RNA-RNA interaction prediction based on multiple sequence alignments

Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments. Compared to the single sequence-pair folding algorithm \texttt{rip}, \texttt{ripalign} requires negligible additional memory resource. Furthermore, we incorporate possible structure constraints as input parameters into our algorithm. The algorithm described here is implemented in C as part of the \texttt{rip} package. The supplemental material, source code and input/output files can freely be downloaded from \url{http://www.combinatorics.cn/cbpc/ripalign.html}. \section{Contact} Christian Reidys \texttt{[email protected]}Comment: 8 pages, 9 figure

Andreev experiments on superconductor/ferromagnet point contacts

Andreev reflection is a smart tool to investigate the spin polarisation P of the current through point contacts between a superconductor and a ferromagnet. We compare different models to extract P from experimental data and investigate the dependence of P on different contact parameters.Comment: 14 pages, 5 figures, accepted for publication in Fizika Nizkikh Temperatu

Andreev experiments on superconductor/ferromagnet point contacts

Andreev reflection is a smart tool to investigate the spin polarization P of the current through point contacts between a superconductor and a ferromagnet. We compare different models to extract P from experimental data and investigate the dependence of P on different contact parameters

Surgical Specialization and Standardization of Care Improves Outcomes in Mechanical Circulatory Support: A Single Center Experience

Purpose: Cardiac surgery continues to transform into areas of sub-specialization and expertise to reduce variability and have superior outcomes. We sought to analyze the impact of surgical sub-specialization and use of protocol and clinical pathways on outcomes with MCS at the time of LVAD implantation. Methods: A single center retrospective analysis of long term durable MCS patients between 2004-2019 was performed. The analysis was conducted comparing management of patients before (Era 1: 2004-2011) vs. after (Era 2: 2012-2019) based on before and after introduction of MCS sub-specialization. Since 2012, multiple initiatives were introduced namely recruitment of specialized MCS/transplant surgeons, multidisciplinary team rounds, establishment of a shock team, development of clinical care pathways, electronic medical record order sets and clinical practice guidelines. Results: A total of 542 patients were included. During Era 1, five cardiac surgeons implanted LVADs in 123 patients, while in Era 2, two MCS/transplant trained surgeons implanted LVADs in 419 patients. Era 2 included higher number of INTERMACS 1 and 2 profile patients (41% vs. 63%) reflecting higher-acuity patient population. With implementation of the sub-specialization services, 1-year survival improved from 70% to 90%. Median ICU stay decreased from 13 to 8 days and percent of patients discharged to home increased from 62% to 95%. Standardized protocols for management of high LDH, GI bleeding, and blood pressure management resulted in significant reduction in overall hospital length of stay. With introduction of clinical care pathways, the average time for workup from admission to LVAD implant decreased from 27.6 days to 8.5 days. Conclusion: Introduction of surgical sub-specialization and standardization of care with the use of clinical pathways and protocols in managing patients with LVADs can help improve survival, reduce variability in medical care, and reduce ICU length of stay

Big Data Analysis

The value of big data is predicated on the ability to detect trends and patterns and more generally to make sense of the large volumes of data that is often comprised of a heterogeneous mix of format, structure, and semantics. Big data analysis is the component of the big data value chain that focuses on transforming raw acquired data into a coherent usable resource suitable for analysis. Using a range of interviews with key stakeholders in small and large companies and academia, this chapter outlines key insights, state of the art, emerging trends, future requirements, and sectorial case studies for data analysis

Manipulating chemistry through nanoparticle morphology

We demonstrate that the protonation chemistry of molecules adsorbed at nanometer distances from the surface of anisotropic gold nanoparticles can be manipulated through the effect of surface morphology on the local proton density of an organic coating. Direct evidence of this remarkable effect was obtained by monitoring surface-enhanced Raman scattering (SERS) from mercaptobenzoic acid and 4-aminobenzenethiol molecules adsorbed on gold nanostars. By smoothing the initially sharp nanostar tips through a mild thermal treatment, changes were induced on protonation of the molecules, which can be observed through changes in the measured SERS spectra. These results shed light on the local chemical environment near anisotropic colloidal nanoparticles and open an alternative avenue to actively control chemistry through surface morphology.LL and LML-M acknowledge funding from European Commission Grant (EUSMI 731019). Funding is also acknowledged from the Spanish MINECO (MAT2017-86659-R and MDM-2017-0720 to LML-M; MAT2017-88492-R and SEV2015-0522 to JGA) and the European Research Council (Advanced Grant 787510 4DBIOSERS to LML-M; Advanced Grant 789104-eNANO to JGA)