Morpheus: Automated Safety Verification of Data-Dependent Parser Combinator Programs

Parser combinators are a well-known mechanism used for the compositional construction of parsers, and have shown to be particularly useful in writing parsers for rich grammars with data-dependencies and global state. Verifying applications written using them, however, has proven to be challenging in large part because of the inherently effectful nature of the parsers being composed and the difficulty in reasoning about the arbitrarily rich data-dependent semantic actions that can be associated with parsing actions. In this paper, we address these challenges by defining a parser combinator framework called Morpheus equipped with abstractions for defining composable effects tailored for parsing and semantic actions, and a rich specification language used to define safety properties over the constituent parsers comprising a program. Even though its abstractions yield many of the same expressivity benefits as other parser combinator systems, Morpheus is carefully engineered to yield a substantially more tractable automated verification pathway. We demonstrate its utility in verifying a number of realistic, challenging parsing applications, including several cases that involve non-trivial data-dependent relations

O-GlcNAc modification: why so intimately associated with phosphorylation?

Post-translational modification of proteins at serine and threonine side chains by β-N-acetylglucosamine (O-GlcNAc) mediated by the enzyme β-N-acetylglucosamine transferase has been emerging as a fundamental regulatory mechanism encompassing a wide range of proteins involved in cell division, metabolism, transcription and cell signaling. Furthermore, an extensive interplay between O-GlcNAc modification and serine/threonine phosphorylation in a variety of proteins has been reported to exist. However, our understanding of the regulatory mechanisms involved in O-GlcNAc modification and its interplay with serine/threonine phosphorylation in proteins is still elusive. Recent success in the mapping of O-GlcNAc modification sites in proteins as a result of technological advancement in mass spectrometry have revealed two important clues which may be inherently connected to the regulation of O-GlcNAc modification and its interplay with phosphorylation in proteins. First, almost all O-GlcNAc modified proteins are known phospho proteins. Second, the prevalence of tyrosine phosphorylation among O-GlcNAc modified proteins is exceptionally higher (~68%) than its normal occurrence (~2%) alone. We hypothesize that phosphorylation may be a requisite for O-GlcNAc modification and tyrosine phosphorylation plays a role in the interplay between O-GlcNAc modification and serine/threonine phosphorylation in proteins. In other words, the interplay between O-GlcNAc modification and phosphorylation is not limited to serine/threonine phosphorylation but also includes tyrosine phosphorylation. Our hypothesis provides an opportunity to understand the underlying mechanism involved in O-GlcNAc modification and its interplay with serine/threonine phosphorylation in proteins. Furthermore, implication of our hypothesis extends to tyrosine kinase signaling

Towards Improved Imbalance Robustness in Continual Multi-Label Learning with Dual Output Spiking Architecture (DOSA)

Algorithms designed for addressing typical supervised classification problems can only learn from a fixed set of samples and labels, making them unsuitable for the real world, where data arrives as a stream of samples often associated with multiple labels over time. This motivates the study of task-agnostic continual multi-label learning problems. While algorithms using deep learning approaches for continual multi-label learning have been proposed in the recent literature, they tend to be computationally heavy. Although spiking neural networks (SNNs) offer a computationally efficient alternative to artificial neural networks, existing literature has not used SNNs for continual multi-label learning. Also, accurately determining multiple labels with SNNs is still an open research problem. This work proposes a dual output spiking architecture (DOSA) to bridge these research gaps. A novel imbalance-aware loss function is also proposed, improving the multi-label classification performance of the model by making it more robust to data imbalance. A modified F1 score is presented to evaluate the effectiveness of the proposed loss function in handling imbalance. Experiments on several benchmark multi-label datasets show that DOSA trained with the proposed loss function shows improved robustness to data imbalance and obtains better continual multi-label learning performance than CIFDM, a previous state-of-the-art algorithm.Comment: 8 pages, 4 figures, 4 tables, 45 references. Submitted to IJCNN 202

Advanced Low-Floor Vehicle (ALFV) Specification Research

This report details the results of research on market comparison, operational cost efficiencies, and prototype tests conducted on a novel design for an Advanced Low Floor Vehicle (ALFV), flex-route transit bus. Section I describes how the need for such a bus arises from a combination of diminishing transit funding from the federal government and demographic and transportation factors. Section II describes the unique features of this bus design that render it suitable for rural and urban operation, including improved transit passenger and wheelchair accessibility, reduced maintenance, structural design features, safety provisions, and the technical specifications of this design. Section III details the potential differences in capital and operational costs of procuring and operating this bus in a fleet. Potential cost reductions due to the long-life vehicle concept, maneuverability, operational savings (from APTA Bus Roadeo tests), and reserve fleet savings are explored. Section IV refers to the Federal Transit Administration (FTA) new model bus tests (“Altoona Testing”). However, at the this time, the Altoona Bus Test Report for these tests is not yet released by the bus manufacturer, Ride Solution, Inc., as is its right under the Bus Testing Regulation. The report must be released to the public before this bus can be purchased by a transit agency using FTA funds. In addition to the standard Altoona Bus Test, additional research was conducted to determine the turning ability, suspension travel, ramp travel index, field of view for the driver, compliance to Americans with Disabilities Act (ADA) requirements, and timed assessment of wheelchair securement. Section IV also presents the results of these tests. Section V presents results from a market comparison that included the buses in this mid-size category that were tested at Altoona and are expected to be available for FTA grantees to purchase. The specifications and performance of the ALFV bus are compared with these buses. Section VI presents a flex-route utilization plan, and Section VII provides the results from a survey of transit professionals about their interest in the features of this bus design. Section VIII gives Ride Solution’s experience in developing the concept for ALFV. Conclusions of this report are presented in Section IX, followed by the references and appendices

Transglutaminase 2 Kinase Activity Facilitates Protein Kinase A-induced Phosphorylation of Retinoblastoma Protein

Transglutaminase 2 (TG2, tissue transglutaminase) is a multifunctional protein involved in cross-linking a variety of proteins, including retinoblastoma protein (Rb). Here we show that Rb is also a substrate for the recently identified serine/threonine kinase activity of TG2 and that TG2 phosphorylates Rb at the critically important Ser780 residue. Furthermore, phosphorylation of Rb by TG2 destabilizes the Rb.E2F1 complex. TG2 phosphorylation of Rb was abrogated by high Ca2+ concentrations, whereas TG2 transamidating activity was inhibited by ATP. TG2 was itself phosphorylated by protein kinase A (PKA). Phosphorylation of TG2 by PKA attenuated its transamidating activity and enhanced its kinase activity. Activation of PKA in mouse embryonic fibroblasts (MEF) with dibutyryl-cAMP enhanced phosphorylation of both TG2 and Rb by a process that was inhibited by the PKA inhibitor H89. Treatment with dibutyryl-cAMP enhanced Rb phosphorylation in MEFtg2+/+ cells but not in MEFtg2-/- cells. These data indicate that Rb is a substrate for TG2 kinase activity and suggest that phosphorylation of Rb, which results from activation of PKA in fibroblasts, is indirect and requires TG2 kinase activity

IZLJEV NAFTE U MORSKOME OKOLIŠU: ZAHTJEVI NAKON ODOBALNOGA IZLJEVA NAFTE

The global lifestyle of this modern world has become more dependent on petroleum-based products, whose applications are involved almost everywhere. Since a large quantity of oil is being used on a daily basis, the spilling of oil by various means during its storage and transportation has become inevitable. This work focuses on the spilling of oil in a marine environment, generally referred to as an offshore oil spill, in contrast to an onshore oil spill associated with a terrestrial environment. These oil spills not only devastate the natural resources and unsettle the economy, they also jeopardize marine life, as well as human health. The remediation of an oil spill remains very challenging, when the disaster is associated with a large aerial extent. In this context, a sound understanding is required on the origin, seeping, composition and properties of the spilled oil in order to better monitor the spreading of the oil spill. In this manuscript, a detailed list of fundamental queries, which will be required to be addressed at the instance of an oil spill has been deduced, which will be extremely useful for the oil spill respondents as there are no previous studies that exclusively provide the type and nature of data required to be collected, immediately following an oil spill. Furthermore, this manuscript has deduced a list of sensitive and essential plots that will be required in order to analyse and forecast the spreading of an oil spill. An essence of weathering and its associated movement of oil spill has been included.Globalni stil života modernoga svijeta postao je sve ovisniji o proizvodima na osnovi nafte, koji se gotovo svugdje primjenjuju. Budući da je u svakodnevnoj upotrebi velika količina nafte, izljevi nafte u okoliš tijekom njezina transporta i skladištenja neizbježni su. Ovaj rad usmjeren je na izljeve nafte u morski okoliš, koji se razlikuju od izljeva nafte u terestrički okoliš. Izljevi nafte u morski okoliš devastiraju prirodne resurse i utječu na gospodarstvo, ali i ugrožavaju morske ekosustave, kao i zdravlje ljudi. Kod velikih onečišćenih područja sanacija izljeva nafte dodatan je izazov. U tome kontekstu, a kako bi se bolje pratilo širenje nafte u okolišu, potrebno je dobro razumijevanje izljeva nafte, njegova izvora te sastava i svojstava izlivene nafte. S obzirom na nedostatak sustavno prikazanih podataka u literaturi, u ovome je radu izrađen detaljan popis temeljnih pitanja na koja je potrebno odgovoriti u slučaju izljeva nafte, kao pomoć odgovornim osobama u definiranju tipa i prirode podataka koje moraju prikupiti odmah nakon što se izljev nafte dogodi. Nadalje, izveden je popis temeljnih grafičkih dijagrama koji su nužni za analizu i predviđanje širenja izlivene nafte. Uzeto je u obzir i djelovanje vremenskih prilika i s njima povezano kretanje izlivene nafte