gebhart/patrepeval huggingface dataset:
Adsorption of a Polyampholyte Chain on a Charged Surface. (1997)

We discuss the adsorption of a single polyampholyte chain with degree of polymerization N carrying Nf charges, (Nf+ positive and Nf- negative charges) on a charged surface with σ charges per unit area. The adsorption is due to the electrostatic polarization of the polyampholyte chain, which acquires a dipole moment in the surface electric field. Symmetric Gaussian polyampholytes with equal numbers of positive and negative charges adsorb if the surface charge density σ is larger than (1/alBN)· (1/f 1/2) (lB is the Bjerrum length and a is the bond size). Polyampholyte chains carrying a charge of the same sign as the surface can also adsorb if the surface charge is large enough. For a typical asymmetry |f- − f+| ≈ (f/N)1/2, the adsorption threshold is σ > (1/alBN3/4)(1/f 1/4). The effect of the added salt on the adsorption is considered. Finally, we determine the adsorption threshold of a collapsed polyampholyte globule.
Common mechanism links spiral wave meandering and wave-front–obstacle separation (1997)

Spiral waves rotate either around a circular core or meander, inscribing a noncircular pattern. The medium properties determining the transition of meandering were found to be equivalent to those defining the transition from wave tip separation and attachment around the end of an unexcitable strip of thickness comparable to zero velocity wave-front thickness. The transition from circular to noncircular tip movement is analytically predicted by the balance of the diffusive fluxes within the boundary layer at the wave tip.
Ultrahigh speed spectral/Fourier domain OCT imaging in ophthalmology (2009)

Ultrahigh speed Spectral/Fourier domain ophthalmic OCT imaging at 70,000-312,500 axial scans per second is demonstrated using a high speed CMOS camera at 800 nm. Comparative imaging results of the fovea illustrate the performance tradeoffs between different imaging speeds and spectrometer configurations. Dense 3D volumetric acquisitions show minimal motion artifacts when acquired at 250,000 axial scans per second. The porous structure of the lamina cribrosa is shown in en face images extracted from a dense volumetric acquisition of the optical nerve head acquired at 106, 382 axial scans per second. Rapid repeated volume imaging (4D-OCT) shows blood flow in retinal capillaries. Boundaries of the capillary network are enhanced by motion contrast. 3D volumetric data acquired at 49,000 axial scans per second using an InGaAs camera at 1050 nm is compared to volumetric data acquired at 101, 010 axial scans per second using a CMOS camera at 800nm. Averaging of adjacent cross sectional scans in the volume is shown to increase contrast in the images and reduce speckle. The enhanced penetration of the 1050 nm compared to the 800 nm OCT imaging system is shown. Dense 2D/3D data sets and 4D-OCT repeated volume imaging promise alternative methods for diagnosis and monitoring of disease.
Variable power assist control of twin direct-drive motor system based on human stiffness estimation (2008)

This paper presents a novel sensor-less force control approach for the robot-assisted motion of human arm movements. The twin direct-drive motor system with wire rope mechanism has been developed in order to provide precise force sensation for human-robot interaction. The proposed control is obtained by using two disturbance observers combined with modal space design. In the common mode of modal space design, each motor has almost the same characteristics of the friction effect and other nonlinearity. Therefore, it is easy for the proposed system to compensate these nonlinear effects. Moreover, the bandwidth and the stiffness of mechanism can be enlarged by increasing the wire rope tension command. In the differential mode, the purity of human external force with compensation of friction force is obtained based on modal space design. This mode is useful for control interaction force of human arm movements. Variable powers assist control method based on a real-time estimation of the stiffness of the human arms is also introduced. By considering the stiffness of human arm movements, this method increases the efficiency of force control system and realizes comfortable force for human-robot interaction. The effectiveness of the method is verified by experimental results.
Influence of Superplasticizer Adsorption on the Rheology of Cement Paste (1999)

The production of high performance concrete requires the development of new superplasticizers with increased efficiencies. The knowledge of the mechanisms by which these admixtures act is of primary importance for the design of new polymers. They are believed to be linked to the dispersion cement agglomerates by electrostatic, steric or entropic repulsion, or improved wetting (capillary effect). The two first are directly linked to adsorbed polymers. The third is linked to both adsorbed and solvated polymers, while the last is mainly linked to polymers remaining in solution. To elucidate the effects of the superplasticizers, two approaches were used. On one hand, adsorption isotherms of polymers were measured by solution depletion. On the other hand, rheological testing leading to the determination of the amount of superplasticizer needed to reach a minimum yield stress. A comparison of both results reveals the relative importance of the possible mechanisms contributing to superplasticizer efficiency. It is shown that molecular mass distribution effects polymer adsorption. It is also shown how a cement obtained by grinding with and without a grinding aid has different adsorption properties and different polymer requirements. Results are discussed in the light of understanding by which mechanisms polymers are acting. 1.
Multiresolution X-ray CT Imaging of Fiber Reinforced Composite Materials (2011)

International audience
Feasibility and design considerations for an iris acquisition system for smartphones (2014)

Iris biometrics has the potential to provide the security required by next generation smartphones. This paper deals with the feasibility of an iris acquisition system for smartphones and similar hand held devices. When it comes to smartphones, a number of image acquisition challenges tend to surface. This paper discusses some of these challenges along with a brief description of acquisition system wavelength, iris image size and iris image spatial resolution and various other image quality parameters which affect iris recognition performance such as usable iris area, iris-pupil and iris-sclera contrast, image sharpness, gaze angle, SNR etc. Some preliminary results and design ideas for practical iris image acquisition are also presented.
Involvement of Fatty Acid Synthase in Azacytidine-Induced Cytotoxicity in Waldenstrom's Macroglobulinemia. (2009)

Abstract Abstract 3731 Poster Board III-667 Azacytidine is a potent demethylation agent and has been used for the treatment of myelodysplastic syndrome. Despite a role in reactivating epigenetically silenced tumor-suppressor genes, the mechanisms of action for azacytidine are not well understood. The relationships between the reactivation of tumor-suppressor genes and the significance for clinical responses also remain to be established. Azacytidine can incorporate into both RNA and DNA strands and may therefore act through multiple pathways. We therefore investigated the therapeutic potential of azacytidine in Waldenstrom's Macroglobulinemia (WM), and characterized certain molecular changes associated with azacytidine. We found that azacytidine exhibited significant dose-dependent cytotoxicity against WM cell lines, and primary WM cells. Treatment of BCWM.1 WM cells with 2 uM of azacytidine rapidly induced cell cycle arrest at G1, and also induced apoptosis at 48 hours. Cleavage of caspase 3, 7, 8, 9 and PARP-1 suggested an involvement of mitochondrial and death receptor pathways in azacytidine-induced apoptosis. The BH3 proteins Puma and Bim, and the pro-apoptotic protein Bax were up-regulated while the anti-apoptotic proteins Bcl-2 and Bcl-xl remained unchanged after treatment with azacytidine. In addition, azacytidine did not induce Akt and NFκB pathways. To further elucidate molecular changes associated with azacytidine treatment, we performed genome-wide microarray expression in BCWM.1 WM cells treated with azacytidine. We observed that the gene encoding fatty acid synthase (FASN) was among the most down-regulated of targets. FASN has been linked to tumor cell proliferation, and its expression was observed by us to be upregulated by microarray studies in WM patients, and further validated as a highly over-expressed target by quantitative RT-PCR analysis in WM patients versus healthy donors. Moreover, by these studies we show that knockdown of FASN by small interfering RNA resulted in growth arrest, and also induced apoptosis in BCWM.1 WM cells. Cerulenin, a specific inhibitor of FASN derived from a natural product, induced strong cytotoxicity against BCWM.1 and primary WM cells at 20 uM in 24 hours. In addition, a synergistic induction of apoptosis in BCWM.1 WM cells was observed in the presence of both azacytidine and cerulenin. The results of this study support an important role for FASN in azacytidine-induced cytotoxicity in WM cells, and highlight a novel mechanistic pathway for this agent, as well as a novel target for drug therapy in WM. A clinical study investigating the activity of azacytidine in WM is planned. Disclosures: No relevant conflicts of interest to declare.
Fluorescence microscopy techniques for quantitative evaluation of organic biocide distribution in antifouling paint coatings: application to model antifouling coatings (2012)

A test matrix of antifouling (AF) coatings including pMMA, an erodible binder and a novel trityl copolymer incorporating Cu₂O and a furan derivative (FD) natural product, were subjected to pontoon immersion and accelerated rotor tests. Fluorescence and optical microscopy techniques were applied to these coatings for quantification of organic biocide and pigment distribution. Total leaching of the biocide from the novel copolymer binder was observed within 6 months of rotor immersion, compared to 35% from the pMMA coating. In pontoon immersions, 61% of the additive was lost from the pMMA coating, and 53% from the erodible binder. Profiles of FD content in the binders revealed an accelerated loss of additive from the surface of the CDP resulting from rosin degradation, compared to even depletion from pMMA. In all samples, release of the biocide was inhibited beyond the Cu₂O front, corresponding to the leached layer in samples where Cu₂O release occurred.
Accumulation of Golgi-specific mannosyltransferases inCandida albicanscells grown in the presence of brefeldin A (1995)

The fungal metabolite brefeldin A (BFA) is known for its ability to block the secretory process in eukaryotic cells by interfering in the endoplasmic reticulum (ER) to Golgi membrane traffic, causing the disassembly of Golgi apparatus and redistribution of Golgi enzymes into the ER. In sensitive yeasts, underglycosylated forms of secretory proteins accumulate in the cytoplasm in the presence of BFA. We investigated whether the incomplete glycosylation of mannoproteins could be due to repression of the synthesis of Golgi-located terminal mannosyltransferases and whether the underglycosylated mannoproteins can be incorporated into the cell walls in Candida albicans. However, we found that the microsomal membranes isolated from the yeast cells grown in the presence of 14 micrograms.mL-1 of BFA had on average three times higher overall specific activity of mannan synthase than membranes from control cells. The increase in specific activity of mannan synthase was mainly due to accumulation of Golgi-specific mannosyltransferases responsible for elongation of the O-glycosidically linked mannooligosaccharides and for the synthesis of the N-glycosidically linked mannan outer chain. As a consequence, the mannans synthesized in vitro from GDP-[U-14C]mannose by the membranes from cells grown in the presence of BFA had longer O-glycosidically linked oligosaccharides and longer side-chains in the N-glycosidically linked polymannose part of the molecule than mannans synthesized by membranes from the control cells. Contrary to results obtained in vitro, the structural features of cell wall mannans isolated from intact BFA-grown and from control cells were almost indistinguishable.
Low-Loss and High-Extinction-Ratio Silica-Based Strictly Nonblocking 16 16 (1998)

A low-loss and high-extinction-ratio silica-based 16 16 thermooptic matrix switch is demonstrated. The switch, which employs a double Mach-Zehnder interferometer switching unit and a matrix arrangement which reduces the total wave- guide length, is fabricated with 0.75% refractive index difference waveguides on a 6-in silicon wafer. The average insertion loss and the average extinction ratio are 6.6 and 55 dB, respectively. The total power consumption is 17 W.
Transendothelial Electrical Resistance Measurement across the Blood–Brain Barrier: A Critical Review of Methods (2021)

The blood-brain barrier (BBB) represents the tightest endothelial barrier within the cardiovascular system characterized by very low ionic permeability. Our aim was to describe the setups, electrodes, and instruments to measure electrical resistance across brain microvessels and culture models of the BBB, as well as critically assess the influence of often neglected physical and technical parameters such as temperature, viscosity, current density generated by different electrode types, surface size, circumference, and porosity of the culture insert membrane. We demonstrate that these physical and technical parameters greatly influence the measurement of transendothelial electrical resistance/resistivity (TEER) across BBB culture models resulting in severalfold differences in TEER values of the same biological model, especially in the low-TEER range. We show that elevated culture medium viscosity significantly increases, while higher membrane porosity decreases TEER values. TEER data measured by chopstick electrodes can be threefold higher than values measured by chamber electrodes due to different electrode size and geometry, resulting in current distribution inhomogeneity. An additional shunt resistance at the circumference of culture inserts results in lower TEER values. A detailed description of setups and technical parameters is crucial for the correct interpretation and comparison of TEER values of BBB models.
EP874 Serologic markers of Chlamydia trachomatis and other sexually transmitted infections and subsequent ovarian cancer risk: results from the EPIC cohort (2019)

<h3>Introduction/Background</h3> Sexually transmitted infections (STI) and pelvic inflammatory disease may cause damage to the fallopian tube where a substantial proportion of epithelial ovarian cancer (EOC) likely arises. The aim of this study was to determine whether <i>Chlamydia trachomatis</i> antibodies are associated with higher EOC risk. As secondary objectives, we investigated <i>Mycoplasma genitalium,</i>herpes simplex virus type 2 (HSV-2) and human papillomavirus (HPV) 16, 18 and 45 and EOC risk. <h3>Methodology</h3> In a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort,791 cases and 1,669 matched controls with pre-diagnosis blood samples were analyzed. Cases and controls were matched on study center, and at blood collection age, time of day, fasting status, exogenous hormone use, menopausal status, and menstrual cycle phase. Antibodies against <i>C. trachomatis</i>, <i>M. genitalium</i>, HSV-2, and HPV 16, 18 and 45 (E6, E7, L1) were assessed using multiplex fluorescent bead-based serology. Conditional logistic regression was used to estimate relative risks (RR) and 95% confidence intervals [CI] comparing women with positive vs. negative serology. <h3>Results</h3> A total of 40% of the study population was seropositive to at least one STI. Positive serology to <i>C. trachomatis</i> Pgp3 antibodies was not associated with EOC risk overall, but was associated with higher risk of the mucinous histotype (RR=2.56 [95% CI=1.3–5.05]). Positive serology for chlamydia heat shock protein 60 (cHSP60-1), produced during persistent infection, was associated with higher risk of EOC overall (1.33 [1.09–1.62]) and of the serous subtype (1.42 [1.09–1.84]). None of the other evaluated STIs were associated with EOC risk overall; in analyses by histotype, HSV-2 was associated with higher risk of endometrioid EOC (2.93 [1.50–5.74]). <h3>Conclusion</h3> <i>C. trachomatis</i> infection may influence carcinogenesis of serous and mucinous EOC, while HSV-2 might promote endometrioid disease. Mechanisms linking STIs to EOC need to be further elucidated. <h3>Disclosure</h3> Financial support: This work was supported by grants from The Cancer Research Foundation in Northern Sweden and The County Council of Västerbotten, Sweden, and the German Cancer Research Center. The coordination of EPIC is financially supported by the European Commission (DG-SANCO) and the International Agency for Research on Cancer. The national cohorts are supported by grant givers in the separate countries. Detailed information on demand.
Fireiron: A Scheduling Language for High-Performance Linear Algebra on GPUs (2020)

Achieving high-performance GPU kernels requires optimizing algorithm implementations to the targeted GPU architecture. It is of utmost importance to fully use the compute and memory hierarchy, as well as available specialised hardware. Currently, vendor libraries like cuBLAS and cuDNN provide the best performing implementations of GPU algorithms. However the task of the library programmer is incredibly challenging: for each provided algorithm, high-performance implementations have to be developed for all commonly used architectures, input sizes, and different storage formats. These implementations are generally provided as optimized assembly code because performance-critical architectural features are only exposed at this level. This prevents reuse between different implementations of even the same algorithm, as simple differences can have major effects on low-level implementation details. In this paper we introduce Fireiron, a DSL and compiler which allows the specification of high-performance GPU implementations as compositions of simple and reusable building blocks. We show how to use Fireiron to optimize matrix multiplication implementations, achieving performance matching hand-coded CUDA kernels, even when using specialised hardware such as NIVIDA Tensor Cores, and outperforming state-of-the-art implementations provided by cuBLAS by more than 2x.
Membrane‐aerated microbioreactor for high‐throughput bioprocessing (2004)

A microbioreactor with a volume of microliters is fabricated out of poly(dimethylsiloxane) (PDMS) and glass. Aeration of microbial cultures is through a gas-permeable PDMS membrane. Sensors are integrated for on-line measurement of optical density (OD), dissolved oxygen (DO), and pH. All three parameter measurements are based on optical methods. Optical density is monitored via transmittance measurements through the well of the microbioreactor while dissolved oxygen and pH are measured using fluorescence lifetime-based sensors incorporated into the body of the microbioreactor. Bacterial fermentations carried out in the microbioreactor under well-defined conditions are compared to results obtained in a 500-mL bench-scale bioreactor. It is shown that the behavior of the bacteria in the microbioreactor is similar to that in the larger bioreactor. This similarity includes growth kinetics, dissolved oxygen profile within the vessel over time, pH profile over time, final number of cells, and cell morphology. Results from off-line analysis of the medium to examine organic acid production and substrate utilization are presented. By changing the gaseous environmental conditions, it is demonstrated that oxygen levels within the microbioreactor can be manipulated. Furthermore, it is demonstrated that the sensitivity and reproducibility of the microbioreactor system are such that statistically significant differences in the time evolution of the OD, DO, and pH can be used to distinguish between different physiological states. Finally, modeling of the transient oxygen transfer within the microbioreactor based on observed and predicted growth kinetics is used to quantitatively characterize oxygen depletion in the system.
Discovery of 4-Aryl-4H-chromenes as a New Series of Apoptosis Inducers Using a Cell- and Caspase-based High-Throughput Screening Assay. 1. Structure−Activity Relationships of the 4-Aryl Group (2004)

By applying a novel cell- and caspase-based HTS assay, 2-amino-3-cyano-7-(dimethylamino)-4-(3-methoxy-4,5-methylenedioxyphenyl)-4H-chromene (1a) has been identified as a potent apoptosis inducer. Compound 1a was found to induce nuclear fragmentation and PARP cleavage, as well as to arrest cells at the G(2)/M stage and to induce apoptosis as determined by the flow cytometry analysis assay in multiple human cell lines (e.g. Jurkat, T47D). Through structure-activity relationship (SAR) studies of the 4-aryl group, a 4- and 7-fold increase in potency was obtained from the screening hit 1a to the lead compounds 2-amino-4-(3-bromo-4,5-dimethoxyphenyl)-3-cyano-7-(dimethylamino)-4H-chromene (1c) and 2-amino-3-cyano-7-(dimethylamino)-4-(5-methyl-3-pyridyl)-4H-chromene (4e), with an EC(50) of 19 and 11 nM in the caspase activation assay in T47D breast cancer cells, respectively. The 2-amino-4-aryl-3-cyano-7-(dimethylamino)-4H-chromenes also were found to be highly active in the growth inhibition MTT assay, with GI(50) values in the low nanomolar range for compound 1c. Significantly, compound 1c was found to have a GI(50) value of 2 nM in the paclitaxel resistant, p-glycoprotein overexpressed, MES-SA/DX5 tumor cells. Functionally, compound 1c was found to be a potent inhibitor of tubulin polymerization and to effectively inhibit the binding of colchicine to tubulin. These results confirm that the cell-based caspase activation assay is a powerful tool for the discovery of potent apoptosis inducers and suggest that the 4-aryl-4H-chromenes have the potential to be developed into future anticancer agents.
A Precise and Scalable Post-Modification of Mesoporous Metal-Organic Framework NU-1000 Via Atomic Layer Deposition (2016)

The connectivity of NU-1000, a metal-organic framework, gives rise to Zr 6 nodes with hydroxyl-containing functional groups pointing into the large 1D mesoporous hexagonal channels of the framework. These free and exposed –OH groups are ideal grafting sites, and they can be easily tailored to serve a specific function. Through atomic layer deposition in MOFs (AIM), we demonstrate the ability to form several oxides with atomic precision at the exposed –OH sites of NU-1000. Importantly, this process occurs without changing the overall structure of the framework. Recent progress in scaling AIM process of the ultrahigh surface area (2300 m 2 /g) framework as well as progress in pinpointing the location and mechanism of surface chemical reactions of catalytically relevant metals is discussed. Computational, synchrotron, and in-situ analytical methods including DFT, differential electron diffraction, and in situ FTIR are brought to bear on several new metal systems, many of which show remarkably self-limiting behavior.