Culture Shock

Take one week living in our culture: Monday: A student quotes other students on Overheard at Gettysburg. “In the commons at 8:50am. Two girls. Completely serious. Girl 1: Have you been outside? Girl 2: Yea! It’s rape weather. Girl 1: I know. A girl could totally get raped out there.” [excerpt

Transferable neural networks for enhanced sampling of protein dynamics

Variational auto-encoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single non-linear embedding. In this work, we illustrate how this non-linear latent embedding can be used as a collective variable for enhanced sampling, and present a simple modification that allows us to rapidly perform sampling in multiple related systems. We first demonstrate our method is able to describe the effects of force field changes in capped alanine dipeptide after learning a model using AMBER99. We further provide a simple extension to variational dynamics encoders that allows the model to be trained in a more efficient manner on larger systems by encoding the outputs of a linear transformation using time-structure based independent component analysis (tICA). Using this technique, we show how such a model trained for one protein, the WW domain, can efficiently be transferred to perform enhanced sampling on a related mutant protein, the GTT mutation. This method shows promise for its ability to rapidly sample related systems using a single transferable collective variable and is generally applicable to sets of related simulations, enabling us to probe the effects of variation in increasingly large systems of biophysical interest.Comment: 20 pages, 10 figure

Coronal response to an EUV wave from DEM analysis

EUV (Extreme-Ultraviolet) waves are globally propagating disturbances that have been observed since the era of the SoHO/EIT instrument. Although the kinematics of the wave front and secondary wave components have been widely studied, there is not much known about the generation and plasma properties of the wave. In this paper we discuss the effect of an EUV wave on the local plasma as it passes through the corona. We studied the EUV wave, generated during the 2011 February 15 X-class flare/CME event, using Differential Emission Measure diagnostics. We analyzed regions on the path of the EUV wave and investigated the local density and temperature changes. From our study we have quantitatively confirmed previous results that during wave passage the plasma visible in the Atmospheric Imaging Assembly (AIA) 171A channel is getting heated to higher temperatures corresponding to AIA 193A and 211A channels. We have calculated an increase of 6 - 9% in density and 5 - 6% in temperature during the passage of the EUV wave. We have compared the variation in temperature with the adiabatic relationship and have quantitatively demonstrated the phenomenon of heating due to adiabatic compression at the wave front. However, the cooling phase does not follow adiabatic relaxation but shows slow decay indicating slow energy release being triggered by the wave passage. We have also identified that heating is taking place at the front of the wave pulse rather than at the rear. Our results provide support for the case that the event under study here is a compressive fast-mode wave or a shock.Comment: Accepted for publication in Ap

Limits on Clouds and Hazes for the TRAPPIST-1 Planets

The TRAPPIST-1 planetary system is an excellent candidate for study of the evolution and habitability of M-dwarf planets. Transmission spectroscopy observations performed with the Hubble Space Telescope (HST) suggest the innermost five planets do not possess clear hydrogen atmospheres. Here we reassess these conclusions with recently updated mass constraints and expand the analysis to include limits on metallicity, cloud top pressure, and the strength of haze scattering. We connect recent laboratory results of particle size and production rate for exoplanet hazes to a one-dimensional atmospheric model for TRAPPIST-1 transmission spectra. Doing so, we obtain a physically-based estimate of haze scattering cross sections. We find haze scattering cross sections on the order of 1e-26 to 1e-19 cm squared are needed in hydrogen-rich atmospheres for TRAPPIST-1 d, e, and f to match the HST data. For TRAPPIST-1 g, we cannot rule out a clear hydrogen-rich atmosphere. We also modeled the effects an opaque cloud deck and substantial heavy element content have on the transmission spectra. We determine that hydrogen-rich atmospheres with high altitude clouds, at pressures of 12mbar and lower, are consistent with the HST observations for TRAPPIST-1 d and e. For TRAPPIST-1 f and g, we cannot rule out clear hydrogen-rich cases to high confidence. We demonstrate that metallicities of at least 60xsolar with tropospheric (0.1 bar) clouds agree with observations. Additionally, we provide estimates of the precision necessary for future observations to disentangle degeneracies in cloud top pressure and metallicity. Our results suggest secondary, volatile-rich atmospheres for the outer TRAPPIST-1 planets d, e, and f.Comment: 15 pages, 3 figures, 2 tables, accepted in the Astronomical Journa

Adding a Youth Flavor to Extension\u27s Programs

Youths not only participate in Extension services but also can be equipped as facilitators to extend information about a critical topic to new audiences. Our interdisciplinary team of Extension professionals created a program to equip youths as peer educators, increase youths\u27 awareness and understanding of a new topic (local foods), promote youths\u27 positive development, and establish a model for involving teens in existing Extension programs. Other Extension professionals can use the program\u27s model, amending the topic area as needed, to promote positive youth development outcomes while engaging youths in helping with Extension\u27s mission

Effects of sunrise/sunset lighting on corticosterone levels in Coturnix quail (Coturnix coturnix)

Both genetics and environment play important roles in the growth, performance, and overall welfare of poultry species. Current commercial production practices typically do not mimic the natural environmental conditions of ancestral poultry species, specifically lighting. The current study aimed to evaluate the impact of genetics and the effect of sunrise/sunset lighting on the stress response of 4 genetic lines of Coturnix quail. The 4 lines utilized in this study included high stress (H), low stress (L), stress control (R), and Arkansas randombred (A) quail lines. Day old chicks from these lines were placed in one of two environmentally controlled rooms. All conditions were kept similar between the rooms until week 4. At week 4, half of the quail in each room were relocated to the other room and the experimental conditions began. One room was subjected to sudden on/off lighting while the other room was subjected to a 1-hour long sunrise/sunset treatment. At 8 weeks of age, blood was collected from one bird in each line of quail at 5 time points: before lights on, 3 points during sunrise lighting, and after lights were on at full intensity. The subsequent plasma samples were evaluated for their corticosterone concentrations. Quail housed in the sunrise/sunset lighting room had numerically lower corticosterone concentrations overall and transferred quail had numerically elevated corticosterone concentrations. In conclusion, sunrise/sunset lighting has the potential to improve overall production, regardless of genetic line

Interactions of the Gasotransmitters Contribute to Microvascular Tone (Dys)regulation in the Preterm Neonate

Background & Aims Hydrogen sulphide (H2S), nitric oxide (NO), and carbon monoxide (CO) are involved in transitional microvascular tone dysregulation in the preterm infant; however there is conflicting evidence on the interaction of these gasotransmitters, and their overall contribution to the microcirculation in newborns is not known. The aim of this study was to measure the levels of all 3 gasotransmitters, characterise their interrelationships and elucidate their combined effects on microvascular blood flow. Methods 90 preterm neonates were studied at 24h postnatal age. Microvascular studies were performed by laser Doppler. Arterial COHb levels (a measure of CO) were determined through co-oximetry. NO was measured as nitrate and nitrite in urine. H2S was measured as thiosulphate by liquid chromatography. Relationships between levels of the gasotransmitters and microvascular blood flow were assessed through partial correlation controlling for the influence of gestational age. Structural equation modelling was used to examine the combination of these effects on microvascular blood flow and derive a theoretical model of their interactions. Results No relationship was observed between NO and CO (p = 0.18, r = 0.18). A positive relationship between NO and H2S (p = 0.008, r = 0.28) and an inverse relationship between CO and H2S (p = 0.01, r = -0.33) exists. Structural equation modelling was used to examine the combination of these effects on microvascular blood flow. The model with the best fit is presented. Conclusions The relationships between NO and H2S, and CO and H2S may be of importance in the preterm newborn, particularly as NO levels in males are associated with higher H2S levels and higher microvascular blood flow and CO in females appears to convey protection against vascular dysregulation. Here we present a theoretical model of these interactions and their overall effects on microvascular flow in the preterm newborn, upon which future mechanistic studies may be based.The authors would like to acknowledge the parents of the neonates enrolled in the 2CANS study for their participation, the staff of the Kaleidoscope Neonatal Intensive Care Unit at the John Hunter Children’s Hospital, and Kimberly-Clark Australia for providing the diapers used in this stud

The group-based social skills training SOSTA-FRA in children and adolescents with high functioning autism spectrum disorder - study protocol of the randomised, multi-centre controlled SOSTA - net trial

Background: Group-based social skills training (SST) has repeatedly been recommended as treatment of choice in high-functioning autism spectrum disorder (HFASD). To date, no sufficiently powered randomised controlled trial has been performed to establish efficacy and safety of SST in children and adolescents with HFASD. In this randomised, multi-centre, controlled trial with 220 children and adolescents with HFASD it is hypothesized, that add-on group-based SST using the 12 weeks manualised SOSTA–FRA program will result in improved social responsiveness (measured by the parent rated social responsiveness scale, SRS) compared to treatment as usual (TAU). It is further expected, that parent and self reported anxiety and depressive symptoms will decline and pro-social behaviour will increase in the treatment group. A neurophysiological study in the Frankfurt HFASD subgroup will be performed pre- and post treatment to assess changes in neural function induced by SST versus TAU. Methods/design: The SOSTA – net trial is designed as a prospective, randomised, multi-centre, controlled trial with two parallel groups. The primary outcome is change in SRS score directly after the intervention and at 3 months follow-up. Several secondary outcome measures are also obtained. The target sample consists of 220 individuals with ASD, included at the six study centres. Discussion: This study is currently one of the largest trials on SST in children and adolescents with HFASD worldwide. Compared to recent randomised controlled studies, our study shows several advantages with regard to in- and exclusion criteria, study methods, and the therapeutic approach chosen, which can be easily implemented in non-university-based clinical settings. Trial registration: ISRCTN94863788 – SOSTA – net: Group-based social skills training in children and adolescents with high functioning autism spectrum disorder

Molecular Distribution, 13C-Isotope, and Enantiomeric Compositions of Carbonaceous Chondrite Monocarboxylic Acids

The watersoluble organic compounds in carbonaceous chondrite meteorites constitute a record of the synthetic reactions occurring at the birth of the solar system and those taking place during parent body alteration and may have been important for the later origins and development of life on Earth. In this present work, we have developed a novel methodology for the simultaneous analysis of the molecular distribution, compoundspecific 13C, and enantiomeric compositions of aliphatic monocarboxylic acids (MCA) extracted from the hotwater extracts of 16 carbonaceous chondrites from CM, CR, CO, CV, and CK groups. We observed high concentrations of meteoritic MCAs, with total carbon weight percentages which in some cases approached those of carbonates and insoluble organic matter. Moreover, we found that the concentration of MCAs in CR chondrites is higher than in the other meteorite groups, with acetic acid exhibiting the highest concentration in all samples. The abundance of MCAs decreased with increasing molecular weight and with increasing aqueous and/or thermal alteration experienced by the meteorite sample. The 13C isotopic values of MCAs ranged from 52 to +27, and aside from an inverse relationship between 13C value and carbon straightchain length for C3C6 MCAs in Murchison, the 13Cisotopic values did not correlate with the number of carbon atoms per molecule. We also observed racemic compositions of 2methylbutanoic acid in CM and CR chondrites. We used this novel analytical protocol and collective data to shed new light on the prebiotic origins of chondritic MCAs

High temperature condensate clouds in super-hot Jupiter atmospheres

Deciphering the role of clouds is central to our understanding of exoplanet atmospheres, as they have a direct impact on the temperature and pressure structure, and observational properties of the planet. Super-hot Jupiters occupy a temperature regime similar to low mass M-dwarfs, where minimal cloud condensation is expected. However, observations of exoplanets such as WASP-12b (Teq ~ 2500 K) result in a transmission spectrum indicative of a cloudy atmosphere. We re-examine the temperature and pressure space occupied by these super-hot Jupiter atmospheres, to explore the role of the initial Al- and Ti-bearing condensates as the main source of cloud material. Due to the high temperatures a majority of the more common refractory material is not depleted into deeper layers and would remain in the vapor phase. The lack of depletion into deeper layers means that these materials with relatively low cloud masses can become significant absorbers in the upper atmosphere. We provide condensation curves for the initial Al- and Ti-bearing condensates that may be used to provide quantitative estimates of the effect of metallicity on cloud masses, as planets with metal-rich hosts potentially form more opaque clouds because more mass is available for condensation. Increased metallicity also pushes the point of condensation to hotter, deeper layers in the planetary atmosphere further increasing the density of the cloud. We suggest that planets around metal-rich hosts are more likely to have thick refractory clouds, and discuss the implication on the observed spectra of WASP-12b.Comment: Accepted for publication in MNRAS, 10 pages, 1 table, 5 figure