Background: As part of a coordinated effort to expand research activity around rigor, reproducibility, and transparency (RRT) across scientific disciplines, a team of investigators at the Indiana ...University School of Public Health-Bloomington hosted a workshop in October 2019 with international leaders to discuss key opportunities for RRT research.
Objective: The workshop aimed to identify research priorities and opportunities related to RRT.
Design: Over two-days, workshop attendees gave presentations and participated in three working groups: (1) Improving Education & Training in RRT, (2) Reducing Statistical Errors and Increasing Analytic Transparency, and (3) Looking Outward: Increasing Truthfulness and Accuracy of Research Communications. Following small-group discussions, the working groups presented their findings, and participants discussed the research opportunities identified. The investigators compiled a list of research priorities, which were circulated to all participants for feedback.
Results: Participants identified the following priority research questions: (1) Can RRT-focused statistics and mathematical modeling courses improve statistics practice?; (2) Can specialized training in scientific writing improve transparency?; (3) Does modality (e.g. face to face, online) affect the efficacy RRT-related education?; (4) How can automated programs help identify errors more efficiently?; (5) What is the prevalence and impact of errors in scientific publications (e.g., analytic inconsistencies, statistical errors, and other objective errors)?; (6) Do error prevention workflows reduce errors?; (7) How do we encourage post-publication error correction?; (8) How does 'spin' in research communication affect stakeholder understanding and use of research evidence?; (9) Do tools to aid writing research reports increase comprehensiveness and clarity of research reports?; and (10) Is it possible to inculcate scientific values and norms related to truthful, rigorous, accurate, and comprehensive scientific reporting?
Conclusion: Participants identified important and relatively unexplored questions related to improving RRT. This list may be useful to the scientific community and investigators seeking to advance meta-science (i.e. research on research).
Purpose: We investigate how an intrinsic speckle tracking approach to speckle-based x-ray imaging is used to extract an object’s effective dark-field (DF) signal, which is capable of providing object ...information in three dimensions.
Approach: The effective DF signal was extracted using a Fokker–Planck type formalism, which models the deformations of illuminating reference beam speckles due to both coherent and diffusive scatter from the sample. Here, we assumed that (a) small-angle scattering fans at the exit surface of the sample are rotationally symmetric and (b) the object has both attenuating and refractive properties. The associated inverse problem of extracting the effective DF signal was numerically stabilized using a “weighted determinants” approach.
Results: Effective DF projection images, as well as the DF tomographic reconstructions of the wood sample, are presented. DF tomography was performed using a filtered back projection reconstruction algorithm. The DF tomographic reconstructions of the wood sample provided complementary, and otherwise inaccessible, information to augment the phase contrast reconstructions, which were also computed.
Conclusions: An intrinsic speckle tracking approach to speckle-based imaging can tomographically reconstruct an object’s DF signal at a low sample exposure and with a simple experimental setup. The obtained DF reconstructions have an image quality comparable to alternative x-ray DF techniques.
Abstract
BACKGROUND
As intraventricular thrombolysis for intraventricular hemorrhage (IVH) has developed over the last 2 decades, hemorrhagic complications have remained a concern despite general ...validation of its safety in controlled trials in the Clot Lysis: Evaluation of Accelerated Resolution of Intraventricular Hemorrhage Phase III (CLEAR-IVH) program.
OBJECTIVE
To analyze factors associated with symptomatic bleeding following IVH with and without thrombolysis in conjunction with the recently completed CLEAR III trial.
METHODS
We reviewed safety reports on symptomatic bleeding events reported during the first year after randomization among subjects enrolled in the CLEAR III trial. Clinical and imaging data were retrieved through the trial database as part of ongoing quality and safety monitoring. A posthoc root-cause analysis was performed to identify potential factors predisposing to rebleeding in each case. Cases were classified according to onset of rebleeding (during dosing, early after dosing and delayed), the pattern of bleeding, and treatment rendered (alteplase vs saline).
RESULTS
Twenty subjects developed a secondary symptomatic intracranial hemorrhage constituting 4% of subjects. Symptomatic rebleeding events occurred during the dosing protocol (n = 9, 67% alteplase), early after the protocol (n = 5, 40% alteplase), and late (n = 6, 0% alteplase). Catheter-related hemorrhages were the most common (n = 7, 35%) followed by expansion or new intraventricular (n = 6, 30%) and intracerebral (n = 5, 25%) hemorrhages. Symptomatic hemorrhages during therapy resulted from a combination of treatment- and patient-related factors and were at most partially attributable to alteplase. Rebleeding after the dosing protocol primarily reflected patients’ risk factors.
CONCLUSION
Intraventricular thrombolysis marginally increases the overall risk of symptomatic hemorrhagic complications after IVH, and only during the treatment phase.
Ultra-short period (USP) planets are a class of low-mass planets with periods shorter than one day. Their origin is still unknown, with photo-evaporation of mini-Neptunes and in situ formation being ...the most credited hypotheses. Formation scenarios differ radically in the predicted composition of USP planets, and it is therefore extremely important to increase the still limited sample of USP planets with precise and accurate mass and density measurements. We report here the characterization of a USP planet with a period of 0.28 days around K2-141 (EPIC 246393474), and the validation of an outer planet with a period of 7.7 days in a grazing transit configuration. We derived the radii of the planets from the K2 light curve and used high-precision radial velocities gathered with the HARPS-N spectrograph for mass measurements. For K2-141b, we thus inferred a radius of 1.51 0.05 R and a mass of 5.08 0.41 M , consistent with a rocky composition and lack of a thick atmosphere. K2-141c is likely a Neptune-like planet, although due to the grazing transits and the non-detection in the RV data set, we were not able to put a strong constraint on its density. We also report the detection of secondary eclipses and phase curve variations for K2-141b. The phase variation can be modeled either by a planet with a geometric albedo of 0.30 0.06 in the Kepler bandpass, or by thermal emission from the surface of the planet at ∼3000 K. Only follow-up observations at longer wavelengths will allow us to distinguish between these two scenarios.
The abdominal compartment syndrome is a potentially life-threatening condition with frequent renal involvement. There are few if any means of inferring subclinical effects before organ dysfunction. ...Because intrarenal pressure correlates with renal sonographic indices in other renal diseases, the purpose of this study was to determine the relationship between increasing intraabdominal hypertension and renal vascular flow velocities in a porcine model using renal Doppler ultrasound.
Animal study.
University research laboratory.
Eight anesthetized, mechanically ventilated, well-hydrated, 30-kg female Yorkshire pigs.
Intraabdominal hypertension was induced by instillation of warmed intraperitoneal saline through a midline laparoscopic port. Intraabdominal pressure (IAP) was continuously monitored directly from the peritoneum and indirectly from the bladder. IAP was varied from 0 to 50 mm Hg in increments of 5 mm Hg. At each IAP level, gray-scale, color, and spectral Doppler renal arcuate artery ultrasound was obtained and resistive index (RI) and peak airway pressure calculated.
Excellent agreement between direct and indirect IAP was found (bias, 0.032 mm Hg; 95% limits, -5.5 to 5.6 mm Hg). A linear relationship between RI and indirect IAP was observed and was defined by the regression equation: RI = 0.553 + 0.0104 x bladder pressure. There was a trend toward different RIs between left and right kidneys (p = .052) at the same IAP. RI varied in a linear fashion at low peak airway pressure and demonstrated an inflection point with steeper subsequent slope after peak airway pressure of 30 cm H2O. RI values rapidly returned to near baseline after abdominal decompression.
In this model, the renal artery RI correlated strongly and linearly with the severity of intraabdominal hypertension, making renal Doppler ultrasound a potential noninvasive screening tool for the renal effects of intraabdominal hypertension. Further studies are warranted.
We report the detection of a Saturn-size exoplanet orbiting HD 332231 (TOI 1456) in light curves from the Transiting Exoplanet Survey Satellite (TESS). HD 332231-an F8 dwarf star with a V-band ...magnitude of 8.56-was observed by TESS in Sectors 14 and 15. We detect a single-transit event in the Sector 15 presearch data conditioning (PDC) light curve. We obtain spectroscopic follow-up observations of HD 332231 with the Automated Planet Finder, Keck I, and SONG telescopes. The orbital period we infer from radial velocity (RV) observations leads to the discovery of another transit in Sector 14 that was masked by PDC due to scattered light contamination. A joint analysis of the transit and RV data confirms the planetary nature of HD 332231 b, a Saturn-size ( ), sub-Saturn-mass ( ) exoplanet on a 18.71 day circular orbit. The low surface gravity of HD 332231 b and the relatively low stellar flux it receives make it a compelling target for transmission spectroscopy. Also, the stellar obliquity is likely measurable via the Rossiter-McLaughlin effect, an exciting prospect given the 0.14 au orbital separation of HD 332231 b. The spectroscopic observations do not provide substantial evidence for any additional planets in the HD 332231 system, but continued RV monitoring is needed to further characterize this system. We also predict that the frequency and duration of masked data in the PDC light curves for TESS Sectors 14-16 could hide transits of some exoplanets with orbital periods between 10.5 and 17.5 days.
The first monochromatic X‐ray tomography experiments conducted at the Imaging and Medical beamline of the Australian Synchrotron are reported. The sample was a phantom comprising nylon line, Al wire ...and finer Cu wire twisted together. Data sets were collected at four different X‐ray energies. In order to quantitatively account for the experimental values obtained for the Hounsfield (or CT) number, it was necessary to consider various issues including the point‐spread function for the X‐ray imaging system and harmonic contamination of the X‐ray beam. The analysis and interpretation of the data includes detailed considerations of the resolution and efficiency of the CCD detector, calculations of the X‐ray spectrum prior to monochromatization, allowance for the response of the double‐crystal Si monochromator used (via X‐ray dynamical theory), as well as a thorough assessment of the role of X‐ray phase‐contrast effects. Computer simulations relating to the tomography experiments also provide valuable insights into these important issues. It was found that a significant discrepancy between theory and experiment for the Cu wire could be largely resolved in terms of the effect of the point‐spread function. The findings of this study are important in respect of any attempts to extract quantitative information from X‐ray tomography data, across a wide range of disciplines, including materials and life sciences.
The Imaging and Medical beamline at the Australian Synchrotron achieved `first light' in December 2008. Here, the first experiments performed on the beamline are reported, which involved both X‐ray ...imaging and tomography studies for a range of samples. The use of a plastic‐edge phantom for quantitative measurements of contrast and resolution proved to be very instructive and helped to confirm certain parameter values such as the effective horizontal source size, detector resolution and average X‐ray energy for the polychromatic beam.
We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) on the basis of multidimensional and comprehensive characterization, including mtDNA and ...whole-genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared with other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT upregulation in cancer distinct from previously observed amplifications and point mutations.
•Comprehensive molecular analysis is performed on 66 kidney chromophobe cases•Global molecular patterns provide clues as to this cancer’s cell of origin•mtDNA sequencing reveals loss-of-function mutations in NADH dehydrogenase subunits•Genomic structural rearrangements involving TERT promoter region are assessed
Davis et al. describe the landscape of somatic genomic alterations of chromophobe renal cell carcinomas, showing that changes in mitochondrial function are an inherent component of the disease biology and identifying genomic rearrangement as a mechanism for elevated TERT expression.
Most planetary discoveries with the K2 and Transiting Exoplanet Survey Satellite (TESS) missions are restricted to short periods because of the limited duration of observation. However, the ...re-observation of sky area allows for the detection of longer period planets. We describe new transits detected in six candidate planetary systems that were observed by multiple K2 mission campaigns. One of these systems is a multiplanet system with four candidate planets; we present new period constraints for two planets in this system. In the other five systems, only one transit is observed in each campaign, and we derive period constraints from this new data. The period distributions are highly multimodal resulting from missed potential transits in the gap between observations. Each peak in the distribution corresponds to transits at an integer harmonic of the two observed transits. We further detail a generalized procedure to constrain the period for planets with multiple observations with intervening gaps. Because long-period photometrically discovered planets are rare, these systems are interesting targets for follow-up observations and confirmation. Specifically, all six systems are bright enough (V = 10.4-12.7) to be amenable to radial velocity follow-up. This work serves as a template for period constraints in a host of similar yet-to-be-discovered planets in long baseline, temporally gapped observations conducted by the TESS mission.
PDF
