Teaching computers to fold proteins

A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. In a test with 24 peptides of known structure, none folded correctly with the initial potential functions, but two-thirds came within 3{\AA} to their native fold after optimizing the potential functions.Comment: 4 pages, 3 figure

Cyclic AMP pathway activation and extracellular zinc induce rapid intracellular zinc mobilization in Candida albicans

LK was supported by Innovation Fund Denmark, DK (4019-00019B). Pcovery ApS received funding from Wellcome Trust, Research Councils, UK (100480/Z/12), Novo Seeds, DK and Boehringer Ingelheim Venture Fund, D. DW is supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (102549/Z/13/Z), the Medical Research Council and University of Aberdeen (MR/N006364/1) and received support from a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology (097377/Z/11/Z). The funders had no part in study design, data collection and interpretation, or the decision to submit the work for publication.Peer reviewedPublisher PD

Medical Data Architecture Platform and Recommended Requirements for a Medical Data System for Exploration Missions

The Medical Data Architecture (MDA) project supports the Exploration Medical Capability (ExMC) risk to minimize or reduce the risk of adverse health outcomes and decrements in performance due to in-flight medical capabilities on human exploration missions. To mitigate this risk, the ExMC MDA project addresses the technical limitations identified in ExMC Gap Med 07: We do not have the capability to comprehensively process medically- relevant information to support medical operations during exploration missions. This gap identifies that the current in-flight medical data management includes a combination of data collection and distribution methods that are minimally integrated with on-board medical devices and systems. Furthermore, there are a variety of data sources and methods of data collection. For an exploration mission, the seamless management of such data will enable a more medically autonomous crew than the current paradigm of medical data management on the International Space Station. ExMC has recognized that in order to make informed decisions about a medical data architecture framework, current methods for medical data management must not only be understood, but an architecture must also be identified that provides the crew with actionable insight to medical conditions. This medical data architecture will provide the necessary functionality to address the challenges of executing a self-contained medical system that approaches crew health care delivery without assistance from ground support. Hence, the products derived from the third MDA prototype development will directly inform exploration medical system requirements for Level of Care IV in Gateway missions. In fiscal year 2019, the MDA project developed Test Bed 3, the third iteration in a series of prototypes, that featured integrations with cognition tool data, ultrasound image analytics and core Flight Software (cFS). Maintaining a layered architecture design, the framework implemented a plug-in, modular approach in the integration of these external data sources. An early version of MDA Test Bed 3 software was deployed and operated in a simulated analog environment that was part of the Next Space Technologies for Exploration Partnerships (NextSTEP) Gateway tests of multiple habitat prototypes. In addition, the MDA team participated in the Gateway Test and Verification Demonstration, where the MDA cFS applications was integrated with Gateway-in-a-Box software to send and receive medically relevant data over a simulated vehicle network. This software demonstration was given to ExMC and Gateway Program stakeholders at the NASA Johnson Space Center Integrated Power, Avionics and Software (iPAS) facility. Also, the integrated prototypes served as a vehicle to provide Level 5 requirements for the Crew Health and Performance Habitat Data System for Gateway Missions (Medical Level of Care IV). In the upcoming fiscal year, the MDA project will continue to provide systems engineering and vertical prototypes to refine requirements for medical Level of Care IV and inform requirements for Level of Care V

Multipole Expansion for Relativistic Coulomb Excitation

We derive a general expression for the multipole expansion of the electro-magnetic interaction in relativistic heavy-ion collisions, which can be employed in higher-order dynamical calculations of Coulomb excitation. The interaction has diagonal as well as off-diagonal multipole components, associated with the intrinsic and relative coordinates of projectile and target. A simple truncation in the off-diagonal components gives excellent results in first-order perturbation theory for distant collisions and for beam energies up to 200 MeV/nucleon.Comment: 3 figures, Accepted for publication in Phys. Rev.

Real-time observations of single bacteriophage λ DNA ejections in vitro

The physical, chemical, and structural features of bacteriophage genome release have been the subject of much recent attention. Many theoretical and experimental studies have centered on the internal forces driving the ejection process. Recently, Mangenot et al. [Mangenot S, Hochrein M, Rädler J, Letellier L (2005) Curr Biol 15:430–435.] reported fluorescence microscopy of phage T5 ejections, which proceeded stepwise between DNA nicks, reaching a translocation speed of 75 kbp/s or higher. It is still unknown how high the speed actually is. This paper reports real-time measurements of ejection from phage {lambda}, revealing how the speed depends on key physical parameters such as genome length and ionic state of the buffer. Except for a pause before DNA is finally released, the entire 48.5-kbp genome is translocated in {approx}1.5 s without interruption, reaching a speed of 60 kbp/s. The process gives insights particularly into the effects of two parameters: a shorter genome length results in lower speed but a shorter total time, and the presence of divalent magnesium ions (replacing sodium) reduces the pressure, increasing ejection time to 8–11 s. Pressure caused by DNA–DNA interactions within the head affects the initiation of ejection, but the close packing is also the dominant source of friction: more tightly packed phages initiate ejection earlier, but with a lower initial speed. The details of ejection revealed in this study are probably generic features of DNA translocation in bacteriophages and have implications for the dynamics of DNA in other biological systems

Anharmonicities of giant dipole excitations

The role of anharmonic effects on the excitation of the double giant dipole resonance is investigated in a simple macroscopic model.Perturbation theory is used to find energies and wave functions of the anharmonic ascillator.The cross sections for the electromagnetic excitation of the one- and two-phonon giant dipole resonances in energetic heavy-ion collisions are then evaluated through a semiclassical coupled-channel calculation.It is argued that the variations of the strength of the anharmonic potential should be combined with appropriate changes in the oscillator frequency,in order to keep the giant dipole resonance energy consistent with the experimental value.When this is taken into account,the effects of anharmonicities on the double giant dipole resonance excitation probabilities are small and cannot account for the well-known discrepancy between theory and experiment

Double Giant Dipole Resonance in ^{208}Pb

Double-dipole excitations in ^{208}Pb are analyzed within a microscopic model explicitly treating 2p2h-excitations. Collective states built from such 2p2h-excitations are shown to appear at about twice the energy of the isovector giant dipole resonance, in agreement with the experimental findings. The calculated cross section for Coulomb excitation at relativistic energies cannot explain simultaneously the measured single-dipole and double-dipole cross sections, however.Comment: 7 pages, Latex, 5 postscript figure

Use of 18F-NaF PET in the staging of skeletal metastases of newly diagnosed, high-risk prostate cancer patients:a nationwide cohort study

OBJECTIVE: To determine whether preoperative staging of high-risk prostate cancer with (18)F-sodium-fluoride ((18)F-NaF) positron emission tomography (PET) reduces the risk of skeletal metastases. DESIGN: Nationwide, population-based cohort study using real-world data. SETTING: The study used national health registries, including all sites in Denmark from 2011 to 2018. PARTICIPANTS: Newly diagnosed high-risk prostate cancer patients who underwent radical prostatectomy from 2011 to 2018. Patients were stratified into two groups according to the preoperative imaging modality of either (18)F-NaF PET or bone scintigraphy. MAIN OUTCOME MEASURES: The risk of skeletal-related events (SREs) as a proxy for skeletal metastases following radical prostatectomy. The secondary endpoint was overall survival. RESULTS: Between 1 January 2011 and 31 December 2018, 4183 high-risk patients underwent radical prostatectomy. Of these patients, 807 (19.3%) underwent (18)F-NaF PET and 2161 (51.7%) underwent bone scintigraphy. The remaining 30% were examined by a different imaging method or did not undergo imaging. Using the inverse probability of treatment weighting to control potential confounding, the HR of experiencing an SRE for patients in the (18)F-NaF PET group versus the bone scintigraphy group was 1.15 (95% CI 0.86 to 1.54). The 3-year survival rates were 97.4% (95% CI 96.1 to 98.7) and 97.1% (95% CI 96.4 to 97.9) for patients receiving (18)F-NaF PET and bone scintigraphy, respectively. CONCLUSION: Patients with high-risk prostate cancer undergoing preoperative staging with (18)F-NaF PET did not display a lower risk of developing SREs after prostatectomy compared with patients undergoing bone scintigraphy. The survival rates were similar between the two groups