Estimating the reproducibility & transparency of smoking cessation behaviour change interventions

Introduction: Activities promoting research reproducibility and transparency are crucial for generating trustworthy evidence. Evaluation of smoking interventions is one area where vested interests may motivate reduced reproducibility and transparency. / Aims: Assess markers of transparency and reproducibility in smoking behaviour change intervention evaluation reports. Methods: One hundred evaluation reports of smoking behaviour change intervention randomised controlled trials published in 2018-2019 were identified. Reproducibility markers of pre-registration, protocol sharing, data-, materials- and analysis script-sharing, replication of a previous study and open access publication were coded in identified reports. Transparency markers of funding and conflict of interest declarations were also coded. Coding was performed by two researchers, with inter-rater reliability calculated using Krippendorff’s alpha. / Results: Seventy-one percent of reports were open access and 73% pre-registered. However, only 13% provided accessible materials, 7% accessible data and 1% accessible analysis scripts. No reports were replication studies. Ninety-four percent of reports provided a funding source statement and eighty-eight percent of reports provided a conflict of interest statement. / Conclusions: Open data, materials, analysis and replications are rare in smoking behaviour change interventions, whereas funding source and conflict of interest declarations are common. Future smoking research should be more reproducible to enable knowledge accumulation

Structured Sparsity: Discrete and Convex approaches

Compressive sensing (CS) exploits sparsity to recover sparse or compressible signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity is also used to enhance interpretability in machine learning and statistics applications: While the ambient dimension is vast in modern data analysis problems, the relevant information therein typically resides in a much lower dimensional space. However, many solutions proposed nowadays do not leverage the true underlying structure. Recent results in CS extend the simple sparsity idea to more sophisticated {\em structured} sparsity models, which describe the interdependency between the nonzero components of a signal, allowing to increase the interpretability of the results and lead to better recovery performance. In order to better understand the impact of structured sparsity, in this chapter we analyze the connections between the discrete models and their convex relaxations, highlighting their relative advantages. We start with the general group sparse model and then elaborate on two important special cases: the dispersive and the hierarchical models. For each, we present the models in their discrete nature, discuss how to solve the ensuing discrete problems and then describe convex relaxations. We also consider more general structures as defined by set functions and present their convex proxies. Further, we discuss efficient optimization solutions for structured sparsity problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure

New measurement of θ13\theta_{13} via neutron capture on hydrogen at Daya Bay

This article reports an improved independent measurement of neutrino mixing angle $\theta_{13}$ at the Daya Bay Reactor Neutrino Experiment. Electron antineutrinos were identified by inverse $\beta$-decays with the emitted neutron captured by hydrogen, yielding a data-set with principally distinct uncertainties from that with neutrons captured by gadolinium. With the final two of eight antineutrino detectors installed, this study used 621 days of data including the previously reported 217-day data set with six detectors. The dominant statistical uncertainty was reduced by 49%. Intensive studies of the cosmogenic muon-induced $^9$Li and fast neutron backgrounds and the neutron-capture energy selection efficiency, resulted in a reduction of the systematic uncertainty by 26%. The deficit in the detected number of antineutrinos at the far detectors relative to the expected number based on the near detectors yielded $\sin^22\theta_{13} = 0.071 \pm 0.011$ in the three-neutrino-oscillation framework. The combination of this result with the gadolinium-capture result is also reported.Comment: 26 pages, 23 figure

Improved Measurement of the Reactor Antineutrino Flux and Spectrum at Daya Bay

A new measurement of the reactor antineutrino flux and energy spectrum by the Daya Bay reactor neutrino experiment is reported. The antineutrinos were generated by six 2.9~GW$_{\mathrm{th}}$ nuclear reactors and detected by eight antineutrino detectors deployed in two near (560~m and 600~m flux-weighted baselines) and one far (1640~m flux-weighted baseline) underground experimental halls. With 621 days of data, more than 1.2 million inverse beta decay (IBD) candidates were detected. The IBD yield in the eight detectors was measured, and the ratio of measured to predicted flux was found to be $0.946\pm0.020$ ($0.992\pm0.021$) for the Huber+Mueller (ILL+Vogel) model. A 2.9~$\sigma$ deviation was found in the measured IBD positron energy spectrum compared to the predictions. In particular, an excess of events in the region of 4-6~MeV was found in the measured spectrum, with a local significance of 4.4~$\sigma$. A reactor antineutrino spectrum weighted by the IBD cross section is extracted for model-independent predictions.Comment: version published in Chinese Physics

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW$_{\textrm{th}}$ reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective $^{239}$Pu fission fractions, $F_{239}$, from 0.25 to 0.35, Daya Bay measures an average IBD yield, $\bar{\sigma}_f$, of $(5.90 \pm 0.13) \times 10^{-43}$ cm$^2$/fission and a fuel-dependent variation in the IBD yield, $d\sigma_f/dF_{239}$, of $(-1.86 \pm 0.18) \times 10^{-43}$ cm$^2$/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the $^{239}$Pu fission fraction at 10 standard deviations. The variation in IBD yield was found to be energy-dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1$\sigma$. This discrepancy indicates that an overall deficit in measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes $^{235}$U, $^{239}$Pu, $^{238}$U, and $^{241}$Pu. Based on measured IBD yield variations, yields of $(6.17 \pm 0.17)$ and $(4.27 \pm 0.26) \times 10^{-43}$ cm$^2$/fission have been determined for the two dominant fission parent isotopes $^{235}$U and $^{239}$Pu. A 7.8% discrepancy between the observed and predicted $^{235}$U yield suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.Comment: 7 pages, 5 figure

: a cis antisense RNA operates in trans in S. aureus

International audienceAntisense RNAs (asRNAs) pair to RNAs expressed from the complementary strand, and their functions are thought to depend on nucleotide overlap with genes on the opposite strand. There is little information on the roles and mechanisms of asRNAs. We show that a cis asRNA acts in trans, using a domain outside its target complementary sequence. SprA1 small regulatory RNA (sRNA) and SprA1(AS) asRNA are concomitantly expressed in S. aureus. SprA1(AS) forms a complex with SprA1, preventing translation of the SprA1-encoded open reading frame by occluding translation initiation signals through pairing interactions. The SprA1 peptide sequence is within two RNA pseudoknots. SprA1(AS) represses production of the SprA1-encoded cytolytic peptide in trans, as its overlapping region is dispensable for regulation. These findings demonstrate that sometimes asRNA functional domains are not their gene-target complementary sequences, suggesting there is a need for mechanistic re-evaluation of asRNAs expressed in prokaryotes and eukaryotes

Structure of hadron resonances with a nearby zero of the amplitude

We discuss the relation between the analytic structure of the scattering amplitude and the origin of an eigenstate represented by a pole of the amplitude.If the eigenstate is not dynamically generated by the interaction in the channel of interest, the residue of the pole vanishes in the zero coupling limit. Based on the topological nature of the phase of the scattering amplitude, we show that the pole must encounter with the Castillejo-Dalitz-Dyson (CDD) zero in this limit. It is concluded that the dynamical component of the eigenstate is small if a CDD zero exists near the eigenstate pole. We show that the line shape of the resonance is distorted from the Breit-Wigner form as an observable consequence of the nearby CDD zero. Finally, studying the positions of poles and CDD zeros of the KbarN-piSigma amplitude, we discuss the origin of the eigenstates in the Lambda(1405) region.Comment: 7 pages, 3 figures, v2: published versio