Inverse Protein Folding Using Deep Bayesian Optimization

Inverse protein folding -- the task of predicting a protein sequence from its backbone atom coordinates -- has surfaced as an important problem in the "top down", de novo design of proteins. Contemporary approaches have cast this problem as a conditional generative modelling problem, where a large generative model over protein sequences is conditioned on the backbone. While these generative models very rapidly produce promising sequences, independent draws from generative models may fail to produce sequences that reliably fold to the correct backbone. Furthermore, it is challenging to adapt pure generative approaches to other settings, e.g., when constraints exist. In this paper, we cast the problem of improving generated inverse folds as an optimization problem that we solve using recent advances in "deep" or "latent space" Bayesian optimization. Our approach consistently produces protein sequences with greatly reduced structural error to the target backbone structure as measured by TM score and RMSD while using fewer computational resources. Additionally, we demonstrate other advantages of an optimization-based approach to the problem, such as the ability to handle constraints

Optimization of care for patients with hereditary angioedema living in rural areas

BACKGROUND: People living in rural areas of the United States experience greater health inequality than individuals residing in urban or suburban locations and encounter several barriers to obtaining optimal health care. Health disparities are compounded for patients with rare diseases such as hereditary angioedema (HAE), an autosomal dominant genetic disorder characterized by recurrent, severe abdominal pain and life-threatening oropharyngeal or laryngeal swelling. OBJECTIVE: To explore the challenges of managing patients with HAE in rural areas and suggest possible improvements for optimizing care. DATA SOURCES: PubMed was searched for articles on patient care management, treatment challenges, rural health, and HAE. STUDY SELECTIONS: Relevant articles were selected and reviewed. RESULTS: Challenges in managing HAE in the rural setting were identified, including obtaining a diagnosis of HAE, easy access to a physician with expertise in HAE, continuity of care, availability of telemedicine services, access to approved HAE therapies, patient education, and economic barriers to treatment. Ways to improve HAE patient care in rural areas include health care provider recognition of the patient with undiagnosed HAE, development of individualized management plans, expansion of telemedicine, effective care at the local level, appropriate access to HAE medication, and increased awareness of patient support and advocacy groups. CONCLUSION: For patients with HAE living in rural areas, optimal care is complicated by health disparities. Given the scarcity with which these topics have been covered in the literature to date, it is intended that this article will serve as the impetus for a range of further initiatives focused on improving access to care

Electrostatic carrier doping of GdTiO3/SrTiO3 interfaces

Heterostructures and superlattices consisting of a prototype Mott insulator, GdTiO3, and the band insulator SrTiO3 are grown by molecular beam epitaxy and show intrinsic electronic reconstruction, approximately 1/2 electron per surface unit cell at each GdTiO3/SrTiO3 interface. The sheet carrier densities in all structures containing more than one unit cell of SrTiO3 are independent of layer thicknesses and growth sequences, indicating that the mobile carriers are in a high concentration, two-dimensional electron gas bound to the interface. These carrier densities closely meet the electrostatic requirements for compensating the fixed charge at these polar interfaces. Based on the experimental results, insights into interfacial band alignments, charge distribution and the influence of different electrostatic boundary conditions are obtained.Comment: The article has been accepted by Applied Physics Letters. After it is published, it will be found at http://apl.aip.org

A combined measurement of cosmic growth and expansion from clusters of galaxies, the CMB and galaxy clustering

Combining galaxy cluster data from the ROSAT All-Sky Survey and the Chandra X-ray Observatory, cosmic microwave background data from the Wilkinson Microwave Anisotropy Probe, and galaxy clustering data from the WiggleZ Dark Energy Survey, the 6-degree Field Galaxy Survey and the Sloan Digital Sky Survey III, we test for consistency the cosmic growth of structure predicted by General Relativity (GR) and the cosmic expansion history predicted by the cosmological constant plus cold dark matter paradigm (LCDM). The combination of these three independent, well studied measurements of the evolution of the mean energy density and its fluctuations is able to break strong degeneracies between model parameters. We model the key properties of cosmic growth with the normalization of the matter power spectrum, sigma_8, and the cosmic growth index, gamma, and those of cosmic expansion with the mean matter density, Omega_m, the Hubble constant, H_0, and a kinematical parameter equivalent to that for the dark energy equation of state, w. For a spatially flat geometry, w=-1, and allowing for systematic uncertainties, we obtain sigma_8=0.785+-0.019 and gamma=0.570+0.064-0.063 (at the 68.3 per cent confidence level). Allowing both w and gamma to vary we find w=-0.950+0.069-0.070 and gamma=0.533+-0.080. To further tighten the constraints on the expansion parameters, we also include supernova, Cepheid variable and baryon acoustic oscillation data. For w=-1, we have gamma=0.616+-0.061. For our most general model with a free w, we measure Omega_m=0.278+0.012-0.011, H_0=70.0+-1.3 km s^-1 Mpc^-1 and w=-0.987+0.054-0.053 for the expansion parameters, and sigma_8=0.789+-0.019 and gamma=0.604+-0.078 for the growth parameters. These results are in excellent agreement with GR+LCDM (gamma~0.55; w=-1) and represent the tightest and most robust simultaneous constraint on cosmic growth and expansion to date.Comment: 14 pages, 5 figures, 1 table. Matches the accepted version for MNRAS. New sections 3 and 6 added, containing 2 new figures. Table extended. The results including BAO data have been slightly modified due to an updated BAO analysis. Conclusions unchange

Asymmetric function theory

The classical theory of symmetric functions has a central position in algebraic combinatorics, bridging aspects of representation theory, combinatorics, and enumerative geometry. More recently, this theory has been fruitfully extended to the larger ring of quasisymmetric functions, with corresponding applications. Here, we survey recent work extending this theory further to general asymmetric polynomials.Comment: 36 pages, 8 figures, 1 table. Written for the proceedings of the Schubert calculus conference in Guangzhou, Nov. 201

Molten Salt Heat Transport Loop: Materials Corrosion and Heat Transfer Phenomena

An experimental system for corrosion testing of candidate materials in molten FLiNaK salt at 850 degree C has been designed and constructed. While molten FLiNaK salt was the focus of this study, the system can be utilized for evaluation of materials in other molten salts that may be of interest in the future. Using this system, the corrosion performance of a number of code-certified alloys of interest to NGNP as well as the efficacy of Ni-electroplating have been investigated. The mechanisums underlying corrosion processes have been elucidated using scanning electron microscopy, x-ray diffraction, and x-ray photoelectron spectroscopy of the materials after the corrosion tests, as well as by the post-corrosion analysis of the salts using inductively coupled plasma (ICP) and neutron activation analysis (NAA) techniques

Angular momenta creation in relativistic electron-positron plasma

Creation of angular momentum in a relativistic electron-positron plasma is explored. It is shown that a chain of angular momentum carrying vortices is a robust asymptotic state sustained by the generalized nonlinear Schrodinger equation characteristic to the system. The results may suggest a possible electromagnetic origin of angular momenta when it is applied to the MeV epoch of the early Universe.Comment: 20 pages, 6 figure

How can frontline expertise and new models of care best contribute to safely reducing avoidable acute admissions? A mixed-methods study of four acute hospitals

BackgroundHospital emergency admissions have risen annually, exacerbating pressures on emergency departments (EDs) and acute medical units. These pressures have an adverse impact on patient experience and potentially lead to suboptimal clinical decision-making. In response, a variety of innovations have been developed, but whether or not these reduce inappropriate admissions or improve patient and clinician experience is largely unknown.AimsTo investigate the interplay of service factors influencing decision-making about emergency admissions, and to understand how the medical assessment process is experienced by patients, carers and practitioners.MethodsThe project used a multiple case study design for a mixed-methods analysis of decision-making about admissions in four acute hospitals. The primary research comprised two parts: value stream mapping to measure time spent by practitioners on key activities in 108 patient pathways, including an embedded study of cost; and an ethnographic study incorporating data from 65 patients, 30 carers and 282 practitioners of different specialties and levels. Additional data were collected through a clinical panel, learning sets, stakeholder workshops, reading groups and review of site data and documentation. We used a realist synthesis approach to integrate findings from all sources.FindingsPatients’ experiences of emergency care were positive and they often did not raise concerns, whereas carers were more vocal. Staff’s focus on patient flow sometimes limited time for basic care, optimal communication and shared decision-making. Practitioners admitted or discharged few patients during the first hour, but decision-making increased rapidly towards the 4-hour target. Overall, patients’ journey times were similar, although waiting before being seen, for tests or after admission decisions, varied considerably. The meaning of what constituted an ‘admission’ varied across sites and sometimes within a site. Medical and social complexity, targets and ‘bed pressure’, patient safety and risk, each influenced admission/discharge decision-making. Each site responded to these pressures with different initiatives designed to expedite appropriate decision-making. New ways of using hospital ‘space’ were identified. Clinical decision units and observation wards allow potentially dischargeable patients with medical and/or social complexity to be ‘off the clock’, allowing time for tests, observation or safe discharge. New teams supported admission avoidance: an acute general practitioner service filtered patients prior to arrival; discharge teams linked with community services; specialist teams for the elderly facilitated outpatient treatment. Senior doctors had a range of roles: evaluating complex patients, advising and training juniors, and overseeing ED activity.ConclusionsThis research shows how hospitals under pressure manage complexity, safety and risk in emergency care by developing ‘ground-up’ initiatives that facilitate timely, appropriate and safe decision-making, and alternative care pathways for lower-risk, ambulatory patients. New teams and ‘off the clock’ spaces contribute to safely reducing avoidable admissions; frontline expertise brings value not only by placing senior experienced practitioners at the front door of EDs, but also by using seniors in advisory roles. Although the principal limitation of this research is its observational design, so that causation cannot be inferred, its strength is hypothesis generation. Further research should test whether or not the service and care innovations identified here can improve patient experience of acute care and safely reduce avoidable admissions.FundingThe National Institute for Health Research (NIHR) Health Services and Delivery Research programme (project number 10/1010/06). This research was supported by the NIHR Collaboration for Leadership in Applied Health Research and Care South West Peninsula

Variability in Blood Pressure Assessment in Patients Supported with the HeartMate 3TM

Targeted blood pressure (BP) control is a goal of left ventricular assist device medical management, but the interpretation of values obtained from noninvasive instruments is challenging. In the MOMENTUM 3 Continued Access Protocol, paired BP values in HeartMate 3 (HM3) patients were compared from arterial (A)-line and Doppler opening pressure (DOP) (319 readings in 261 patients) and A-line and automated cuff (281 readings in 247 patients). Pearson (R) correlations between A-line mean arterial (MAP) and systolic blood pressures (SBP) were compared with DOP and cuff measures according to the presence (\u3e1 pulse in 5 seconds) or absence of a palpable radial pulse. There were only moderate correlations between A-line and noninvasive measurements of SBP (DOP R = 0.58; cuff R = 0.47) and MAP (DOP R = 0.48; cuff R = 0.37). DOP accuracy for MAP estimation, defined as the % of readings within ± 10 mmHg of A-line MAP, decreased from 80% to 33% for DOP ≤ 90 vs. \u3e90 mmHg, and precision also diminished (mean absolute difference [MAD] increased from 6.3 ± 5.6 to 16.1 ± 11.4 mmHg). Across pulse pressures, cuff MAPs were within ±10 mmHg of A-line 62.9%-68.8% of measures and MADs were negligible. The presence of a palpable pulse reduced the accuracy and precision of the DOP-MAP estimation but did not impact cuff-MAP accuracy or precision. In summary, DOP may overestimate MAP in some patients on HM3 support. Simultaneous use of DOP and automated cuff and radial pulse may be needed to guide antihypertensive medication titration in outpatients on HM3 support

Expression and trans-specific polymorphism of self-incompatibility RNases in Coffea (Rubiaceae)

Self-incompatibility (SI) is widespread in the angiosperms, but identifying the biochemical components of SI mechanisms has proven to be difficult in most lineages. Coffea (coffee; Rubiaceae) is a genus of old-world tropical understory trees in which the vast majority of diploid species utilize a mechanism of gametophytic self-incompatibility (GSI). The S-RNase GSI system was one of the first SI mechanisms to be biochemically characterized, and likely represents the ancestral Eudicot condition as evidenced by its functional characterization in both asterid (Solanaceae, Plantaginaceae) and rosid (Rosaceae) lineages. The S-RNase GSI mechanism employs the activity of class III RNase T2 proteins to terminate the growth of "self" pollen tubes. Here, we investigate the mechanism of Coffea GSI and specifically examine the potential for homology to S-RNase GSI by sequencing class III RNase T2 genes in populations of 14 African and Madagascan Coffea species and the closely related self-compatible species Psilanthus ebracteolatus. Phylogenetic analyses of these sequences aligned to a diverse sample of plant RNase T2 genes show that the Coffea genome contains at least three class III RNase T2 genes. Patterns of tissue-specific gene expression identify one of these RNase T2 genes as the putative Coffea S-RNase gene. We show that populations of SI Coffea are remarkably polymorphic for putative S-RNase alleles, and exhibit a persistent pattern of trans-specific polymorphism characteristic of all S-RNase genes previously isolated from GSI Eudicot lineages. We thus conclude that Coffea GSI is most likely homologous to the classic Eudicot S-RNase system, which was retained since the divergence of the Rubiaceae lineage from an ancient SI Eudicot ancestor, nearly 90 million years ago.United States National Science Foundation [0849186]; Society of Systematic Biologists; American Society of Plant Taxonomists; Duke University Graduate Schoolinfo:eu-repo/semantics/publishedVersio