Functional Description Research Articles

On importance of explicit account of non-complementary contacts in scoring functions

Based both on the practice of post-processing by a human expert and on the higher values of the accuracy metrics of machine learning scoring functions, it is suggested that when estimating the free energy of binding in a ligand–receptor complex, a significant part of intermolecular interactions is still not explicitly taken into account. An assessment is made of how explicit consideration of non-complementary ligand–receptor interactions could improve the accuracy of the description of contemporary classical scoring functions, which tend to use only terms of complementary/favorable interactions.

Tendon Transfers to Improve Grip and Pinch in Patients with Sporadic Inclusion Body Myositis.

Sporadic inclusion body myositis (sIBM) is a rare and slowly progressive skeletal muscle disease that can cause hand dysfunction, which is a major source of disability. Tendon transfers have been reliably used to improve function in other neuromuscular settings. Given that sIBM patients often present with flexion impairments and mostly functioning extensors, we investigated the potential opportunity for tendon transfer surgery to improve hand dysfunction in sIBM patients. We conducted a scoping review for studies of sIBM and tendon transfers, extracted descriptions of hand function and surgical technique, and recorded results in terms of hand function. We also conducted an institutional review board-approved survey with 470 participants to determine baseline patient-reported function and to determine participant perceptions and expectations for tendon transfer surgery to improve hand function in sIBM. We identified three published case reports on tendon transfers in sIBM patients with subjectively improved grip and pinch strength, but standardized measures of hand function or quality-of-life were not reported. Within the surveyed cohort, half of participants reported that they would consider surgery, yet only 8% had been referred to a hand surgeon. Fifty four percent of participants reported that they would consider surgery if there would be 1-2 years of benefit after surgery. All participants who would consider surgery also had significant upper extremity disability. Tendon transfer surgery has the potential to improve quality-of-life for sIBM patients, and there is significant patient interest in this approach. To objectively assess its efficacy, we propose conducting a surgical trial.

Neutron rearrangement of the magic number 90Zr-core determined by the matter density difference between 90Zr and 92Zr

Matter density distributions and root-mean-square matter radii for 90Zr and 92Zr were determined through fitting the small-angle differential cross sections of proton elastic scattering at 0.8 GeV with the Glauber model. With the obtained neutron densities, a neutron rearrangement beyond the expectation for the magic number 90Zr-core was found from 90Zr to 92Zr by adding two valence neutrons. By considering the surface-peaked term, the rearrangement was reproduced by the shell model calculations with the realistic Woods-Saxon potentials. It indicates that the surface-peaked term related to surface nucleon interactions plays an important role in describing the nucleon rearrangement, since the surface-peaked term would improve the description of the radial wave functions.

Comprehensive assessment of executive functioning following childhood severe traumatic brain injury: clinical utility of the child executive functions battery

ObjectivesTo perform a detailed description of executive functioning following moderate-to-severe childhood traumatic brain injury (TBI), and to study demographic and severity factors influencing outcome.MethodsA convenience sample of children/adolescents aged 7–16 years, referred to a rehabilitation department after a TBI (n = 43), was compared to normative data using a newly developed neuropsychological test battery (Child Executive Functions Battery—CEF-B) and the BRIEF.ResultsPerformance in the TBI group was significantly impaired in most of the CEF-B subtests, with moderate to large effect sizes. Regarding everyday life, patients were significantly impaired in most BRIEF clinical scales, either in parent or in teacher reports. Univariate correlations in the TBI group did not yield significant correlations between the CEF-B and socio-economic status, TBI severity, age at injury, or time since injury.ConclusionExecutive functioning is severely altered following moderate-to-severe childhood TBI and is best assessed using a combination of developmentally appropriate neuropsychological tests and behavioral ratings to provide a comprehensive understanding of children’s executive functions.

Distal myopathy due to digenic inheritance of TIA1 and SQSTM1 variants in two unrelated Spanish patients

Welander distal myopathy typically manifests in late adulthood and is caused by the founder TIA1 c.1150G>A (p.Glu384Lys) variant in families of Swedish and Finnish descent. Recently, a similar phenotype has been attributed to the digenic inheritance of TIA1 c.1070A>G (p.Asn357Ser) and SQSTM1 c.1175C>T (p.Pro392Leu) variants. We describe two unrelated Spanish patients presenting with slowly progressive gait disturbance, distal-predominant weakness, and mildly elevated creatine kinase (CK) levels since their 6th decade. Electromyography revealed abnormal spontaneous activity and a myopathic pattern. Muscle magnetic resonance imaging (MRI) showed marked fatty replacement in distal leg muscles. A muscle biopsy, performed on one patient, revealed myopathic changes with rimmed vacuoles. Both patients carried the TIA1 p.Asn357Ser and SQSTM1 p.Pro392Leu variants. Digenic inheritance is supported by evidence from unrelated pedigrees and a plausible biological interaction between both proteins in protein quality control processes. Recent functional studies and additional case descriptions further support this. Clinical suspicion is necessary to seek both variants.

HTLV-1 biofilm polarization maintained by tetraspanin CD82 is required for efficient viral transmission.

In the early stages of infection, human T-lymphotropic virus type 1 (HTLV-1) dissemination within its host is believed to rely mostly on cell-to-cell contacts. Past studies unveiled a novel mechanism of HTLV-1 intercellular transmission based on the remodeling of the host-cell extracellular matrix and the generation of cell-surface viral assemblies whose structure, composition, and function resemble bacterial biofilms. These polarized aggregates of infectious virions, identified as viral biofilms, allow the bulk delivery of viruses to target cells and may help to protect virions from immune attacks. However, viral biofilms' molecular and functional description is still in its infancy, although it is crucial to fully decipher retrovirus pathogenesis. Here, we explore the function of cellular tetraspanins (CD9, CD81, CD82) that we detect inside HTLV-1 particles within biofilms. Our results demonstrate specific roles for CD82 in the cell-surface distribution and intercellular transmission of HTLV-1 biofilms, which we document as two essential parameters for efficient viral transmission. At last, our findings indicate that N-glycosylation of cell-surface molecules, including CD82, is required for the polarization of HTLV-1 biofilms and for the efficient transmission of HTLV-1 between T-lymphocytes.

Design and Implementation of a Book Borrowing Management System Based on Intelligent Recommendation Algorithm

A library is an institution that collects and organizes book materials for people to read and reference. The design of this system is aimed at information-based management of the library's borrowing function, enabling it to achieve the practical goal of improving the work efficiency of administrators. The book borrowing management system in this article adopts a B/S architecture, PHP language, and MySQL database. The administrator of this system can manage the library's book information, reader information, and borrowing and returning information; Readers and users can query book information, modify personal information, and report the loss of their own documents. Unlike general book borrowing management systems, this system uses intelligent recommendation algorithms to recommend books to readers based on their borrowing records. The article provides a detailed introduction to the technical architecture used in the development of the system, as well as a description of various functions of the system. It also studies the functional requirements, usage process, architecture, and database table design of the book borrowing management system.

How Important are Good Method Names in Neural Code Generation? A Model Robustness Perspective

Pre-trained code generation models (PCGMs) have been widely applied in neural code generation which can generate executable code from functional descriptions in natural languages, possibly together with signatures. Despite substantial performance improvement of PCGMs, the role of method names in neural code generation has not been thoroughly investigated. In this paper, we study and demonstrate the potential of benefiting from method names to enhance the performance of PCGMs, from a model robustness perspective. Specifically, we propose a novel approach, namedRADAR(neuRAl coDe generAtorRobustifier).RADARconsists of two components:RADAR-Attack andRADAR-Defense. The former attacks a PCGM by generating adversarial method names as part of the input, which are semantic and visual similar to the original input, but may trick the PCGM to generate completely unrelated code snippets. As a countermeasure to such attacks,RADAR-Defense synthesizes a new method name from the functional description and supplies it to the PCGM. Evaluation results show thatRADAR-Attack can reduce the CodeBLEU of generated code by 19.72% to 38.74% in three state-of-the-art PCGMs (i.e., CodeGPT, PLBART, and CodeT5) in the fine-tuning code generation task, and reduce the Pass@1 of generated code by 32.28% to 44.42% in three state-of-the-art PCGMs (i.e., Replit, CodeGen, and CodeT5+) in the zero-shot code generation task. Moreover,RADAR-Defense is able to reinstate the performance of PCGMs with synthesized method names. These results highlight the importance of good method names in neural code generation and implicate the benefits of studying model robustness in software engineering.

Nonorthogonal Multireference Wave Function Description of Triplet-Triplet Energy Transfer Couplings.

In this study, the use of self-consistent field quasi-diabats is investigated for calculation of triplet energy transfer diabatic coupling elements. It is proposed that self-consistent field quasi-diabats are particularly useful for studying energy transfer (EnT) processes because orbital relaxation in response to changes in electron configuration is implicitly built into the model. The conceptual model that is developed allows for the simultaneous evaluation of direct and charge-transfer mechanisms to establish the importance of the different possible EnT mechanisms. The method's performance is evaluated using two model systems: the ethylene dimer and ethylene with the methaniminium cation. While states that mediate the charge-transfer mechanism were found to be higher in energy than the states involved in the direct mechanism, the coupling elements that control the kinetics were found to be significantly larger in the charge-transfer mechanism. Subsequently, we discuss the advantage of the approach in the context of practical difficulties with the use of established approaches.

Quasianalytic Functionals and Ultradistributions as Boundary Values of Harmonic Functions

We study boundary values of harmonic functions in spaces of quasianalytic functionals and spaces of ultradistributions of non-quasianalytic type. As an application, we provide a new approach to Hörmander’s support theorem for quasianalytic functionals. Our main technical tool is a description of ultradifferentiable functions by almost harmonic functions, a concept that we introduce in this article. We work in the setting of ultradifferentiable classes defined via weight matrices. In particular, our results simultaneously apply to the two standard classes defined via weight sequences and via weight functions.

Hemodynamic response function description in patients with glioma

IntroductionFunctional magnetic resonance imaging is a powerful tool that has provided many insights into cognitive sciences. Yet, as its analysis is mostly based on the knowledge of an a priori canonical hemodynamic response function (HRF), its reliability in patients’ applications has been questioned. There have been reports of neurovascular uncoupling in patients with glioma, but no specific description of the Hemodynamic Response Function (HRF) in glioma has been reported so far. The aim of this work is to describe the HRF in patients with glioma. MethodsForty patients were included. MR images were acquired on a 1.5T scanner. Activated clusters were identified using a fuzzy general linear model; HRFs were adjusted with a double-gamma function. Analyses were undertaken considering the tumor grade, age, sex, tumor location, and activated location. ResultsDifferences are found in the occipital, limbic, insular, and sub-lobar areas, but not in the frontal, temporal, and parietal lobes. The presence of a glioma slows the time-to-peak and onset times by 5.2 and 3.8 % respectively; high-grade gliomas present 8.1 % smaller HRF widths than low-grade gliomas. Discussion and conclusionThere is significant HRF variation due to the presence of glioma, but the magnitudes of the observed differences are small. Most processing pipelines should be robust enough for this magnitude of variation and little if any impact should be visible on functional maps. The differences that have been observed in the literature between functional mapping obtained with magnetic resonance vs. that obtained with direct electrostimulation during awake surgery are more probably due to the intrinsic difference in the mapping process: fMRI mapping detects all recruited areas while intra-surgical mapping indicates only the areas indispensable for the realization of a certain task. Surgical mapping might not be the gold standard to use when trying to validate the fMRI mapping process.

AdS3 orbifolds, BTZ black holes, and holography

Conical defects of the form (AdS3 × S3\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ {\\mathbbm{S}}^3 $$\\end{document})/ℤk have an exact orbifold description in worldsheet string theory, which we derive from their known presentation as gauged Wess-Zumino-Witten models. The configuration of strings and fivebranes sourcing this geometry is well-understood, as is the correspondence to states/operators in the dual CFT2. One can analytically continue the construction to Euclidean AdS3 (i.e. the hyperbolic ball ℍ3+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ {\\mathbb{H}}_3^{+} $$\\end{document}) and consider the orbifold by any infinite discrete (Kleinian) group generated by a set of elliptic elements γi ∈ SL(2, ℂ), γiki\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ {\\gamma}_i^{{\ extrm{k}}_i} $$\\end{document} = \U0001d7d9, i = 1, . , K. The resulting geometry consists of multiple conical defects traveling along geodesics in ℍ3+\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$ {\\mathbb{H}}_3^{+} $$\\end{document}, and provides a semiclassical bulk description of correlation functions in the dual CFT involving the corresponding defect operators, which is nonperturbatively exact in α′. The Lorentzian continuation of these geometries describes a collection of defects colliding to make a BTZ black hole. We comment on a recent proposal to use such correlators to prepare a basis of black hole microstates, and elaborate on a picture of black hole formation and evaporation in terms of the underlying brane dynamics in the bulk.

Questions of studying Yakut fairy tales: a comparative analysis of stories about Granny Taаl-Taаl and Chaarchakhaan

The article is devoted to the study of Yakut fairy tales. The works of I. A. Khudyakov, E. K. Pekarsky, G. U. Ergis, N. V. Emelyanov, modern researchers V. V. Illarionov, Yu. N. Dyakonova, N. A. Orosina and others are presented in the context of theoretical positions in the writings of Russian folklorists. The semantics of the study text is actualized as a process and result of live communication of carriers of cultural memory of ancestors, accompanied by targeted actions to rethink individual parts or episodes of its content. The preservation of interest in an ethnic literature in the modern world is facilitated by the availability of variants of fairy tales and images, but the early recordings of fairy tales are particularly significant. The aim of the work is to seek to substantiate various directions of analysis of folklore texts collected and systematized at the beginning of the 20th century; to identify static and dynamic episodes in stories, descriptions of portraits and functions of main characters. The methodological basis of the research are the works of V. Y. Propp, V. P. Anikin, S. Y. Neklyudov, Yakut ethnographers and folklorists A. E. Kulakovsky and G. V. Ksenophontov. In the process of work, source and textual methods of philology are used. The results consist in the analysis of the “Bibliography of the Yakut Fairy Tale” by Pekarsky (1912) and Ergis (1964 - 1967); in the characterization of the archival sources of features of the early folklore texts of Granny Taаl-Taаl and Chaarchakhaan. In this regard, one of the significant conclusions is the clarification of common places in their stories, and in the functions of the characters - analogies with mythological images and ancient rites.

Design of metal-cutting tool coatings at the atomic level

The research aims to lower tooling costs by reducing the time allotted to designing coatings on domestic cemented carbide metal-cutting tools by using the atomic force approach. The object of the study is coatings on cemented carbides of the tungsten carbide group such as titanium carbide (TiC), titanium nitride (TiN), and titanium (Ti) coatings or a nitride-based titanium, chromium and aluminum (Ti,Cr,Al)N composite coating. To select the most rational coatings, the article employed the method of calculating the functionals of interatomic systems using the density functional description of single atoms. The simplest measure to reduce the cost of designing metal-cutting instruments for manufacturing parts made of difficult-to-machine materials is to develop coatings for this tool type. The article considers various atomic arrangements in the coating material in relation to the WCo8 cemented carbide (VK8, tungsten carbide-cobalt alloy containing 8% cobalt). The calculated values of the interaction energy of the coating material atoms with one another and with the cemented carbide material ranged from 3.04 to 3.5 J/m2. Moreover, the research has established a correlation between the calculation results and the performance parameter of metal-cutting tools considering fracture toughness K1c (MPa ∙ √m). The main result of the study is that the employed computational method made it possible to determine the adhesion value for the atoms of the above-mentioned coating materials with tungsten carbide and cobalt atoms packed in different scale configurations. This enables the classification of coatings from the perspective of ensuring maximum performance properties of the tooling material. The present article assumes that the higher the adhesion value, the better the performance properties. The hypothesis has been confirmed experimentally as well as by the values of fracture toughness K1c. Thus, the most rational coating options have been selected for specified operating conditions of a metal-cutting tool, which permits reduction of tool design costs and makes it possible to predict the performance properties of tools at the design stage.

Data-Driven Policy Iteration for Nonlinear Optimal Control Problems.

The design of optimal control laws for nonlinear systems is tackled without knowledge of the underlying plant and of a functional description of the cost function. The proposed data-driven method is based only on real-time measurements of the state of the plant and of the (instantaneous) value of the reward signal and relies on a combination of ideas borrowed from the theories of optimal and adaptive control problems. As a result, the architecture implements a policy iteration strategy in which, hinging on the use of neural networks, the policy evaluation step and the computation of the relevant information instrumental for the policy improvement step are performed in a purely continuous-time fashion. Furthermore, the desirable features of the design method, including convergence rate and robustness properties, are discussed. Finally, the theory is validated via two benchmark numerical simulations.

VEHICLES FOR DISABLED PEOPLE ON TESTS AT THE MOTOR TRANSPORT INSTITUTE IN WARSAW (1945-1990)

This extensive analytical article presents vehicles for disabled people, thatwere driving on the Polish roads in the years 1945-1990. Over the years,they have undergone detailed type-approval tests at the Motor TransportInstitute in Warsaw, thanks to which the original technical characteristicsand functional description of this type of vehicles have been analysed andpresented for the first time. The material was illustrated with numerousphotographs, drawings and tables, and appropriate conclusions were presentedat the end.

Genome-wide Identification of HvPP2C Genes and Expression Profiling in Response to Cold and Heat Stresses in Barley (Hordeum vulgare L.)

Background: Protein phosphatases (PP2Cs) are the main classes of protein phosphatases in plants, having pivotal functions in different plant stages and abiotic stresses. The PP2C genes are suggested to have critical roles in barley by exposure to heat and cold treatments. Objectives: We surveyed HvPP2C genes from the barley genome in the present study. Phylogenetic analysis, functional annotation, synteny analysis, chromosomal distribution, prediction of cis-elements, and gene expression of HvPP2Cs under abiotic stresses were studied. Methods: In this study, HvPP2Cs of barley were surveyed using bioinformatics tools, and HvPP2C gene expression profiles under cold and heat stresses in 3 tissues (root, leaf, and stem) were analyzed. Results: In this study, 61 HvPP2C genes were detected from barley, and a phylogenetic tree was divided into 13 subfamilies. The results of chromosomal distribution showed that the HvPP2C genes were located on 7 chromosomes. Real-time quantitative reverse transcription PCR (qRT-PCR) analysis of HvPP2Cs showed that they were largely expressed in different tissues (root, stem, and leaf) in the Azaran and Jolge barley cultivars. In Azaran, the HvPP2C gene expression increased in response to cold stress, whereas, in the Jolge cultivar, the HvPP2C gene expression increased in response to heat stress. The analysis of synteny revealed that HvPP2C24b with HvPP2C24a, HvPP2C24 with HvPP2C24a and HvPP2C24b; HvPP2C5 with HvPP2C5a, and HvPP2C41 with HvPP2C41a were paralogous. Conclusions: Results revealed a broad understanding of the HvPP2C gene family in barley, which can be valuable for the functional description of HvPP2Cs in plant response to abiotic stresses.

Semantic-Enriched Code Knowledge Graph to Reveal Unknowns in Smart Contract Code Reuse

Programmers who work with smart contract development often encounter challenges in reusing code from repositories. This is due to the presence of two unknowns that can lead to non-functional and functional failures. These unknowns are implicit collaborations between functions and subtle differences among similar functions. Current code mining methods can extract syntax and semantic knowledge (known knowledge), but they cannot uncover these unknowns due to a significant gap between the known and the unknown. To address this issue, we formulate knowledge acquisition as a knowledge deduction task and propose an analytic flow that uses the function clone as a bridge to gradually deduce the known knowledge into the problem-solving knowledge that can reveal the unknowns. This flow comprises five methods: clone detection, co-occurrence probability calculation, function usage frequency accumulation, description propagation, and control flow graph annotation. This provides a systematic and coherent approach to knowledge deduction. We then structure all of the knowledge into a semantic-enriched code Knowledge Graph (KG) and integrate this KG into two software engineering tasks: code recommendation and crowd-scaled coding practice checking. As a proof of concept, we apply our approach to 5,140 smart contract files available on Etherscan.io and confirm high accuracy of our KG construction steps. In our experiments, our code KG effectively improved code recommendation accuracy by 6% to 45%, increased diversity by 61% to 102%, and enhanced NDCG by 1% to 21%. Furthermore, compared to traditional analysis tools and the debugging-with-the-crowd method, our KG improved time efficiency by 30 to 380 seconds, vulnerability determination accuracy by 20% to 33%, and vulnerability fixing accuracy by 24% to 40% for novice developers who identified and fixed vulnerable smart contract functions.

Basic algorithm for approximation of the boundary trajectory of short-focus electron beam using the root-polynomial functions of the fourth and fifth order

The new iterative method of approximating the boundary trajectory of a short-focus electron beam propagating in a free drift mode in a low-pressure ionized gas under the condition of compensation of the space charge of electrons is considered and discussed in the article. To solve the given approximation task, the root-polynomial functions of the fourth and fifth order were applied, the main features of which are the ravine character and the presence of one global minimum. As an initial approach to solving the approximation problem, the values of the polynomial coefficients are calculated by solving the interpolation problem. After this, the approximation task is solved iteratively. All necessary polynomial coefficients are calculated multiple times, taking into account the values of the function and its derivative at the reference points. The final values of polynomial coefficients of high-order root-polynomial functions are calculated using the dichotomy method. The article also provides examples of the applying fourth-order and fifth-order root-polynomial functions to approximate sets of numerical data that correspond to the description of ravine functions. The obtained theoretical results are interesting and important for the experts who study the physics of electron beams and design modern industrial electron beam technological equipment.

МЕХАНИЗМЫ АКТУАЛИЗАЦИИ ТРУДОВЫХ ФУНКЦИЙ ДОЛЖНОСТНЫХ ЛИЦ В ОБЛАСТИ ИНФОРМАЦИОННОЙ БЕЗОПАСНОСТИ МЧС РОССИИ

The problem of adapting competency models of officials to the practice of current activities of employees is considered, using the example of solving problems of updating and specifying the labor functions of officials of EMERCOM of Russia, carrying out professional activities in the field of ensuring information security and information protection in the dynamic conditions of new threats to information security and innovative technologies for information protection. It is substantiated that in order to update the ontology of the subject area of labor functions in the field of information security in the specifics of the mission of EMERCOM of Russia, it is necessary to constantly update the list of labor functions taking into account modern conditions and trends in the development of science and technologies, as well as their specification for the accumulation of information, its rapid management for the formation of individual educational trajectories to reduce the deficit of competence qualities. To implement an infological description of job functions, it is advisable to use formalized approaches based on the automated generation of job descriptions. In order to implement a less time- and resource-intensive approach to managing the information entities of the job functions of officials and their specifications, it is proposed to use a problem-oriented information system to formulate job descriptions. The article presents artifacts of the conceptual, logical and physical levels of design of the corresponding software tool.