gebhart/patrepeval huggingface dataset:
Spatio-temporal approach for time-varying image motion estimation (2002)

Image motion estimation using the spatio-temporal approach has largely relied on the constant velocity assumption. Spatio-temporal algorithms are developed in this paper to handle time-varying motion. Time-variation is modeled either as a polynomial or as a periodic function of time. Under these models, it is shown that time-varying image motion estimation is equivalent to parameter estimation of one-dimensional polynomial phase or phase modulated signals. Simulation results are provided to illustrate the proposed algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Abstract B44: Targeting Notch signaling with a dual Notch 2/3 antagonist, OMP-59R5, inhibits tumor growth and decreases cancer stem cell frequency in pancreatic cancer. (2012)

Clinical management of pancreatic cancer is challenging and in recent years has not been dramatically improved and this disease remains the fourth most common cause of cancer-related death. Dysregulated Notch2 and/or Notch3 activity has been associated with several human tumor types including pancreatic cancer. In this report, we describe the development of OMP-59R5, an antibody isolated originally by binding to Notch2 and subsequently found to also bind Notch3. OMP-59R5 potently blocks Notch2 and Notch3 signaling and inhibits the growth pancreatic cancer patient derived xenograft tumors, as a single agent and in combination with gemcitabine. The anti-tumor effects were associated with modulation of Notch target genes in tumor and stromal cells. Inclusion of OMP-59R5 delayed pancreatic tumor recurrence following termination of gemcitabine, correlated with an effect of anti-Notch2/3 in decreasing in cancer stem cell frequency and tumorigenicity. Gene set enrichment analysis showed that a subset of the stem cell gene sets and gene set related to epithelial-to-mesenchymal transistion, EMT, was up-regulated in tumors by gemcitabine alone, but down-regulated by the combination of gemcitabine plus OMP-59R5 treatment. Findings from the present study suggest that agents that reduce cancer cell frequency may improve cancer treatment by delaying or preventing tumor recurrence, and reducing the metastatic spread of the disease. In particular, blocking Notch-mediated proliferation of bulk tumor cells and cancer stem cells may provide an attractive strategy for novel therapy in pancreatic cancer treatment. Citation Format: Wan-Ching Yen, Marcus Fischer, Aaron Sato, Min Wang, Ann M. Kapoun, John Lewicki, Austin Gurney, Timothy Hoey. Targeting Notch signaling with a dual Notch 2/3 antagonist, OMP-59R5, inhibits tumor growth and decreases cancer stem cell frequency in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Progress and Challenges; Jun 18-21, 2012; Lake Tahoe, NV. Philadelphia (PA): AACR; Cancer Res 2012;72(12 Suppl):Abstract nr B44.
Broadband dual-mode HIFU array for therapy monitoring and 3D target motion estimation (2015)

This project implements previously developed techniques for guiding and monitoring thermal HIFU therapy using imaging arrays with a spherically shaped therapeutic array for dual-mode operation. Three-dimensional motion tracking, thermal strain measurement, and radiation force rebound measurement within the HIFU steering volume are performed using only the therapy array. The techniques have typically been studied for conventional ultrasound imaging using linear, curvilinear, or phased arrays which are usually placed coaxially in the center of the HIFU array. While the dual-mode approach does not provide the image quality and wide field of view of an imaging array, the perfect co-registration of the therapy array, and its 3D view of the region of interest present a valuable opportunity for ultrasound-guided focused ultrasound (USgFUS) therapy systems. A family of Sonic Concepts broadband spherically-focused HIFU array transducers, driven with the Verasonics HIFU-configured ultrasound system, is used to assess real-time performance of the dual-mode approach, in simulation and experiment. Simulations using the Verasonics acquisition software with a set of point scatterers produce the RF backscatter data used by the monitoring algorithms. The particles are displaced in time using motions that mimic the true or apparent displacements of tissue-like media either in translation, heated by a HIFU focus, or deformed by a radiation force beam. Preliminary experiments using a 128-element HIFU array and a scattering hydrogel phantom indicate that the simulations are effective for studying a range of tradeoffs in transducer design and therapy monitoring approaches.
Modification of current-voltage characteristics of double-barrier tunnel junctions under the influence of quasiparticle extraction (1997)

Enhancement of the magnitude of the value corresponding to the superconducting energy gap of Al${}^{\ensuremath{'}}$ in Nb/Al-AlO${}_{x}$-Al${}^{\ensuremath{'}}$-AlO${}_{x}$-Al/Nb and Nb/Al/Nb/Al-AlO${}_{x}$-Al${}^{\ensuremath{'}}$-AlO${}_{x}$-Al/Nb/Al/Nb devices by tunnel extraction of quasiparticles has been investigated experimentally. The enhancement is observed both at the gap-difference and gap-sum voltage. In addition to the gap-difference and gap-sum features, there is a feature in the $I$-$V$ characteristic which corresponds to the sum of the energy gaps of the external electrodes. The dc and ac Josephson currents appear in the devices below the same critical temperature ${T}_{\mathrm{c}\mathrm{}\mathrm{eq}},$ which is found to be ${T}_{\mathrm{c}\mathrm{}\mathrm{eq}}=2.35$ and 2.60 K for the devices of the first and second types, respectively. Below ${T}_{\mathrm{c}\mathrm{}\mathrm{eq}},$ an enhancement of the dc component of ac Josephson current has been observed at $V&gt;0$, as compared with the magnitude of the dc Josephson current at $V=0$.
Correction: Targeted Isolation of Antibodies Directed against Major Sites of SIV Env Vulnerability (2016)

[This corrects the article DOI: 10.1371/journal.ppat.1005537.].
Nanocomposites of TiO2and Siloxane Copolymers as Environmentally Safe Flame-Retardant Materials† (2008)

Composites of titanium dioxide (TiO2) nanoparticles and biocatalytically synthesized dimethylsiloxane copolyamides were prepared, and their thermal and flame-retardant properties were investigated. The flammability properties such as heat release capacity and total heat release were measured from microscale cumbustion calorimetry (MCC). The thermal degradation temperatures, char yields, and the heat-release capacities of these nanocomposites were significantly improved over the pure polymers. The heat-release capacities of the siloxane copolymer nanocomposites with 20wt% of TiO2 were found to be 167 and 129 J/g K, which is a 35% less than the pure polymers (260 and 194 J/g K, respectively). The SEM/EDAX surface-analysis studies on nanocomposite films and their char revealed that nanocrystalline-TiO2 plays an important role in forming carbonaceous silicate char on the surface as a protective layer.
The macrophage-derived protein PTMA induces filamentation of the human fungal pathogen Candida albicans (2021)

Evasion of killing by immune cells is crucial for fungal survival in the host. For the human fungal pathogen Candida albicans, internalization by macrophages induces a transition from yeast to filaments that promotes macrophage death and fungal escape. Nutrient deprivation, alkaline pH, and oxidative stress have been implicated as triggers of intraphagosomal filamentation; however, the impact of other host-derived factors remained unknown. Here, we show that lysates prepared from macrophage-like cell lines and primary macrophages robustly induce C. albicans filamentation. Enzymatic treatment of lysate implicates a phosphorylated protein, and bioactivity-guided fractionation coupled to mass spectrometry identifies the immunomodulatory phosphoprotein PTMA as a candidate trigger of C. albicans filamentation. Immunoneutralization of PTMA within lysate abolishes its activity, strongly supporting PTMA as a filament-inducing component of macrophage lysate. Adding to the known repertoire of physical factors, this work implicates a host protein in the induction of C. albicans filamentation within immune cells.
Spatiotemporal inpainting for recovering texture maps of partially occluded building facades (2005)

We present a technique for constructing a "clean" texture map of a partially occluded building facade from a series of images taken from a moving camera. Building regions blocked by trees, signs, people, and other foreground objects in a minority of views can be recovered via temporal median filtering on a registered image mosaic of the planar facade. However, when such areas are occluded in the majority of camera views, appearance information from other visible portions of the facade provides a critical cue to correctly complete the mosaic. In this paper we apply a robust measure of spread to infer whether a particular mosaic pixel is occluded in a majority of views, and introduce a novel spatiotemporal timeline-based inpainting algorithm that uses an additional motion cue in order to fill the texture map in majority-occluded regions.
The pharmacology of shame, or Promethean, Epimethean and Antigonian temporality (2017)

Our institutions, corporations and communities today abound in unadorned shamelessness in a manner not only public but political. In short, our relationship to the instrument is fundamentally a matter of knowledge and practice. The loss of such knowledge results in what Anders calls dehumanization, which is here another name for what Stiegler calls proletarianization, a loss of that knowledge on the basis of which behavioural bifurcations, that is, decisions, become possible. Biological automatisms and sociological automatisms are today all placed on 'one side' of a struggle, confronted with technological automatisms operating more rapidly and more powerfully than either nature or culture, overtaking them and outstripping them. The hyper-diachronization engendered by the hyper-synchronization of consumer capitalism is relatively new, but the possibility of such obstructions of the psycho-social individuation process is as old as the process itself. This amounts to the injunction to practise, thoughtfully and therapeutically, a positive pharmacology, as scientific wisdom of life tends always to do.
Inference of genetic regulatory networks from time series gene expression data (2005)

Large-scale gene expression data coming from microarray
Breast Implant Safety (1999)

When reading Jocelyn Kaiser's article “Scientific panel clears breast implants” (News of the Week, 11 Dec. p. [1963][1]), one should not confuse the failure to accumulate sufficient human evidence that silicone breast implants damage the health of some people with evidence that no such link, in
The Tandem‐Crosspoint Switch (2001)

Chapter 9 presents an input-output-buffered switch, called a tandem-crosspoint (TDXP) switch, that fully utilizes current CMOS technologies. It starts with a brief review of basic input and output buffered switch architectures, and then describes the TDXP switch architecture and its performance. The switch supports unicast and multicast traffic.
A CD200FC immunoadhesin prolongs rat islet xenograft survival in mice1 (2002)

CD200:CD200R interactions are important in regulating rat islet xenograft survival.
Transient mid-IR study of electron dynamics in TiO2 conduction band (2013)

The dynamics of TiO2 conduction band electrons were followed with a novel broadband synchrotron-based transient mid-IR spectroscopy setup. The lifetime of conduction band electrons was found to be dependent on the injection method used. Direct band gap excitation results in a lifetime of 2.5 ns, whereas indirect excitation at 532 nm via Ru-N719 dye followed by injection from the dye into TiO2 results in a lifetime of 5.9 ns.
Mitochondrial calcium and its regulation in neurodegeneration induced by oxidative stress (2011)

A proposed mechanism of neuronal death associated with a variety of neurodegenerative diseases is the response of neurons to oxidative stress and consequent cytosolic Ca(2+) overload. One hypothesis is that cytosolic Ca(2+) overload leads to mitochondrial Ca(2+) overload and prolonged opening of the permeability transition pore (PTP), resulting in mitochondrial dysfunction. Elimination of cyclophilin D (CyPD), a key regulator of the PTP, results in neuroprotection in a number of murine models of neurodegeneration in which oxidative stress and high cytosolic Ca(2+) have been implicated. However, the effects of oxidative stress on the interplay between cytosolic and mitochondrial Ca(2+) in adult neurons and the role of the CyPD-dependent PTP in these dynamic processes have not been examined. Here, using primary cultured cerebral cortical neurons from adult wild-type (WT) mice and mice missing cyclophilin D (CyPD-KO), we directly assess cytosolic and mitochondrial Ca(2+) , as well as ATP levels, during oxidative stress. Our data demonstrate that during acute oxidative stress mitochondria contribute to neuronal Ca(2+) overload by release of their Ca(2+) stores. This result contrasts with the prevailing view of mitochondria as a buffer of cytosolic Ca(2+) under stress conditions. In addition, we show that CyPD deficiency reverses the release of mitochondrial Ca(2+) , leading to lower of cytosolic Ca(2+) levels, attenuation of the decrease in cytosolic and mitochondrial ATP, and a significantly higher viability of adult CyPD-knockout neurons following exposure of neurons oxidative stress. The study offers a first insight into the mechanism underlying CyPD-dependent neuroprotection during oxidative stress.
Factors Influencing Self-Reported Use of Antioxidant Supplements in Patients with Age-Related Macular Degeneration (2014)

Despite the recommendation of oral antioxidant supplements in the ARED Study for patients with AMD of category 3 or 4, only about half of these patients took the supplements in this study. Identifying the factors, which influenced the decision against supplement use, may help to better support patients in the prevention of severe vision loss caused by AMD.
Model-based multiscale detection of 3D vessels (2002)

In this paper, we present a new approach to segment vessels from 3D angiography of the brain. Our approach is based on a vessel model and uses a multiscale analysis in order to extract the vessel network surrounding an aneurysm. Our model allows us to choose a criterion based on the eigenvalues of the Hessian matrix for selecting a subset of interesting points near the vessel center. It also allows us to choose a good parameter for a /spl gamma/-normalization of the single scale response. The response at one scale is obtained by integrating along a circle the first derivative of the intensity in the radial direction. Once the multiscale response is obtained, we create a smoothed skeleton of the vessels combined with a MIP or a volume rendering to enhance their visualization. The method has been tested on a large variety of 3-D images of the brain, with excellent results. Vessels of various size and contrast are detected with a remarkable robustness, and most junctions are preserved.
Interfacial Activity of Characterized Middle Eastern Asphaltenes (2018)

Asphaltene molecules play a pivotal role in reservoir fluid characterization. As a result of the high complexity of these molecules, there is still an active debate in the scientific community about their physicochemical properties and the structural elucidation, despite a myriad of published studies. It is commonly agreed that asphaltenes, a fraction of reservoir crude oils, exhibit strong interfacial activity and cause many production challenges. In this work, the structure and interfacial activity of 11 characterized asphaltene samples, extracted from 11 different reservoir crude oils from the Middle Eastern region, were analyzed using Raman spectroscopy and pendent drop tensiometry. Additionally, contact angle measurements and atomic force microscopy (AFM) were executed on selected samples. The Raman analysis revealed that the 11 asphaltene batches have similar structural characteristics with the annulated core ranging from 1.43 to 1.66 nm in diameter, which corresponds to 6–7 fused aromatic rings. Interfacial tension (IFT) was measured using the pendent drop technique, by creating a drop of deionized water in a bulk of the respective asphaltene solution in toluene. IFT 90 min values were in the range between 28.3 and 32.6 mN m–1. For one of the asphaltenes, aggregation in the toluene solution was visible by the naked eye. Interestingly, this asphaltene sample showed the weakest influence in terms of IFT reduction, indicating that aggregation reduces the interfacial activity. On the basis of the IFT results, three of the asphaltene samples, exercising different interfacial activity, were investigated for their adsorption tendency toward a carbonate surface using AFM. Topographic images show asphaltene adsorption. The contact angle for water on asphaltene-conditioned surfaces was higher than that for unconditioned surfaces, indicating that the calcite surface was rendered more oil-wet. Increasing the concentration of the asphaltenes in the conditioning solution did not alter the surface to more oil-wet.
Impact of Scrambling on Barcode Entropy (2011)

Security barcodes and other barcodes linked to on-line databases have become commonplace due to the increased availability of mobile phones equipped with high-quality cameras. In this article, the authors provide methods for quantifying the entropy of the embedded barcode data, assuming methods other than the standards-specified error-correcting code (ECC) approaches can be adopted. Higher entropy, which reduces the likelihood of a fraudulent agent being able to "guess" correct barcodes, is measured directly using a variety of novel algorithms and applied to large sets of barcodes. The authors data, however, show that removing ECC provides the additional advantage of increasing the entropy. Thus, all other settings (data payload size, printing technology, substrate used, etc.) being equal, eliminating the ECC increases the security of the information content for the barcodes (DataMatrix) tested.
Optimal pagination techniques for automatic typesetting systems (1981)

This thesis considers how to use a computer to break a document into pages suitable for printing. Although this problem is easy to solve when the document consists of just text, it becomes complicated when footnotes, displays, and figures are introduced. These elements add some freedom of choice in the way breaks are chosen, since the white space around the displays and the exact placement of the figures can be decided by the pagination algorithm. Out of the many possible ways to paginate such a document, the pagination algorithm should pick the one that is in some sense optimal. The approach taken here is to define a badness function that depends on the way the document is broken up, and then to design an algorithm to find a way to minimize the value of this function.
The document is modelled by two lists, the text list and the figure list. Each item in the text list is either a 'box', corresponding to something that will print such as a line of text, a 'glue' item, corresponding to the white space between the lines, a 'penalty' item, corresponding to a legal place to break the list, or a 'citation', marking a reference to one of the figures. The items in the figure list indicate the size of each figure, and by how much each figure is allowed to stretch or shrink. This model is based on the one used in the TEX typesetting system.
The optimizing pagination algorithm uses dynamic programming to find, for each i, j, and k, the best way to put the first i lines of text and the first j figures onto the first k pages; to make the program run in a reasonable amount of time, this calculation includes only those subproblems that are feasible, i.e., likely to lead to a solution with a small badness value.
The badness function must be chosen carefully in order to get a problem that can be solved by these techniques. For certain simple badness functions, the pagination problem is NP-complete; two such functions are described in the thesis.
Characterization Of The HLA Class II Ligandome In Acute Myeloid Leukemia (AML) Reveals Novel Candidates For Peptide-Based Immunotherapy (2013)

Abstract CD4+ T cells are crucial for the induction and maintenance of cytotoxic T cell responses, but can also mediate direct tumor rejection. The therapeutic efficacy of peptide-based cancer vaccines may thus be improved by including HLA class II epitopes to stimulate T helper cells. In contrast to HLA class I ligands, only a small number of class II ligands of TAA has been described so far. We recently reported on the overexpression of HLA class II in AML cells as compared to autologous monocytes and granulocytes as well as on the first HLA class I leukemia associated antigens identified directly on the cell surface of primary AML cells (Stickel et. al. abstract in Blood 2012). In this study we characterized the HLA class II ligandome in AML to identify additional ligands for a peptide-based immunotherapy approach. HLA class II ligands from primary AML cells as well as bone marrow and peripheral blood mononuclear cell (BMNCs/PBMCs) of healthy donors were analyzed using the approach of direct isolation and identification of naturally presented HLA peptides by affinity chromatography and mass spectrometry (LC-MS/MS). LC-MS/MS peptide analysis provided qualitative and semi-quantitative information regarding the composition of the respective ligandomes. Comparative analysis of malignant and benign samples served to identify ligandome-derived tumor associated antigens (LiTAAs) and to select peptide vaccine candidates. Most abundantly detected peptides were functionally characterized with regard to their ability to induce a specific CD4+ T-cell response in healthy donors and in tumor patients using ELISpot. Samples from 10 AML patients (5 FLT3-ITD mutated) and 18 healthy donors were analyzed. We identified more than 2,100 AML-derived HLA class II ligands representing &gt;1,000 different source proteins, of which 315 were exclusively represented in AML, but not in healthy PBMC/BMNC. Data mining for broadly represented LiTAAs pinpointed 26 HLA class II ligands from 8 source proteins that were presented exclusively on more than 40% of all analyzed AML samples as most promising targets. Amongst them were already described TAAs (e.g., RAB5A) as well as several so far understated proteins (e.g. calsyntenin 1, glycophorin A, mannose-binding lectin 2). Subset analysis revealed 58 LiTAAs presented exclusively on FLT3-ITD mutated AML cells. Additional screening for HLA class II ligands from described leukemia associated antigens showed positive results for NPM1 (1 peptide sequence) and MPO (13 peptide sequences). Peptides from calsyntenin 1 and RAB5A were able to elicit CD4+-T-cell response in 25% of tested AML patients (n=16). Thus, our study identified, for the first time, HLA class II tumor associated antigens directly obtained from the HLA ligandomes of AML patients and thereby represents a further step to our goal of developing a multipeptide vaccine for immunotherapy of AML. Disclosures: No relevant conflicts of interest to declare.
Experimental and numerical investigations of the vacuum‐forming process (1992)

Abstract This paper exmines the influence of process variables on final thickness distributions for vacuum‐formed thermoplastic parts. The process variables investigated include evacuation rate, sheet surface temperature, mold temperature, and material slip over the mold surface. The experimental data presented include, in addition to thicknesses, sheet surface temperature obtained via infrared thermography. A finite element program to model the vacuum‐forming process is discussed, and the wall thickness distribution predicted by this program for a vacuum‐formed part is compared with the results of the experiments.