gebhart/patrepeval huggingface dataset:
Surface Polarity of Dimethylsiloxane‐Grafted Silica Particles (2005)

Abstract Summary: The surface polarity of dimethylsiloxane‐grafted silica particles (DMS/silica) has been studied as a function of surface coverage by measuring the UV/Vis spectra of coadsorbed solvatochromic probes. Fe(phen) 2 (CN) 2 [ cis ‐dicyano‐bis‐(1,10)‐phenanthroline‐iron( II ), ( 1 )] Michler's ketone [4,4′‐bis( N , N ‐dimethylamino)‐benzophenone, ( 2 )], coumarine 153 ( 3 ) and 3‐(4‐amino‐3‐methylphenyl)‐7‐phenylbenzo[1,2 b :4,5 b ′]difuran‐2,6‐dione ( 4 ) were used as solvatochromic surface polarity indicators. Kamlet–Taft's α (hydrogen bond acidity), β (hydrogen bond basicity), and π * (dipolarity/polarizability) parameters of the DMS/solid acid interfaces were calculated using different LSE relationships of data sets of the probes 1 and 2 or 3 (for α and π *) as well as 1 and 4 (for β ). The values for α decrease significantly with increasing conversion of silanol groups with grafted DMS chains. Then, α asymptotically approachs a constant value when more than about 75% of the residual silanols on the surface are grafted with DMS when measured in 1,2‐dichloroethane slurry. The π * values of DMS/silica solvent interfaces seems unaffected by the degree of surface functionalization. The β values of DMS and grafted DMS/silica are clearly lower than the values for α and π *. Solvatochromic probes used for the study of the surface polarity of dimethylsiloxane‐grafted silica particles. magnified image Solvatochromic probes used for the study of the surface polarity of dimethylsiloxane‐grafted silica particles.
Pharmacological Inhibition of O-GlcNAcase Does Not Increase Sensitivity of Glucocorticoid Receptor-Mediated Transrepression (2015)

Glucocorticoid signaling regulates target genes by multiple mechanisms, including the repression of transcriptional activities of nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) though direct protein-protein interactions and subsequent O-GlcNAcylation of RNA polymerase II (pol II). Recent studies have shown that overexpression of O-linked β-N-acetylglucosamine transferase (OGT), which adds an O-linked β-N-acetylglucosamine (O-GlcNAc) group to the C-terminal domain of RNA pol II, increases the transrepression effects of glucocorticoids (GC). As O-GlcNAcase (OGA) is an enzyme that removes O-GlcNAc from O-GlcNAcylated proteins, we hypothesized that the potentiation of GC effects following OGT overexpression could be similarly observed via the direct inhibition of OGA, inhibiting O-GlcNAc removal from pol II. Here we show that despite pharmacological evidence of target engagement by a selective small molecule inhibitor of OGA, there is no evidence for a sensitizing effect on glucocorticoid-mediated effects on TNF-α promoter activity, or gene expression generally, in human cells. Furthermore, inhibition of OGA did not potentiate glucocorticoid-induced apoptosis in several cancer cell lines. Thus, despite evidence for O-GlcNAc modification of RNA pol II in GR-mediated transrepression, our data indicate that pharmacological inhibition of OGA does not potentiate or enhance glucocorticoid-mediated transrepression.
Atrial fibrillation complicating acute myocardial infarction: how should it be interpreted and how should it be treated and prevented? (2009)

clinical features and prognostic implications' , by J. Schmitt et al., on page 1038 Atrial fibrillation (AF) has been reported to complicate the course of acute myocardial infarction (AMI) in 6-21% of hospitalized patients. 1 Possible precipitating factors of AF in this setting include atrial ischaemia or infarction, right ventricular infarction, pericardial inflammation, acute hypoxia or hypokalaemia, and haemodynamic impairment secondary to left ventricular (LV) dysfunction. 2 -4 Endogenous or exogenous catecholamines may also precipitate AF. These factors can be found alone or in combination, and may superimpose on predisposing diseases affecting cardiac anatomy and physiology, such as previous cardiomyopathy, valvular impairment, or chronic lung disease. Finally, AF in the setting of AMI has been reported to be associated with ageing, severely impaired LV function, presence of mitral regurgitation, or frequent ventricular arrhythmias plus right bundle branch block, and presence of left bundle branch block. Although most of these factors are claimed to be causative of AF, the intimate relationship between their presence and AF occurrence is not known. Despite the variability of factors and conditions associated with AF in clinical practice, patients developing this arrhythmia during AMI are usually reported as a uniform category.
On the Planar Damped Linear Vibrations of a Rigid Body (1999)

Abstract The planar motion associated with a damped mode of a vibrating rigid body is actually not well understood. This paper shows that a damped mode is a rotation about a point that is either translating along a straight line or is stationary, depending on how much damping is present. The transition between each type of damping is explained and an example illustrates the results.
Unwrapping differential x-ray phase-contrast images through phase estimation from multiple energy data (2013)

We present a spectral phase unwrapping approach for grating-based differential phase-contrast data where the unwrapped interferometer phase shift is estimated from energy discriminated measurements using maximum likelihood principles. We demonstrate the method on tomographic data sets of a test specimen taken at different x-ray energies using synchrotron radiation. The proposed unwrapping technique was demonstrated to successfully correct the data set for phase wrapping.
Abstract 2056: MicroRNA-126 inhibits SOX2 expression in gastric cancer cells (2010)

Abstract A transcription factor SOX2 is essential for embryonic development and play critical roles in the maintenance of embryonic stem cell's pluripotency. We previously reported that SOX2 plays important roles in growth inhibition through cell cycle arrest and apoptosis, and SOX2 expression was frequently down-regulated in gastric cancers, some of which were due to aberrant DNA methylation. However, the mechanisms underlying loss of SOX2 expression and its target genes involved in gastric carcinogenesis remain largely unknown. In this study, we initially assessed whether microRNAs, small noncoding RNAs, control SOX2 expression in gastric cancers. In silico analysis revealed that microRNA-126 (miR-126) has two predictive target sites in the 3′-UTR of the SOX2 mRNA. Gain- and loss-of function experiments demonstrated that miR-126 inhibited SOX2 expression in gastric cancer cell lines. Luciferase reporter assays with a pGL4-SOX2 3′-UTR vector revealed that miR-126 directly inhibits SOX2 expression by targeting two binding sites in the 3′-UTR of the SOX2 mRNA independently. Some primary gastric cancer tissues with low expression of SOX2 exhibited markedly high levels of miR-126 expression compared with paired non-cancerous mucosae. To further understand the potential effects of miR-126-induced down-regulation of SOX2 on gastric carcinogenesis, we next attempted to identify the downstream target genes of SOX2 in gastric cancer cells. The microarray analysis after SOX2 over-expression in a gastric cancer cell line showed that 437 genes were up-regulated (&amp;gt;2-fold) and 447 genes were down-regulated (&amp;lt;0.5-fold), some of which were cancer-related genes. Taken together, we identified miR-126 as a novel microRNA which inhibits SOX2 expression in gastric cancer cells, and suggest that aberrant miR-126 expression and consequent SOX2 down-regulation may contribute to gastric carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2056.
Nano-electromechanical spatial light modulator enabled by asymmetric resonant dielectric metasurfaces (2022)

Spatial light modulators (SLMs) play essential roles in various free-space optical technologies, offering spatio-temporal control of amplitude, phase, or polarization of light. Beyond conventional SLMs based on liquid crystals or microelectromechanical systems, active metasurfaces are considered as promising SLM platforms because they could simultaneously provide high-speed and small pixel size. However, the active metasurfaces reported so far have achieved either limited phase modulation or low efficiency. Here, we propose nano-electromechanically tunable asymmetric dielectric metasurfaces as a platform for reflective SLMs. Exploiting the strong asymmetric radiation of perturbed high-order Mie resonances, the metasurfaces experimentally achieve a phase-shift close to 290<sup>∘</sup>, over 50% reflectivity, and a wavelength-scale pixel size. Electrical control of diffraction patterns is also achieved by displacing the Mie resonators using nano-electro-mechanical forces. This work paves the ways for future exploration of the asymmetric metasurfaces and for their application to the next-generation SLMs.
Bactericidal/permeability‐increasing protein's signaling pathways and its retinal trophic and anti‐angiogenic effects (2006)

Bactericidal/permeability-increasing protein (BPI) was originally identified as a lipopolysaccharide (LPS) binding protein with gram-negative bactericidal activity in the leukocytes. In this study, we characterized the previously unknown effects of BPI in the eye and the molecular mechanisms involved in its action. BPI mRNA was detected in bovine retina; retinal pigment epithelium; and primary cultures of bovine retinal pigment epithelial cells (RPE), pericytes (RPC), and endothelial cells (REC); while BPI protein was measured in human vitreous and plasma. BPI, but not control protein thaumatin, activated extracellular regulated kinase (ERK) and AKT, and increased DNA synthesis in RPE and RPC but not in REC. A human recombinant 21 kDa modified amino-terminal fragment of BPI (rBPI21) reduced H2O2-induced apoptosis in RPE and inhibited vascular endothelial growth factor (VEGF)-stimulated ERK phosphorylation in REC when preincubated with VEGF. Intraperitoneal (i.p.)-injected rBPI21 reduced ischemia-induced retinal neovascularization and diabetes-induced retinal permeability. Since BPI has unusual dual properties of promoting RPC and RPE growth while suppressing VEGF-induced REC growth and vascular permeability, the mechanistic understanding of BPI's action may provide novel therapeutic opportunities for diabetic retinopathy and age-related macular degeneration.
FewNLU: Benchmarking State-of-the-Art Methods for Few-Shot Natural Language Understanding (2021)

The few-shot natural language understanding (NLU) task has attracted much recent attention. However, prior methods have been evaluated under a disparate set of protocols, which hinders fair comparison and measuring progress of the field. To address this issue, we introduce an evaluation framework that improves previous evaluation procedures in three key aspects, i.e., test performance, dev-test correlation, and stability. Under this new evaluation framework, we re-evaluate several state-of-the-art few-shot methods for NLU tasks. Our framework reveals new insights: (1) both the absolute performance and relative gap of the methods were not accurately estimated in prior literature; (2) no single method dominates most tasks with consistent performance; (3) improvements of some methods diminish with a larger pretrained model; and (4) gains from different methods are often complementary and the best combined model performs close to a strong fully-supervised baseline. We open-source our toolkit, FewNLU, that implements our evaluation framework along with a number of state-of-the-art methods.
Complete Disruption of Autism-Susceptibility Genes by Gene-Editing Predominantly Reduces Functional Connectivity of Isogenic Human Neurons (2018)

Summary Autism Spectrum Disorder is phenotypically and genetically heterogeneous, but genomic analyses have identified candidate susceptibility genes. We present a CRISPR gene editing strategy to insert a protein tag and premature termination sites creating an induced pluripotent stem cell (iPSC) knockout resource for functional studies of 10 ASD-relevant genes ( AFF2/FMR2, ANOS1, ASTN2, ATRX , CACNA1C , CHD8, DLGAP2, KCNQ2 , SCN2A , TENM1 ). Neurogenin 2 (NEUROG2)-directed differentiation of iPSCs allowed production of cortical excitatory neurons, and mutant proteins were not detectable. RNAseq revealed convergence of several neuronal networks. Using both patch-clamp and multi-electrode array approaches, the electrophysiological deficits measured were distinct for different mutations. However, they culminated in a consistent reduction in synaptic activity, including reduced spontaneous excitatory post-synaptic current frequencies in AFF2/FMR2- , ASTN2-, ATRX -, KCNQ2 - and SCN2A -null neurons. Despite ASD susceptibility genes belonging to different gene ontologies, isogenic stem cell resources can reveal common functional phenotypes, such as reduced functional connectivity.
Design considerations and performance of a variable gain, variable bandwidth signal processing circuit for acoustoelectric imaging (2017)

Acoustoelectric imaging (AEI) is a new technique for mapping current densities at high resolution depending on the size of the ultrasound (US) focus. The design and performance of the recording system is crucial for efficient AEI because the amplitude of the AE signal in biological tissue is on the order of a microvolt or less. In this direction, an AE signal processing circuit (AE-SPC), containing high voltage pulse suppressor, variable gain amplifiers, and variable frequency bandpass filters (BPF) is developed to minimize sources of noise and maximize sensitivity for signal detection. AE-SPC is tested and evaluated using both simulations and bench-top testing. The design may be optimal for AE mapping of weak electric currents in excitable tissue, such as the heart and brain.
Entropically Driven Self‐Assembly of Lysinibacillus sphaericus S‐Layer Proteins Analyzed Under Various Environmental Conditions (2009)

S-Layer proteins are an example of bionanostructures that can be exploited in nanofabrication. In addition to their ordered structure, the ability to self-assembly is a key feature that makes them a promising technological tool. Here, in vitro self-assembly kinetics of SpbA was investigated, and found that it occurs at a rate that is dependent on temperature, its concentration, and the concentration of calcium ions and sodium chloride. The activation enthalpy (120.81 kJ . mol(-1)) and entropy (129.34 J . mol(-1) . K(-1)) obtained infers that the incorporation of monomers incurs in a net loss of hydrophobic surface. By understanding how the protein monomers drive the self-assembly at different conditions, the rational optimization of this process was feasible.
Long-term efficacy and predictors of remission following adalimumab treatment in peripheral spondyloarthritis: 3-year results from ABILITY-2 (2018)

In patients with pSpA, early response to adalimumab, but not baseline demographics or disease characteristics, was a better predictor of long-term remission.
The Effect of Articular Cartilage Focal Defect Size and Location in Whole Knee Biomechanics Models (2019)

Articular cartilage focal defects are common soft tissue injuries potentially linked to osteoarthritis (OA) development. Although several defect characteristics likely contribute to osteoarthritis, their relationship to local tissue deformation remains unclear. Using finite element models with various femoral cartilage geometries, we explore how defects change cartilage deformation and joint kinematics assuming loading representative of the maximum joint compression during the stance phase of gait. We show how defects, in combination with location-dependent cartilage mechanics, alter deformation in affected and opposing cartilages, as well as joint kinematics. Small and average sized defects increased maximum compressive strains by approximately 50% and 100%, respectively, compared to healthy cartilage. Shifts in the spatial locations of maximum compressive strains of defect containing models were also observed, resulting in loading of cartilage regions with reduced initial stiffnesses supporting the new, elevated loading environments. Simulated osteoarthritis (modeled as a global reduction in mean cartilage stiffness) did not significantly alter joint kinematics, but exacerbated tissue deformation. Femoral defects were also found to affect healthy tibial cartilage deformations. Lateral femoral defects increased tibial cartilage maximum compressive strains by 25%, while small and average sized medial defects exhibited decreases of 6% and 15%, respectively, compared to healthy cartilage. Femoral defects also affected the spatial distributions of deformation across the articular surfaces. These deviations are especially meaningful in the context of cartilage with location-dependent mechanics, leading to increases in peak contact stresses supported by the cartilage of between 11% and 34% over healthy cartilage.
Stray-light effects of diffractive beam-shaping elements in optical microsystems (1999)

The use of diffractive beam-shaping elements in hybrid or monolithic microsystems is investigated. Compact optical systems require diffractive structures with small grating periods for creating large deflection angles. Such elements are difficult to fabricate while a low stray-light level is maintained. In addition, because of the small geometrical dimensions and the short propagation lengths in an optomechanical microsystem, any stray light generated by the diffractive structure critically affects the overall optical performance. A model for the estimation of the interference effects between the designed and the unwanted diffraction orders is developed and applied to an example of a collimating diffractive optical element. On the basis of theoretical and experimental results, design rules for the application of diffractive beam-shaping elements in microsystems are derived.
Severe Acute Respiratory Syndrome (2004)

Lung changes on thin-section computed tomography of severe acute respiratory syndrome patients improved with time during the convalescent period and showed a significant correlation with advanced age, parameters indicating severe illness, and diffusion capacity adjusted for hemoglobin on follow-up.
Vocabulometer, a Web Platform for Ubiquitous Language Learning (2018)

The Vocabulometer is a reading assistant system designed to record the reading activity of a user and to extract mutual information about the users and the read documents. The Vocabulometer stands as a web platform and offers services for analyzing which word is read at which time, estimating the reading skill of the user, the level of difficulty of a document, and recommending reading materials according to the user's vocabulary. For now the system is based on eye tracking but in the future we plan to make a smartphone application which do not need additional hardware.
Cognitive Distributed Computing and Its Impact on Information Technology (IT) as We Know It (2017)

The International Summit is4si-2017, Digitalisation for a Sustainable Society: Embodied, Embedded, Networked, Empowered through Information, Computation &amp; Cognition, was held 12–16 June 2017 at Chalmers University of Technology Conference Center in Gothenburg, Sweden. [...]
Supplementary Figure 3 from Fibroblast Growth Factor Receptor 1–Transformed Mammary Epithelial Cells Are Dependent on RSK Activity for Growth and Survival (2023)

Supplementary Figure 3 from Fibroblast Growth Factor Receptor 1–Transformed Mammary Epithelial Cells Are Dependent on RSK Activity for Growth and Survival
Sound Waves and the Absence of Galilean Invariance in Flocks (1998)

We study a model of flocking for a very large system $(N\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}320000)$ numerically. We find that in the long wavelength, long time limit, the fluctuations of the velocity and density fields are carried by propagating sound modes, whose dispersion and damping agree quantitatively with the predictions of our previous work using a continuum equation. We find that the sound velocity is anisotropic and characterized by its speed $c$ for propagation perpendicular to the mean velocity $〈\stackrel{\ensuremath{\rightarrow}}{v}〉$, $〈\stackrel{\ensuremath{\rightarrow}}{v}〉$ itself, and a third velocity $\ensuremath{\lambda}〈\stackrel{\ensuremath{\rightarrow}}{v}〉$, arising explicitly from the lack of Galilean invariance in flocks.
Zur Synthese von 1,3‐Dimercaptobenzolen aus Resorcinen über die Newman‐Kwart‐Umlagerung (1973)

Abstract Resorcin und seine substituierten Derivate 3b–d, 7a und b werden mit Dimethylthiocarbamoylchlorid zu den entsprechenden Thiocarbamidsäure‐ O ‐arylestern 5a–d, 8a und b umgesetzt. Bei höherer Temperatur isomerisieren diese O ‐Arylester – in der sogenannten Newman‐Kwart ‐Umlagerung – zu den Thiocarbamidsäure‐S‐arylestern 10a–c, 11a und b , deren anschließende alkalische Hydrolyse die Mercapto‐ und 1,3‐Dimercaptobenzole 12a–e liefert.
StackVault: Protection from Untrusted Functions (2019)

Data exfiltration attacks have led to huge data breaches. Recently, the Equifax attack affected 147M users and a third-party library - Apache Struts - was alleged to be responsible for it. These attacks often exploit the fact that sensitive data are stored unencrypted in process memory and can be accessed by any function executing within the same process, including untrusted third-party library functions. This paper presents StackVault, a kernel-based system to prevent sensitive stack-based data from being accessed in an unauthorized manner by intra-process functions. Stack-based data includes data on stack as well as data pointed to by pointer variables on stack. StackVault consists of three components: (1) a set of programming APIs to allow users to specify which data needs to be protected, (2) a kernel module which uses unforgeable function identities to reliably carry out the sensitive data protection, and (3) an LLVM compiler extension that enables transparent placement of stack protection operations. The StackVault system automatically enforces stack protection through spatial and temporal access monitoring and control over both sensitive stack data and untrusted functions. We implemented StackVault and evaluated it using a number of popular real-world applications, including gRPC. The results show that StackVault is effective and efficient, incurring only up to 2.4% runtime overhead.