NASSAM: a server to search for and annotate tertiary interactions and motifs in three-dimensional structures of complex RNA molecules

Similarities in the 3D patterns of RNA base interactions or arrangements can provide insights into their functions and roles in stabilization of the RNA 3D structure. Nucleic Acids Search for Substructures and Motifs (NASSAM) is a graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications. The NASSAM program is freely accessible without any login requirement at http://mfrlab.org/grafss/nassam/

Competitive stochastic noises in coherently driven two-level atoms and quantum interference

A system of coherently-driven two-level atoms is analyzed in presence of two independent stochastic perturbations: one due to collisions and a second one due to phase fluctuations of the driving field. The behaviour of the quantum interference induced by the collisional noise is considered in detail. The quantum-trajectory method is utilized to reveal the phase correlations between the dressed states involved in the interfering transition channels. It is shown that the quantum interference induced by the collisional noise is remarkably robust against phase noise. This effect is due to the fact that the phase noise, similarly to collisions, stabilizes the phase-difference between the dressed states.Comment: accepted for publication in J. Opt.

Valuing the unpaid contribution of community health volunteers to mass drug administration programs

Community health volunteers (CHVs) are being used within a growing number of healthcare interventions, and they have become a cornerstone for the delivery of mass drug administration within many neglected tropical disease control programs. However, a greater understanding of the methods used to value the unpaid time CHVs contribute to healthcare programs is needed. We outline the two main approaches used to value CHVs' unpaid time (the opportunity cost and the replacement cost approaches). We found that for mass drug administration programs the estimates of the economic costs relating to the CHVs' unpaid time can be significant, with the averages of the different studies varying between US$0.05-0.16 per treatment. We estimated that the time donated by CHVs' to the African Programme for Onchocerciasis Control alone would be valued between US$60-90 million. There is a need for greater transparency and consistency in the methods used to value CHVs' unpaid time

The Buckling Spectra of Nanoparticle Surfactant Assemblies

Fine control over the mechanical properties of thin sheets underpins transcytosis, cell shape, and morphogenesis. Applying these principles to artificial, liquid-based systems has led to reconfigurable materials for soft robotics, actuation, and chemical synthesis. However, progress is limited by a lack of synthetic two-dimensional membranes that exhibit tunable mechanical properties over a comparable range to that seen in nature. Here, we show that the bending modulus, B, of thin assemblies of nanoparticle surfactants (NPSs) at the oil–water interface can be varied continuously from sub-kBT to 106kBT, by varying the ligands and particles that comprise the NPS. We find extensive departure from continuum behavior, including enormous mechanical anisotropy and a power law relation between B and the buckling spectrum width. Our findings provide a platform for shape-changing liquid devices and motivate new theories for the description of thin-film wrinkling

Integrating animal movement with habitat suitability for estimating dynamic landscape connectivity

Context: High-resolution animal movement data are becoming increasingly available, yet having a multitude of trajectories alone does not allow us to easily predict animal movement. To answer ecological and evolutionary questions at a population level, quantitative estimates of a species' potential to act as a link between patches, populations, or ecosystems are of importance. Objectives: We introduce an approach that combines movement-informed simulated trajectories with an environment-informed estimate of their ecological likelihood. With this approach, we estimated connectivity at the landscape level throughout the annual cycle of bar-headed geese (Anser indicus) in its native range. Methods: We used a tracking dataset of bar-headed geese to parameterise a multi-state movement model and to estimate temporally explicit habitat suitability within the species' range. We simulated migratory movements between range fragments, and estimated their ecological likelihood. The results are compared to expectations derived from published literature. Results: Simulated migrations matched empirical trajectories in key characteristics such as stopover duration. The estimated likelihood of simulated migrations was similar to that of empirical trajectories. We found that the predicted connectivity was higher within the breeding than in wintering areas, corresponding to previous findings for this species. Conclusions: We show how empirical tracking data and environmental information can be fused to make meaningful predictions about future animal movements. These are temporally explicit and transferable even outside the spatial range of the available data. Our integrative framework will prove useful for modelling ecological processes facilitated by animal movement, such as seed dispersal or disease ecology

Integrated Batch Reactive Distillation Column Configurations for Optimal Synthesis of Methyl Lactate

YesAlthough batch reactive distillation process outperforms traditional reactor-distillation processes due to simultaneous reaction and separation of products for many reaction systems, synthesis of Methyl lactate (ML) through esterification of lactic acid (LA) with methanol in such process is very challenging due to difficulty of keeping the reactants together when one of the reactants (in this case methanol) has the lowest boiling point than the reaction products. To overcome this challenge, two novel reactive distillation column configurations are proposed in this work and are investigated in detail. These are: (1) integrated conventional batch distillation column (i-CBD) with recycled methanol and (2) integrated semi-batch and conventional batch distillation columns (i-SBD) with methanol recovery and recycle. Performances of each of these configurations are evaluated in terms of profitability for a defined separation task. In i-SBD column, an additional constraint is included to avoid overflow of the reboiler due to continuous feeding of methanol into the reboiler as the reboiler is initially charged to its maximum capacity. This study clearly indicates that both integrated column configurations outperform the traditional column configurations (batch or semi-batch) in terms of batch time, energy consumption, conversion of LA to ML, and the achievable profit

Suzaku broad-band spectroscopy of RX J1347.5-1145: constraints on the extremely hot gas and non-thermal emission

We present the results from the analysis of long Suzaku observations of the most X-ray luminous galaxy cluster RX J1347.5-1145 at z=0.451. Aims: We study physical properties of the hot (~20 keV) gas clump in the south-east (SE) region discovered by the Sunyaev-Zel'dovich (SZ) effect observations, to understand the gas physics of a violent cluster merger. We also explore a signature of non-thermal emission using the hard X-ray data. Results: We find that the single-temperature model fails to reproduce the continuum emission and Fe-K lines measured by XIS simultaneously. The two-temperature model with a very hot component improves the fit, although the XIS data can only give a lower bound on its temperature. We detect the hard X-ray emission in the 12-40 keV band at the 7 sigma level; however, the significance becomes marginal when the systematic error in the background estimation is included. With the Suzaku + Chandra joint analysis, we determine the temperature of the SE excess component to be 25.3^{+6.1}_{-4.5} ^{+6.9}_{-9.5} keV (90% statistical and systematic errors), which is in an excellent agreement with the previous SZ + X-ray analysis. This is the first time that the X-ray spectroscopy alone gives a good measurement of the temperature of the hot component in the SE region, which is made possible by Suzaku's unprecedented sensitivity to the wide X-ray band. These results strongly indicate that the cluster has undergone a recent, violent merger. The spectral analysis shows that the SE component is consistent with being thermal. We find the 3 sigma upper limit on the non-thermal flux, F < 8e-12 erg s^{-1} cm^{-2} in the 12-60 keV band. Combining this limit with a recent discovery of the radio mini halo at 1.4 GHz, we find a lower limit on the strength of the intracluster magnetic field, B > 0.007 micro G.Comment: 15 pages, 13 figures. Accepted for publication in A&

Social Determinants of Health Among Family Caregiver Centered Outcomes in Lung Cancer: A Systematic Review

Background: Lung cancer is the leading cause of cancer death globally. Both lung cancer patients and family caregivers (FCGs) have unmet quality of life (QOL) needs. An understudied topic in lung cancer research is the role of social determinants of health (SDOH) on QOL outcomes for this population. The purpose of this review was to explore the state of research on SDOH FCGs centered outcomes in lung cancer. Methods: The databases PubMed/MEDLINE, Cochrane Library, Cumulative Index to Nursing and Allied Health Literature, and American Psychological Association (APA) PsycInfo were searched for peer-reviewed manuscripts evaluating defined SDOH domains on FCGs published within the last ten years. The information extracted using Covidence included patients, FCGs and study characteristics. Level of evidence and quality of articles were assessed using the Johns Hopkins Nursing Evidence-Based Practice Rating Scale. Results: Of the 344 full-text articles assessed, 19 were included in this review. The social and community context domain focused on caregiving stressors and interventions to reduce its effects. The health care access and quality domain showed barriers and underuse of psychosocial resources. The economic stability domain indicated marked economic burdens for FCGs. Four interconnected themes emerged among articles on the influence of SDOH on FCG-centered outcomes in lung cancer: (I) psychological well-being, (II) overall quality of life, (III) relationship quality, and (IV) economic hardship. Notably, most participants in the studies were White females. The tools used to measure SDOH factors included primarily demographic variables. Conclusions: Current studies provide evidence on the role of SDOH factors on lung cancer FCGs’ QOL. Expanded utilization of validated SDOH measures in future studies would provide greater consistency in data, that could in turn inform interventions to improve QOL. Further research focusing on the domains of education quality and access and neighborhood and built environment should be carried out to bridge gaps in knowledge

Quantum trajectory approach to stochastically-induced quantum interference effects in coherently-driven two-level atoms

Stochastic perturbation of two-level atoms strongly driven by a coherent light field is analyzed by the quantum trajectory method. A new method is developed for calculating the resonance fluorescence spectra from numerical simulations. It is shown that in the case of dominant incoherent perturbation, the stochastic noise can unexpectedly create phase correlation between the neighboring atomic dressed states. This phase correlation is responsible for quantum interference between the related transitions resulting in anomalous modifications of the resonance fluorescence spectra.Comment: paper accepted for publicatio

Peptide exchange on MHC-I by TAPBPR is driven by a negative allostery release cycle.

Chaperones TAPBPR and tapasin associate with class I major histocompatibility complexes (MHC-I) to promote optimization (editing) of peptide cargo. Here, we use solution NMR to investigate the mechanism of peptide exchange. We identify TAPBPR-induced conformational changes on conserved MHC-I molecular surfaces, consistent with our independently determined X-ray structure of the complex. Dynamics present in the empty MHC-I are stabilized by TAPBPR and become progressively dampened with increasing peptide occupancy. Incoming peptides are recognized according to the global stability of the final pMHC-I product and anneal in a native-like conformation to be edited by TAPBPR. Our results demonstrate an inverse relationship between MHC-I peptide occupancy and TAPBPR binding affinity, wherein the lifetime and structural features of transiently bound peptides control the regulation of a conformational switch located near the TAPBPR binding site, which triggers TAPBPR release. These results suggest a similar mechanism for the function of tapasin in the peptide-loading complex