Integrating single-molecule FRET and biomolecular simulations to study diverse interactions between nucleic acids and proteins

The conformations of biological macromolecules are intimately related to their cellular functions. Conveniently, the well-characterized dipole–dipole distance-dependence of Förster resonance energy transfer (FRET) makes it possible to measure and monitor the nanoscale spatial dimensions of these conformations using fluorescence spectroscopy. For this reason, FRET is often used in conjunction with single-molecule detection to study a wide range of conformationally dynamic biochemical processes. Written for those not yet familiar with the subject, this review aims to introduce biochemists to the methodology associated with single-molecule FRET, with a particular emphasis on how it can be combined with biomolecular simulations to study diverse interactions between nucleic acids and proteins. In the first section, we highlight several conceptual and practical considerations related to this integrative approach. In the second section, we review a few recent research efforts wherein various combinations of single-molecule FRET and biomolecular simulations were used to study the structural and dynamic properties of biochemical systems involving different types of nucleic acids (e.g., DNA and RNA) and proteins (e.g., folded and disordered)

Measurement of the α Asymmetry Parameter for the Ω-→ΛK- Decay

We have measured the α parameter of the Ω-→ΛK- decay using data collected with the HyperCP spectrometer during the 1997 fixed-target run at Fermilab. Analyzing a sample of 0.96×106 Ω-→ΛK-, Λ→pπ- decays, we obtain αΩαΛ=[1.33±0.33(stat)±0.52(syst)]×10-2. With the accepted value ofαΛ, αΩ is found to be [2.07±0.51(stat)±0.81(syst)]×10-2

Scaling Tests of the Cross Section for Deeply Virtual Compton Scattering

We present the first measurements of the e⃗p→epγ cross section in the deeply virtual Compton scattering (DVCS) regime and the valence quark region. The Q2 dependence (from 1.5 to 2.3  GeV2) of the helicity-dependent cross section indicates the twist-2 dominance of DVCS, proving that generalized parton distributions (GPDs) are accessible to experiment at moderate Q2. The helicity-independent cross section is also measured at Q2=2.3  GeV2. We present the first model-independent measurement of linear combinations of GPDs and GPD integrals up to the twist-3 approximation

Adjusting Overall Survival Estimates after Treatment Switching: a Case Study in Metastatic Castration-Resistant Prostate Cancer

Background If patients in oncology trials receive subsequent therapy, standard intention-to-treat (ITT) analyses may inaccurately estimate the overall survival (OS) effect of the investigational product. In this context, a post-hoc analysis of the phase 3 PREVAIL study was performed with the aim to compare enzalutamide with placebo in terms of OS, adjusting for potential confounding from switching to antineoplastic therapies that are not part of standard metastatic castration-resistant prostate cancer (mCRPC) treatment pathways in some jurisdictions. Methods The PREVAIL study, which included 1717 chemotherapy-naïve men with mCRPC randomized to treatment with enzalutamide 160 mg/day or placebo, was stopped after a planned interim survival analysis revealed a benefit in favor of enzalutamide. Data from this cutoff point were confounded by switching from both arms and so were evaluated in terms of OS using two switching adjustment methods: the two-stage accelerated failure time model (two-stage method) and inverse probability of censoring weights (IPCW). Results Following adjustment for switching to nonstandard antineoplastic therapies by 14.8 (129/872 patients) and 21.3% (180/845 patients) of patients initially randomized to enzalutamide and placebo, respectively, the two-stage and IPCW methods both resulted in numerical reductions in the hazard ratio (HR) for OS [HR 0.66, 95% confidence interval (CI) 0.57–0.81 and HR 0.63, 95% CI 0.52–0.75, respectively] for enzalutamide compared to placebo versus the unadjusted ITT analysis (HR 0.71, 95% CI 0.60–0.84). These results suggest a slightly greater effect of enzalutamide on OS than originally reported. Conclusion In the PREVAIL study, switching to nonstandard antineoplastic mCRPC therapies resulted in the ITT analysis of primary data underestimating the benefit of enzalutamide on OS

Well-Being: From Concept to Practice?

‘Well-being’ has become a high-profile and contested issue, for both policy and practice, since its introduction as an integral part of the Care Act (2014). A dynamic and fluid concept, the researchers were interested in how qualified social workers conceptualise concept of well-being. This small-scale qualitative study, arising from a partnership between a university and a local authority within England, explored how social workers, in one adult social work service, conceptualized ‘well-being’ in relation to service users who both did have the mental capacity, and also those who lacked capacity, to make informed decisions in relation to their care and support needs. The researchers adopted an interpretivist, qualitative approach to the research and used thematic analysis of the rich data arising from individual and group discussions. Interesting differences emerged that, we propose, related to the practitioners’ dominant ‘cognitive style’ or over-arching approach to considering how individuals, with and without capacity, defined their own well-being, becoming more risk-averse when considering the well-being (as defined within the Care Act 2014) of an individual who lacked capacity. Whilst local authorities have a duty under the Care Act to promote an individual’s well-being, firmly locating the well-being principle at the heart of adult social work assessments, it is important to remember that this is a concept that is mainly self-defined. However, the ways in which practitioners conceptualise well-being influence both how they approach an assessment, and indeed how they seek to build relationships with the person being assessed. Bringing the different cognitive styles to practitioners’ attention, we believe, provides an opportunity to challenge their own and their colleagues’ biases, whether systemic or individual, and free them to embrace the fluidity of experience and well-being, for all individuals seeking to access services

Exclusive neutral pion electroproduction in the deeply virtual regime

We present measurements of the ep -\u3e ep pi(0) cross section extracted at two values of four-momentum transfer Q(2) = 1.9 GeV(2) and Q(2) = 2.3 GeV(2) at Jefferson Lab Hall A. The kinematic range allows one to study the evolution of the extracted cross section as a function of Q(2) and W. Results are confronted with Regge-inspired calculations and GPD predictions. An intepretation of our data within the framework of semi-inclusive deep inelastic scattering is also discussed

ECCC TEST PROGRAMME AND DATA ASSESSMENT ON GTD111 CREEP RUPTURE, STRAIN AND DUCTILITY

GTD111, a creep resistant Ni-based superalloy developed by GE, is widely used in land-based gas turbine first stage blades. However, there is little published information on its creep properties and microstructure. The European Creep Collaborative Committee (ECCC) Working Group 3C consequently selected GTD111 as a model material for testing and complementary data assessment. The aim of this paper is to present the results from the ECCC test program and data assessment, and to compare equiaxed (EA) and directionally solidified (DS) material performance. Testing and metallographic laboratories from six European nations collaborated to produce strain monitored creep rupture data on four EA and DS materials out to beyond 10,000 hours within a wide range of temperatures, 850-950°C, and stresses, 293-99 MPa. Available (generally short term) results from other sources were also included in the compiled, small but viable, 51-test data set. Assessment was carried out by three different assessors using different tools and adopting different prediction models. Conventional ECCC post-assessment techniques and novel “back-fitting” methods were used to identify a preferred model. It was shown that assessing all the EA and DS data together can lead to non-conservative predictions for EA materials, but separating the two classes creates small data subsets which cannot be modelled effectively. As a pragmatic compromise, the DS data and those EA data which also showed good ductility were included in a final "ductile GTD111" assessment. The resulting creep rupture material models and rupture strength predictions are presented up to 3 times the longest test duration. It was then shown that the performance of lower ductility EA materials can also be predicted effectively with the "ductile" model by truncating the rupture time at the measured fracture strain. For this exercise, a creep strain model based on rupture and time to strain data was fitted. In parallel, microstructural examination was performed to characterize the damage modes involved in the low ductility failures. It was thereby shown that the creep rupture strength shortfall of an EA material compared to its DS equivalent is not a constant factor, but is primarily governed by the reduced creep ductility. Hence, the shortfall varies between different EA casts, and tends to become greater in the longer term.JRC.F.4-Innovative Technologies for Nuclear Reactor Safet

THE RESULTS OF PANCREATIC RESECTIONS AND LONG- TERM SURVIVAL FOR PANCREATIC DUCTAL ADENOCARCINOMA : A SINGLE-INSTITUTION EXPERIENCE

Objectives: Since the early 1990s, low long-term survival rates following pancreatic surgery for pancreatic ductal adenocarcinoma have challenged us to improve treatment. In this series, we aim to show improved survival from pancreatic ductal adenocarcinoma during the era of centralized pancreatic surgery. Methods: Analysis of all pancreatic resections performed at Helsinki University Hospital and survival of pancreatic ductal adenocarcinoma patients during 2000-2013 were included. Post-operative complications such as fistulas, reoperations, and mortality rates were recorded. Patient and tumor characteristics were compared with survival data. Results: Of the 853 patients undergoing pancreatic surgery, 581 (68%) were pancreaticoduodenectomies, 195 (21%) distal resections, 28 (3%) total pancreatectomies, and 49 (6%) other procedures. Mortality after pancreaticoduodenectomy was 2.1%. The clinically relevant B/C fistula rate was 7% after pancreaticoduodenectomy and 13% after distal resection, and the re-operation rate was 5%. The 5- and 10-year survival rates for pancreatic ductal adenocarcinoma were 22% and 14%; for T1-2, N0 and R0 tumors, the corresponding survival rates were 49% and 31%. Carbohydrate antigen 19-9 >75 kU/L, carcinoembryonic antigen >5 mu g/L, N1, lymph-node ratio >20%, R1, and lack of adjuvant therapy were independent risk factors for decreased survival. Conclusion: After centralization of pancreatic surgery in southern Finland, we have managed to enable pancreatic ductal adenocarcinoma patients to survive markedly longer than in the early 1990s. Based on a 1.7-million population in our clinic, mortality rates are equal to those of other high-volume centers and long-term survival rates for pancreatic ductal adenocarcinoma have now risen to some of the highest reported.Peer reviewe

Search for the Lepton-Number-Violating Decay Ξ−→pμ−μ−\Xi^- \to p \mu^- \mu^-

A sensitive search for the lepton-number-violating decay $\Xi^-\to p \mu^-\mu^-$ has been performed using a sample of $\sim10^9$ $\Xi^-$ hyperons produced in 800 GeV/$c$ $p$-Cu collisions. We obtain $\mathcal{B}(\Xi^-\to p \mu^-\mu^-)< 4.0\times 10^{-8}$ at 90% confidence, improving on the best previous limit by four orders of magnitude.Comment: 9 pages, 5 figures, to be published in Phys. Rev. Let

Spectroscopy of Li-9(Lambda) by electroproduction

Background: In the absence of accurate data on the free two-body hyperon-nucleon interaction, the spectra of hypernuclei provides information on the details of the effective hyperon-nucleon interaction. Purpose: To obtain a high-resolution binding-energy spectrum for the Be-9(e, e\u27 K+) Li-9(Lambda) reaction. Method: Electroproduction of the hypernucleus Li-9(Lambda) has been studied for the first time with sub-MeV energy resolution in Hall A at Jefferson Lab on a Be-9 target. In order to increase the counting rate and to provide unambiguous kaon identification, two superconducting septum magnets and a ring imaging Cherenkov detector were added to the Hall A standard equipment. Results: The cross section to low-lying states of Li-9(Lambda) is concentrated within 3 MeV of the ground state and can be fit with four peaks. The positions of the doublets agree with theory while a disagreement could exist with respect to the relative strengths of the peaks in the doublets. The Lambda separation energy, B-Lambda, of 8.36 +/- 0.08 (stat.) +/- 0.08 (syst.) MeV was measured, in agreement with an earlier experiment