gebhart/patrepeval huggingface dataset:
Dynamic surface matching for patient positioning in radiotherapy (2002)

Curative radiotherapy of localised cancer delivers discrete doses of radiation to diseased tissue over many days. Computer driven multileaf collimators now closely conform radiation dose fields to the shape of any tumour. This technology invites the reduction of beam margins in order to maximally spare healthy tissue, reducing side-effects, but placing more emphasis on the precision of dose delivery. However, tumour motion and body surface variation demand more accurate patient set-ups. Software has been developed to assist in the task of aligning a patient on the treatment couch with his/her previously planned CT scan in true three-dimensions. A body surface height-map is constructed from a B-spline skinned model of the planned CT scan outline set and compared with a height-map from an optical sensor. This type of co-registration does not depend entirely on skin surface markers which unavoidably move due to the dynamics of internal/external anatomical forces.
First-Principles Predictions and <i>in Situ</i> Experimental Validation of Alumina Atomic Layer Deposition on Metal Surfaces (2014)

The atomic layer deposition (ALD) of metal oxides on metal surfaces is of great importance in applications such as microelectronics, corrosion resistance, and catalysis. In this work, Al2O3 ALD using trimethylaluminum (TMA) and water was investigated on Pd, Pt, Ir, and Cu surfaces by combining in situ quartz crystal microbalance (QCM), quadrupole mass spectroscopy (QMS), and scanning tunneling microscopy (STM) measurements with density functional theory (DFT) calculations. These studies revealed that TMA undergoes dissociative chemisorption to form monomethyl aluminum (AlCH3*, the asterisk designates a surface species) on both Pd and Pt, which transform into Al(OH)3* during the subsequent water exposure. Furthermore, the AlCH3* can further dissociate into Al* and CH3* on stepped Pt(211). Additional DFT calculations predicted that Al2O3 ALD should proceed on Ir following a similar mechanism but not on Cu due to the endothermicity for TMA dissociation. These predictions were confirmed by in situ QCM, QMS, and STM measurements. Our combined theoretical and experimental study also found that the preferential decoration of low-coordination metal sites, especially after high temperature treatment, correlates with the differences in free energy between Al2O3 ALD on the (111) and stepped (211) surfaces. These insights into Al2O3 growth on metal surfaces can guide the future design of advanced metal/metal oxide catalysts with greater durability by protecting the metal against sintering and dissolution and enhanced selectivity by blocking low-coordination metal sites while leaving (111) facets available for catalysis.
Bacterial cellulose modified with xyloglucan bearing the adhesion peptide RGD promotes endothelial cell adhesion and metabolism-a promising modification for vascular grafts (2010)

Today, biomaterials such as polytetrafluorethylene (ePTFE) are used clinically as prosthetic grafts for vascular surgery of large vessels (>5 mm). In small diameter vessels, however, their performance is poor due to early thrombosis. Bacterial-derived cellulose (BC) is a new promising material as a replacement for blood vessels. This material is highly biocompatible in vivo but shows poor cell adhesion. In the native blood vessel, the endothelium creates a smooth non-thrombogenic surface. In order to sustain cell adhesion, BC has to be modified. With a novel xyloglucan (XG) glycoconjugate method, it is possible to introduce the cell adhesion peptide RGD (Arg-Gly-Asp) onto bacterial cellulose. The advantage of the XG-technique is that it is an easy one-step procedure carried out in water and it does not weaken or alter the fiber structure of the hydrogel. In this study, BC was modified with XG and XGRGD to asses primary human vascular endothelial cell adhesion, proliferation, and metabolism as compared with unmodified BC. This XG-RGD-modification significantly increased cell adhesion and the metabolism of seeded primary endothelial cells as compared with unmodified BC whereas the proliferation rate was affected only to some extent. The introduction of an RGD-peptide to the BC surface further resulted in enhanced cell spreading with more pronounced stress fiber formation and mature phenotype. This makes BC together with the XG-method a promising material for synthetic grafts in vascular surgery and cardiovascular research.
Chymase-containing mast cells in human arterial intima: implications for atherosclerotic disease. (1997)

Many of the mast cells present in human atherosclerotic lesions contain chymase. As the lesions progress to more severe forms, the number of such mast cells increases, and their activity (degree of degranulation) increases. Exocytosed heparin-bound chymase may be involved in the development of both early (fatty streaks) and late (thrombotic) atherosclerotic lesions. Experimental studies with rat serosal mast cells have revealed that chymase can degrade the apolipoprotein B-100 component of low-density lipoprotein (LDL) particles and the apolipoprotein A component of high-density lipoprotein (HDL) particles. Both of these chymase actions on apolipoproteins tend to increase the cholesterol content of macrophages and to convert them into the foam cells typical of early atherosclerotic lesions. In atheromatous plaques, the late atherosclerotic lesions, the chymase-containing mast cells may render the plaques unstable and their caps susceptible to rupture when chymase activates the interstitial procollagenase secreted by the macrophages in the plaque caps. Definition of the quantitative importance of chymase in the pathogenesis of atherosclerosis and its complications remains an exciting challenge for the future.
A Notion of Harmonic Clustering in Simplicial Complexes (2019)

We outline a novel clustering scheme for simplicial complexes that produces clusters of simplices in a way that is sensitive to the homology of the complex. The method is inspired by, and can be seen as a higher-dimensional version of, graph spectral clustering. The algorithm involves only sparse eigenproblems, and is therefore computationally efficient. We believe that it has broad application as a way to extract features from simplicial complexes that often arise in topological data analysis.
<title>New contrast agents for optical imaging: acid-cleavable conjugates of cyanine dyes with biomolecules</title> (1999)

The investigation of cyanine dyes as contrast agents in optical tumor imagin has been a focus of our recent work. We have shown that i.v. injected hydrophilic indotricarbocyanine derivatives enable tumor detection by fluorescence imagin and by frequency-domain absorption spectroscopy. Our current objective is to extend this approach by conjugating these dyes with specific biomolecules in order to enhance targetability and to introduce acid-cleavable links that enable dye release in acidic cell compartments. Accordingly, we have synthesized cyanine dyes which contain different acid-cleavable hydrazone links and which were coupled to peptides, proteins and antibodies. We have studied the release of the dyes under various pH conditions. Our results show that dye release from transferrin increased under acidic conditions, while at neutral pH the stability was higher. Additionally, we observed pH-dependent fluorescence enhancement during cleavage. Cellular fluorescence microscopy experiments indicated that intracellular trapping is possible. In conclusion, cyanine dyes bound to biomolecules by acid- cleavable bonds could act as promising optical contrast agents. Further work will include optimization of release rates by chemical modification and in vivo imaging studies.
Psychoacoustical correlates of musically induced chills (2008)

Music listening is often accompanied by the experience of emotions, sometimes even by so-called “strong experiences of music” (SEMs). SEMs can include such pleasurable reactions as shivers down the spine or goose pimples, which are referred to as “chills”. In the present study, the role of psychoacoustical features was investigated with respect to the experience of chills. Psychoacoustical parameters of short musical segments (total duration: 20 s), characterized as chill- inducing, were analyzed and compared with musical excerpts which did not induce chill responses. A significant increase of loudness in the frequency range between 8 and 18 Bark (920–4400 Hz) was found in those excerpts for which chills were reported. Frequency-dependent changes of loudness seem to play an important role in the induction of chills.
Embedded multiple description coding for progressive image transmission over unreliable channels (2002)

A multiple description scalar quantization (MDSQ) based coding system can be regarded as a source coder (quantizer) followed by a channel coder, i.e. the combination of index and codeword assignment. The redundancy, or the correlation between the descriptions, is controlled by the number of diagonals covered by the index assignment. We consider here the usage of multiple description uniform scalar quantization (that we call MDUSQ) for robust and progressive transmission of images over unreliable channels. The progressive feature is an important factor for rate control in non-stationary (varying bandwidth) communication environments. In this context, the paper describes an embedded index assignment strategy that provides improved rate-distortion performances in progressive transmission scenarios, against index assignments defined so far for MDSQ. The MDUSQ together with the embedded index assignment algorithm are incorporated into the JPEG2000 verification model. The approach is compared against a progressive multiple description scheme based on a polyphase transform (PT) decomposition of the signal.
A Novel Cancelable FaceHashing Technique Based on Non-Invertible Transformation With Encryption and Decryption Template (2020)

A novel cancelable FaceHashing technique based on non-invertible transformation with encryption and decryption template has been proposed in this paper. The proposed system has four components: face preprocessing, feature extraction, cancelable feature extraction followed by the classification, and encryption/decryption of cancelable face feature templates. During face preprocessing, the facial region of interest has been extracted out to speed the process for evaluating discriminant features. In feature extraction, some optimization techniques such as Sparse Representation Coding, Coordinate descent, and Block coordinates descent have been employed on facial descriptors to obtain the best representative of those descriptors. The representative descriptors are further arranged in a spatial pyramid matching structure to extract more discriminant and distinctive feature vectors. To preserve them, the existing BioHashing technique has been modified and extended to some higher levels of security attacks and the modified BioHashing technique computes a cancelable feature vector by the combined effect of the facial feature vector and the assigned token correspond to each user. The elements of computed cancelable feature vector are in a numeric form that has been employed to perform both verifications as well as identification task in online while the original facial feature vectors are kept offline either in hard drive or disc. Then, to enhance more security levels and also to preserve the cancelable face features, an RSA based encryption-decryption algorithm has been introduced. The proposed system has been tested using four benchmark face databases: CASIA-FACE-v5, IITK, CVL, and FERET, and performance are obtained as correct recognition rate and equal error rate. The performance are compared to the state-of-the-art methods for the superiority of the proposed feature extraction technique and individual performance analysis has been performed at all the security levels of the proposed Cancelable FaceHashing Technique. These comparisons show the superiority of the proposed system.
Excitation de plasmons et de phonons par battement de deux ondes électromagnétiques transversales dans un plasma (1988)

Le battement de deux ondes électromagnétiques dans un plasma pour produire une onde longitudinale (plasmon ou phonon) est réalisé expérimentalement à l'aide d'un double banc micro-onde en bande centimétrique. La détection du couplage se fait : (a) soit par une méthode d'absorption directe sur l'une des pompes ; (b) soit par diffusion hétérodyne d'une troisième onde dans des conditions de quasi-absorption. Ces méthodes de détection sont optimales : la première satisfait la relation de Manley-Rowe pour le transfert d'action entre les pompes dans le cas d'amortissement convectif ; la seconde produit une onde diffusée qui est anti-conjuguée de phase avec l'onde mère 2, dans la mesure où l'onde 3 diffère peu de l'onde mère 1.
QALM - a tool for automating quantitative analysis of LC-MS-MS/MS data (2010)

The goal of bioinformatics is to support science and research in the field of biology through the application of information technology. Proteomics is a field within biology that deals with the study of proteins. This paper describes QALM, an application developed to automate and simplify a specific type of proteomics analysis. QALM is first and foremost a proof of concept through which certain options for implementing such automation have been explored. Although a functional and usable application has been created, this should primarily be considered a stepping stone for similar applications in the future. Currently QALM is a desktop tool for importing and exporting data, inte- grating and communicating with external systems for the analysis of such data, and finally generating reports to present the results. It currently runs only un- der the Linux operating system, but it should be possible to change this fairly easily.
Development of Novel Aerobic Oxidation Method using N-Hydroxyphthalimide as Catalyst (1999)

Novel methods for the oxidation of alkanes with molecular oxygen using a radical catalyst, N-hydroxyphthalimide (NHPI), have been developed. Thus, a variety of alkanes such as cyclohexane, adamantane and toluene which are very difficult to be oxidized with molecular oxygen by conventional methods could be converted into the corresponding alcohols and/or carbonyl compounds in high yields. The application of the same methodology to adamantane with CO/air led to adamantanecarboxylic acid through radical carbonylation in fair yield. The reaction of benzyl ethers with NO in the presence of NHPI afforded the corresponding aldehydes in good yields. The present method provides a new class of aerobic oxidation which is refered to as radical-catalyzed autoxidation.
Brain manganese and the balance between essential roles and neurotoxicity (2020)

Manganese (Mn) is an essential micronutrient required for the normal development of many organs, including the brain. Although its roles as a cofactor in several enzymes and in maintaining optimal physiology are well-known, the overall biological functions of Mn are rather poorly understood. Alterations in body Mn status are associated with altered neuronal physiology and cognition in humans, and either overexposure or (more rarely) insufficiency can cause neurological dysfunction. The resultant balancing act can be viewed as a hormetic U-shaped relationship for biological Mn status and optimal brain health, with changes in the brain leading to physiological effects throughout the body and vice versa. This review discusses Mn homeostasis, biomarkers, molecular mechanisms of cellular transport, and neuropathological changes associated with disruptions of Mn homeostasis, especially in its excess, and identifies gaps in our understanding of the molecular and biochemical mechanisms underlying Mn homeostasis and neurotoxicity.
Single‐screen triband fss with double‐square‐loop elements (1992)

Abstract A single‐screen double‐square‐loop (DSL) frequency selective surface (FSS) has been developed and tested for triband applications (i.e., to reflect the X‐band and to pass the S‐ and Ku‐band waves). Good agreement between predicted and measured transmission performance is obtained for the DSL FSS on a 0.001‐in.‐thick Kapton with/without a flat Kevlar honeycomb sandwich panel. It is found that this single‐screen DSL FSS with/without the Kevlar honeycomb has a resonant frequency near 8.4 GHz for incident angle steered from normal to 45° and for both TE and TM polarizations.
Bead beating-based continuous flow cell lysis in a microfluidic device (2015)

This paper describes a bead beating-based miniaturized cell lysis device that works in continuous flow allowing the analysis of large volumes of samples without previous treatment.
Physiological concentrations of tissue factor pathway inhibitor do not inhibit prothrombinase (1996)

Tissue factor pathway inhibitor (TFPI) is a Kunitz-type serine proteinase inhibitor that directly inhibits factor Xa and, in a factor Xa dependent manner, inhibits the factor VIIa/tissue factor catalytic complex. The inhibitory effect of TFPI in prothrombin activation assays using purified components of the prothrombinase complex was examined. When factor Xa is added to mixtures containing TFPI, prothrombin, calcium ions, and nonactivated platelets or factor V and phospholipids, TFPI significantly reduces subsequent thrombin generation, and the inhibitory effect is enhanced by heparin. If factor Xa is preincubated with calcium ions and thrombin-activated platelets or factor Va and phospholipids to permit formation of prothrombinase before the addition of prothrombin and physiologic concentrations of TFPI (< 8 nmol/L), minimal inhibition of thrombin generation occurs, even in the presence of heparin. Thus, contrary to results in amidolytic assays with chromogenic substrates, prothrombinase is resistant to inhibition by TFPI in the presence of its physiological substrate, prothrombin. Higher concentrations of TFPI (approximately 100 nmol/L), similar to those used in animal studies testing for therapeutic actions of TFPI, do effectively block prothrombinase activity.
A semantic model of program faults (1996)

Program faults are artifacts that are widely studied, but there are many aspects of faults that we still do not understand. In addition to the simple fact that one important goal during testing is to cause failures and thereby detect faults, a full understanding of the characteristics of faults is crucial to several research areas in testing. These include fault-based testing, testability, mutation testing, and the comparative evaluation of testing strategies. In this workshop paper, we explore the fundamental nature of faults by looking at the differences between a syntactic and semantic characterization of faults. We offer definitions of these characteristics and explore the differentiation. Specifically, we discuss the concept of "size" of program faults --- the measurement of size provides interesting and useful distinctions between the syntactic and semantic characterization of faults. We use the fault size observations to make several predictions about testing and present preliminary data that supports this model. We also use the model to offer explanations about several questions that have intrigued testing researchers.
Cloning and Sequence Analysis of<i>czc</i>Genes in<i>Alcaligenes</i>sp. Strain CT14 (1996)

We have isolated 14 cadmium (Cd)-resistant, soil-borne bacteria. Among those, strain CT14, which was identified as an Alcaligenes sp., has a czc (cadmium, zinc, and cobalt divalent cation resistant determinant) system. Here we report the nucleotide sequence of 4 genes (czcCBAD) of the system. CzcCBA showed over 98% identity with those of A. eutrophus CH34, however, CzcD, the distal gene product, was 117 amino acids longer than that (199 amino acids) of A. eutrophus CH34, and had considerable similarity to the members of the CDF (cation diffusion facilitator) family proteins all over the region.
Detail-preserving smoothing with morphology and fuzzy reasoning (1996)

This study investigates a new approach to removing noise that preserves the fine details which are based on combination of mathematical morphology and fuzzy reasoning. We extract some features from an image using mathematical morphology, then input these features, and the image itself, into fuzzy-rule-based systems to produce a more graceful image.
[Preventive vaccination for viral hepatitis]. (1997)

Viral hepatitis A-E belong to the most important infectious diseases worldwide. Viral hepatitis is highly endemic in most developing countries in Africa, South East Asia, and southern America; however also in industrialized countries as Germany hepatitis A, B and C represent a thread which should not be underestimated. In Germany, there are about 20,000 to 40,000 hepatitis A infections every year, most of them acquired abroad; about 50,000 new hepatitis B infections and about 5,000 to 8,000 infections with hepatitis C virus occur every year. About 500,000 individuals are chronic carriers of hepatitis B virus and roughly the same number is supposed to be chronically infected with hepatitis C virus. As possibilities for therapeutic intervention in chronic hepatitis B and C are still limited, immunoprophylactic measures are of particular importance. Passive and active immunization is available for hepatitis A and B but so far not for hepatitis C. Passive immunization by application of specific immunoglobulins gives protection which is effective within a few hours but is limited according to the amount of immunoglobulin to six to twelve months. Active immunization on the other hand induces a specific immune response starting after a delay of usually days or sometimes weeks but nevertheless lasting for at least several years. The combination of both methods, passive-active immunization, has the advantage of immediate protection due to the immunoglobulin which lasts until the active immunization induces an endogenous antibody production.
Comparison of the glycaemic effect of fructose, sucrose and starch-containing mid-morning snacks in insulin-dependent diabetics. (1983)

Capillary blood glucose levels were measured every 30 min for 2 h after four different 20 g carbohydrate mid-morning snacks of foods containing predominantly fructose, sucrose or starch in eight insulin-dependent diabetics and eight normal control subjects. In the diabetic subjects, there was no significant difference in the glycaemic effect of the four different snacks. This study does not support the view that fructose is a useful alternative sweetener for diabetics or the view that sucrose should be excluded from the diet of insulin-dependent diabetics.
Dynamics of TGF‐β/Smad signaling (2012)

The physiological responses to TGF-β stimulation are diverse and vary amongst different cell types and environmental conditions. Even though the principal molecular components of the canonical and the non-canonical TGF-β signaling pathways have been largely identified, the mechanism that underlies the well-established context dependent physiological responses remains a mystery. Understanding how the components of TGF-β signaling function as a system and how this system functions in the context of the global cellular regulatory network requires a more quantitative and systematic approach. Here, we review the recent progress in understanding TGF-β biology using integration of mathematical modeling and quantitative experimental analysis. These studies reveal many interesting dynamics of TGF-β signaling and how cells quantitatively decode variable doses of TGF-β stimulation.