Preserving Liveness Guarantees from Synchronous Communication to Asynchronous Unstructured Low-Level Languages

In the implementation of abstract synchronous communication in asynchronous unstructured low-level languages, e.g. using shared variables, the preservation of safety and especially liveness properties is a hitherto open problem due to inherently different abstraction levels. Our approach to overcome this problem is threefold: First, we present our notion of handshake refinement with which we formally prove the correctness of the implementation relation of a handshake protocol. Second, we verify the soundness of our handshake refinement, i.e., all safety and liveness properties are preserved to the lower level. Third, we apply our handshake refinement to show the correctness of all implementations that realize the abstract synchronous communication with the handshake protocol. To this end, we employ an exemplary language with asynchronous shared variable communication. Our approach is scalable and closes the verification gap between different abstraction levels of communication

The Ituwa Surge deposits of the Holocene Ngozi caldera, Mbeya Region, Tanzania

The Ituwa Surge deposits belong to the Holocene Ngozi volcano (volcano number 222164 of the Smithsonian Institute Global Volcanism Program; Siebert et al. 2010) of the Rungwe Volcanic Province (RVP; Harkin 1960; Lenhardt and Oppenheimer 2014). They are named after their type locality and place of best exposure, the village of Ituwa in the Mbeya Region of southwestern Tanzania. Volcanism within the RVP started approximately 9 Ma ago and can be divided into a Late Miocene (*9.2–5.4 Ma), a Late Pliocene-Early Pleistocene (*3–1.6 Ma) and a Mid-Pleistocene-recent (\*0.6 Ma) phase (Ebinger et al. 1989, 1993; Ivanov et al. 1999).http://link.springer.com/journal/5312016-04-30hb201

Multivariable analysis of outcome predictors and adjustment of main outcome results to baseline data profile in randomized controlled trials: Safe Implementation of Thrombolysis in Stroke-MOnitoring STudy (SITS-MOST)

<p><b>Background and Purpose:</b> The Safe Implementation of Thrombolysis in Stroke-MOnitoring STudy (SITS-MOST) unadjusted results demonstrated that intravenous alteplase is well tolerated and that the effects were comparable with those seen in randomized, controlled trials (RCTs) when used in routine clinical practice within 3 hours of ischemic stroke onset. We aimed to identify outcome predictors and adjust the outcomes of the SITS-MOST to the baseline characteristics of RCTs.</p> <p><b>Methods:</b> The study population was SITS-MOST (n=6483) and pooled RCTs (n=464) patients treated with intravenous alteplase within 3 hours of stroke onset. Multivariable, backward stepwise regression analyses (until P≤0.10) were performed to identify the outcome predictors for SITS-MOST. Variables appearing either in the final multivariable model or differing (P<0.10) between SITS-MOST and RCTs were included in the prediction model for the adjustment of outcomes. Main outcome measures were symptomatic intracerebral hemorrhage, defined as National Institutes of Health Stroke Scale deterioration ≥1 within 7 days with any hemorrhage (RCT definition), mortality, and independency as defined by modified Rankin Score of 0 to 2 at 3 months.</p> <p><b>Results:</b> The adjusted proportion of symptomatic intracerebral hemorrhage for SITS-MOST was 8.5% (95% CI, 7.9 to 9.0) versus 8.6% (6.3 to 11.6) for pooled RCTs; mortality was 15.5% (14.7 to 16.2) versus 17.3% (14.1 to 21.1); and independency was 50.4% (49.6 to 51.2) versus 50.1% (44.5 to 54.7), respectively. In the multivariable analysis, older age, high blood glucose, high National Institutes of Health Stroke Scale score, and current infarction on imaging scans were related to poor outcome in all parameters. Systolic blood pressure, atrial fibrillation, and weight were additional predictors of symptomatic intracerebral hemorrhage. Current smokers had a lower rate of symptomatic intracerebral hemorrhage. Disability before current stroke (modified Rankin Score 2 to 5), diastolic blood pressure, antiplatelet other than aspirin, congestive heart failure, patients treated in new centers, and male sex were related to high mortality at 3 months.</p> <p><b>Conclusions:</b> The adjusted outcomes from SITS-MOST were almost identical to those in relevant RCTs and reinforce the conclusion drawn previously in the unadjusted analysis. We identified several important outcome predictors to better identify patients suitable for thrombolysis.</p&gt

Reconstructing the thermal structure of the upper ocean : insights from planktic foraminifera shell chemistry and alkenones in modern sediments of the tropical eastern Indian Ocean

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 26 (2011): PA3219, doi:10.1029/2011PA002132.Shell chemistry of planktic foraminifera and the alkenone unsaturation index in 69 surface sediment samples in the tropical eastern Indian Ocean off West and South Indonesia were studied. Results were compared to modern hydrographic data in order to assess how modern environmental conditions are preserved in sedimentary record, and to determine the best possible proxies to reconstruct seasonality, thermal gradient and upper water column characteristics in this part of the world ocean. Our results imply that alkenone-derived temperatures record annual mean temperatures in the study area. However, this finding might be an artifact due to the temperature limitation of this proxy above 28°C. Combined study of shell stable oxygen isotope and Mg/Ca ratio of planktic foraminifera suggests that Globigerinoides ruber sensu stricto (s.s.), G. ruber sensu lato (s.l.), and G. sacculifer calcify within the mixed-layer between 20 m and 50 m, whereas Globigerina bulloides records mixed-layer conditions at ∼50 m depth during boreal summer. Mean calcifications of Pulleniatina obliquiloculata, Neogloboquadrina dutertrei, and Globorotalia tumida occur at the top of the thermocline during boreal summer, at ∼75 m, 75–100 m, and 100 m, respectively. Shell Mg/Ca ratios of all species show a significant correlation with temperature at their apparent calcification depths and validate the application of previously published temperature calibrations, except for G. tumida that requires a regional Mg/Ca-temperature calibration (Mg/Ca = 0.41 exp (0.068*T)). We show that the difference in Mg/Ca-temperatures of the mixed-layer species and the thermocline species, particularly between G. ruber s.s. (or s.l.) and P. obliquiloculata, can be applied to track changes in the upper water column stratification. Our results provide critical tools for reconstructing past changes in the hydrography of the study area and their relation to monsoon, El Niño-Southern Oscillation, and the Indian Ocean Dipole Mode.This project was funded by the German Ministry of Education and Research (BMBF project PABESIA) and the “Deutsche Forschungsgemeinschaft” (DFG project HE 3412/15–1)

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls

Report on computational assessment of Tumor Infiltrating Lymphocytes from the International Immuno-Oncology Biomarker Working Group

Funder: U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)Funder: National Center for Research Resources under award number 1 C06 RR12463-01, VA Merit Review Award IBX004121A from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University.Funder: Susan G Komen Foundation (CCR CCR18547966) and a Young Investigator Grant from the Breast Cancer Alliance.Funder: The Canadian Cancer SocietyFunder: Breast Cancer Research Foundation (BCRF), Grant No. 17-194Abstract: Assessment of tumor-infiltrating lymphocytes (TILs) is increasingly recognized as an integral part of the prognostic workflow in triple-negative (TNBC) and HER2-positive breast cancer, as well as many other solid tumors. This recognition has come about thanks to standardized visual reporting guidelines, which helped to reduce inter-reader variability. Now, there are ripe opportunities to employ computational methods that extract spatio-morphologic predictive features, enabling computer-aided diagnostics. We detail the benefits of computational TILs assessment, the readiness of TILs scoring for computational assessment, and outline considerations for overcoming key barriers to clinical translation in this arena. Specifically, we discuss: 1. ensuring computational workflows closely capture visual guidelines and standards; 2. challenges and thoughts standards for assessment of algorithms including training, preanalytical, analytical, and clinical validation; 3. perspectives on how to realize the potential of machine learning models and to overcome the perceptual and practical limits of visual scoring

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Funder: Breast Cancer Research Foundation (BCRF); doi: https://doi.org/10.13039/100001006Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting