bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpolation and Model Checking for Nonlinear Arithmetic
Authors: Jovanović Dejan , Dutertre Bruno 
Published: July 2021

AbstractWe present a new model-based interpolation procedure for satisfiability modulo theories (SMT). The procedure uses a new mode of interaction with the SMT solver that we call solving modulo a model. This either extends a given partial model into a full model for a set of assertions or returns an explanation (a model interpolant) when no solution exists. This mode of interaction fits well into the model-constructing satisfiability (MCSAT) framework of SMT. We use it to develop an interpolation procedure for any MCSAT-supported theory. In particular, this method leads to an effective interpolation procedure for nonlinear real arithmetic. We evaluate the new procedure by integrating it into a model checker and comparing it with state-of-art model-checking tools for nonlinear arithmetic.
Progress in Certifying Hardware Model Checking Results
Authors: Yu Emily , Biere Armin , Heljanko Keijo 
Published: July 2021

AbstractWe present a formal framework to certifyk-induction-based model checking results. The key idea is the notion of ak-witness circuit which simulates the given circuit and has a simple inductive invariant serving as proof certificate. Our approach allows to check proofs with an independent proof checker by reducing the certification problem to pure SAT checks and checking a simple QBF with one quantifier alternation. We also presentCertifaiger, the resulting certification toolkit, and evaluate it on instances from the hardware model checking competition. Our experiments show the practical use of our certification method.
Model-Checking Structured Context-Free Languages
Authors: Chiari Michele , Mandrioli Dino , Pradella Matteo 
Published: July 2021

AbstractThe problem of model checking procedural programs has fostered much research towards the definition of temporal logics for reasoning on context-free structures. The most notable of such results are temporal logics on Nested Words, such as CaRet and NWTL. Recently, the logic OPTL was introduced, based on the class of Operator Precedence Languages (OPL), more powerful than Nested Words. We define the new OPL-based logic POTL, and provide a model checking procedure for it. POTL improves on NWTL by enabling the formulation of requirements involving pre/post-conditions, stack inspection, and others in the presence of exception-like constructs. It improves on OPTL by being FO-complete, and by expressing more easily stack inspection and function-local properties. We developed a model checking tool for POTL, which we experimentally evaluate on some interesting use-cases.
Model Checking $$\omega $$-Regular Properties with Decoupled Search
Authors: Gnad Daniel , Eisenhut Jan , Lluch Lafuente Alberto , Hoffmann Jörg 
Published: July 2021

AbstractDecoupled search is a state space search method originally introduced in AI Planning. Similar to partial-order reduction methods, decoupled search exploits the independence of components to tackle the state explosion problem. Similar to symbolic representations, it does not construct the explicit state space, but sets of states are represented in a compact manner, exploiting component independence. Given the success of both partial-order reduction and symbolic representations when model checking liveness properties, our goal is to add decoupled search to the toolset of liveness checking methods. Specifically, we show how decoupled search can be applied to liveness verification for composed Büchi automata by adapting, and showing correct, a standard algorithm for detecting lassos (i.e., infinite accepting runs), namely nested depth-first search. We evaluate our approach using a prototype implementation.
Ghost Signals: Verifying Termination of Busy Waiting
Authors: Reinhard Tobias , Jacobs Bart 
Published: July 2021

AbstractPrograms for multiprocessor machines commonly perform busy waiting for synchronization. We propose the first separation logic for modularly verifying termination of such programs under fair scheduling. Our logic requires the proof author to associate a ghost signal with each busy-waiting loop and allows such loops to iterate while their corresponding signal $$s$$
s
is not set. The proof author further has to define a well-founded order on signals and to prove that if the looping thread holds an obligation to set a signal $$s'$$

s
′

, then $$s'$$

s
′

is ordered above $$s$$
s
. By using conventional shared state invariants to associate the state of ghost signals with the state of data structures, programs busy-waiting for arbitrary conditions over arbitrary data structures can be verified.
AIGEN: Random Generation of Symbolic Transition Systems
Authors: Jacobs Swen , Sakr Mouhammad 
Published: July 2021

AbstractAIGEN is an open source tool for the generation of transition systems in a symbolic representation. To ensure diversity, it employs a uniform random sampling over the space of all Boolean functions with a given number of variables. AIGEN relies on reduced ordered binary decision diagrams (ROBDDs) and canonical disjunctive normal form (CDNF) as canonical representations that allow us to enumerate Boolean functions, in the former case with an encoding that is inspired by data structures used to implement ROBDDs. Several parameters allow the user to restrict generation to Boolean functions or transition systems with certain properties, which are then output in AIGER format. We report on the use of AIGEN to generate random benchmark problems for the reactive synthesis competition SYNTCOMP 2019, and present a comparison of the two encodings with respect to time and memory efficiency in practice.
Reflections on Termination of Linear Loops
Authors: Zhu Shaowei , Kincaid Zachary 
Published: July 2021

AbstractThis paper shows how techniques for linear dynamical systems can be used to reason about the behavior of general loops. We present two main results. First, we show that every loop that can be expressed as a transition formula in linear integer arithmetic has a best model as a deterministic affine transition system. Second, we show that for any linear dynamical system f with integer eigenvalues and any integer arithmetic formula G, there is a linear integer arithmetic formula that holds exactly for the states of f for which G is eventually invariant. Combining the two, we develop a monotone conditional termination analysis for general loops.
Model-Free Reinforcement Learning for Branching Markov Decision Processes
Authors: Hahn Ernst Moritz , Perez Mateo , Schewe Sven , Somenzi Fabio , Trivedi Ashutosh , Wojtczak Dominik 
Published: July 2021

AbstractWe study reinforcement learning for the optimal control of Branching Markov Decision Processes (BMDPs), a natural extension of (multitype) Branching Markov Chains (BMCs). The state of a (discrete-time) BMCs is a collection of entities of various types that, while spawning other entities, generate a payoff. In comparison with BMCs, where the evolution of a each entity of the same type follows the same probabilistic pattern, BMDPs allow an external controller to pick from a range of options. This permits us to study the best/worst behaviour of the system. We generalise model-free reinforcement learning techniques to compute an optimal control strategy of an unknown BMDP in the limit. We present results of an implementation that demonstrate the practicality of the approach.
Cameleer: A Deductive Verification Tool for OCaml
Authors: Pereira Mário , Ravara António 
Published: July 2021

AbstractWe present , an automated deductive verification tool for OCaml. We leverage on the recently proposed GOSPEL (Generic OCaml SPEcification Language) to attach rigorous, yet readable, behavioral specification to OCaml code. The formally-specified program is fed to our toolchain, which translates it into an equivalent one in WhyML, the programming and specification language of the Why3 verification framework. We report on successful case studies conducted in .
LLMC: Verifying High-Performance Software
Authors: van der Berg Freark I. 
Published: July 2021

AbstractMulti-threaded unit tests for high-performance thread-safe data structures typically do not test all behaviour, because only a single scheduling of threads is witnessed per invocation of the unit tests. Model checking such unit tests allows to verify all interleavings of threads. These tests could be written in or compiled to LLVM IR. Existing LLVM IR model checkers like divine and Nidhugg, use an LLVM IR interpreter to determine the next state. This paper introduces llmc, a multi-core explicit-state model checker of multi-threaded LLVM IR that translates LLVM IR to LLVM IR that is executed instead of interpreted. A test suite of 24 tests, stressing data structures, shows that on average llmc clearly outperforms the state-of-the-art tools divine and Nidhugg.
An SMT Encoding of LLVM’s Memory Model for Bounded Translation Validation
Authors: Lee Juneyoung , Kim Dongjoo , Hur Chung-Kil , Lopes Nuno P. 
Published: July 2021

AbstractSeveral automatic verification tools have been recently developed to verify subsets of LLVM’s optimizations. However, none of these tools has robust support to verify memory optimizations.In this paper, we present the first SMT encoding of LLVM’s memory model that 1) is sufficiently precise to validate all of LLVM’s intra-procedural memory optimizations, and 2) enables bounded translation validation of programs with up to hundreds of thousands of lines of code. We implemented our new encoding in Alive2, a bounded translation validation tool, and used it to uncover 21 new bugs in LLVM memory optimizations, 10 of which have been already fixed. We also found several inconsistencies in LLVM IR’s official specification document (LangRef) and fixed LLVM’s code and the document so they are in agreement.
Lower-Bound Synthesis Using Loop Specialization and Max-SMT
Authors: Albert Elvira , Genaim Samir , Martin-Martin Enrique , Merayo Alicia , Rubio Albert 
Published: July 2021

AbstractThis paper presents a new framework to synthesize lower-bounds on the worst-case cost for non-deterministic integer loops. As in previous approaches, the analysis searches for a metering function that under-approximates the number of loop iterations. The key novelty of our framework is the specialization of loops, which is achieved by restricting their enabled transitions to a subset of the inputs combined with the narrowing of their transition scopes. Specialization allows us to find metering functions for complex loops that could not be handled before or be more precise than previous approaches. Technically, it is performed (1) by using quasi-invariants while searching for the metering function, (2) by strengthening the loop guards, and (3) by narrowing the space of non-deterministic choices. We also propose a Max-SMT encoding that takes advantage of the use of soft constraints to force the solver look for more accurate solutions. We show our accuracy gains on benchmarks extracted from the 2020 Termination and Complexity Competition by comparing our results to those obtained by the
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system.
ATLAS: Automated Amortised Complexity Analysis of Self-adjusting Data Structures
Authors: Leutgeb Lorenz , Moser Georg , Zuleger Florian 
Published: July 2021

AbstractBeing able to argue about the performance of self-adjusting data structures such as splay trees has been a main objective, when Sleator and Tarjan introduced the notion ofamortisedcomplexity.Analysing these data structures requires sophisticated potential functions, which typically contain logarithmic expressions. Possibly for these reasons, and despite the recent progress in automated resource analysis, they have so far eluded automation. In this paper, we report on the first fully-automated amortised complexity analysis of self-adjusting data structures. Following earlier work, our analysis is based on potential function templates with unknown coefficients.We make the following contributions: 1) We encode the search for concrete potential function coefficients as an optimisation problem over a suitable constraint system. Our target function steers the search towards coefficients that minimise the inferred amortised complexity. 2) Automation is achieved by using a linear constraint system in conjunction with suitable lemmata schemes that encapsulate the required non-linear facts about the logarithm. We discuss our choices that achieve a scalable analysis. 3) We present our tool$$\mathsf {ATLAS}$$ATLASand report on experimental results forsplay trees,splay heapsandpairing heaps. We completely automatically infer complexity estimates that match previous results (obtained by sophisticated pen-and-paper proofs), and in some cases even infer better complexity estimates than previously published.
Improving clinical utility of GAD65 autoantibodies by electrochemiluminescence assay and clinical phenotype when identifying autoimmune adult-onset diabetes
Authors: Gu Yong , Jia Xiaofan , Vartak Tanwi , Miao Dongmei , Dong Fran , Jerram Samuel T. , Rewers Marian , Ferrara Assiamira , Lawrence Jean M. , Yu Liping , Leslie R. David ,   the Action LADA consortium and the Diabetes in Young Adults (DiYA) Study Group, Leslie Richard David , Hawa Mohammed I , Pozzilli Paolo , Beck-Nielsen Henning , Yderstraede Knud , Hunter Steven , Hadden David , Buzzetti Raffaella , Scherbaum Werner , Kolb Hubert , Schloot Nanette C. , Seissler Jochen , Schernthaner Guntram , Tuomilehto Jaakko , Sarti Cinzia , De Leiva Alberto , Brugues Eulalia , Mauricio Didac , Thivolet Charles , Lawrence Jean M , Ferrara Assiamira , Slezak Jeff M. , Quesenberry Charles , Saydah Sharon , Yu Liping , Rewers Marian 
Published: July 2021

Abstract
Aims/hypothesis
It is important to differentiate the two major phenotypes of adult-onset diabetes, autoimmune type 1 diabetes and non-autoimmune type 2 diabetes, especially as type 1 diabetes presents in adulthood. Serum GAD65 autoantibodies (GADA) are the most sensitive biomarker for adult-onset autoimmune type 1 diabetes, but the clinical value of GADA by current standard radiobinding assays (RBA) remains questionable. The present study focused on the clinical utility of GADA differentiated by a new electrochemiluminescence (ECL) assay in patients with adult-onset diabetes.

Methods
Two cohorts were analysed including 771 diabetic participants, 30–70 years old, from the Action LADA study (n = 6156), and 2063 diabetic participants, 20–45 years old, from the Diabetes in Young Adults (DiYA) study. Clinical characteristics of participants, including requirement of early insulin treatment, BMI and development of multiple islet autoantibodies, were analysed according to the status of RBA-GADA and ECL-GADA, respectively, and compared between these two assays.

Results
GADA was the most prevalent and predominant autoantibody, >90% in both cohorts. GADA positivity by either RBA or ECL assay significantly discriminated clinical type 1 from type 2 diabetes. However, in both cohorts, participants with ECL-GADA positivity were more likely to require early insulin treatment, have multiple islet autoantibodies, and be less overweight (for all p < 0.0001). However, clinical phenotype, age at diagnosis and BMI independently improved positive predictive value (PPV) for the requirement of insulin treatment, even augmenting ECL-GADA. Participants with GADA detectable by RBA, but not confirmed by ECL, had a phenotype more similar to type 2 diabetes. These RBA-GADA positive individuals had lower affinity GADA compared with participants in which GADA was confirmed by ECL assay.

Conclusions/interpretation
Detection of GADA by ECL assay, given technical advantages over RBA-GADA, identified adult-onset diabetes patients at higher risk of requiring early insulin treatment, as did clinical phenotype, together allowing for more accurate clinical diagnosis and management.

Graphical abstract
Experimental analysis and development of an in-house CFD condensation hood model
Authors: Tokarski Mieszko , Ryfa Arkadiusz , Bulinski Piotr , Rojczyk Marek , Ziarko Krzysztof , Ostrowski Ziemowit , Nowak Andrzej J. 
Published: July 2021

AbstractAn existing condensation hood has been numerically investigated using k-ε turbulence and species transport models. Due to the geometrical complexity of the appliance, two additional mathematical models were introduced with the use of User Defined Functions (UDFs). They were a model of a fan and a model of the internally finned pipes of a heat exchanger. The latter also involved a condensation model of steam implemented by mass and energy source terms. Such an approach allowed us to avoid troublesome two-phase flow simulation and thus significantly reduced the computational effort. Based on the results provided by the numerical model, potential improvements of the heat exchanger were proposed and implemented into a second, modified numerical model. Reduction of the number of the pipes by 25% is the most important change of the developed device. Its negative effect on condensation efficiency was to be compensated by improvements of steam flow in the device. Once the modifications had been evaluated, the prototype of the device was built and tested experimentally. Both the numerical and experimental results agree and show that, the modified condensation hood is comparable to the original construction in terms of condensation efficiency, despite the significant heat transfer surface area reduction.
D-Galacturonic acid reduction by S. cerevisiae for L-galactonate production from extracted sugar beet press pulp hydrolysate
Authors: Wagner J. , Schäfer D. , von den Eichen N. , Haimerl C. , Harth S. , Oreb M. , Benz J. P. , Weuster-Botz D. 
Published: July 2021

Abstract
Pectin-rich residues are considered as promising feedstocks for sustainable production of platform chemicals. Enzymatic hydrolysis of extracted sugar beet press pulp (SBPP) releases the main constituent of pectin, d-galacturonic acid (d-GalA). Using engineered Saccharomyces cerevisiae, d-GalA is then reduced to l-galactonate (l-GalOA) with sorbitol as co-substrate. The current work addresses the combination of enzymatic hydrolysis of pectin in SBPP with a consecutive optimized biotransformation of the released d-GalA to l-GalOA in simple batch processes in stirred-tank bioreactors. Process conditions were first identified with synthetic media, where a product concentration of 9.9 g L-1 L-GalOA was obtained with a product selectivity of 99% (L-GalOA D-GalA-1) at pH 5 with 4% (w/v) sorbitol within 48 h. A very similar batch process performance with a product selectivity of 97% was achieved with potassium citrate buffered SBPP hydrolysate, demonstrating for the first time direct production of L-GalOA from hydrolyzed biomass using engineered S. cerevisiae. Combining the hydrolysis process of extracted SBPP and the biotransformation process with engineered S. cerevisiae paves the way towards repurposing pectin-rich residues as substrates for value-added chemicals.

Key points
• Efficient bioreduction of D-GalA with S. cerevisiae in stirred-tank reactors
• Batch production of L-GalOA by engineered S. cerevisiae with high selectivity
• Direct L-GalOA production from hydrolyzed sugar beet press pulp

Graphical abstract
Age estimation comparison between whole and thin-sectioned otoliths and pelvic fin-ray sections of long-lived lake trout, Salvelinus namaycush, from Great Bear Lake, Northwest Territories, Canada
Authors: Gallagher Colin P. , Wastle Rick J. , Marentette Julie R. , Chavarie Louise , Howland Kimberly L. 
Published: July 2021

AbstractStudies to determine precision and bias of both methods and age-readers are important to evaluate reliability of age data used for developing fisheries management objectives. We assessed within-reader, between-reader, and between-method precision (coefficient of variation, CV%) and bias of age estimations for long-lived lake trout, Salvelinus namaycush, from Great Bear Lake using three readers with different levels of experience. The assessment used independent age estimates (n = 3 per reader) from whole and transverse-sectioned otoliths (range = 1–67 years), and pelvic fin-ray sections (range = 3–26 years). We also examined between-method differences in assigned confidence scores. Within readers, age estimates from sectioned otoliths were more precise (2.6–3.0%) than whole (3.6–4.5%) otoliths. Between whole and sectioned otoliths, precision of age estimates was 5.4% and bias was low up to age 20. Age was typically under-estimated from whole otoliths compared to sections for fish ≥ 34 years. Increased reader confidence was correlated with greater precision and younger age estimates, particularly for whole otoliths, but less so for fin rays. Age was estimated with higher confidence from otolith sections than other methods. The least experienced reader estimated age with the lowest precision, and between-reader bias was evident among older ages. Age was consistently under-estimated and less precise from pelvic fins compared to sectioned otoliths, and are therefore an unsuitable non-lethal alternative. Sectioned otoliths revealed longevity was greater (67 years) than historically documented using whole otoliths (53 years) for these fish. Our findings contribute to those relying on otoliths or pelvic fin rays to estimate ages of long-lived lake trout populations, which are a key component of freshwater fauna in polar North America.
In vivo cardiopulmonary impact of skeletal M3Dq DREADD expression: a pilot study
Authors: Vincent Sandra G. , Fisher John T. 
Published: July 2021

AbstractThe muscarinic M3 receptor (M3R) is implicated in cardiopulmonary control and many other peripheral physiologic functions. Previous observations report mortality in mice expressing a Gq-linked designer G-protein coupled receptor (Dq) selectively in striated muscle, while M3Dq DREADD (Designer Receptor Exclusively Activated by Designer Drug), selectively expressed in skeletal muscle (SKM) impacts glucose metabolism. We investigated whether activation of SKM M3Dq impacts cardiopulmonary function. Heart rate (HR), body temperature (Tb) and locomotor activity (ACT) were measured in 4 conscious, chronically instrumented M3Dq DREADD mice and 4 wildtype controls. Circadian values of HR, BT and ACT were not different between genotypes (p > 0.05). Activation of the M3Dq DREADD by clozapine N-oxide (CNO; 0.1 mg/kg) resulted in: a significant drop in heart rate, 2 h after injection, compared with a time-matched baseline control period from the same animals (460 ± 28 vs. 532 ± 6, p < 0.05), significantly lower ACT compared to the baseline control (p < 0.05) and reduced pulmonary minute ventilation compared to pre-CNO control (p < 0.05). M3Dq DREADD activation did not cause bronchoconstriction (separate protocol), however, there was a concomitant reduction in HR, Tb and ventilation, accompanied by cardiac arrhythmias. We speculate that reductions in Tb, HR and ventilation reflect a mechanistic link between SKM Gq signaling and the metabolic responses associated with the initiation of torpor. Supported by the Canadian Institutes of Health Research (CIHR MOP-81211).
Sufficient Spectral Radius Conditions for Hamilton-Connectivity of k-Connected Graphs
Authors: Zhou Qiannan , Broersma Hajo , Wang Ligong , Lu Yong 
Published: July 2021

AbstractWe present two new sufficient conditions in terms of the spectral radius $$\rho (G)$$

ρ
(
G
)

guaranteeing that a k-connected graph G is Hamilton-connected, unless G belongs to a collection of exceptional graphs. We use the Bondy–Chvátal closure to characterize these exceptional graphs.