Structured specifications for better verification of heap-manipulating programs

Abstract. Conventional specifications typically have a flat structure that is based primarily on the underlying logic. Such specifications lack structures that could have provided better guidance to the verification process. In this work, we propose to add three new structures to a specification framework for separation logic to achieve a more precise and better guided verification for pointer-based programs. The newly introduced structures empower users with more control over the verification process in the following ways: (i) case analysis can be invoked to take advantage of disjointness conditions in the logic. (ii) early, as opposed to late, instantiation can minimise on the use of existential quantification. (iii) formulae that are staged provide better reuse of the verification process. Initial experiments have shown that structured specifications can lead to more precise verification without incurring any performance overhead.

The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and x chromosome specific allelic properties.

Background: In female mammalian cells, random X chromosome inactivation (XCI) equalizes the dosage of X-encoded gene products to that in male cells. XCI is a stochastic process, in which each X chromosome has a probability to be inactivated. To obtain more insight in the factors setting up this probability, we studied the role of the X to autosome (X:A) ratio in initiation of XCI, and have used the experimental data in a computer simulation model to study the cellular population dynamics of XCI. Methodology/Principal Findings: To obtain more insight in the role of the X:A ratio in initiation of XCI, we generated triploid mouse ES cells by fusion of haploid round spermatids with diploid female and male ES cells. These fusion experiments resulted in only XXY triploid ES cells. XYY and XXX ES lines were absent, suggesting cell death related either to insufficient X-chromosomal gene dosage (XYY) or to inheritance of an epigenetically modified X chromosome (XXX). Analysis of active (Xa) and inactive (Xi) X chromosomes in the obtained triploid XXY lines indicated that the initiation frequency of XCI is low, resulting in a mixed population of XaXiY and XaXaY cells, in which the XaXiY cells have a small proliferative advantage. This result, and findings on XCI in diploid and tetraploid ES cell lines with different X:A ratios, provides evidence that the X:A ratio determines the probability for a given X chromosome to be inactivated. Furthermore, we found that the kinetics of the XCI process can be simulated using a probability for an X chromosome to be inactivated that is proportional to the X:A ratio. These simulation studies re-emphasize our hypothesis that the probability is a function of the concentration of an X-encoded activator of XCI, and of X chromosome specific allelic properties determining the threshold for this activator. Conclusions: The present findings reveal that the probability for an X chromosome to be inactivated is proportional to the X:A ratio. This finding supports the presence of an X-encoded activator of the XCI process. © 2009 Monkhorst et al

Trade-Offs Between Carbon Stocks and Timber Recovery in Tropical Forests are Mediated by Logging Intensity

Forest degradation accounts for ~70% of total carbon losses from tropical forests. Substantial emissions are from selective logging, a land-use activity that decreases forest carbon density. To maintain carbon values in selectively logged forests, climate change mitigation policies and government agencies promote the adoption of reduced-impact logging (RIL) practices. However, whether RIL will maintain both carbon and timber values in managed tropical forests over time remains uncertain. In this study, we quantify the recovery of timber stocks and aboveground carbon at an experimental site where forests were subjected to different intensities of RIL (4, 8, and 16 trees/ha). Our census data span 20 years postlogging and 17 years after the liberation of future crop trees from competition in a tropical forest on the Guiana Shield, a globally important forest carbon reservoir. We model recovery of timber and carbon with a breakpoint regression that allowed us to capture elevated tree mortality immediately after logging. Recovery rates of timber and carbon were governed by the presence of residual trees (i.e., trees that persisted through the first harvest). The liberation treatment stimulated faster recovery of timber albeit at a carbon cost. Model results suggest a threshold logging intensity beyond which forests managed for timber and carbon derive few benefits from RIL, with recruitment and residual growth not sufficient to offset losses. Inclusion of the breakpoint at which carbon and timber gains outpaced postlogging mortality led to high predictive accuracy, including out-of-sample R2 values \u3e90%, and enabled inference on demographic changes postlogging. Our modeling framework is broadly applicable to studies that aim to quantify impacts of logging on forest recovery. Overall, we demonstrate that initial mortality drives variation in recovery rates, that the second harvest depends on old growth wood, and that timber intensification lowers carbon stocks

Use of a Single Hybrid Imaging Agent for Integration of Target Validation with In Vivo and Ex Vivo Imaging of Mouse Tumor Lesions Resembling Human DCIS

Screening of biomarker expression levels in tumor biopsy samples not only provides an assessment of prognostic and predictive factors, but may also be used for selection of biomarker-specific imaging strategies. To assess the feasibility of using a biopsy specimen for a personalized selection of an imaging agent, the chemokine receptor 4 (CXCR4) was used as a reference biomarker. Methods: A hybrid CXCR4 targeting peptide (MSAP-Ac-TZ14011) containing a fluorescent dye and a chelate for radioactive labeling was used to directly compare initial flow cytometry–based target validation in fresh tumor tissue to $in$ $vivo$ single photon emission computed tomography (SPECT) imaging and $in$ $vivo$ and $ex$ $vivo$ fluorescence imaging. Results: Flow cytometric analysis of mouse tumor derived cell suspensions enabled discrimination between 4T1 control tumor lesions (with low levels of CXCR4 expression) and CXCR4 positive early, intermediate and late stage MIN-O lesions based on their CXCR4 expression levels; CXCR4$^{basal}$, CXCR4$^+$ and CXCR4$^{++}$ cell populations could be accurately discriminated. Mean fluorescent intensity ratios between expression in MIN-O and 4T1 tissue found with flow cytometry were comparable to ratios obtained with in vivo SPECT/CT and fluorescence imaging, ex vivo fluorescence evaluation and standard immunohistochemistry. Conclusion: The hybrid nature of a targeting imaging agent like MSAP-Ac-TZ14011 enables integration of target selection, in vivo imaging and ex vivo validation using a single agent. The use of biopsy tissue for biomarker screening can readily be expanded to other targeting hybrid imaging agents and can possibly help increase the clinical applicability of tumor-specific imaging approaches

The ASCIZ-DYNLL1 axis promotes 53BP1-dependent non-homologous end joining and PARP inhibitor sensitivity

53BP1 controls a specialized non-homologous end joining (NHEJ) pathway that is essential for adaptive immunity, yet oncogenic in BRCA1 mutant cancers. Intra-chromosomal DNA double-strand break (DSB) joining events during immunoglobulin class switch recombination (CSR) require 53BP1. However, in BRCA1 mutant cells, 53BP1 blocks homologous recombination (HR) and promotes toxic NHEJ, resulting in genomic instability. Here, we identify the protein dimerization hub—DYNLL1—as an organizer of multimeric 53BP1 complexes. DYNLL1 binding stimulates 53BP1 oligomerization, and promotes 53BP1’s recruitment to, and interaction with, DSB-associated chromatin. Consequently, DYNLL1 regulates 53BP1-dependent NHEJ: CSR is compromised upon deletion of Dynll1 or its transcriptional regulator Asciz, or by mutation of DYNLL1 binding motifs in 53BP1; furthermore, Brca1 mutant cells and tumours are rendered resistant to poly-ADP ribose polymerase (PARP) inhibitor treatments upon deletion of Dynll1 or Asciz. Thus, our results reveal a mechanism that regulates 53BP1-dependent NHEJ and the therapeutic response of BRCA1-deficient cancers

Effect of No Prehydration vs Sodium Bicarbonate Prehydration Prior to Contrast-Enhanced Computed Tomography in the Prevention of Postcontrast Acute Kidney Injury in Adults With Chronic Kidney Disease The Kompas Randomized Clinical Trial

Importance Prevention of postcontrast acute kidney injury in patients with stage 3 chronic kidney disease (CKD) by means of prehydration has been standard care for years. However, evidence for the need for prehydration in this group is limited. Objective To assess the renal safety of omitting prophylactic prehydration prior to iodine-based contrast media administration in patients with stage 3 CKD. Design, Setting, and Participants The Kompas trial was a multicenter, noninferiority, randomized clinical trial conducted at 6 hospitals in the Netherlands in which 523 patients with stage 3 CKD were randomized in a 1:1 ratio to receive no prehydration or prehydration with 250 mL of 1.4% sodium bicarbonate administered in a 1-hour infusion before undergoing elective contrast-enhanced computed tomography from April 2013 through September 2016. Final follow-up was completed in September 2017. Data were analyzed from January 2018 to June 2019. Interventions In total, 262 patients were allocated to the no prehydration group and 261 were allocated to receive prehydration. Analysis on the primary end point was available in 505 patients (96.6%). Main Outcomes and Measures The primary end point was the mean relative increase in serum creatinine level 2 to 5 days after contrast administration compared with baseline (noninferiority margin of less than 10% increase in serum creatinine level). Secondary outcomes included the incidence of postcontrast acute kidney injury 2 to 5 days after contrast administration, mean relative increase in creatinine level 7 to 14 days after contrast administration, incidences of acute heart failure and renal failure requiring dialysis, and health care costs. Results Of 554 patients randomized, 523 were included in the intention-to-treat analysis. The median (interquartile range) age was 74 (67-79) years; 336 (64.2%) were men and 187 (35.8%) were women. The mean (SD) relative increase in creatinine level 2 to 5 days after contrast administration compared with baseline was 3.0% (10.5) in the no prehydration group vs 3.5% (10.3) in the prehydration group (mean difference, 0.5; 95% CI, -1.3 to 2.3; P <.001 for noninferiority). Postcontrast acute kidney injury occurred in 11 patients (2.1%), including 7 of 262 (2.7%) in the no prehydration group and 4 of 261 (1.5%) in the prehydration group, which resulted in a relative risk of 1.7 (95% CI, 0.5-5.9; P = .36). None of the patients required dialysis or developed acute heart failure. Subgroup analyses showed no evidence of statistical interactions between treatment arms and predefined subgroups. Mean hydration costs were euro119 (US $143.94) per patient in the prehydration group compared with euro0 (US$0) in the no prehydration group (P <.001). Other health care costs were similar. Conclusions and Relevance Among patients with stage 3 CKD undergoing contrast-enhanced computed tomography, withholding prehydration did not compromise patient safety. The findings of this study support the option of not giving prehydration as a safe and cost-efficient measure

Proximity Dimensions and Scientific Collaboration among Academic Institutions in Europe: The Closer, the Better?

The main objective of this paper is to examine the effect of various proximity dimensions (geographical, cognitive, institutional, organizational, social and economic) on academic scientific collaborations (SC). The data to capture SC consists of a set of co-authored articles published between 2006 and 2010 by universities located in EU-15, indexed by the Science Citation Index (SCI Expanded) of the ISI Web of Science database. We link this data to institution-level information provided by the EUMIDA dataset. Our final sample consists of 240,495 co-authored articles from 690 European universities that featured in both datasets. Additionally, we also retrieved data on regional R&D funding from Eurostat. Based on the gravital equation, we estimate several econometrics models using aggregated data from all disciplines as well as separated data for Chemistry & Chemical Engineering, Life Sciences and Physics & Astronomy. Our results provide evidence on the substantial role of geographical, cognitive, institutional, social and economic distance in shaping scientific collaboration, while the effect of organizational proximity seems to be weaker. Some differences on the relevance of these factors arise at discipline level