gebhart/patrepeval huggingface dataset:
Dip-and-Drag Lateral Force Spectroscopy for Measuring Adhesive Forces between Nanofibers (2016)

Adhesive interactions between nanofibers strongly influence the mechanical behavior of soft materials composed of fibrous networks. We use atomic force microscopy in lateral force mode to drag a cantilever tip through fibrous networks, and use the measured lateral force response to determine the adhesive forces between fibers of the order of 100 nm diameter. The peaks in lateral force curves are directly related to the detachment energy between two fibers; the data is analyzed using the Jarzynski equality to yield the average adhesion energy of the weakest links. The method is successfully used to measure adhesion forces arising from van der Waals interactions between electrospun polymer fibers in networks of varying density. This approach overcomes the need to isolate and handle individual fibers, and can be readily employed in the design and evaluation of advanced materials and biomaterials which, through inspiration from nature, are increasingly incorporating nanofibers. The data obtained with this technique may also be of critical importance in the development of network models capable of predicting the mechanics of fibrous materials.
High Performance Normally-off GaN MOSFETs on Si Substrates (2013)

The enhancement mode AlGaN/GaN hybrid MOS-HFETs on Si substrates have been demonstrated. The breakdown voltage of over 1.71 kV was achieved by investigating the epitaxial structure. Furthermore, a high integrity SiO 2 /Al 2 O 3 gate stack has been demonstrated for GaN MOSFETs. The SiO 2 film formed on GaN by the MW-PECVD exhibits good properties compared that by the LP-CVD. Then, by incorporating the advantages of both of SiO 2 with a high insulating characteristics and Al 2 O 3 with good interface characteristics, the SiO 2 /Al 2 O 3 gate stack structure has been employed in GaN MOS devices. It is shown that a low interface state density between gate insulator and GaN, a high breakdown field, and a large charge-to-breakdown by applying 3-nm Al 2 O 3 in this structure. The SiO 2 /Al 2 O 3 gate stack has also been applied to AlGaN/GaN hybrid MOS-HFET and excellent properties with the threshold voltage of 4.2 V and the maximum field-effect mobility of 192 cm 2 /Vs are shown in the transistor.
BayesImposter: Bayesian Estimation Based .bss Imposter Attack on Industrial Control Systems (2022)

Over the last six years, several papers used memory deduplication to trigger various security issues, such as leaking heap-address and causing bit-flip in the physical memory. The most essential requirement for successful memory deduplication is to provide identical copies of a physical page. Recent works use a brute-force approach to create identical copies of a physical page that is an inaccurate and time-consuming primitive from the attacker's perspective. Our work begins to fill this gap by providing a domain-specific structured way to duplicate a physical page in cloud settings in the context of industrial control systems (ICSs). Here, we show a new attack primitive - \textit{BayesImposter}, which points out that the attacker can duplicate the .bss section of the target control DLL file of cloud protocols using the \textit{Bayesian estimation} technique. Our approach results in less memory (i.e., 4 KB compared to GB) and time (i.e., 13 minutes compared to hours) compared to the brute-force approach used in recent works. We point out that ICSs can be expressed as state-space models; hence, the \textit{Bayesian estimation} is an ideal choice to be combined with memory deduplication for a successful attack in cloud settings. To demonstrate the strength of \textit{BayesImposter}, we create a real-world automation platform using a scaled-down automated high-bay warehouse and industrial-grade SIMATIC S7-1500 PLC from Siemens as a target ICS. We demonstrate that \textit{BayesImposter} can predictively inject false commands into the PLC that can cause possible equipment damage with machine failure in the target ICS. Moreover, we show that \textit{BayesImposter} is capable of adversarial control over the target ICS resulting in severe consequences, such as killing a person but making it looks like an accident. Therefore, we also provide countermeasures to prevent the attack.
Delphinidin Reduces Glucose Uptake in Mice Jejunal Tissue and Human Intestinal Cells Lines through FFA1/GPR40 (2017)

Anthocyanins are pigments with antihyperglycemic properties, and they are potential candidates for developing functional foods for the therapy or prevention of Diabetes mellitus type 2 (DM2). The mechanism of these beneficial effects of anthocyanins are, however, hard to explain, given their very low bioavailability due to poor intestinal absorption. We propose that free fatty acid receptor 1 (FFA1, also named GPR40), is involved in an inhibitory effect of the anthocyanidin delphinidin over intestinal glucose absorption. We show the direct effects of delphinidin on the intestine using jejunum samples from RF/J mice, and the human intestinal cell lines HT-29, Caco-2, and NCM460. By the use of specific pharmacological antagonists, we determined that delphinidin inhibits glucose absorption in both mouse jejunum and a human enterocytic cell line in a FFA1-dependent manner. Delphinidin also affects the function of sodium-glucose cotransporter 1 (SGLT1). Intracellular signaling after FFA1 activation involved cAMP increase and cytosolic Ca<sup>2+</sup> oscillations originated from intracellular Ca<sup>2+</sup> stores and were followed by store-operated Ca<sup>2+</sup> entry. Taken together, our results suggest a new GPR-40 mediated local mechanism of action for delphinidin over intestinal cells that may in part explain its antidiabetic effect. These findings are promising for the search for new prevention and pharmacological treatment strategies for DM2 management.
Plasmolysis induced by toluene in a cyoB mutant of Pseudomonas putida (2004)

The cyoABCDE gene cluster of Pseudomonas putida DOT-T1E encodes a terminal cytochrome oxidase. A 500-bp 'cyoB' DNA fragment was cloned in pCHESI Omega Km and used to generate a cyoB knock-out mutant in vivo. The mutant strain was not limited in the generation of proton-motif force, although when grown on minimal medium with glucose or citrate, the CyoB mutant exhibited a slight increase in duplication time with respect to the wild-type strain. This effect was even more pronounced when toluene was supplied in the gas phase. In consonance with the negative effect of toluene on the growth was the finding that the CyoB mutant was hypersensitive to sudden 0.3% (v/v) toluene shocks, in contrast with the wild-type strain. This effect was particularly exacerbated in cells that reached the stationary phase. The increased sensitivity to solvents of the CyoB mutant did not appear to be related to the inability of the cells to strengthen the membrane package or to induce the efflux pumps in response to the solvent, but rather to solvent-induced plasmolysis that may be triggered by wrinkles in the cytoplasmic membrane at the poles of the mutant cells, and invagination of the outer membranes, which eventually lead to cell death.
Making Personal Digital Assistants Aware of What They Do Not Know (2016)

Personal digital assistants (PDAs) are spoken (and typed) dialog systems that are expected to assist users without being constrained to a particular domain. Typically, it is possible to construct deep multi-domain dialog systems focused on a narrow set of head domains. For the long tail (or when the speech recognition is not correct) the PDA does not know what to do. Two common fallback approaches are to either acknowledge its limitation or show web search results. Either approach can severely undermine the user’s trust in the PDA’s intelligence if invoked at the wrong time. In this paper, we propose features that are helpful in predicting the right fallback response. We then use these features to construct dialog policies such that the PDA is able to correctly decide between invoking web search or acknowledging its limitation. We evaluate these dialog policies on real user logs gathered from a PDA, deployed to millions of users, using both offline (judged) and online (user-click) metrics. We demonstrate that our hybrid dialog policy significantly increases the accuracy of choosing the correct response, measured by analyzing click-rate in logs, and also enhances user satisfaction, measured by human evaluations of the replayed experience.
Direct Skin Friction Measurements with Shock-Impingement Compensation in Complex Turbulent Flows (2006)

Skin friction measurements are necessary to determine aerodynamic force impact on system performance. Direct and indirect methods are available to quantify skin friction, but only direct measurements eliminate the need for prior detailed understandi ng of the flow. One such direct measure gage uses a movable wall element or floating head, which is connected to some sort of flexure. A cantilever beam version of this gage allows the beam to flex to weaker wall shear forces while remaining stiff relati ve to stronger pressure forces normal to the head. Because shock impingement on or near the floating element has been shown to lead to major errors, this paper provides the results of employing a four -strain gage configuration into two separate Wheatstone bridges. This provides a way to separately measure the moment caused by any pressure differentials across the element surface, such as that produced by an impinging shock, in addition to the shear. Initial testing in a Mach 4 flow with and without shock impingement has demonstrated the utility of the approach. This design successfully measures shear and moment while obviating pressure and acceleration effects.
ChemInform Abstract: Radical Addition to the Carbonyl Carbon of Ketones Promoted by Aqueous Titanium Trichloride in Acidic Medium: One Step Synthesis of Pinacols and Lactones. (1986)

Abstract Die Ketone (Ia)‐(Id) reagieren nach A) unter Bildung der Pinakole (II), wobei neben (IIb)‐(IId) auch der Alkohol (III) und das Dimere (IV) entstehen.
Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots (2016)

Massive parallel analysis using array technology has become the mainstay for analysis of genomes and transcriptomes. Analogously, the predominance of phosphorylation as a regulator of cellular metabolism has fostered the development of peptide arrays of kinase consensus substrates that allow the charting of cellular phosphorylation events (often called kinome profiling). However, whereas the bioinformatical framework for expression array analysis is well-developed, no advanced analysis tools are yet available for kinome profiling. Especially intra-array and interarray normalization of peptide array phosphorylation remain problematic, due to the absence of "housekeeping" kinases and the obvious fallacy of the assumption that different experimental conditions should exhibit equal amounts of kinase activity. Here we describe the development of analysis tools that reliably quantify phosphorylation of peptide arrays and that allow normalization of the signals obtained. We provide a method for intraslide gradient correction and spot quality control. We describe a novel interarray normalization procedure, named repetitive signal enhancement, RSE, which provides a mathematical approach to limit the false negative results occuring with the use of other normalization procedures. Using in silico and biological experiments we show that employing such protocols yields superior insight into cellular physiology as compared to classical analysis tools for kinome profiling.
Synthesis and biological activity of L-5-deazafolic acid and L-deazaaminopterin: synthetic strategies to 5-deazapteridines (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and biological activity of L-5-deazafolic acid and L-deazaaminopterin: synthetic strategies to 5-deazapteridinesEdward C. Taylor, David C. Palmer, Thomas J. George, Stephen R. Fletcher, Chi Ping Tseng, Peter J. Harrington, G. Peter Beardsley, Donald J. Dumas, Andre Rosowsky, and Michael WickCite this: J. Org. Chem. 1983, 48, 25, 4852–4860Publication Date (Print):December 1, 1983Publication History Published online1 May 2002Published inissue 1 December 1983https://pubs.acs.org/doi/10.1021/jo00173a014https://doi.org/10.1021/jo00173a014research-articleACS PublicationsRequest reuse permissionsArticle Views449Altmetric-Citations66LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cyclin D–Cdk4 is regulated by GATA-1 and required for megakaryocyte growth and polyploidization (2007)

Endomitosis is a unique form of cell cycle used by megakaryocytes, in which the latter stages of mitosis are bypassed so that the cell can increase its DNA content and size. Although several transcription factors, including GATA-1 and RUNX-1, have been implicated in this process, the link between transcription factors and polyploidization remains undefined. Here we show that GATA-1-deficient megakaryocytes, which display reduced size and polyploidization, express nearly 10-fold less cyclin D1 and 10-fold increased levels of p16 compared with their wild-type counterparts. We further demonstrate that cyclin D1 is a direct GATA-1 target in megakaryocytes, but not erythroid cells. Restoration of cyclin D1 expression, when accompanied by ectopic overexpression of its partner Cdk4, resulted in a dramatic increase in megakaryocyte size and DNA content. However, terminal differentiation was not rescued. Of note, polyploidization was only modestly reduced in cyclin D1-deficient mice, likely due to compensation by elevated cyclin D3 expression. Finally, consistent with an additional defect conferred by increased levels of p16, inhibition of cyclin D-Cdk4 complexes with a TAT-p16 fusion peptide significantly blocked polyploidization of wild-type megakaryocytes. Together, these data show that GATA-1 controls growth and polyploidization by regulating cyclin D-Cdk4 kinase activity.
ON THE POTENTIAL FOR GUIDANCE OF ABLATION THERAPY USING ACOUSTIC RADIATION FORCE IMPULSE IMAGING (2007)

Acoustic radiation force imaging methods utilize acoustic radiation force to mechanically excite tissue, and the tissue response is monitored with conventional imaging methods. Radiation force based methods comprise a subset of elasticity imaging, in which images reflect relative differences in tissue stiffness. Acoustic radiation force impulse (ARFI) imaging is one such method that is implemented on a modified diagnostic ultrasound scanner, using the same transducer for the excitation and monitoring of the tissue response. ARFI imaging is under investigation for its potential to monitor thermal ablation procedures because thermal lesions are associated with considerable (> 4 times) stiffness increases as compared to viable tissue. Applications include monitoring radiofrequency ablation procedures in the liver, kidney, and heart, and monitoring focused ultrasound ablation procedures. We present results from ongoing studies in these areas
Low‐Temperature Sintering and Dielectric Properties of Ag(Nb,Ta)O 3 Composite Ceramics (2002)

The sintering behavior and dielectric properties of perovskite Ag(Nb 1− x Ta x )O 3 (0 &lt; x &lt; 1) solid solutions and two‐phase composite assemblages were explored. A small amount of CuO (1 wt%) was used for liquid‐phase sintering and led to high densification at temperatures &lt;950°C. The temperature coefficient of capacitance, TCC, was adjusted by varying the Nb:Ta ratio within the solid‐solution series and by creating composite microstructures. Two‐phase assemblages consisting of Ag(Nb 3/4 Ta 1/4 )O 3 and Ag(Nb 1/4 Ta 3/4 )O 3 were synthesized to achieve a temperature‐stable dielectric material for high‐frequency applications. The composite dielectric with CuO addition had an average dielectric constant of 390 and a Q × f factor of 410 GHz at 2 GHz, with a stable TCC (0 to −180 ppm/°C) in the temperature range from −20° to +60°C. In addition, process compatibility with a silver conductor was confirmed by high‐frequency ring‐resonator measurements and microstructural characterization. The Ag(Nb 1− x Ta x )O 3 solid solutions and composites are promising candidates as embedded capacitors for radio‐frequency/microwave applications.
Sensitivity analysis and optimization of sub-wavelength optical gratings using adjoints (2014)

Numerical optimization of photonic devices is often limited by a large design space the finite-differences gradient method requires as many electric field computations as there are design parameters. Adjoint-based optimization can deliver the same gradients with only two electric field computations. Here, we derive the relevant adjoint formalism and illustrate its application for a waveguide slab, and for the design of optical sub-wavelength gratings.
The viscosity of short polyelectrolyte solutions (2013)

We consider the viscosity of solutions of highly charged short polyelectrolytes. Our system is a poly(styrene-maleic acid) copolymer solution (SMA) with various added salt concentrations in dilute and semidilute regimes. The SMA solutions show some particular features: (i) variations of the specific viscosity measured for different values of concentration and ionic strength can be rescaled on two universal curves when plotted as a function of the effective volume fraction; (ii) the reduced viscosity is proportional to the Debye length. In order to describe the viscosity of such a system we model the motion of the charged rods considering a simpler system: we replace each charged rod and its corresponding charge cloud by an effective neutral rod. This modified system is yet below the concentrated regime and, at most, steric interactions are left. In the semidilute regime, we model the rescaled rods moving under a mean field potential and obtain a dynamical equation for the orientational tensor, considered small, and the viscosity is derived from it. Within our mean field approach, the effects due to the rod Brownian motion and due to the potential cancel each other and the behavior of the viscosity is explained in terms of the effective volume fraction only. Our predictions are in good qualitative agreement with the experimental results over a wide range of parameters, and suggest a method for obtaining the rotational diffusion constant in the semidilute regime.
Sur la normalisation de la matrice Laplacienne en partitionnement spectral (2017)

International audience
Use of machine learning derived features from CT and H&E whole-slide images to predict overall survival in head and neck squamous cell carcinoma. (2023)

6086 Background: Computed tomography (CT) and H&amp;E whole-slide images (WSI) have been found to carry rich prognostic information for patients diagnosed with head and neck squamous cell carcinoma (HNSCC). However, most machine learning models aimed for outcome prediction only took advantage of single image modality. In this work, we developed and validated a prognostic machine learning method incorporating both CT and WSI to predict overall survival in HNSCC patients. Methods: Matched radiographic CT scans and digitized WSI were acquired from the Cleveland Clinic for 167 HNSCC patients, including 120 HPV-associated oropharyngeal cancer and 47 laryngeal cancer. Both primary tumor and the largest suspicious lymph node were annotated on CT scans and primary tumor was delineated on H&amp;E WSI. We split the dataset into training and validation set using a 7:3 ratio, which resulted in 119 patients in the training set and 48 for hold-out validation. We applied a machine learning model (M_ML) using both CT and WSI as input to perform end-to-end predictions of overall survival. We used the harrell’s concordance index (C-index) to evaluate the prognostic performance. Finally, we performed the multivariable cox proportional hazard analysis adjusting for clinicopathological variables (i.e. age, gender, smoking pack-year [PY], AJCC 7 th edition overall stage, and treatment modality) to validate the independent prognostic significance of the model. Results: The combined machine learning model M_ML (C-index = 0.81) outperformed the model using CT images alone (C-index = 0.63) and WSI alone (C-index = 0.64) on the validation set. In multivariable analysis, M_ML is still statistically significant accounting for clinicopathologic factors (p = 0.0007). Conclusions: This pilot study shows that a multi-omic machine learning model utilizing both radiographic CT and digitized WSI can predict HNSCC overall survival and outperforms models using only a single modality. [Table: see text]
Synthesis and in vitro evaluation of F-18 labeled fluoroalkyl phenylalanine derivatives as potential PET imaging agents (2010)

297 Objectives A number of phenylalanine and tyrosine derivatives have proven to be useful tumor imaging agents. In particular, O-(2-[F-18]fluoroethyl)-L-tyrosine (FET) has shown success in imaging brain tumors but limited applicability in imaging peripheral tumors. Our goal is to develop new phenylalanine derivatives with better tumor-avid characteristics than FET. Two new ligands, p-(2-[F-18]fluoroethyl)-L-phenylalanine (FEP) and p-(3-[F-18]fluoropropyl)-L-phenylalanine (FPP) were synthesized and evaluated. Methods Precursors of FEP and FPP were synthesized via triflation, Stille cross-coupling, hydroboration-oxidation and subsequent tosylation reactions from protected L-tyrosine. The F-18 ligands were prepared via nucleophilic substitution with [F-18]KF-K2.2.2 complex or [F-18]TBAF, followed by deprotection with trifluoroacetic acid. The uptake of ligands into 9L rat glioma cells was determined and the results were compared to FET uptake. Results Precursors for labeling were prepared with 34 to 60% yield. Enantiomerically pure FEP and FPP could be obtained using [F-18]TBAF for radiofluorination. Optically pure ligands were synthesized in 100 min with 17-28% yield and an average specific activity of 15 GBq/µmol at the end of synthesis. In vitro studies showed FPP had comparable uptake with FET, while FEP uptake was significantly (40%) higher than FET in 9L cells. Conclusions Initial studies suggest that the new F-18 fluoroalkyl phenylalaine derivatives are potentially useful amino acid tracers for PET imaging and further development of these ligands is warranted