gebhart/patrepeval huggingface dataset:
Конфигурируемая система статической верификации модулей ядра операционных систем (2014)

Ядро операционной системы (ОС) представляет собой критичную в отношении надежности и производительности программную систему. Качество ядра современных ОС уже находится на достаточно высоком уровне. Иначе обстоит дело с модулями ядра, например, драйверами устройств, которые по ряду причин имеют существенно более низкий уровень качества. Одними из наиболее критичных и распространенных ошибок в модулях ядра являются нарушения правил корректного использования программного интерфейса ядра ОС. Выявить все такие нарушения в модулях или доказать их корректность потенциально можно с помощью инструментов статической верификации, которым для проведения анализа необходимо предоставить контрактные спецификации, описывающие формальным образом обязательства ядра и модулей по отношению друг к другу. В статье рассматриваются существующие методы и системы статической верификации модулей ядра различных ОС. Предлагается новый метод статической верификации модулей ядра ОС Linux, который позволяет конфигурировать процесс проверки на каждом из его этапов. Показывается, каким образом данный метод может быть адаптирован для проверки компонентов ядра других ОС. Описывается архитектура конфигурируемой системы статической верификации модулей ядра ОС Linux, реализующей предложенный метод, и демонстрируются результаты ее практического применения. В заключении рассматриваются направления дальнейшего развития.
Digital Twin as a Proxy for Industrial Cyber-Physical Systems (2023)

Digital twins (DTs) in industrial cyber-physical systems (ICPSs) are an essential concept for Industry 4.0. In recent years, DT architectures and frameworks for industry have been the focus of several research initiatives regarding analytics, predictive maintenance, virtual evaluation & verification, and fault detection & diagnosis. However, the resource constraint and battery-driven devices in an ICPS environment are facing challenges such as short life spans due to high energy consumption, lower availability of the services, and low security capabilities. To meet these challenges, this paper identifies some critical properties for DTs, including energy efficiency, high availability & state persistence, remote & contention control, and security. To provide services in ICPSs, we define the concept of a DT as a proxy (DTaaP) and a four-layer architectural model for the DTaaP that enables meeting the identified properties. We present a generic proof of concept (PoC) implementation by using Eclipse Ditto, which is an open-source digital twin framework. We evaluate our artifact against the listed properties through an experimental scenario. We show that the DTaaP improves energy efficiency, that the DT can serve as an anchor point for security, and that the DTaaP provides availability and persistence for duty cycling devices. We also identify some limitations of Eclipse Ditto for PoC DTaaP implementation, which can be a focus for future research.
Efficient Processing Pathways to Create High Interface Materials (2020)

Whereas physical chemistry and phase separation of the constituents can be used to direct the organization of multiphase materials, processing flows could be an alternative to create intricate multiphase structures. Generating interfaces on the bulk scale through traditional batch- or continuous-mixing processes is, however, energy and material intensive, and offers poor control. Here, we discuss an alternative based on interface creation using laminar flow in specific static mixers that force immiscible streams through splitting and recombination elements, which multiplies the layers per unit volume in a fractal manner and maximizes the area of interfacial contact. These techniques have mainly been used for polymeric systems so far, but the notion of hierarchical and fractal processing can be extended to other classes of soft materials. Increasingly thin multilayered liquid structures are remarkably stable, leading to very small droplets when they finally break up, thus opening a possible route towards energy-efficient emulsification, as will be discussed at the end of this chapter.
High-Mass-Loading Porous Ti3C2TxFilms for Ultrahigh-Rate Pseudocapacitors (2020)

Mass production of ordered and porous three-dimensional (3D) electrodes is a crucial prerequisite for practical energy storage devices. MXenes have drawn considerable attention as pseudocapacitive materials for outstanding electric conductivity and surface redox reactions; however, they face challenges for achieving 3D porous architectures especially at high mass loadings. Herein we propose a reduced-repulsion freeze-casting assembly concept via interlayer interaction engineering for constructing 3D porous Ti3C2Tx films, wherein interlayer repulsion is minimized via less electronegative functional groups and charge screening effect based on quantum calculations. 3D Ti3C2Tx films deliver a capacitance of 207.9 F g-1 at 10 V s-1, which demonstrates 58.6% capacitance retention with a 1000-fold scan rate increase. The capacitive performance is almost independent of electrode mass loading up to 16.18 mg cm-2, exhibiting ultrahigh areal capacitance of 3731 mF cm-2 and energy density of 336.7 μWh cm-2.
Reconstructing sharply folding surfaces: A convex formulation (2009)

In recent years, 3D deformable surface reconstruction from single images has attracted renewed interest. It has been shown that preventing the surface from either shrinking or stretching is an effective way to resolve the ambiguities inherent to this problem. However, while the geodesic distances on the surface may not change, the Euclidean ones decrease when folds appear. Therefore, when applied to discrete surface representations, such constant-distance constraints are only effective for smoothly deforming surfaces, and become inaccurate for more flexible ones that can exhibit sharp folds. In such cases, surface points must be allowed to come closer to each other. In this paper, we show that replacing the equality constraints of earlier approaches by inequality constraints that let the mesh representation of the surface shrink but not expand yields not only a more faithful representation, but also a convex formulation of the reconstruction problem. As a result, we can accurately reconstruct surfaces undergoing complex deformations that include sharp folds from individual images.
Prostate cancer susceptibility genes: lessons learned and challenges posed. (2003)

In most developed countries, prostate cancer is the most frequently diagnosed malignancy in men. The extent to which the marked racial/ethnic difference in its incidence rate is attributable to screening methods, environmental, hormonal and/or genetic factors remains unknown. A positive family history is among the strongest epidemiological risk factors for prostate cancer. It is now well recognized that the role of candidate genetic markers to this multifactorial malignancy is more difficult to identify than the identification of other cancer susceptibility genes. Indeed, despite the localization of several susceptibility loci, there has been limited success in identifying high-risk susceptibility genes analogous to BRCA1 or BRCA2 for breast and ovarian cancer. Nonetheless, three strong candidate susceptibility genes have been described, namely ELAC2 (chromosome 17p11/HPC2 region), 2'-5'-oligoadenylate-dependent ribonuclease L (RNASEL), a gene in the HPC1 region, and Macrophage Scavenger Receptor 1 (MSR1), a gene within a region of linkage on chromosome 8p. Additional studies using larger cohorts are needed to fully evaluate the role of these susceptibility genes in prostate cancer risk. It is also of interest to mention that a significant percentage of men with early-onset prostate cancer harbor germline mutation in the BRCA2 gene thus confirming its role as a high-risk prostate cancer susceptibility gene. Although initial segregation analyses supported the hypothesis that a number of rare highly penetrant loci contribute to the Mendelian inheritance of prostate cancer, current experimental evidence better supports the hypothesis that some of the familial risks may be due to inheritance of multiple moderate-risk genetic variants. In this regard, it is not surprising that analyses of genes encoding key proteins involved in androgen biosynthesis and action led to the observation of a significant association between a susceptibility to prostate cancer and common genetic variants in some of those genes.
A Novel Form of Neurotensin Post-translationally Modified by Arginylation (2005)

A novel bioactive form of neurotensin post-translationally modified at a Glu residue was isolated from porcine intestine. Purification of the peptide was guided by detection of intracellular Ca2+ release in SK-N-SH neuroblastoma cells. Using high resolution accurate mass analysis on an ion trap Fourier transform mass spectrometer, the post-translational modification was identified as arginine linked to the gamma-carboxyl of Glu via an isopeptide bond, and we named the newly identified peptide "arginylated neurotensin" (R-NT, N-(neurotensin-C5-4-yl)arginine). Although arginylation is a known modification of N-terminal amino groups in proteins, its presence at a Glu side chain is unique. The finding places neurotensin among the few physiologically active peptides that occur both in post-translationally modified and unmodified forms. Pharmacologically, we characterized R-NT for its ligand activity on three known neurotensin receptors, NTR1, -2, and -3, and found that R-NT has similar pharmacological properties to those of neurotensin, however, with a slightly higher affinity to all three receptors. We expressed the intracellular receptor NTR3 as a soluble protein secreted into the cell culture medium, which allowed characterization of its R-NT and neurotensin binding properties. The creation of soluble NTR3 also provides a potential tool for neutralizing neurotensin action in vivo and in vitro. We have shown that SK-N-SH neuroblastoma cells express NTR1 and NTR3 but not NTR2, suggesting that the Ca2+ mobilization elicited by R-NT is via NTR1.
IN SITU MONITORING OF THE ANTICANCER DRUG EFFLUX FROM DRUG RESISTANT LUNG CANCER CELLS (2008)

This paper presents the in situ quantitative monitoring of the anticancer drug doxorubicin (DOX) efflux from the drug resistant lung cancer cells NCI-H69AR by using a microelectrode array integrated compact electrochemical system. This ap- proach achieves a sensitive, quantitative, non invasive and real-time efflux assay that can help address drug resistance, a major therapeutic stumbling block for cancer chemotherapy. The efflux of anticancer drug doxorubicin (DOX) from NCI-H69AR lung cancer cells was extensively studied.
Formation of H2+ by Ultra-Low-Energy Collisions of Protons with Water Ice Surfaces (2011)

The molecular ion of dihydrogen (H2+) is produced by 1 eV collisions of protons (H+) on amorphous water ice surfaces. The reaction is also observed on crystalline ice surfaces, but with lower efficiency. Collisions of D+ on amorphous H2O and D2O ices yield D2+ on the former, subsequent to isotope exchange on the H2O surface. Ultra-low-energy collision-induced dihydrogen ion production is also observed from alkanol surfaces, with decreasing efficiency as the alkyl chain length increases. There is no corresponding reaction on solid hexane. This endothermic reaction, with implications for interstellar chemistry and plasma etching processes, is proposed to occur as a result of stabilization of the other reaction product, a hydroxyl radical (OH•), on water surfaces through hydrogen-bonding interactions with the surface. These results point to an interesting chemistry involving ultra-low-energy ions on molecular solids.
Securing Biochemical Samples Using Molecular Barcoding on Digital Microfluidic Biochips (2021)

Microfluidic biochips are being adopted today in point-of-care diagnostics, e.g., COVID-19 testing; therefore, it is critical to ensure integrity of bio-sample before bioassays are run on-chip. A security technique called molecular barcoding was recently proposed to thwart sample-forgery attacks in DNA forensics. Molecular barcoding refers to addition of unique DNA molecules in bio-samples, and the sequence of the added DNA sample serves as a distinct “barcode” for the sample. The existence of the added molecule can be validated using polymerase chain reaction (PCR) and gel electrophoresis. However, this security solution has several limitations: (1) the lack of robustness of the barcode molecules when they are added to other genomic DNA (e.g., samples collected for diagnostics); (2) the need for special bulk instrumentation for validation; (3) the need for human intervention during the overall process. To overcome the limitations, we design a set of robust molecular barcodes that can be validated using both traditional polymerase chain reaction and loop mediated isothermal amplification (LAMP). The validation using LAMP can be executed on a small-in-size and portable digital microfluidic biochip (DMFB). Our LAMP workflow includes a color-changing visual indicator for simple, rapid identification of the barcode existence in solutions. We first demonstrate the proposed security workflow using benchtop techniques. Next, we fabricate a printed circuit board (PCB)-based DMFB with heaters and demonstrate, for the first time, the LAMP assay on a DMFB.
Investigation of photorefractive self-pumped phase-conjugate mirrors in the presence of loss and high modulation depth (1992)

Previous theoretical models for linear and ring self-pumped phase-conjugate mirrors are reviewed and modified to include the effects of linear absorption. The nonlinear photorefractive response at high modulation depths, present when large electric fields are applied in semiconductor and sillenite materials, is included in the coupled wave equations for the ring mirror, and the equations are solved numerically. Results of the analysis show that phase-conjugate reflectivities can be severely limited because of both linear absorption and large-signal effects. The calculations are compared with actual measurements of ring mirrors by using InP and Bi12TiO2o.
Supplementary Data from Targeting the Temporal Dynamics of Hypoxia-Induced Tumor-Secreted Factors Halts Tumor Migration (2023)

&lt;p&gt;Supplementary Information includes supplemental experimental procedures, description of gene regulatory network, two tables, eight figures and a supplementary video. Supplementary Table S1. List of primers used Supplementary Table S2. Parameters used in the ODEs Supplementary Figure S1: Large T47D microtumors exhibit collective migration, hypoxia and aggressive phenotype. Supplementary video showing migration of a microtumor Supplementary Figure S2: Treatment of 150 and 600μm microtumors with conditioned media of 150μm microtumors (150/CM). Supplementary Figure S3: Morphology and multi-parameter flow cytometry on breast cancer metastatic pleural effusion cells. Supplementary Figure S4: Large microtumors of patient-derived primary cancer cells and xenograft cells showed migratory behavior. Supplementary Figure S5: Integrated regulatory network of tumor secretome factors and signaling molecules involved in microtumor migration. Supplementary Figure S6: HIF-1α inhibition at later time points does not inhibit migration of 600μm microtumors. Supplementary Figure S7: Effect of MMP inhibitor treatment on the collective migration of large microtumors of T47D cell line and patient-derived metastatic breast cancer (mBC) cells. Supplementary Figure S8: Effect of Anti-sE-CAD antibody treatment on the collective migration of large microtumors of T47D cells and patient-derived metastatic breast cancer (mBC) cells.&lt;/p&gt;
Mononuclear Phagocyte Differentiation, Activation, and Viral Infection Regulate Matrix Metalloproteinase Expression: Implications for Human Immunodeficiency Virus Type 1-Associated Dementia (2001)

The pathogenesis of human immunodeficiency virus type 1 (HIV-1)-associated dementia (HAD) is mediated mainly by mononuclear phagocyte (MP) secretory products and their interactions with neural cells. Viral infection and MP immune activation may affect leukocyte entry into the brain. One factor that influences central nervous system (CNS) monocyte migration is matrix metalloproteinases (MMPs). In the CNS, MMPs are synthesized by resident glial cells and affect the integrity of the neuropil extracellular matrix (ECM). To ascertain how MMPs influence HAD pathogenesis, we studied their secretion following MP differentiation, viral infection, and cellular activation. HIV-1-infected and/or immune-activated monocyte-derived macrophages (MDM) and human fetal microglia were examined for production of MMP-1, -2, -3, and -9. MMP expression increased significantly with MP differentiation. Microglia secreted high levels of MMPs de novo that were further elevated following CD40 ligand-mediated cell activation. Surprisingly, HIV-1 infection of MDM led to the down-regulation of MMP-9. In encephalitic brain tissue, MMPs were expressed within perivascular and parenchymal MP, multinucleated giant cells, and microglial nodules. These data suggest that MMP production in MP is dependent on cell type, differentiation, activation, and/or viral infection. Regulation of MMP expression by these factors may contribute to neuropil ECM degradation and leukocyte migration during HAD.
A simple method for the synthesis of perdeuterated aromatic hydrocarbons and heterocyclic compounds (1987)

A general method has been developed for the preparation of deuterated aromatic compounds that are useful for coal reaction studies and as internal standards for GC/MS analysis. The method requires little specialized equipment or synthesis expertise. A reaction mixture containing Cl, D/sub 2/O, and chromium is used to exchange deuterium for aromatic hydrogens at temperatures of 200/sup 0/ to 300/sup 0/C. A single set of reaction conditions can be used to prepare a wide range of deuterated aromatics with nearly complete exchange of aromatic hydrogen for deuterium and little or no chemical degradation of the reactant. When a 20:1 molar ratio of deuterium to aromatic hydrogen was used the isotopic purity of most species tested.
Semantic Representation of Neural Circuit Knowledge in Caenorhabditis elegans (2023)

In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology Causal Activity Modelling, or GO-CAM). In this study, we explored whether the GO-CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode <i>C. elegans</i> (<i>C. elegans</i> Neural Circuit Causal Activity Modelling (<i>Ce</i>N-CAM)). We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO<sub>2</sub>) avoidance behaviors could be faithfully represented with <i>Ce</i>N-CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate the <i>C. elegans</i> connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge.
Compact Transient Thermal Model of Microfluidically Cooled Three-Dimensional Stacked Chips With Pin-Fin Enhanced Microgap (2021)

Abstract Three-dimensional (3D) stacked integrated circuit (SIC) chips are one of the most promising technologies to achieve compact, high-performance, and energy-efficient architectures. However, they face a heat dissipation bottleneck due to the increased volumetric heat generation and reduced surface area. Previous work demonstrated that pin-fin enhanced microgap cooling, which provides fluidic cooling between layers could potentially address the heat dissipation challenge. In this paper, a compact multitier pin-fin single-phase liquid cooling model has been established for both steady-state and transient conditions. The model considers heat transfer between layers via pin-fins, as well as the convective heat removal in each tier. Spatially and temporally varying heat flux distribution, or power map, in each tier can be modeled. The cooling fluid can have different pumping power and directions for each tier. The model predictions are compared with detailed simulations using computational fluid dynamics/heat transfer (CFD/HT). The compact model is found to run 120–600 times faster than the CFD/HT model, while providing acceptable accuracy. Actual leakage power estimation is performed in this codesign model, which is an important contribution for codesign of 3D-SICs. For the simulated cases, temperatures could decrease 3% when leakage power estimation is adopted. This model could be used as electrical-thermal codesign tool to optimize thermal management and reduce leakage power.
Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis (2017)

Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL) approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS), and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients <i>ex vivo</i>. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models.