Verification of a Rust Implementation of Knuth's Dancing Links using ACL2

Dancing Links connotes an optimization to a circular doubly-linked list data structure implementation which provides for fast list element removal and restoration. The Dancing Links optimization is used primarily in fast algorithms to find exact covers, and has been popularized by Knuth in Volume 4B of his seminal series The Art of Computer Programming. We describe an implementation of the Dancing Links optimization in the Rust programming language, as well as its formal verification using the ACL2 theorem prover. Rust has garnered significant endorsement in the past few years as a modern, memory-safe successor to C/C++ at companies such as Amazon, Google, and Microsoft, and is being integrated into both the Linux and Windows operating system kernels. Our interest in Rust stems from its potential as a hardware/software co-assurance language, with application to critical systems. We have crafted a Rust subset, inspired by Russinoff's Restricted Algorithmic C (RAC), which we have imaginatively named Restricted Algorithmic Rust, or RAR. In previous work, we described our initial implementation of a RAR toolchain, wherein we simply transpile the RAR source into RAC. By so doing, we leverage a number of existing hardware/software co-assurance tools with a minimum investment of time and effort. In this paper, we describe the RAR Rust subset, describe our improved prototype RAR toolchain, and detail the design and verification of a circular doubly-linked list data structure employing the Dancing Links optimization in RAR, with full proofs of functional correctness accomplished using the ACL2 theorem prover.Comment: In Proceedings ACL2-2023, arXiv:2311.08373. arXiv admin note: substantial text overlap with arXiv:2205.1170

Development of a Translator from LLVM to ACL2

In our current work a library of formally verified software components is to be created, and assembled, using the Low-Level Virtual Machine (LLVM) intermediate form, into subsystems whose top-level assurance relies on the assurance of the individual components. We have thus undertaken a project to build a translator from LLVM to the applicative subset of Common Lisp accepted by the ACL2 theorem prover. Our translator produces executable ACL2 formal models, allowing us to both prove theorems about the translated models as well as validate those models by testing. The resulting models can be translated and certified without user intervention, even for code with loops, thanks to the use of the def::ung macro which allows us to defer the question of termination. Initial measurements of concrete execution for translated LLVM functions indicate that performance is nearly 2.4 million LLVM instructions per second on a typical laptop computer. In this paper we overview the translation process and illustrate the translator's capabilities by way of a concrete example, including both a functional correctness theorem as well as a validation test for that example.Comment: In Proceedings ACL2 2014, arXiv:1406.123

The IMS New Researchers\u27 Survival Guide

Statistics is a wonderfully diverse profession and graduate students making career choices have many options — especially in light of the dearth of students moving into the statistical sciences today. The three main career paths at the PhD level are in academics, industry/business and government. Each of these job types offers its own mix of intellectual challenges, financial reward, pressure and security. How a new researcher selects (or is selected by) a specific occupation in the statistical sciences sometimes seems more a function of luck than of conscious decision making. This consideration was one of the first concerns addressed by the New Researchers Committee (NRC) of the Institute of Mathematical Statistics in 1988, and this guide is the product of that (and later) thinking. We believe that if students were better informed about their choices, they would be less apprehensive, pursue their goals more effectively and, ultimately, be far more likely to find positions for which they are well suited. Similarly, if doctoral students were generally more familiar with various aspects of professional life, the entire statistical community would benefit. Among the transitional facts of life with which we believe new researchers should be acquainted are: 1. mechanisms for applying for jobs, 2. expectations associated with different types of jobs, 3. techniques for initiating an active research program, and 4. methods of becoming more involved with the broader statistical community. The Survival Guide addresses these issues, but it also offers advice on a variety of other topics which new researchers may wish to consider as they prepare to leave graduate school. This guide is based on the Statistical Science article by the New Researchers Committee of IMS (1991). See Kruse (2002) on inspiration for statistics as a career path and Stasny (2001) on the big picture with respect to academic jobs. DeMets et al (1998) and Shettle and Gaddy (1998) provide job outlooks for statisticians

Evaluation of Multiple Models to Distinguish Closely Related Forms of Disease Using DNA Microarray Data: an Application to Multiple Myeloma

Motivation: Standard laboratory classification of the plasma cell dyscrasia monoclonal gammopathy of undetermined significance (MGUS) and the overt plasma cell neoplasm multiple myeloma (MM) is quite accurate, yet, for the most part, biologically uninformative. Most, if not all, cancers are caused by inherited or acquired genetic mutations that manifest themselves in altered gene expression patterns in the clonally related cancer cells. Microarray technology allows for qualitative and quantitative measurements of the expression levels of thousands of genes simultaneously, and it has now been used both to classify cancers that are morphologically indistinguishable and to predict response to therapy. It is anticipated that this information can also be used to develop molecular diagnostic models and to provide insight into mechanisms of disease progression, e.g., transition from healthy to benign hyperplasia or conversion of a benign hyperplasia to overt malignancy. However, standard data analysis techniques are not trivial to employ on these large data sets. Methodology designed to handle large data sets (or modified to do so) is needed to access the vital information contained in the genetic samples, which in turn can be used to develop more robust and accurate methods of clinical diagnostics and prognostics.Results: Here we report on the application of a panel of statistical and data mining methodologies to classify groups of samples based on expression of 12,000 genes derived from a high density oligonucleotide microarray analysis of highly purified plasma cells from newly diagnosed MM, MGUS, and normal healthy donors. The three groups of samples are each tested against each other. The methods are found to be similar in their ability to predict group membership; all do quite well at predicting MM vs. normal and MGUS vs. normal. However, no method appears to be able to distinguish explicitly the genetic mechanisms between MM and MGUS. We believe this might be due to the lack of genetic differences between these two conditions, and may not be due to the failure of the models. We report the prediction errors for each of the models and each of the methods. Additionally, we report ROC curves for the results on group prediction.Availability: Logistic regression: standard software, available, for example in SAS. Decision trees and boosted trees: C5.0 from www.rulequest.com. SVM: SVM-light is publicly available from svmlight.joachims.org. Naïve Bayes and ensemble of voters are publicly available from www.biostat.wisc.edu/~mwaddell/eov.html. Nearest Shrunken Centroids is publicly available from http://www-stat.stanford.edu/~tibs/PAM

Failure of physiologic transformation of spiral arteries, endothelial and trophoblast cell activation, and acute atherosis in the basal plate of the placenta

BACKGROUND: Failure of physiologic transformation of spiral arteries has been reported in preeclampsia, fetal growth restriction, fetal death, and spontaneous preterm labor with intact or ruptured membranes. Spiral arteries with failure of physiologic transformation are prone to develop atherosclerotic-like lesions of atherosis. There are striking parallels between preeclampsia and atherosclerotic disease, and between lesions of atherosis and atherosclerosis. Endothelial activation, identified by intercellular adhesion molecule-1 expression, is present in atherosclerotic-like lesions of heart transplantation, and is considered a manifestation of rejection. Similarly, endothelial activation/dysfunction has been implicated in the pathophysiology of atherosclerosis and preeclampsia. Intercellular adhesion molecule-1-overexpressing-activated endothelial cells are more resistant to trophoblast displacement than nonactivated endothelium, and may contribute to shallow spiral artery trophoblastic invasion in obstetrical syndromes having failure of physiologic transformation. OBJECTIVE: We sought to determine whether failure of spiral artery physiologic transformation was associated with activation of interstitial extravillous trophoblasts and/or spiral artery endothelium and presence of acute atherosis in the placental basal plate. STUDY DESIGN: A cross-sectional study of 123 placentas (19-42 weeks' gestation) obtained from normal pregnancies (n = 22), preterm prelabor rupture of membranes (n = 26), preterm labor (n = 23), preeclampsia (n = 27), intrauterine fetal death (n = 15), and small for gestational age (n = 10) was performed. Failure of spiral artery physiologic transformation and presence of cell activation was determined using immunohistochemistry of placental basal plates containing a median of 4 (minimum: 1; maximum: 9) vessels per placenta. Endothelial/trophoblast cell activation was defined by the expression of intercellular adhesion molecule-1. Investigators examining microscopic sections were blinded to clinical diagnosis. Pairwise comparisons among placenta groups were performed with Fisher exact test and Wilcoxon rank sum test using a Bonferroni-adjusted level of significance (.025). RESULTS: We found that 87% (94/108) of placentas having spiral arteries with failure of physiologic transformation (actin-positive and cytokeratin-negative) in the basal plate, and 0% (0/15) of placentas having only spiral arteries with complete physiologic transformation (cytokeratin-positive and actin-negative), had arterial endothelial and/or interstitial extravillous trophoblasts reactive with the intercellular adhesion molecule-1 activation marker (P < .001). A significant correlation (R2 = 0.84) was found between expression of spiral artery endothelial and interstitial extravillous trophoblast intercellular adhesion molecule-1 (P < .001) in activated placentas. Lesions of atherosis were found in 31.9% (30/94) of placentas with complete and/or partial failure of physiologic transformation of spiral arteries that were intercellular adhesion molecule-1-positive, in none of the 14 placentas with failure of physiologic transformation that were intercellular adhesion molecule-1-negative, and in none of the 15 placentas with complete spiral artery physiologic transformation without failure (P = .001). All placentas (30/30, 100%) with atherosis were identified in placentas having concomitant spiral artery endothelial and interstitial extravillous trophoblast activation. CONCLUSION: Failure of spiral artery physiologic transformation in the placental basal plate is associated with interstitial extravillous trophoblast and arterial endothelial activation along with increased frequency of spiral artery atherosis. These findings may be used to improve the characterization of different disorders of the placental bed such as in refining the existing tools for the early prediction of risk for preterm, preeclamptic, and other abnormal pregnancies

Inter-Colony Comparison of Diving Behavior of an Arctic Top Predator: Implications for Warming in the Greenland Sea

The goal of this study was to assess how diverse oceanographic conditions and prey communities affect the foraging behavior of little auks Alle alle. The Greenland Sea is characterized by 3 distinct water masses: (1) the East Greenland Current (EGC), which carries Arctic waters southward; (2) the Sørkapp Current (SC), which originates in the Arctic Ocean but flows north along the west coast of Spitsbergen; and (3) the West Spitsbergen Current (WSC), which carries warm Atlantic-derived water north. Each of these 3 water masses is characterized by a distinct mesozooplankton community. Little auks breeding adjacent to the EGC have access to large, lipid-rich Calanus copepods, whereas those adjacent to the SC have medium sized prey, while those near the WSC are limited to even smaller, less profitable prey. We used time−depth recorders to compare the time allocation and diving behavior of little auks adjacent to each of these 3 water masses. We predicted that birds in the EGC would not have to forage as intensively as those in the SC or WSC. We found that little auks foraging in the EGC spent less time at sea, spent less time flying, dived less often, made fewer long, deep dives, and made fewer V-shaped searching dives. This indicates that the EGC provides a more favorable foraging environment than do the warmer water masses to the east. Comparing the foraging behavior of little auk populations confined to Arctic versus Atlantic-influenced waters can provide insight into the potential impacts of future warming in the Greenland Sea

The bending of cell sheets - from folding to rolling

The bending of cell sheets plays a major role in multicellular embryonic morphogenesis. Recent advances are leading to a deeper understanding of how the biophysical properties and the force-producing behaviors of cells are regulated, and how these forces are integrated across cell sheets during bending. We review work that shows that the dynamic balance of apical versus basolateral cortical tension controls specific aspects of invagination of epithelial sheets, and recent evidence that tissue expansion by growth contributes to neural retinal invagination in a stem cell-derived, self-organizing system. Of special interest is the detailed analysis of the type B inversion in Volvox reported in BMC Biology by Höhn and Hallmann, as this is a system that promises to be particularly instructive in understanding morphogenesis of any monolayered spheroid system

Solar thermoelectricity Via Advanced Latent Heat Storage

An aspect of the present disclosure is a system that includes a thermal valve having a first position and a second position, a heat transfer fluid, and an energy converter where, when in the first position, the thermal valve prevents the transfer of heat from the heat transfer fluid to the energy converter, and when in the second position, the thermal valve allows the transfer of heat from the heat transfer fluid to the energy converter, such that at least a portion of the heat transferred is converted to electricity by the energy converter

Expression of the SmB′ splicing protein in rodent cells capable of following an alternative RNA splicing pathway

AbstractThe expression of the SmB and SmB′ spliceosome proteins in a variety of cell types and tissues has been investigated. Although SmB is found in all cells studied, the SmB′ protein is found only in a small number of rodent cell types. The presence of this protein is correlated with the ability to utilize an alternative pathway of RNA splicing which is not available in most cell types. This is the first demonstration of tissue specific expression of a protein component of the spliceosome and suggests a role for SmB′ in the regulation of some cases of alternative RNA splicing