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Book ; Online: Synthesis with Explicit Dependencies

Golia, Priyanka / Roy, Subhajit / Meel, Kuldeep S.

2023

Abstract: Quantified Boolean Formulas (QBF) extend propositional logic with quantification $\forall, \exists$. In QBF, an existentially quantified variable is allowed to depend on all universally quantified variables in its scope. Dependency Quantified Boolean ... ...

Abstract	Quantified Boolean Formulas (QBF) extend propositional logic with quantification $\forall, \exists$. In QBF, an existentially quantified variable is allowed to depend on all universally quantified variables in its scope. Dependency Quantified Boolean Formulas (DQBF) restrict the dependencies of existentially quantified variables. In DQBF, existentially quantified variables have explicit dependencies on a subset of universally quantified variables called Henkin dependencies. Given a Boolean specification between the set of inputs and outputs, the problem of Henkin synthesis is to synthesize each output variable as a function of its Henkin dependencies such that the specification is met. Henkin synthesis has wide-ranging applications, including verification of partial circuits, controller synthesis, and circuit realizability. This work proposes a data-driven approach for Henkin synthesis called Manthan3. On an extensive evaluation of over 563 instances arising from past DQBF solving competitions, we demonstrate that Manthan3 is competitive with state-of-the-art tools. Furthermore, Manthan3 could synthesize Henkin functions for 26 benchmarks for which none of the state-of-the-art techniques could synthesize. Comment: To be published in Design, Automation and Test in Europe Conference (DATE), 2023
Keywords	Computer Science - Logic in Computer Science ; Computer Science - Artificial Intelligence
Subject code	005
Publishing date	2023-01-25
Publishing country	us
Document type	Book ; Online
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Article ; Online: Host microbiome associated low intestinal acetate correlates with progressive NLRP3-dependent hepatic-immunotoxicity in early life microcystin-LR exposure.

More, Madhura / Chatterjee, Somdatta / Saha, Punnag / Bose, Dipro / Trivedi, Ayushi / Roy, Subhajit / Chatterjee, Saurabh

BMC pharmacology & toxicology

2023 Volume 24, Issue 1, Page(s) 78

Abstract: Background: Microcystins (MCs), potent hepatotoxins pose a significant health risk to humans, particularly children, who are more vulnerable due to higher water intake and increased exposure during recreational activities.: Methods: Here, we ... ...

Abstract	Background: Microcystins (MCs), potent hepatotoxins pose a significant health risk to humans, particularly children, who are more vulnerable due to higher water intake and increased exposure during recreational activities. Methods: Here, we investigated the role of host microbiome-linked acetate in modulating inflammation caused by early-life exposure to the cyanotoxin Microcystin-LR (MC-LR) in a juvenile mice model. Results: Our study revealed that early-life MC-LR exposure disrupted the gut microbiome, leading to a depletion of key acetate-producing bacteria and decreased luminal acetate concentration. Consequently, the dysbiosis hindered the establishment of a gut homeostatic microenvironment and disrupted gut barrier function. The NOD-like receptor family pyrin domain - containing 3 (NLRP3) inflammasome, a key player in MC-induced hepatoxicity emerged as a central player in this process, with acetate supplementation effectively preventing NLRP3 inflammasome activation, attenuating hepatic inflammation, and decreasing pro-inflammatory cytokine production. To elucidate the mechanism underlying the association between early-life MC-LR exposure and the progression of metabolic dysfunction associated steatotic liver disease (MASLD), we investigated the role of acetate binding to its receptor -G-protein coupled receptor 43 (GPR43) on NLRP3 inflammasome activation. Our results demonstrated that acetate-GPR43 signaling was crucial for decreasing NLRP3 protein levels and inhibiting NLRP3 inflammasome assembly. Further, acetate-induced decrease in NLRP3 protein levels was likely mediated through proteasomal degradation rather than autophagy. Overall, our findings underscore the significance of a healthy gut microbiome and its metabolites, particularly acetate, in the progression of hepatotoxicity induced by early life toxin exposure, crucial for MASLD progression. Conclusions: This study highlights potential therapeutic targets in gut dysbiosis and NLRP3 inflammasome activation for mitigating toxin-associated inflammatory liver diseases.
MeSH term(s)	Animals ; Mice ; Acetates ; Dysbiosis/chemically induced ; Gastrointestinal Microbiome ; Inflammasomes ; Inflammation/drug therapy ; Microcystins/toxicity ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Chemical Substances	Acetates ; cyanoginosin LR (EQ8332842Y) ; Inflammasomes ; Microcystins ; NLR Family, Pyrin Domain-Containing 3 Protein
Language	English
Publishing date	2023-12-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2680259-4
ISSN	2050-6511 ; 2050-6511
ISSN (online)	2050-6511
ISSN	2050-6511
DOI	10.1186/s40360-023-00721-7
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Book ; Online: Synthesis of Semantic Actions in Attribute Grammars

Kalita, Pankaj Kumar / Kumar, Miriyala Jeevan / Roy, Subhajit

2022

Abstract: Attribute grammars allow the association of semantic actions to the production rules in context-free grammars, providing a simple yet effective formalism to define the semantics of a language. However, drafting the semantic actions can be tricky and a ... ...

Abstract	Attribute grammars allow the association of semantic actions to the production rules in context-free grammars, providing a simple yet effective formalism to define the semantics of a language. However, drafting the semantic actions can be tricky and a large drain on developer time. In this work, we propose a synthesis methodology to automatically infer the semantic actions from a set of examples associating strings to their meanings. We also propose a new coverage metric, derivation coverage. We use it to build a sampler to effectively and automatically draw strings to drive the synthesis engine. We build our ideas into our tool, PANINI, and empirically evaluate it on twelve benchmarks, including a forward differentiation engine, an interpreter over a subset of Java bytecode, and a mini-compiler for C language to two-address code. Our results show that PANINI scales well with the number of actions to be synthesized and the size of the context-free grammar, significantly outperforming simple baselines. Comment: 12 pages, 11 Figures, 2 tables, 48 References
Keywords	Computer Science - Programming Languages
Subject code	005
Publishing date	2022-08-14
Publishing country	us
Document type	Book ; Online
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Article ; Online: Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV.

Roy, Priti / Roy, Subhajit / Sengupta, Neelanjana

Biophysical journal

2020 Volume 119, Issue 8, Page(s) 1525–1537

Abstract: The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, ... ...

Abstract	The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the nonstructural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant β-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intramonomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability, and asymmetric salt-bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (S
MeSH term(s)	Disulfides ; Humans ; Viral Nonstructural Proteins/genetics ; Virus Replication ; Zika Virus ; Zika Virus Infection
Chemical Substances	Disulfides ; Viral Nonstructural Proteins
Language	English
Publishing date	2020-09-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2020.08.036
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Book ; Online: Debug-Localize-Repair

Verma, Sahil / Roy, Subhajit

A Symbiotic Construction for Heap Manipulations

2020

Abstract: We present Wolverine, an integrated Debug-Localize-Repair environment for heap manipulating programs. Wolverine packages a new bug localization algorithm that reduces the search space of repairs and a novel, proof-directed repair algorithm to synthesize ... ...

Abstract	We present Wolverine, an integrated Debug-Localize-Repair environment for heap manipulating programs. Wolverine packages a new bug localization algorithm that reduces the search space of repairs and a novel, proof-directed repair algorithm to synthesize the repair patches. While concretely executing a program, Wolverine displays the abstract program states (as box-and-arrow diagrams) as a visual aid to the programmer. Wolverine supports "hot-patching" of the generated patches to provide a seamless debugging environment, and the bug localization enkindles tremendous speedups in repair timing. Wolverine also facilitates new debug-localize-repair possibilities, specification refinement, and checkpoint-based hopping. We evaluate our framework on 6400 buggy programs (generated using automated fault injection) on a variety of data-structures like singly, doubly, and circular linked lists, AVL trees, Red-Black trees, Splay Trees, and Binary Search Trees; Wolverine could repair all the buggy instances within realistic programmer wait-time (less than 5 sec in most cases). Wolverine could also repair more than 80% of the 247 (buggy) student submissions (where a reasonable attempt was made). Comment: 24 pages, 20 figures
Keywords	Computer Science - Programming Languages ; Computer Science - Software Engineering
Subject code	005
Publishing date	2020-11-26
Publishing country	us
Document type	Book ; Online
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Article ; Online: Distinct molecular phenotypes involving several human diseases are induced by IFN-λ3 and IFN-λ4 in monocyte-derived macrophages.

De, Manjarika / Bhushan, Anand / Grubbe, William S / Roy, Subhajit / Mendoza, Juan L / Chinnaswamy, Sreedhar

Genes and immunity

2022 Volume 23, Issue 2, Page(s) 73–84

Abstract: Human Interferon (IFN) lambda 3 (IFN-λ3) and IFN-λ4 are closely linked at the IFNL locus and show association with several diseases in genetic studies. Since they are only ~30% identical to each other, to better understand their roles in disease ... ...

Abstract	Human Interferon (IFN) lambda 3 (IFN-λ3) and IFN-λ4 are closely linked at the IFNL locus and show association with several diseases in genetic studies. Since they are only ~30% identical to each other, to better understand their roles in disease phenotypes, comparative studies are needed. Monocytes are precursors to macrophages (monocyte-derived macrophages; MDMs) that get differentiated under the influence of various immune factors, including IFNs. In a recent study, we characterized lipopolysaccharide-activated M1 and M2-MDMs that were differentiated in presence of IFN-λ3 or IFN-λ4. In this study, we performed transcriptomics on these M1 and M2-MDMs to further understand their molecular phenotypes. We identified over 760 genes that were reciprocally regulated by IFN-λ3 and IFN-λ4, additionally we identified over 240 genes that are significantly affected by IFN-λ4 but not IFN-λ3. We observed that IFN-λ3 was more active in M2-MDMs while IFN-λ4 showed superior response in M1-MDMs. Providing a structural explanation for these functional differences, molecular modeling showed differences in expected interactions of IFN-λ3 and IFN-λ4 with the extracellular domain of IFN-λR1. Further, pathway analysis showed several human infectious diseases and even cancer-related pathways being significantly affected by IFN-λ3 and/or IFN-λ4 in both M1 and M2-MDMs.
MeSH term(s)	Antiviral Agents ; Humans ; Interferons/genetics ; Interferons/pharmacology ; Macrophages/metabolism ; Monocytes/metabolism ; Phenotype ; Interferon Lambda
Chemical Substances	Antiviral Agents ; Interferons (9008-11-1) ; Interferon Lambda
Language	English
Publishing date	2022-02-03
Publishing country	England
Document type	Journal Article
ZDB-ID	2060566-3
ISSN	1476-5470 ; 1466-4879
ISSN (online)	1476-5470
ISSN	1466-4879
DOI	10.1038/s41435-022-00164-w
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Article ; Online: Hepatic NLRP3-Derived Hsp70 Binding to TLR4 Mediates MASLD to MASH Progression upon Inhibition of PP2A by Harmful Algal Bloom Toxin Microcystin, a Second Hit.

Roy, Subhajit / Saha, Punnag / Bose, Dipro / Trivedi, Ayushi / More, Madhura / Xiao, Shuo / Diehl, Anna Mae / Chatterjee, Saurabh

International journal of molecular sciences

2023 Volume 24, Issue 22

Abstract: Harmful algal bloom toxin microcystin has been associated with metabolic dysfunction-associated steatotic liver disease (MASLD) progression and hepatocellular carcinoma, though the mechanisms remain unclear. Using an established mouse model of MASLD, we ... ...

Abstract	Harmful algal bloom toxin microcystin has been associated with metabolic dysfunction-associated steatotic liver disease (MASLD) progression and hepatocellular carcinoma, though the mechanisms remain unclear. Using an established mouse model of MASLD, we show that the NLRP3-Hsp70-TLR4 axis drives in part the inflammation of the liver lobule that results in the progression of MASLD to metabolic dysfunction-associated steatohepatitis (MASH). Results showed that mice deficient in NLRP3 exhibited decreased MASH pathology, blocked Hsp70 expression, and co-binding with NLRP3, a crucial protein component of the liver inflammasome. Hsp70, both in the liver lobule and extracellularly released in the liver vasculature, acted as a ligand to TLR4 in the liver, primarily in hepatocytes to activate the NF-κB pathway, ultimately leading to hepatic cell death and necroptosis, a crucial pathology of MASH progression. The above studies show a novel insight into an inflammasome-triggered Hsp70-mediated inflammation that may have broader implications in MASLD pathology. MASLD to MASH progression often requires multiple hits. One of the mediators of progressive MASLD is environmental toxins. In this research report, we show for the first time a novel mechanism where microcystin-LR, an environmental toxin, advances MASLD to MASH by triggering the release of Hsp70 as a DAMP to activate TLR4-induced inflammation in the liver.
MeSH term(s)	Mice ; Animals ; Inflammasomes/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/genetics ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Toll-Like Receptor 4/genetics ; Toll-Like Receptor 4/metabolism ; Harmful Algal Bloom ; Microcystins/toxicity ; Non-alcoholic Fatty Liver Disease/metabolism ; Inflammation/metabolism
Chemical Substances	Inflammasomes ; NLR Family, Pyrin Domain-Containing 3 Protein ; Toll-Like Receptor 4 ; Microcystins
Language	English
Publishing date	2023-11-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms242216354
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Article ; Online: Prolonged Antibiotic Use in a Preclinical Model of Gulf War Chronic Multisymptom-Illness Causes Renal Fibrosis-like Pathology via Increased micro-RNA 21-Induced PTEN Inhibition That Is Correlated with Low Host

Trivedi, Ayushi / Bose, Dipro / Saha, Punnag / Roy, Subhajit / More, Madhura / Skupsky, Jonathan / Klimas, Nancy G / Chatterjee, Saurabh

Cells

2023 Volume 13, Issue 1

Abstract: Gulf War (GW) veterans show gastrointestinal disturbances and gut dysbiosis. Prolonged antibiotic treatments commonly employed in veterans, especially the use of fluoroquinolones and aminoglycosides, have also been associated with dysbiosis. This study ... ...

Abstract	Gulf War (GW) veterans show gastrointestinal disturbances and gut dysbiosis. Prolonged antibiotic treatments commonly employed in veterans, especially the use of fluoroquinolones and aminoglycosides, have also been associated with dysbiosis. This study investigates the effect of prolonged antibiotic exposure on risks of adverse renal pathology and its association with gut bacterial species abundance in underlying GWI and aims to uncover the molecular mechanisms leading to possible renal dysfunction with aging. Using a GWI mouse model, administration of a prolonged antibiotic regimen involving neomycin and enrofloxacin treatment for 5 months showed an exacerbated renal inflammation with increased NF-κB activation and pro-inflammatory cytokines levels. Involvement of the high mobility group 1 (HMGB1)-mediated receptor for advanced glycation end products (RAGE) activation triggered an inflammatory phenotype and increased transforming growth factor-β (TGF-β) production. Mechanistically, TGF-β- induced microRNA-21 upregulation in the renal tissue leads to decreased phosphatase and tensin homolog (PTEN) expression. The above event led to the activation of protein kinase-B (AKT) signaling, resulting in increased fibronectin production and fibrosis-like pathology. Importantly, the increased miR-21 was associated with low levels of
MeSH term(s)	Animals ; Mice ; Anti-Bacterial Agents/adverse effects ; Proto-Oncogene Proteins c-akt ; Dysbiosis ; Gulf War ; HMGB1 Protein ; Kidney Diseases ; Chronic Disease ; Clostridiales ; Fibrosis ; Inflammation ; Transforming Growth Factor beta ; MicroRNAs
Chemical Substances	Anti-Bacterial Agents ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; HMGB1 Protein ; Transforming Growth Factor beta ; MicroRNAs
Language	English
Publishing date	2023-12-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells13010056
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Book ; Online: Input Validation with Symbolic Execution

Mehrotra, Anay / Bansal, Ayush / Pandey, Awanish / Roy, Subhajit

2021

Abstract: Symbolic execution has always been plagued by the inability to handle programs that require highly structured inputs. Most often, the symbolic execution engine gets overwhelmed by the sheer number of infeasible paths and fails to explore enough feasible ... ...

Abstract	Symbolic execution has always been plagued by the inability to handle programs that require highly structured inputs. Most often, the symbolic execution engine gets overwhelmed by the sheer number of infeasible paths and fails to explore enough feasible paths to gain any respectable coverage. In this paper, we propose a system, InVaSion, that attempts to solve this problem for forking-based symbolic execution engines. We propose an input specification language (ISL) that is based on a finite-state automaton but includes guarded transitions, a set of registers and a set of commands to update the register states. We demonstrate that our language is expressive enough to handle complex input specifications, like the Tiff image format, while not requiring substantial human effort; even the Tiff image specification could be specified in our language with an automaton of about 35 states. InVaSion translates the given program and the input specification into a non-deterministic program and uses symbolic execution to instantiate the non-determinism. This allows our tool to work with any forking-based symbolic execution engine and with no requirement of any special theory solver. Over our set of benchmarks, on an average, InVaSion was able to increase branch coverage from 24.97% to 67.84% over baseline KLEE.
Keywords	Computer Science - Programming Languages
Subject code	004
Publishing date	2021-04-03
Publishing country	us
Document type	Book ; Online
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Book ; Online: Learning Differentially Private Mechanisms

Roy, Subhajit / Hsu, Justin / Albarghouthi, Aws

2021

Abstract: Differential privacy is a formal, mathematical definition of data privacy that has gained traction in academia, industry, and government. The task of correctly constructing differentially private algorithms is non-trivial, and mistakes have been made in ... ...

Abstract	Differential privacy is a formal, mathematical definition of data privacy that has gained traction in academia, industry, and government. The task of correctly constructing differentially private algorithms is non-trivial, and mistakes have been made in foundational algorithms. Currently, there is no automated support for converting an existing, non-private program into a differentially private version. In this paper, we propose a technique for automatically learning an accurate and differentially private version of a given non-private program. We show how to solve this difficult program synthesis problem via a combination of techniques: carefully picking representative example inputs, reducing the problem to continuous optimization, and mapping the results back to symbolic expressions. We demonstrate that our approach is able to learn foundational algorithms from the differential privacy literature and significantly outperforms natural program synthesis baselines.
Keywords	Computer Science - Cryptography and Security ; Computer Science - Machine Learning ; Computer Science - Programming Languages
Subject code	006 ; 005
Publishing date	2021-01-04
Publishing country	us
Document type	Book ; Online
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