Local sequence features that influence AP-1 cis-regulatory activity

In the genome, most occurrences of transcription factor binding sites (TFBS) have no cis-regulatory activity, which suggests that flanking sequences contain information that distinguishes functional from nonfunctional TFBS. We interrogated the role of flanking sequences near Activator Protein 1 (AP-1) binding sites that reside in DNase I Hypersensitive Sites (DHS) and regions annotated as Enhancers. In these regions, we found that sequence features directly adjacent to the core motif distinguish high from low activity AP-1 sites. Some nearby features are motifs for other TFs that genetically interact with the AP-1 site. Other features are extensions of the AP-1 core motif, which cause the extended sites to match motifs of multiple AP-1 binding proteins. Computational models trained on these data distinguish between sequences with high and low activity AP-1 sites and also predict changes in cis-regulatory activity due to mutations in AP-1 core sites and their flanking sequences. Our results suggest that extended AP-1 binding sites, together with adjacent binding sites for additional TFs, encode part of the information that governs TFBS activity in the genome.</jats:p

Markov Chain Monitoring

In networking applications, one often wishes to obtain estimates about the number of objects at different parts of the network (e.g., the number of cars at an intersection of a road network or the number of packets expected to reach a node in a computer network) by monitoring the traffic in a small number of network nodes or edges. We formalize this task by defining the 'Markov Chain Monitoring' problem. Given an initial distribution of items over the nodes of a Markov chain, we wish to estimate the distribution of items at subsequent times. We do this by asking a limited number of queries that retrieve, for example, how many items transitioned to a specific node or over a specific edge at a particular time. We consider different types of queries, each defining a different variant of the Markov chain monitoring. For each variant, we design efficient algorithms for choosing the queries that make our estimates as accurate as possible. In our experiments with synthetic and real datasets we demonstrate the efficiency and the efficacy of our algorithms in a variety of settings.Comment: 13 pages, 10 figures, 1 tabl

PTRE-seq reveals mechanism and interactions of RNA binding proteins and miRNAs

A large number of RNA binding proteins (RBPs) and miRNAs bind to the 3′ untranslated regions of mRNA, but methods to dissect their function and interactions are lacking. Here the authors introduce post-transcriptional regulatory element sequencing (PTRE-seq) to dissect sequence preferences, interactions and consequences of RBP and miRNA binding

Test Experiment for Time-Reversal Symmetry Breaking Superconductivity

A new experiment is proposed to probe the time-reversal symmetry of a superconductor. It is shown that a time-reversal symmetry breaking superconductor can be identified by the observation of a fractional flux in connection with a Josephson junction in a special geometry.Comment: 4 pages, 2 figures available upon request, Revtex, MIT-CMT-OC

Genetic analysis of east and west coast populations of Penaeus monodon from India based on random amplified polymorphic DNA

The east and west coast populations of wild Penaeus monodon in India were genetically characterized by RAPD analysis using six highly polymorphic primers reported earlier. The average genetic similarities within populations, based on profiles generated by all the six primers, were 0.828 and 0.851 for the east and west coast populations, respectively, values with individual primers ranging from 0.744 to 0.889. The average genetic similarity between populations across all the primers was 0.774. The number of bands found to be polymorphic were 38 (51.35%) and 37 (50.68%) in the east and west coast populations, respectively. Primer 5 yielded the highest level of polymorphism (63.63%) in the east coast population whereas primer 3 yielded the lowest level of polymorphism (36.36%) in the west coast population. The study reveals the existence of genetic variation in P. monodon stocks providing scope for genetic improvement through selective breeding. It also provides baseline data for future work on population structure analysis of P. monodon

Estimation of RNA/DNA ratio in two north-Indian natural populations of mahseer (Tor tor) and its relationship with growth and hydrobiology

Samples of Tor tor were collected from Bari Reservoir of Udaipur and Narmada River at Hoshangabad (India), in the months of July and November 2005, respectively. Twenty-five samples were collected from each location. Bari Reservoir samples ranged from 17.0 to 24.5 cm in total length and from 75 to 155 g in weight, while Narmada samples ranged from 20.0 to 42.0 cm in length and 90 to 425 g in weight. The nucleic acid content in body muscle of Tor tor and the RNA/DNA ratio were estimated. The age of fishes was estimated by the scale study method and specimens were classified into four age groups. RNA/DNA ratio showed significant linear increase with increase in weight and age till the age of three years after which, the growth rate reduced. The 1-2 year group was the only one common between the two water bodies and a comparison of RNA/DNA ratios showed higher growth rate in Bari Reservoir. The gross primary productivity was also higher in Bari Reservoir being 551 mg cmˉ³ dˉ¹ compared to 404 mg cmˉ³ dˉ¹ observed for Narmada River. The condition factor (K) was found to be higher (1.21) in the fish from the Bari Reservoir compared to those of Narmada River (1.14). The growth rate was higher in females compared to males in >100 g specimens

Dipole-dipole interaction of Josephson diamagnetic moments

The role of dipole-dipole interaction between Josephson diamagnetic moments is considered within a model system of two clusters (each cluster contains three weakly connected superconducting grains). The sign of the resulting critical current is shown to depend on the orientation between clusters, allowing for both 0 and $\pi$ type junctions behavior. The possibility of the experimental verification of the model predictions is discussed

Association Between Empathy and Burnout Among Emergency Medicine Physicians

Background: The association between physician self-reported empathy and burnout has been studied in the past with diverse findings. We aimed to determine the association between empathy and burnout among United States emergency medicine (EM) physicians using a novel combination of tools for validation. Methods: This was a prospective single-center observational study. Data were collected from EM physicians. From December 1, 2018 to January 31, 2019, we used the Jefferson scale of empathy (JSE) to assess physician empathy and the Copenhagen burnout inventory (CBI) to assess burnout. We divided EM physicians into different groups (residents in each year of training, junior/senior attendings). Empathy, burnout scores and their association were analyzed and compared among these groups. Results: A total of 33 attending physicians and 35 EM residents participated in this study. Median self-reported empathy scores were 113 (interquartile range (IQR): 105 - 117) in post-graduate year (PGY)-1, 112 (90 - 115) in PGY-2, 106 (93 - 118) in PGY-3 EM residents, 112 (105 - 116) in junior and 114 (101 - 125) in senior attending physicians. Overall burnout scores were 43 (33 - 50) in PGY-1, 51 (29 - 56) in PGY-2, 43 (42 - 53) in PGY-3 EM residents, 33 (24 - 47) in junior attending and 25 (22 - 53) in senior attending physicians separately. The Spearman correlation (ρ) was -0.11 and β-weight was -0.23 between empathy and patient-related burnout scores. Conclusion: Self-reported empathy declines over the course of EM residency training and improves after graduation. Overall high burnout occurs among EM residents and improves after graduation. Our analysis showed a weak negative correlation between self-reported empathy and patient-related burnout among EM physicians

Electronic states of PrCoO3_3: X-ray photoemission spectroscopy and LDA+U density of states studies

Electronic states of PrCoO$_3$ are studied using x-ray photoemission spectroscopy. Pr 3d$_{5/2}$ core level and valence band (VB) were recorded using Mg K$_\beta$ source. The core level spectrum shows that the 3d$_{5/2}$ level is split into two components of multiplicity 4 and 2, respectively due to coupling of the spin states of the hole in 3d$_{5/2}$ with Pr 4f holes spin state. The observed splitting is 4.5 eV. The VB spectrum is interpreted using density of states (DOS) calculations under LDA and LDA+U. It is noted that LDA is not sufficient to explain the observed VB spectrum. Inclusion of on-site Coulomb correlation for Co 3d electrons in LDA+U calculations gives DOS which is useful in qualitative explanation of the ground state. However, it is necessary to include interactions between Pr 4f electrons to get better agreement with experimental VB spectrum. It is seen that the VB consists of Pr 4f, Co 3d and O 2p states. Pr 4f, Co 3d and O 2p bands are highly mixed indicating strong hybridization of these three states. The band near the Fermi level has about equal contributions from Pr 4f and O 2p states with somewhat smaller contribution from Co 3d states. Thus in the Zaanen, Sawatzky, and Allen scheme PrCoO$_3$ can be considered as charge transfer insulator. The charge transfer energy $\Delta$ can be obtained using LDA DOS calculations and the Coulomb-exchange energy U' from LDA+U. The explicit values for PrCoO$_3$ are $\Delta$ = 3.9 eV and U' = 5.5 eV; the crystal field splitting and 3d bandwidth of Co ions are also found to be 2.8 and 1.8 eV, respectively.Comment: 12 pages, 7 figures; to appear J. Phys.: Condens. Matte