bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-shot deterministic complex amplitude imaging with a single-layer metalens
Authors: Li Liu , Wang Shuai , Zhao Feng , Zhang Yixin , Wen Shun , Chai Huichao , Gao Yunhui , Wang Wenhui , Cao Liangcai , Yang Yuanmu
Published: January 2024

Conventional imaging systems can only capture light intensity. Meanwhile, the lost phase information may be critical for a variety of applications such as label-free microscopy and optical metrology. Existing phase retrieval techniques typically require a bulky setup, multiframe measurements, or prior information of the target scene. Here, we proposed an extremely compact system for complex amplitude imaging, leveraging the extreme versatility of a single-layer metalens to generate spatially multiplexed and polarization phase–shifted point spread functions. Combining the metalens with a polarization camera, the system can simultaneously record four polarization shearing interference patterns along both in-plane directions, thus allowing the deterministic reconstruction of the complex amplitude light field in a single shot. Using an incoherent light-emitting diode as the illumination, we experimentally demonstrated speckle-noise–free complex amplitude imaging for both static and moving objects with tailored magnification ratio and field of view. The miniaturized and robust system may open the door for complex amplitude imaging in portable devices for point-of-care applications.
In a wild germinal center, what determines survival of the fittest?
Authors: Flowers Emily M. , Eisenbarth Stephanie C.
Published: January 2024

Mice with natural BCR frequencies have plasma cells enriched for high-affinity clones, but high-affinity clones persist in the germinal center, leaving the rules for plasma cell selection still murky.
IL-10mpting T
H
17 cell fate in the gut
Authors: Danielson Sarah Mann , Kuhn Kristine A.
Published: January 2024

Interleukin-10 mediates regulatory functions of commensal-specific TH17 cells in murine small intestine.
Microneme-located VP2 in
Eimeria acervulina
elicits effective protective immunity against infectious bursal disease virus
Authors: Yu Ying , Tang Xinming , Duan Chunhui , Suo Jingxia , Crouch Colin , Zhang Sixin , Liu Xianyong , Liu Jie , Bruton Beth , Tarpey Ian , Suo Xun
Published: January 2024

Using transgenic
Eimeria
spp. to deliver exogenous antigens is a viable option for developing multivalent live vaccines. Previous research revealed that the location of antigen expression in recombinant
Eimeria
dictates the magnitude and type of immune responses. In this study, we constructed genetically modified
Eimeria acervulina
that expressed VP2 protein, a protective antigen from infectious bursal disease virus (IBDV), on the surface or in the microneme of sporozoites. After vaccination, VP2-specific antibody was readily detected in specific pathogen-free chickens receiving transgenic
E. acervulina
parasites expressing VP2 in microneme, but animals vaccinated with which expressing VP2 on surface failed to produce detectable antibody after two times immunizations. Moreover, the bursal lesion of microneme-located VP2 transgenic
E. acervulina
immunized chickens was less severe compared with un-immunized animals after IBDV challenge infection. Therefore, genetically modified
E. acervulina
that express IBDV-derived VP2 in micronemes are effective in inducing specific antibody responses against VP2, while parasites that have VP2 expression on cell surface are not suitable. Thus, the use of
Eimeria
parasites as vaccine vectors needs to consider the proper targeting of exogenous immunogens. Our results have implications for the design of other vector vaccines.
Genome-scale metabolic model of the versatile bacterium
Paracoccus denitrificans
Pd1222
Authors: Bordel Sergio , Martín-González Diego , Börner Tim , Muñoz Raúl , Santos-Beneit Fernando
Published: January 2024

Paracoccus denitrificans
has been broadly used as a model denitrifying organism. It grows on a large portfolio of carbon sources, under aerobic and anoxic conditions. These characteristics, together with its amenability to genetic manipulations, make
P. denitrificans
a promising cell factory for industrial biotechnology. This paper presents and validates the first functional genome-scale metabolic model for
P. denitrificans
, which is a key tool to enable
P. denitrificans
as a platform for metabolic engineering and industrial biotechnology. Optimization of the biomass yield led to accurate predictions in a broad scope of substrates.
Bleomycin reduces
Vairimorpha (Nosema) ceranae
infection in honey bees with some evident host toxicity
Authors: Parrella Parker , Elikan Annabelle B. , Kogan Helen V. , Wague Fatoumata , Marshalleck Corey A. , Snow Jonathan W.
Published: January 2024

Microsporidia cause disease in many beneficial insects, including honey bees, yet few pathogen control tools are available for protecting these important organisms against infection. Some evidence suggests that microsporidia possess a reduced number of genes encoding DNA repair proteins. We hypothesized that microsporidia would thus be susceptible to treatment with DNA-damaging agents and tested this hypothesis using a novel, rapid method for achieving robust and homogenous experimental infection of large numbers of newly emerged honey bees with one of its microsporidia pathogens,
Vairimorpha
(
Nosema
)
ceranae
. In carrying out these experiments, we found this novel
V. ceranae
inoculation method to have similar efficacy as other traditional methods. We show that the DNA-damaging agent bleomycin reduces
V. ceranae
levels, with minimal but measurable effects on honey bee survival and increased expression of midgut cellular stress genes, including those encoding SHSP. Increased expression of
UpdlC
suggests the occurrence of epithelial regeneration, which may contribute to host resistance to bleomycin treatment. While bleomycin does reduce infection levels, host toxicity issues may preclude its use in the field. However, with further work, bleomycin may provide a useful tool in the research setting as a potential selection agent for genetic modification of microsporidia.

IMPORTANCE

Microsporidia cause disease in many beneficial insects, yet there are few tools available for control in the field or laboratory. Based on the reported paucity of DNA repair enzymes found in microsporidia genomes, we hypothesized that these obligate intracellular parasites would be sensitive to DNA damage. In support of this, we observed that the well-characterized DNA damage agent bleomycin can reduce levels of the microsporidia
Vairimorpha
(
Nosema
)
ceranae
in experimental infections in honey bees. Observation of slightly reduced honey bee survival and evidence of sublethal toxicity likely preclude the use of bleomycin in the field. However, this work identifies bleomycin as a compound that merits further exploration for use in research laboratories as a potential selection agent for generating genetically modified microsporidia.
Independent and combined effects of calorie restriction and AICAR on glucose uptake and insulin signaling in skeletal muscles from 24-month-old female and male rats
Authors: Wang Haiyan , Zheng Amy , Thorley Dominic , Arias Edward B. , Cartee Gregory D.
Published: January 2024

We assessed the effects of two levels of calorie restriction (CR; eating either 15% or 35% less than ad libitum, AL, food intake for 8 weeks) by 24-month-old female and male rats on glucose uptake (GU) and phosphorylation of key signaling proteins (Akt; AMP-activated protein kinase, AMPK; Akt substrate of 160 kDa, AS160) measured in isolated skeletal muscles that underwent four incubation conditions (without either insulin or AICAR, an AMPK activator; with AICAR alone; with insulin alone; or with insulin and AICAR). Regardless of sex: (1) neither CR group versus the AL group had greater GU by insulin-stimulated muscles; (2) phosphorylation of Akt in insulin-stimulated muscles was increased in 35% CR versus AL rats; (3) prior AICAR treatment of muscle resulted in greater GU by insulin-stimulated muscles, regardless of diet; and (4) AICAR caused elevated phosphorylation of acetyl CoA carboxylase, an indicator of AMPK activation, in all diet groups. There was a sexually dimorphic diet effect on AS160 phosphorylation, with 35% CR exceeding AL for insulin-stimulated muscles in male rats, but not in female rats. Our working hypothesis is that the lack of a CR-effect on GU by insulin-stimulated muscles was related to the extended duration of the ex vivo incubation period (290 min compared to 40–50 min that was previously reported to be effective). The observed efficacy of prior treatment of muscles with AICAR to improve glucose uptake in insulin-stimulated muscles supports the strategy of targeting AMPK with the goal of improving insulin sensitivity in older females and males.
Freshwater fish otoliths record signals from both water and physiological processes: new insights from Sr/Ca and Ba/Ca ratios
Authors: Bareille G. , Vignon M. , Chappaz A. , Fontaine A. , Tabouret H. , Morat F. , Martin J. , Aymes J.C. , Daverat F. , Pécheyran C. , Donard O.
Published: January 2024

Using strontium (Sr) and barium (Ba) in otoliths to determine natal origins and understand patterns of fish movements is based on the fundamental assumption that otoliths record water chemistry signals without any major alterations. Although prior studies highlighted that fish physiology can modify the water signal in otoliths, studies for freshwater fish are scarce. We exposed different groups of Atlantic salmon parr Salmo salar to different scenarios of ambient-level variations in Sr/Ca and Ba/Ca ratios and then combined otolith chemical profiles with environmental data (water chemistry and temperature), Fulton's index, and otolith growth rates to assess what factors explain/influence the elemental ratios of Sr and Ba in otoliths. Generalized additive mixed models (GAMMs) using water-based otolith composition, temperature, Fulton's index, and “individual” as explanatory variables allow to demonstrate that water chemistry alone cannot fully explain measured ratios in otoliths, except in scenarios involving significant changes in water chemistry. Other factors (physiological effects) should be accounted for reproducing short and minimal seasonal variations in water composition, considering that inter-individual variability contributes quite significantly in most scenarios.
Quantum system ascribed to the Oppenheimer–Snyder model of massive stars
Authors: Góźdź Andrzej , Ostrowski Jan J. , Pȩdrak Aleksandra , Piechocki Włodzimierz
Published: January 2024

We quantize the Oppenheimer–Snyder model of black holes using the integral quantization method. We treat spatial and temporal coordinates on the same footing at both the classical and quantum levels. Our quantization resolves or smears the singularities of the classical curvature invariants. Quantum trajectories with bounces can replace singular classical trajectories. The considered quantum black hole may have finite bouncing time. As a by-product, we obtain the resolution of the gravitational singularity of the Schwarzschild black hole at the quantum level.
INFORMATION AND COMMUNICATION TECHNOLOGIES, INCLUSIVE FINANCE AND ENTREPRENEURSHIP IN AFRICA: A GENDER-SPECIFIC PERSPECTIVE
Authors: UCHE EMMANUEL , ODIONYE JOSEPH C. , NGEPAH NICHOLAS
Published: January 2024

The potential for information and communication technologies (ICT) and inclusive finance to drive entrepreneurial activity in an African context remain unclear. We specifically consider effects on male versus female entrepreneurs. This study unveils new insights based on an annual panel series for 52 African countries from 2005–2019. The system-generalized method-of-moments (sysGMM) and the novel method-of-moments quantile regression (MM-QR) aided the analysis. The estimates of both procedures demonstrate that entrepreneurship in Africa is self-promoting. The sysGMM estimator demonstrates that financial inclusion produced unsubstantial effects on entrepreneurial activity. However, the estimates of the MM-QR produced varying significant positive relationships mostly at the upper quantiles for all entrepreneurs. The sysGMM reveals that ICT produced marginal positive effects for entrepreneurs in general but not for female entrepreneurs. Additionally, the MM-QR unveiled a significant positive influence of ICT at the lower and middle quantiles for aggregate levels of entrepreneurship. ICT produced significant positive effects at the lower quantiles for men, and at the upper quantiles for women. Policy options to promote entrepreneurship in the continent are highlighted.
ALLIANCE PORTFOLIO DIVERSITY AS A LEVER OF PRODUCT INNOVATION IN DEVELOPING COUNTRIES
Authors: PAULA FÁBIO DE OLIVEIRA , MACEDO-SOARES T. DIANA
Published: January 2024

Most authors agree that alliance portfolio diversity (APD) has an inverted U-shaped influence on innovation performance and is particularly important for firms with a high absorptive capacity (AC), which moderates this relationship positively. However, the reality of developing countries with weaker national innovation systems (NIS) and firms with lower AC may influence these relationships. To test these hypotheses in such a context, we tested a longitudinal structural model in a sample of 1,237 Colombian manufacturing firms. The results indicated that, in a developing country context, APD at the appropriate level is especially relevant for firms with low AC, even the letter maintaining the positive moderation effect on the inverted U-shaped relationship of the former with innovation. Besides, the longitudinal structural equation modelling (SEM) chosen to conduct the analysis mitigates endogeneity issues presented in more commonly used cross-section analyses.
On the Time-Dilation Paradox—Can it be Removed?
Authors: Valldor Martin
Published: January 2024

In special relativity theory, the velocity of light is assumed to be constant, independent of the reference frame. This creates paradoxes when observations in different reference frames are compared. The so-called twin-paradox is based on a Gedanken experiment with identical twins, one traveling in a spaceship and one remaining on Earth. Due to the time-dilation effect, the traveling twin, when returning to Earth is younger than the other twin. This paradox has been tentatively resolved by inserting asymmetry, but the fully symmetrical twin-paradox remains within the relativity theory. However, if the light velocity, instead of being absolute, is taken to be relative, the paradox can be resolved. By reevaluating the light-clock experiment and performing various other Gedanken experiments, it becomes apparent that constant movement, independent of velocity, is the same as “at rest” for any one reference frame and does not need to involve any relativistic effects. This would make the Lorentz–Voigt factor void, and red- and blue-shifts of electromagnetic (EM) radiation can be explained as true changes in light-velocities. Based on thinking experiments, new rules for light-velocities are proposed, which also could explain anomalous observations regarding Jupiter’s moon Io’s movement. Gravity and its effect on light are examined, and it is argued that planetary lensing of light can be simply explained as refraction in a planet’s atmosphere or by diffraction on the planet itself. Further, the light pressure can resolve the indistinguishability principle. Alternatives to relativity explanations are suggested for several observations that nullify Fresnel dragging and oppose the existence of an aether medium. A modified Mach–Zehnder interferometer is proposed as an instrument for measuring sub-c and super-c velocities of EM-waves. The “old” relativity theories are replaced by a novel postulate that an applied force, leading to changes in velocity, is the reason for time-dilation: what may be called mechanical relativity. A mathematical suggestion of mechanical relativity is presented, along with discussions on connections between time, energy, and gravity.
Dolomite formation during penecontemporaneous subaerial diagenesis: evidence from modern dolomite crusts forming in lagoon Brejo do Espinho, Brazil
Authors: Ning Meng , Wang Yao , McKenzie Judith A. , Vasconcelos Crisogono , Li Chenqing , Shen Anjiang , Liang Feng , Shen Bing
Published: January 2024

The early lithification of carbonate mud during the subaerial exposure stage under semiarid conditions has been proposed to facilitate dolomite formation. However, how the biogeochemical processes during subaerial diagenesis promote dolomite formation remains unclear. Here, we employ a multiproxy approach to investigate the process of dolomite formation by analysing modern dolomite crusts forming in lagoon Brejo do Espinho. Petrological analysis reveals that the crusts consist of coexisting high-Mg calcite and dolomite. Low Fe and Mn concentrations indicate the formation of dolomite under oxic conditions, whereas a higher Sr concentration in well-lithified crust suggests primary bacterial-induced dolomite precipitation. The Mg isotopic composition of the crusts exhibits a lighter value than that of modern sabkha dolomite, suggesting different dolomitization processes and Mg sources. The more negative

δ

13
C values of the crusts than those of the unlithified carbonate mud in lagoon Brejo do Espinho indicate the incorporation of
13
C-depleted organic carbon. The biogeochemical processes related to decaying organic matter during subaerial diagenesis generate partially oxidized organic matter that promotes Mg
2+
dehydration and enhances the dissolution of primary high-Mg calcite, ultimately triggering the transition of high-Mg calcite to dolomite and/or the direct precipitation of dolomite. The ancient ‘dolomite factory’ operated through the cyclic deposition of carbonate sediments and penecontemporaneous subaerial diagenesis.

Thematic collection:
This article is part of the Towards unravelling the ‘Dolomite Problem’: new approaches and novel perspectives collection available at:
https://www.lyellcollection.org/topic/collections/towards-unravelling-the-dolomite-problem
Early Jurassic and Late Cretaceous plagiogranites in Nain–Baft ophiolitic mélange zone in Iran: remnants of rift–drift and SSZ evolution of a Neotethyan seaway
Authors: Shirdashtzadeh Nargess , Dilek Yildirim , Furnes Harald , Dantas Elton Luiz
Published: January 2024

We have investigated the geology, geochemistry and geochronology of various plagiogranite intrusions that are spatially associated with ophiolitic subunits in a mélange terrain exposed within the Nain–Baft fault zone along the western boundary of the Central–East Iranian Microcontinent (CEIM). One group of plagiogranites is intrusive into foliated amphibolites, whereas the plagiogranites of the other group are intrusive into gabbros, dyke swarms and pillow lavas that are tectonically juxtaposed. U–Pb zircon dating of the first group of plagiogranites has revealed near-concordant crystallization ages of 176.94 ± 0.71, 179.84 ± 0.92 and 190.40 ± 2.1 Ma, indicating the early Jurassic timing of their emplacement. U–Pb zircon dating of the second group of plagiogranites has revealed a weighted average age of 92.34 ± 0.38 Ma, indicating that they were emplaced in the early Late Cretaceous. The Early Jurassic plagiogranites are low-K, sub-alkaline rocks with negative Eu anomalies, low Ti and high La and Ce contents. They display elevated ratios of large ion lithophile elements to high field strength elements. They were part of a magmatic system that facilitated the earliest rift–drift stages of a Neotethyan seaway development, and their magmas were produced by fractional crystallization of a mafic melt associated with asthenospheric upwelling beneath a rift system. The Late Cretaceous plagiogranites are low-K, sub-alkaline rocks with negative Eu anomalies, high Y and low Ta contents. They show light REE depletion relative to flat heavy REE patterns, and high Ba/Th ratios. Magmas of these plagiogranites were the products of partial melting of amphibolites in the subducting oceanic lithosphere in the same Neotethyan seaway. Thus, we posit that plagiogranite rocks in suture zones can be excellent trackers of geochemical, geochronological and magmatic evolution of various types of oceanic crust through rift–drift, seafloor spreading and subduction initiation stages within the same ocean basins in the past.

Thematic collection:
This article is part of the Ophiolites, melanges and blueschists collection available at:
https://www.lyellcollection.org/topic/collections/ophiolites-melanges-and-blueschists
Mississippian olistostromes of Iberia revisited: tectonic drivers of synorogenic carbonate platform/reef destruction
Authors: Dias da Silva Ícaro , Pereira Manuel Francisco , Clavijo Emílio González , Silva José Brandão
Published: January 2024

This paper reviews the synorogenic basins formed on the Gondwana side of the Variscan Orogen of Iberia, highlighting the widespread occurrence of calciturbiditic formations and olistostromes containing reef limestone olistoliths in Iberia's Variscan basins. Using key examples from the Variscan Orogen for comparison (the Azrou–Khenifra and Rhenohercynian basins), the significance of these olistostromes and flyschoid deposits is discussed. Our tectonic models of the Variscan belt in Iberia propose possible drivers of synorogenic carbonate platform/reef destruction responsible for the origin of calciturbidites and olistostromes. One model proposes the formation of an orogenic plateau via the lateral flow of partially molten orogenic roots in the context of Laurussia–Gondwana convergence following the destruction of the Rheic Ocean and slab retreat of the Gondwana (lower) plate. An alternative model invokes subduction of Palaeotethys oceanic lithosphere beneath the Gondwana (upper) plate. Both emphasize the Mississippian occurrence of a significant thermal anomaly beneath Gondwana that favoured strong lithosphere thinning, creating ideal conditions for synorogenic carbonate platform/reef destruction and the formation of calciturbidite deposits and olistostromes in Iberia. The Variscan palaeotopography would look similar in both situations. Distinguishing between these models is therefore not straightforward, with differences in the kinematics of regional tectonic transport in the superstructure of Mississippian gneiss domes.

Thematic collection:
This article is part of the Ophiolites, melanges and blueschists collection available at:
https://www.lyellcollection.org/topic/collections/ophiolites-melanges-and-blueschists
Ramsey Quantifiers in Linear Arithmetics
Authors: Bergsträßer Pascal , Ganardi Moses , Lin Anthony W. , Zetzsche Georg
Published: January 2024

We study Satisfiability Modulo Theories (SMT) enriched with the so-called Ramsey quantifiers, which assert the existence of cliques (complete graphs) in the graph induced by some formulas. The extended framework is known to have applications in proving program termination (in particular, whether a transitive binary predicate is well-founded), and monadic decomposability of SMT formulas. Our main result is a new algorithm for eliminating Ramsey quantifiers from three common SMT theories: Linear Integer Arithmetic (LIA), Linear Real Arithmetic (LRA), and Linear Integer Real Arithmetic (LIRA). In particular, if we work only with existentially quantified formulas, then our algorithm runs in polynomial time and produces a formula of linear size. One immediate consequence is that checking well-foundedness of a given formula in the aforementioned theory defining a transitive predicate can be straightforwardly handled by highly optimized SMT-solvers. We show also how this provides a uniform semi-algorithm for verifying termination and liveness with completeness guarantee (in fact, with an optimal computational complexity) for several well-known classes of infinite-state systems, which include succinct timed systems, one-counter systems, and monotonic counter systems. Another immediate consequence is a solution to an open problem on checking monadic decomposability of a given relation in quantifier-free fragments of LRA and LIRA, which is an important problem in automated reasoning and constraint databases. Our result immediately implies decidability of this problem with an optimal complexity (coNP-complete) and enables exploitation of SMT-solvers. It also provides a termination guarantee for the generic monadic decomposition algorithm of Veanes et al. for LIA, LRA, and LIRA. We report encouraging experimental results on a prototype implementation of our algorithms on micro-benchmarks.
Modular Denotational Semantics for Effects with Guarded Interaction Trees
Authors: Frumin Dan , Timany Amin , Birkedal Lars
Published: January 2024

We present
guarded interaction trees
— a structure and a fully formalized framework for representing higher-order computations with higher-order effects in Coq, inspired by domain theory and the recently proposed interaction trees. We also present an accompanying separation logic for reasoning about guarded interaction trees. To demonstrate that guarded interaction trees provide a convenient domain for interpreting higher-order languages with effects, we define an interpretation of a PCF-like language with effects and show that this interpretation is sound and computationally adequate; we prove the latter using a logical relation defined using the separation logic. Guarded interaction trees also allow us to combine different effects and reason about them modularly. To illustrate this point, we give a modular proof of type soundness of cross-language interactions for safe interoperability of different higher-order languages with different effects. All results in the paper are formalized in Coq using the Iris logic over guarded type theory.
Optimal Program Synthesis via Abstract Interpretation
Authors: Mell Stephen , Zdancewic Steve , Bastani Osbert
Published: January 2024

We consider the problem of synthesizing programs with numerical constants that optimize a quantitative objective, such as accuracy, over a set of input-output examples. We propose a general framework for optimal synthesis of such programs in a given domain specific language (DSL), with provable optimality guarantees. Our framework enumerates programs in a general search graph, where nodes represent subsets of concrete programs. To improve scalability, it uses
A
*
search in conjunction with a search heuristic based on abstract interpretation; intuitively, this heuristic establishes upper bounds on the value of subtrees in the search graph, enabling the synthesizer to identify and prune subtrees that are provably suboptimal. In addition, we propose a natural strategy for constructing abstract transformers for monotonic semantics, which is a common property for components in DSLs for data classification. Finally, we implement our approach in the context of two such existing DSLs, demonstrating that our algorithm is more scalable than existing optimal synthesizers.
Regular Abstractions for Array Systems
Authors: Hong Chih-Duo , Lin Anthony W.
Published: January 2024

Verifying safety and liveness over array systems is a highly challenging problem. Array systems naturally capture parameterized systems such as distributed protocols with an unbounded number of processes. Such distributed protocols often exploit process IDs during their computation, resulting in array systems whose element values range over an infinite domain. In this paper, we develop a novel framework for proving safety and liveness over array systems. The crux of the framework is to overapproximate an array system as a string rewriting system (i.e. over a finite alphabet) by means of a new predicate abstraction that exploits the so-called indexed predicates. This allows us to tap into powerful verification methods for string rewriting systems that have been heavily developed in the last two decades or so (e.g. regular model checking). We demonstrate how our method yields simple, automatically verifiable proofs of safety and liveness properties for challenging examples, including Dijkstra's self-stabilizing protocol and the Chang-Roberts leader election protocol.
The Essence of Generalized Algebraic Data Types
Authors: Sieczkowski Filip , Stepanenko Sergei , Sterling Jonathan , Birkedal Lars
Published: January 2024

This paper considers direct encodings of generalized algebraic data types (GADTs) in a minimal suitable lambda-calculus. To this end, we develop an extension of System
F
ω
with recursive types and internalized type equalities with injective constant type constructors. We show how GADTs and associated pattern-matching constructs can be directly expressed in the calculus, thus showing that it may be treated as a highly idealized modern functional programming language. We prove that the internalized type equalities in conjunction with injectivity rules increase the expressive power of the calculus by establishing a non-macro-expressibility result in
F
ω
, and prove the system type-sound via a syntactic argument. Finally, we build two relational models of our calculus: a simple, unary model that illustrates a novel, two-stage interpretation technique, necessary to account for the equational constraints; and a more sophisticated, binary model that relaxes the construction to allow, for the first time, formal reasoning about data-abstraction in a calculus equipped with GADTs.
Quotient Haskell: Lightweight Quotient Types for All
Authors: Hewer Brandon , Hutton Graham
Published: January 2024

Subtypes and quotient types are dual type abstractions. However, while subtypes are widely used both explicitly and implicitly, quotient types have not seen much practical use outside of proof assistants. A key difficulty to wider adoption of quotient types lies in the significant burden of proof-obligations that arises from their use. In this article, we address this issue by introducing a class of quotient types for which the proof-obligations are decidable by an SMT solver. We demonstrate this idea in practice by presenting
Quotient Haskell
, an extension of Liquid Haskell with support for quotient types.
EasyBC: A Cryptography-Specific Language for Security Analysis of Block Ciphers against Differential Cryptanalysis
Authors: Sun Pu , Song Fu , Chen Yuqi , Chen Taolue
Published: January 2024

Differential cryptanalysis is a powerful algorithmic-level attack, playing a central role in evaluating the security of symmetric cryptographic primitives. In general, the resistance against differential cryptanalysis can be characterized by the maximum expected differential characteristic probability. In this paper, we present generic and extensible approaches based on mixed integer linear programming (MILP) to bound such probability. We design a high-level cryptography-specific language EasyBC tailored for block ciphers and provide various rigorous procedures, as differential denotational semantics, to automate the generation of MILP from block ciphers written in EasyBC. We implement an open-sourced tool that provides support for fully automated resistance evaluation of block ciphers against differential cryptanalysis. The tool is extensively evaluated on 23 real-life cryptographic primitives including all the 10 finalists of the NIST lightweight cryptography standardization process. The experiments confirm the expressivity of EasyBC and show that the tool can effectively prove the resistance against differential cryptanalysis for all block ciphers under consideration. EasyBC makes resistance evaluation against differential cryptanalysis easily accessible to cryptographers.
Implementation and Synthesis of Math Library Functions
Authors: Briggs Ian , Lad Yash , Panchekha Pavel
Published: January 2024

Achieving speed and accuracy for math library functions like exp, sin, and log is difficult. This is because low-level implementation languages like C do not help math library developers catch mathematical errors, build implementations incrementally, or separate high-level and low-level decision making. This ultimately puts development of such functions out of reach for all but the most experienced experts. To address this, we introduce MegaLibm, a domain-specific language for implementing, testing, and tuning math library implementations. MegaLibm is safe, modular, and tunable. Implementations in MegaLibm can automatically detect mathematical mistakes like sign flips via semantic wellformedness checks, and components like range reductions can be implemented in a modular, composable way, simplifying implementations. Once the high-level algorithm is done, tuning parameters like working precisions and evaluation schemes can be adjusted through orthogonal tuning parameters to achieve the desired speed and accuracy. MegaLibm also enables math library developers to work interactively, compiling, testing, and tuning their implementations and invoking tools like Sollya and type-directed synthesis to complete components and synthesize entire implementations. MegaLibm can express 8 state-of-the-art math library implementations with comparable speed and accuracy to the original C code, and can synthesize 5 variations and 3 from-scratch implementations with minimal guidance.
Efficient CHAD
Authors: Smeding Tom J. , Vákár Matthijs I. L.
Published: January 2024

We show how the basic Combinatory Homomorphic Automatic Differentiation (CHAD) algorithm can be optimised, using well-known methods, to yield a simple, composable, and generally applicable reverse-mode automatic differentiation (AD) technique that has the correct computational complexity that we would expect of reverse-mode AD. Specifically, we show that the standard optimisations of sparse vectors and state-passing style code (as well as defunctionalisation/closure conversion, for higher-order languages) give us a purely functional algorithm that is most of the way to the correct complexity, with (functional) mutable updates taking care of the final log-factors. We provide an Agda formalisation of our complexity proof. Finally, we discuss how the techniques apply to differentiating parallel functional array programs: the key observations are 1) that all required mutability is (commutative, associative) accumulation, which lets us preserve task-parallelism and 2) that we can write down data-parallel derivatives for most data-parallel array primitives.
Orthologic with Axioms
Authors: Guilloud Simon , Kunčak Viktor
Published: January 2024

We study the proof theory and algorithms for orthologic, a logical system based on ortholattices, which have shown practical relevance in simplification and normalization of verification conditions. Ortholattices weaken Boolean algebras while having polynomial-time equivalence checking that is sound with respect to Boolean algebra semantics. We generalize ortholattice reasoning and obtain an algorithm for proving a larger class of classically valid formulas.

As the key result, we analyze a proof system for orthologic augmented with axioms. An important feature of the system is that it limits the number of formulas in a sequent to at most two, which makes the extension with axioms non-trivial. We show a generalized form of cut elimination for this system, which implies a sub-formula property. From there we derive a cubic-time algorithm for provability from axioms, or equivalently, for validity in finitely presented ortholattices. We further show that propositional resolution of width 5 proves all formulas provable in orthologic with axioms. We show that orthologic system subsumes resolution of width 2 and arbitrarily wide unit resolution and is complete for reasoning about generalizations of propositional Horn clauses.

Moving beyond ground axioms, we introduce effectively propositional orthologic (by analogy with EPR for classical logic), presenting its semantics as well as a sound and complete proof system. Our proof system implies the decidability of effectively propositional orthologic, as well as its fixed-parameter tractability for a bounded maximal number of variables in each axiom. As a special case, we obtain a generalization of Datalog with negation and disjunction.
Polymorphic Type Inference for Dynamic Languages
Authors: Castagna Giuseppe , Laurent Mickaël , Nguyễn Kim
Published: January 2024

We present a type system that combines, in a controlled way,
first-order polymorphism with intersection types, union types, and
subtyping, and prove its safety. We then define a type reconstruction
algorithm that is sound and terminating. This yields a system in which
unannotated functions are given polymorphic types (thanks to
Hindley-Milner) that can express the overloaded behavior of the
functions they type (thanks to the intersection introduction rule) and
that are deduced by applying advanced techniques of type narrowing
(thanks to the union elimination rule). This makes the system a prime
candidate to type dynamic languages.
Fusing Direct Manipulations into Functional Programs
Authors: Zhang Xing , Xie Ruifeng , Guo Guanchen , He Xiao , Zan Tao , Hu Zhenjiang
Published: January 2024

Bidirectional live programming systems (BLP) enable developers to modify a program by directly manipulating the program output, so that the updated program can produce the manipulated output. One state-of-the-art approach to BLP systems is operation-based, which captures the developer's intention of program modifications by taking how the developer manipulates the output into account. The program modifications are usually hard coded for each direct manipulation in these BLP systems, which are difficult to extend. Moreover, to reflect the manipulations to the source program, these BLP systems trace the modified output to appropriate code fragments and perform corresponding code transformations. Accordingly, they require direct manipulation users be aware of the source code and how it is changed, making "direct" manipulation (on output) be "indirect".

In this paper, we resolve this problem by presenting a novel operation-based framework for bidirectional live programming, which can automatically fuse direct manipulations into the source code, thus supporting code-insensitive direct manipulations. Firstly, we design a simple but expressive delta language DM capable of expressing common direct manipulations for output values. Secondly, we present a fusion algorithm that propagates direct manipulations into the source functional programs and applies them to the constants whenever possible; otherwise, the algorithm embeds manipulations into the "proper positions" of programs. We prove the correctness of the fusion algorithm that the updated program executes to get the manipulated output. To demonstrate the expressiveness of DM and the effectiveness of our fusion algorithm, we have implemented FuseDM, a prototype SVG editor that supports GUI-based operations for direct manipulation, and successfully designed 14 benchmark examples starting from blank code using FuseDM.
Internalizing Indistinguishability with Dependent Types
Authors: Liu Yiyun , Chan Jonathan , Shi Jessica , Weirich Stephanie
Published: January 2024

In type systems with dependency tracking, programmers can assign an ordered set of levels to computations and prevent information flow from high-level computations to the low-level ones. The key notion in such systems is
indistinguishability
: a definition of program equivalence that takes into account the parts of the program that an observer may depend on. In this paper, we investigate the use of dependency tracking in the context of dependently-typed languages. We present the Dependent Calculus of Indistinguishability (DCOI), a system that adopts indistinguishability as the definition of equality used by the type checker. DCOI also internalizes that relation as an observer-indexed propositional equality type, so that programmers may reason about indistinguishability within the language. Our design generalizes and extends prior systems that combine dependency tracking with dependent types and is the first to support conversion and propositional equality at arbitrary observer levels. We have proven type soundness and noninterference theorems for DCOI and have developed a prototype implementation of its type checker.
Polyregular Functions on Unordered Trees of Bounded Height
Authors: Bojańczyk Mikołaj , Klin Bartek
Published: January 2024

We consider injective first-order interpretations that input and output trees of bounded height. The corresponding functions have polynomial output size, since a first-order interpretation can use a
k
-tuple of input nodes to represent a single output node. We prove that the equivalence problem for such functions is decidable, i.e. ‍given two such interpretations, one can decide whether, for every input tree, the two output trees are isomorphic.

We also give a calculus of typed functions and combinators which derives exactly injective first-order interpretations for unordered trees of bounded height. The calculus is based on a type system, where the type constructors are products, coproducts and a monad of multisets. Thanks to our results about tree-to-tree interpretations, the equivalence problem is decidable for this calculus.

As an application, we show that the equivalence problem is decidable for first-order interpretations between classes of graphs that have bounded tree-depth. In all cases studied in this paper, first-order logic and MSO have the same expressive power, and hence all results apply also to MSO interpretations.
When Subtyping Constraints Liberate: A Novel Type Inference Approach for First-Class Polymorphism
Authors: Parreaux Lionel , Boruch-Gruszecki Aleksander , Fan Andong , Chau Chun Yin
Published: January 2024

Type inference in the presence of first-class or “impredicative” second-order polymorphism à la System F has been an active research area for several decades, with original works dating back to the end of the 80s. Yet, until now many basic problems remain open, such as how to type check expressions like (𝜆𝑥. (𝑥 123, 𝑥 True)) id reliably. We show that a type inference approach based on multi-bounded polymorphism, a form of implicit polymorphic subtyping with multiple lower and upper bounds, can help us resolve most of these problems in a uniquely simple and regular way. We define F
{≤}
, a declarative type system derived from the existing theory of implicit coercions by Cretin and Rémy (LICS 2014), and we introduce SuperF, a novel algorithm to infer polymorphic multi-bounded F
{≤}
types while checking user type annotations written in the syntax of System F. We use a recursion-avoiding heuristic to guarantee termination of type inference at the cost of rejecting some valid programs, which thankfully rarely triggers in practice. We show that SuperF is vastly more powerful than all first-class-polymorphic type inference systems proposed so far, significantly advancing the state of the art in type inference for general-purpose programming languages.
Validation of Modern JSON Schema: Formalization and Complexity
Authors: Attouche Lyes , Baazizi Mohamed-Amine , Colazzo Dario , Ghelli Giorgio , Sartiani Carlo , Scherzinger Stefanie
Published: January 2024

JSON Schema is the de-facto standard schema language for JSON data. The language went through many minor revisions, but the most recent versions of the language, starting from Draft 2019-09, added two novel features, dynamic references and annotation-dependent validation, that change the evaluation model. Modern JSON Schema is the name used to indicate all versions from Draft 2019-09, which are characterized by these new features, while Classical JSON Schema is used to indicate the previous versions.

These new “modern” features make the schema language quite difficult to understand and have generated many discussions about the correct interpretation of their official specifications; for this reason, we undertook the task of their formalization. During this process, we also analyzed the complexity of data validation in Modern JSON Schema, with the idea of confirming the polynomial complexity of Classical JSON Schema validation, and we were surprised to discover a completely different truth: data validation, which is expected to be an extremely efficient process, acquires, with Modern JSON Schema features, a PSPACE complexity.

In this paper, we give the first formal description of Modern JSON Schema, which we have discussed with the community of JSON Schema tool developers, and which we consider a central contribution of this work. We then prove that its data validation problem is PSPACE-complete. We prove that the origin of the problem lies in the Draft 2020-12 version of dynamic references, and not in annotation-dependent validation. We study the schema and data complexities, showing that the problem is PSPACE-complete with respect to the schema size even with a fixed instance but is in P when the schema is fixed and only the instance size is allowed to vary. Finally, we run experiments that show that there are families of schemas where the difference in asymptotic complexity between dynamic and static references is extremely visible, even with small schemas.
Efficient Bottom-Up Synthesis for Programs with Local Variables
Authors: Li Xiang , Zhou Xiangyu , Dong Rui , Zhang Yihong , Wang Xinyu
Published: January 2024

We propose a new synthesis algorithm that can efficiently search programs with local variables (e.g., those introduced by lambdas). Prior bottom-up synthesis algorithms are not able to evaluate programs with free local variables, and therefore cannot effectively reduce the search space of such programs (e.g., using standard observational equivalence reduction techniques), making synthesis slow. Our algorithm can reduce the space of programs with local variables. The key idea, dubbed lifted interpretation, is to lift up the program interpretation process, from evaluating one program at a time to simultaneously evaluating all programs from a grammar. Lifted interpretation provides a mechanism to systematically enumerate all binding contexts for local variables, thereby enabling us to evaluate and reduce the space of programs with local variables. Our ideas are instantiated in the domain of web automation. The resulting tool, Arborist, can automate a significantly broader range of challenging tasks more efficiently than state-of-the-art techniques including WebRobot and Helena.