or liver/kidney damage. Media stories and advertisements contributed to medication fears. Hopes and expectations for treatment ranged from those that were symptom or functional status-based, such as desiring mood stabilization and elimination of specific symptoms (23%, N=21), to more global hopes such as “being normal” (20%, N=18) or “cured” (18%, N=16). LIMITATIONS: Limitations include relatively small sample, lack of a comparator, inclusion of only depressed individuals and those willing to discuss their illness experience. CONCLUSIONS: While individuals with BD appreciate the effects of medications, concerns regarding adverse effects and discrepancy between actual and hoped-for outcomes can be substantial. Subjective experience with medications using qualitative and quantitative methods should be explored in order to optimize treatment collaboration and outcomes

Watch-wearing as a marker of conscientiousness

Several aspects of an individual’s appearance have been shown to predict personality and related behaviour. While some of these cues are grounded in biology (e.g., the human face), other aspects of a person’s appearance can be actively controlled (e.g., clothing). In this paper, we consider a common fashion accessory, the wristwatch. In an exploratory sample (N > 100) and a confirmatory sample (N > 600), we compared big-five personality traits between individuals who do or do not regularly wear a standard wristwatch. Significantly higher levels of conscientiousness were observed in participants who wore a watch. In a third study (N = 85), watch wearers arrived significantly earlier to appointments in comparison to controls. These results are discussed in relation to enclothed cognition and the rise of wearable technology including smartwatches

Height and Body Mass on the Mating Market: Associations With Number of Sex Partners and Extra-Pair Sex Among Heterosexual Men and Women Aged 18–65

People with traits that are attractive on the mating market are better able to pursue their preferred mating strategy. Men who are relatively tall may be preferred by women because taller height is a cue to dominance, social status, access to resources, and heritable fitness, leading them to have more mating opportunities and sex partners. We examined height, education, age, ethnicity, and body mass index (BMI) as predictors of sexual history among heterosexual men and women (N = 60,058). The linear and curvilinear associations between self-reported height and sex partner number were small for men when controlling for education, BMI, and ethnicity (linear β = .05; curvilinear β = −.03). The mean and median number of sex partners for men of different heights were: very short (9.4; 5), short (11.0; 7), average (11.7; 7), tall (12.0; 7), very tall (12.1; 7), and extremely tall (12.3; 7). Men who were “overweight” reported a higher mean and median number of sex partners than men with other body masses. The results for men suggested limited variation in reported sex partner number across most of the height continuum, but that very short men report fewer partners than other men

Lifting of Ir{100} reconstruction by CO adsorption: An ab initio study

The adsorption of CO on unreconstructed and reconstructed Ir{100} has been studied, using a combination of density functional theory and thermodynamics, to determine the relative stability of the two phases as a function of CO coverage, temperature and pressure. We obtain good agreement with experimentaldata. At zero temperature, the (1X5) reconstruction becomes less stable than the unreconstructed (1X1) surface when the CO coverage exceeds a critical value of 0.09 ML. The interaction between CO molecules is found to be repulsive on the reconstructed surface, but attractive on the unreconstructed, explaining the experimental observation of high CO coverage on growing (1X1) islands. At all temperatures and pressures, we find only two possible stable states: 0.05 ML CO c(2X2) overlayer on the (1X1) substrate, and the clean (1$\times$5) reconstructed surface.Comment: 31 page

Resonance energy transfer: The unified theory revisited

Resonanceenergy transfer (RET) is the principal mechanism for the intermolecular or intramolecular redistribution of electronic energy following molecular excitation. In terms of fundamental quantum interactions, the process is properly described in terms of a virtual photon transit between the pre-excited donor and a lower energy (usually ground-state) acceptor. The detailed quantum amplitude for RET is calculated by molecular quantum electrodynamical techniques with the observable, the transfer rate, derived via application of the Fermi golden rule. In the treatment reported here, recently devised state-sequence techniques and a novel calculational protocol is applied to RET and shown to circumvent problems associated with the usual method. The second-rank tensor describing virtual photon behavior evolves from a Green’s function solution to the Helmholtz equation, and special functions are employed to realize the coupling tensor. The method is used to derive a new result for energy transfer systems sensitive to both magnetic- and electric-dipole transitions. The ensuing result is compared to that of pure electric-dipole–electric-dipole coupling and is analyzed with regard to acceptable transfer separations. Systems are proposed where the electric-dipole–magnetic-dipole term is the leading contribution to the overall rate

Calculation of the heavy-hadron axial couplings g_1, g_2, and g_3 using lattice QCD

In a recent letter [Phys. Rev. Lett. 108, 172003 (2012), arXiv:1109.2480] we have reported on a lattice QCD calculation of the heavy-hadron axial couplings $g_1$, $g_2$, and $g_3$. These quantities are low-energy constants of heavy-hadron chiral perturbation theory (HH$\chi$PT) and are related to the $B^*B\pi$, $\Sigma_b^*\Sigma_b\pi$, and $\Sigma_b^{(*)}\Lambda_b\pi$ couplings. In the following, we discuss important details of the calculation and give further results. To determine the axial couplings, we explicitly match the matrix elements of the axial current in QCD with the corresponding matrix elements in HH$\chi$PT. We construct the ratios of correlation functions used to calculate the matrix elements in lattice QCD, and study the contributions from excited states. We present the complete numerical results and discuss the data analysis in depth. In particular, we demonstrate the convergence of $SU(4|2)$ HH$\chi$PT for the axial-current matrix elements at pion masses up to about 400 MeV and show the impact of the nonanalytic loop contributions. Finally, we present additional predictions for strong and radiative decay widths of charm and bottom baryons.Comment: 42 pages, 20 figures, updated calculation of Xi_b^{*0} width using mass measurement from CMS, published versio

Photodetector Development for the Wheel Abrasion Experiment on the Sojourner Microrover of the Mars Pathfinder Mission

On-board the Mars Pathfinder spacecraft, launched in December of 1996, is a small roving vehicle named Sojourner. On Sojourner is an experiment to determine the abrasive characteristics of the Martian surface, called the Wheel Abrasion Experiment (WAE). The experiment works as follows: one of the wheels of the rover has a strip of black anodized aluminum bonded to the tread. The aluminum strip has thin coatings of aluminum, nickel and platinum deposited in patches. There are five (5) patches or samples of each metal, and the patches range in thickness from 200 A to 1000 A. The different metals were chosen for their differing hardness and their environmental stability. As the wheel is spun in the Martian soil, the thin patches of metal are abraded away, exposing the black anodization. The abrasion is monitored by measuring the amount of light reflected off of the samples. A photodetector was developed for this purpose, and that is the subject of this paper