On the identity of the identity operator in nonadiabatic linearized semiclassical dynamics

Simulating the nonadiabatic dynamics of condensed-phase systems continues to pose a significant challenge for quantum dynamics methods. Approaches based on sampling classical trajectories within the mapping formalism, such as the linearized semiclassical initial value representation (LSC-IVR), can be used to approximate quantum correlation functions in dissipative environments. Such semiclassical methods however commonly fail in quantitatively predicting the electronic-state populations in the long-time limit. Here we present a suggestion to minimize this difficulty by splitting the problem into two parts, one of which involves the identity, and treating this operator by quantum-mechanical principles rather than with classical approximations. This strategy is applied to numerical simulations of spin-boson model systems, showing its potential to drastically improve the performance of LSC-IVR and related methods with no change to the equations of motion or the algorithm in general, but rather by simply using different functional forms of the observables

The Effects of a High Fat Meal on Blood Flow Regulation during Arm Exercise

A diet high in saturated fats results in endothelial dysfunction and can lead to atherosclerosis, a precursor to cardiovascular disease. Exercise training is a potent stimulus though to mitigate the negative effects of a high saturated fat diet; however, it is unclear how high-saturated fat meal (HSFM) consumption impacts blood flow regulation during a single exercise session. PURPOSE: This study sought to examine the impact of a single HSFM on peripheral vascular function during an acute upper limb exercise bout. METHODS: Ten young healthy individuals completed two sessions of progressive handgrip exercise. Subjects either consumed a HSFM (0.84 g of fat/kg of body weight) 4 hours prior or remained fasted before the exercise bout. Progressive rhythmic handgrip exercise (6kg, 12kg, 18kg) was performed for 3 minutes per stage at rate of 1 Hz. The brachial artery (BA) diameter and blood velocity was obtained using Doppler Ultrasound (GE Logiq e) and BA blood flow was calculated with these values. RESULTS: BA blood flow and flow mediated dilation (normalized for shear rate) during the handgrip exercise significant increased from baseline in all workloads, but no differences were revealed in response to the HSFM consumption. CONCLUSION: Progressive handgrip exercise augmented BA blood flow and flow mediated dilation in both testing days; however, there was no significant differences following the HSFM consumption. This suggests that upper limb blood flow regulation during exercise is unaltered by a high fat meal in young healthy individuals.https://scholarscompass.vcu.edu/gradposters/1060/thumbnail.jp

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

BACKGROUND: The mitochondrial genomes of flowering plants vary greatly in size, gene content, gene order, mutation rate and level of RNA editing. However, the narrow phylogenetic breadth of available genomic data has limited our ability to reconstruct these traits in the ancestral flowering plant and, therefore, to infer subsequent patterns of evolution across angiosperms. RESULTS: We sequenced the mitochondrial genome of Liriodendron tulipifera, the first from outside the monocots or eudicots. This 553,721 bp mitochondrial genome has evolved remarkably slowly in virtually all respects, with an extraordinarily low genome-wide silent substitution rate, retention of genes frequently lost in other angiosperm lineages, and conservation of ancestral gene clusters. The mitochondrial protein genes in Liriodendron are the most heavily edited of any angiosperm characterized to date. Most of these sites are also edited in various other lineages, which allowed us to polarize losses of editing sites in other parts of the angiosperm phylogeny. Finally, we added comprehensive gene sequence data for two other magnoliids, Magnolia stellata and the more distantly related Calycanthus floridus, to measure rates of sequence evolution in Liriodendron with greater accuracy. The Magnolia genome has evolved at an even lower rate, revealing a roughly 5,000-fold range of synonymous-site divergence among angiosperms whose mitochondrial gene space has been comprehensively sequenced. CONCLUSIONS: Using Liriodendron as a guide, we estimate that the ancestral flowering plant mitochondrial genome contained 41 protein genes, 14 tRNA genes of mitochondrial origin, as many as 7 tRNA genes of chloroplast origin, >700 sites of RNA editing, and some 14 colinear gene clusters. Many of these gene clusters, genes and RNA editing sites have been variously lost in different lineages over the course of the ensuing ∽200 million years of angiosperm evolution

A MASH simulation of the photoexcited dynamics of cyclobutanone

In response to a community prediction challenge, we simulate the nonadiabatic dynamics of cyclobutanone using the mapping approach to surface hopping (MASH). We consider the first 500 fs of relaxation following photo-excitation to the S2 state and predict the corresponding time-resolved electron-diffraction signal that will be measured by the planned experiment. 397 ab-initio trajectories were obtained on the fly with state-averaged complete active space self-consistent field (SA-CASSCF) using a (12,11) active space. To obtain an estimate of the potential systematic error 198 of the trajectories were calculated using an aug-cc-pVDZ basis set and 199 with a 6-31+G* basis set. MASH is a recently proposed independent trajectory method for simulating nonadiabatic dynamics, originally derived for two-state problems. As there are three relevant electronic states in this system, we used a newly developed multi-state generalisation of MASH for the simulation: the uncoupled spheres multi-state MASH method (unSMASH). This study therefore serves both as an investigation of the photo-dissociation dynamics of cyclobutanone, and also as a demonstration of the applicability of unSMASH to ab-initio simulations. In line with previous experimental studies, we observe that the simulated dynamics is dominated by three sets of dissociation products, C3H6+CO, C2H4+C2H2O and C2H4+CH2+CO, and we interpret our predicted electron-diffraction signal in terms of the key features of the associated dissociation pathways.Comment: 47 pages, 43 figure

The Rice Miniature Inverted Repeat Transposable Element mPing Is an Effective Insertional Mutagen in Soybean

Insertional mutagenesis of legume genomes such as soybean (Glycine max) should aid in identifying genes responsible for key traits such as nitrogen fixation and seed quality. The relatively low throughput of soybean transformation necessitates the use of a transposon-tagging strategy where a single transformation event will produce many mutations over a number of generations. However, existing transposon-tagging tools being used in legumes are of limited utility because of restricted transposition (Ac/Ds: soybean) or the requirement for tissue culture activation (Tnt1: Medicago truncatula). A recently discovered transposable element from rice (Oryza sativa), mPing, and the genes required for its mobilization, were transferred to soybean to determine if it will be an improvement over the other available transposon-tagging tools. Stable transformation events in soybean were tested for mPing transposition. Analysis of mPing excision at early and late embryo developmental stages revealed increased excision during late development in most transgenic lines, suggesting that transposition is developmentally regulated. Transgenic lines that produced heritable mPing insertions were identified, with the plants from the highest activity line producing at least one new insertion per generation. Analysis of the mPing insertion sites in the soybean genome revealed that features displayed in rice were retained including transposition to unlinked sites and a preference for insertion within 2.5 kb of a gene. Taken together these findings indicate that mPing has the characteristics necessary for an effective transposon-tagging resource

Factors influencing the approaches to studying of preclinical and clinical students and postgraduate trainees

<p>Abstract</p> <p>Background</p> <p>Students can be classified into three categories depending on their approaches to studying; namely, deep approach (DA), strategic approach (SA) and surface apathetic or superficial approach (SAA). The aim of this study was to identify factors affecting the approaches to studying among Sri Lankan medical undergraduates and post graduate trainees and to analyze the change in the pattern of study skills with time and experience.</p> <p>Method</p> <p>Pre-clinical and clinical students of the Faculty of Medicine, University of Colombo and postgraduate trainees in Surgery at the National Hospital of Sri Lanka were invited to complete the Approaches and Study Skills Inventory for Students (ASSIST) questionnaire.</p> <p>Results</p> <p>A total of 187 pre clinical (M: F = 96:91), 124 clinical (M: F = 61:63) and 53 post graduate trainees (M: F = 50:3) participated in the study. Approaches of male and female students were similar. SA was significantly affected by age among the preclinical students (p = 0.01), but not in other groups. Among pre-clinical students, males preferred a teacher who supported understanding (p = 0.04) but females preferred a passive transmission of information (p < 0.001). This, too, was not visible among other groups. A linear regression performed on group (batch), gender, island rank at GCE Advance Level (AL) examination, self appraisal score and the preference scores of type of teacher only managed to explain 35% or less of variance observed for each approach in individual groups.</p> <p>Conclusion</p> <p>Different factors affect the approach to studying in different groups but these explain only a small fraction of the variance observed.</p

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

X-ray Crystallographic Structure of an Artificial β-Sheet Dimer

This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution