Logics with Multiteam Semantics

Team semantics is the mathematical basis of modern logics of dependence and independence. In contrast to classical Tarski semantics, a formula is evaluated not for a single assignment of values to the free variables, but on a set of such assignments, called a team. Team semantics is appropriate for a purely logical understanding of dependency notions, where only the presence or absence of data matters, but being based on sets, it does not take into account multiple occurrences of data values. It is therefore insufficient in scenarios where such multiplicities matter, in particular for reasoning about probabilities and statistical independencies. Therefore, an extension from teams to multiteams (i.e. multisets of assignments) has been proposed by several authors. In this paper we aim at a systematic development of logics of dependence and independence based on multiteam semantics. We study atomic dependency properties of finite multiteams and discuss the appropriate meaning of logical operators to extend the atomic dependencies to full-fledged logics for reasoning about dependence properties in a multiteam setting. We explore properties and expressive power of a wide spectrum of different multiteam logics and compare them to second-order logic and to logics with team semantics. In many cases the results resemble what is known in team semantics, but there are also interesting differences. While in team semantics, the combination of inclusion and exclusion dependencies leads to a logic with the full power of both independence logic and existential second-order logic, independence properties of multiteams are not definable by any combination of properties that are downwards closed or union closed and thus are strictly more powerful than inclusion-exclusion logic. We also study the relationship of logics with multiteam semantics with existential second-order logic for a specific class of metafinite structures. It turns out that inclusion-exclusion logic can be characterised in a precise sense by the Presburger fragment of this logic, but for capturing independence, we need to go beyond it and add some form of multiplication. Finally, we also consider multiteams with weights in the reals and study the expressive power of formulae by means of topological properties.

An Adaptive Imitation Learning Framework for Robotic Complex Contact-Rich Insertion Tasks

Complex contact-rich insertion is a ubiquitous robotic manipulation skill and usually involves nonlinear and low-clearance insertion trajectories as well as varying force requirements. A hybrid trajectory and force learning framework can be utilized to generate high-quality trajectories by imitation learning and find suitable force control policies efficiently by reinforcement learning. However, with the mentioned approach, many human demonstrations are necessary to learn several tasks even when those tasks require topologically similar trajectories. Therefore, to reduce human repetitive teaching efforts for new tasks, we present an adaptive imitation framework for robot manipulation. The main contribution of this work is the development of a framework that introduces dynamic movement primitives into a hybrid trajectory and force learning framework to learn a specific class of complex contact-rich insertion tasks based on the trajectory profile of a single task instance belonging to the task class. Through experimental evaluations, we validate that the proposed framework is sample efficient, safer, and generalizes better at learning complex contact-rich insertion tasks on both simulation environments and on real hardware.

An elite broadly neutralizing antibody protects SARS-CoV-2 Omicron variant challenge

The strikingly high transmissibility and antibody evasion of SARS-CoV-2 Omicron variant have posted great challenges on the efficacy of current vaccines and antibody immunotherapy. Here, we screened 34 BNT162b2-vaccinees and cloned a public broadly neutralizing antibody (bNAb) ZCB11 from an elite vaccinee. ZCB11 neutralized all authentic SARS-CoV-2 variants of concern (VOCs), including Omicron and OmicronR346K with potent IC50 concentrations of 36.8 and 11.7 ng/mL, respectively. Functional analysis demonstrated that ZCB11 targeted viral receptor-binding domain (RBD) and competed strongly with ZB8, a known RBD-specific class II NAb. Pseudovirus-based mapping of 57 naturally occurred single mutations or deletions revealed that only S371L resulted in 11-fold neutralization resistance, but this phenotype was not observed in the Omicron variant. Furthermore, prophylactic ZCB11 administration protected lung infection against both the circulating pandemic Delta and Omicron variants in golden Syrian hamsters. These results demonstrated that vaccine-induced ZCB11 is a promising bNAb for immunotherapy against pandemic SARS-CoV-2 VOCs.

Secondary structure specific simpler prediction models for protein backbone angles

Motivation Protein backbone angle prediction has achieved significant accuracy improvement with the development of deep learning methods. Usually the same deep learning model is used in making prediction for all residues regardless of the categories of secondary structures they belong to. In this paper, we propose to train separate deep learning models for each category of secondary structures. Machine learning methods strive to achieve generality over the training examples and consequently loose accuracy. In this work, we explicitly exploit classification knowledge to restrict generalisation within the specific class of training examples. This is to compensate the loss of generalisation by exploiting specialisation knowledge in an informed way. Results The new method named SAP4SS obtains mean absolute error (MAE) values of 15.59, 18.87, 6.03, and 21.71 respectively for four types of backbone angles $$\phi$$ ϕ , $$\psi$$ ψ , $$\theta$$ θ , and $$\tau$$ τ . Consequently, SAP4SS significantly outperforms existing state-of-the-art methods SAP, OPUS-TASS, and SPOT-1D: the differences in MAE for all four types of angles are from 1.5 to 4.1% compared to the best known results. Availability SAP4SS along with its data is available from https://gitlab.com/mahnewton/sap4ss.

Study on technical solutions for shore power supply of motor yacht

The report presents an analysis of modern technical solutions for shore power supply of a specific class of passenger ships - luxury yachts for charter trips. The design data of a motor yacht in its different operating modes are considered, as well as the energy mix related to the fuel consumption at shore supply of the yacht during its stay at the port. The use of modern technical systems for shore supply includes the application of specific frequency converters, through which compatibility between the different voltage standards and the frequency for different shore power supply systems is realized. The costs of onshore power, compared to those of marine fuel, can be calculated from the current prices of onshore electricity and the energy produced from its own generators. The analysis of the basic design data of the motor yacht and the assessment of the energy costs on board, fuel economy and emission reductions will provide a clear answer to the advantages of the power supply from the shore of the vessel.

Assessment of energy efficiency of a motor yacht depending on routes and sailing area

The report presents an analysis of luxury charter yachts which are a specific class of vessels that, in order to meet the schedules and increased requirements of the owners regarding the luxury of the services offered, have relatively high energy consumption for their gross tonnage, compared to other passenger ships. The study focuses on the analysis of energy efficiency of luxury yachts by calculating the energy efficiency index (EEDI). This involves comparing different parameters that affect the value of the EEDI and can lead to energy savings. The report presents theoretical and experimental studies of the energy costs of a 70-meter luxury yacht for charter trips. With the use of the design data of the ship’s electrical equipment at different operating modes, at different routes, under different conditions, dependences for analysis of the optimal modes of movement are obtained, which leads to the realization of maximum savings of electricity and primary energy.

PKD-dependent PARP12-catalyzed mono-ADP-ribosylation of Golgin-97 is required for E-cadherin transport from Golgi to plasma membrane

Adenosine diphosphate (ADP)-ribosylation is a posttranslational modification involved in key regulatory events catalyzed by ADP-ribosyltransferases (ARTs). Substrate identification and localization of the mono-ADP-ribosyltransferase PARP12 at the trans-Golgi network (TGN) hinted at the involvement of ARTs in intracellular traffic. We find that Golgin-97, a TGN protein required for the formation and transport of a specific class of basolateral cargoes (e.g., E-cadherin and vesicular stomatitis virus G protein [VSVG]), is a PARP12 substrate. PARP12 targets an acidic cluster in the Golgin-97 coiled-coil domain essential for function. Its mutation or PARP12 depletion, delays E-cadherin and VSVG export and leads to a defect in carrier fission, hence in transport, with consequent accumulation of cargoes in a trans-Golgi/Rab11–positive intermediate compartment. In contrast, PARP12 does not control the Golgin-245–dependent traffic of cargoes such as tumor necrosis factor alpha (TNFα). Thus, the transport of different basolateral proteins to the plasma membrane is differentially regulated by Golgin-97 mono-ADP-ribosylation by PARP12. This identifies a selective regulatory mechanism acting on the transport of Golgin-97– vs. Golgin-245–dependent cargoes. Of note, PARP12 enzymatic activity, and consequently Golgin-97 mono-ADP-ribosylation, depends on the activation of protein kinase D (PKD) at the TGN during traffic. PARP12 is directly phosphorylated by PKD, and this is essential to stimulate PARP12 catalytic activity. PARP12 is therefore a component of the PKD-driven regulatory cascade that selectively controls a major branch of the basolateral transport pathway. We propose that through this mechanism, PARP12 contributes to the maintenance of E-cadherin–mediated cell polarity and cell–cell junctions.

Biogenesis of mature piRNAs in Caenorhabditis elegans is dependent on orchestration between multiple ribonucleases and PRG-1

Piwi-interacting RNAs (piRNAs) are an animal-specific class of germline-enriched small non-coding RNAs that shape transcriptome, as well as ensure genomic integrity and fertility by regulating transposons and other selfish genetic elements. In Caenorhabditis elegans mature piRNAs are 21-nucleotides long, begin with a monophosphorylated uridine, and they associate with PRG-1 to form piRISCs that scan the transcriptome for non-self sequences. However, these piRNAs are born as longer 5-capped transcripts, where PARN-1, a 3-5 exoribonuclease, contributes to the formation of the mature 3-end. But, till date, the 5-processing events remain elusive. We demonstrate that the recently identified endoribonuclease activity of XRN-2 is involved in the processing of the 5-end of precursor piRNAs in worms. Depletion of XRN-2 results in reduced mature piRNA levels, with concomitant increase in levels of the 5-capped precursors. We also reveal that the piRNAs born as longer precursor molecules (>60 nt), prior to 5-end processing, undergo ENDU-1-mediated endoribonucleolytic processing of their 3-ends. Our in vitro RNA-protein interaction studies unravel the mechanistic interactions between XRN-2 and PRG-1 towards the formation of mature 5-ends of piRNAs. In vivo experiments employing prg-1 mutant worms indicate that XRN-2 has the potential to perform clearance of precursors that are not bound and protected by PRG-1. Finally, we also demonstrate that XRN-2 is not only important for the generation of mature piRNAs and piRNA-dependent endo-siRNAs, but through yet unknown pathways, it also affects piRNA-independent endo-siRNAs that shape transcriptome, as well as contribute to genomic integrity via regulation of transposable elements.

Effect of Traditional Cooking and In Vitro Gastrointestinal Digestion of the Ten Most Consumed Beans from the Fabaceae Family in Thailand on Their Phytochemicals, Antioxidant and Anti-Diabetic Potentials

The edible beans in Fabaceae have been used for foods and medicines since the ancient time, and being used more and more. It is also appeared as a major ingredient in dairy cooking menu in many regions including Thailand, a rich biodiversity country. Many studies reported on health benefits of their flavonoids, but there is no report on the effect of cooking on phytochemical profile and pharmacological potentials. Thus, this present study aims to complete this knowledge, with the 10 most consumed Fabaceae beans in Thailand, by determining the impact of traditional cooking and gastrointestinal digestion on their phytochemicals, their antioxidant and anti-diabetic activities using different in vitro and in cellulo yeast models. The results showed that Vigna unguiculata subsp. sesquipedalis were the richest source of phytochemicals, whereas the population of V. mungo, Phaseolus vulgaris, V. angularis, and V. unguiculata subsp. sesquipedalis were richest in monomeric anthocyanin contents (MAC). Furthermore, the results clearly demonstrated the impact of the plant matrix effect on the preservation of a specific class of phytochemicals. In particular, after cooking and in vitro digestion, total flavonoid contents (TFC) in Glycine max extract was higher than in the uncooked sample. This study is the first report on the influence of cooking and in vitro gastrointestinal digestion on the inhibition capacity toward advanced glycation end products (AGEs). All samples showed a significant capacity to stimulate glucose uptake in yeast model, and V. angularis showed the highest capacity. Interestingly, the increase in glucose uptake after in vitro digestion was higher than in uncooked samples for both P. vulgaris and G. max samples. The current study is the first attempt to investigate at the effects of both processes not only on the natural bioactive compounds but also on antioxidant and anti-diabetic activities of Thailand’s 10 most consumed beans that can be applied for agro-industrial and phytopharmaceutical sectors.

FACTOR ANALYSIS METHOD APPLICATION FOR CONSTRUCTING OBJECTIVE FUNCTIONS OF OPTIMIZATION IN MULTIMODAL TRANSPORT PROBLEMS

The paper regards a specific class of optimization criteria that possess features of probability. Therefore, constructing objective function of optimization problem, the importance is attached to probability indices that show the probability of some criterial event or events to occur. Factor analysis has been taken for the main method of constructing objective function. Algorithm for constructing objective function of optimization is done for criterion of minimization risk level in multimodal transportations that demanded demonstration data. The application of factor analysis in classical problem solution was shown to give the problem a more distinct analytical interpretation in solving it.