gebhart/patrepeval huggingface dataset:
An Assistive Handwashing System with Emotional Intelligence (2014)

Whether emotional intelligence (or, affective reasoning) is included can influence the effectiveness of a cognitive assistive system. This thesis presents a novel emotionally intelligent hand-washing assistant that aims to help older adults with Alzheimer's disease complete hand-washing tasks more independently. The thesis reviews previous works in the development of cognitive assistants and in the study of emotional intelligence, and then designs a hand-washing system prototype that combines the two research streams. The difficulties in designing such a system, including probabilistic and decision-theoretic reasoning of the user's functional and emotional states, computer-vision based activity monitoring and affective recognition, and embodied prompting are discussed. Designing the hand-washing system as an integration of independent components, the thesis also discusses coordination between the components. The thesis implements the system in the end, and shows by preliminary tests in laboratory settings that the system implemented (1) runs in real-time from the perspective of the user group, (2) is able to provide a level of functional assistance, (3) produces system prompts that have encoded to some extent the emotional state of its user. The preliminary tests also indicated that a user with emotions with high potency levels (and high activity levels) is more likely to receive system prompts with low potency levels (and high activity levels).&#13;\n&#13;\nThis thesis is one of the exploratory works in the area of integrating emotional intelligence with cognitive intelligent assistive systems. It provides a solution to fitting emotional intelligence in a functional system, as well as points out directions for future improvements. The framework designed in this thesis is portable and extensible, and can be generalized to be used in other applications.
Motion Compensated Prediction and Interpolation Filter Design in H.265/HEVC (2013)

Coding efficiency gains in the new High Efficiency Video Coding (H.265/HEVC) video coding standard are achieved by improving many aspects of the traditional hybrid coding framework. Motion compensated prediction, and in particular the interpolation filter, is one area that was improved significantly over H.264/AVC. This paper presents the details of the interpolation filter design of the H.265/HEVC standard. First, the improvements of H.265/HEVC interpolation filtering over H.264/AVC are presented. These improvements include novel filter coefficient design with an increased number of taps and utilizing higher precision operations in interpolation filter computations. Then, the computational complexity is analyzed, both from theoretical and practical perspectives. Theoretical complexity analysis is done by studying the worst-case complexity analytically, whereas practical analysis is done by profiling an optimized decoder implementation. Coding efficiency improvements over the H.264/AVC interpolation filter are studied and experimental results are presented. They show a 4.0% average bitrate reduction for the luma component and 11.3% average bitrate reduction for the chroma components. The coding efficiency gains are significant for some video sequences and can reach up to 21.7%.
Structure and function of type II restriction endonucleases (2001)

More than 3000 type II restriction endonucleases have been discovered. They recognize short, usually palindromic, sequences of 4-8 bp and, in the presence of Mg(2+), cleave the DNA within or in close proximity to the recognition sequence. The orthodox type II enzymes are homodimers which recognize palindromic sites. Depending on particular features subtypes are classified. All structures of restriction enzymes show a common structural core comprising four beta-strands and one alpha-helix. Furthermore, two families of enzymes can be distinguished which are structurally very similar (EcoRI-like enzymes and EcoRV-like enzymes). Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone. In contrast, specific binding is characterized by an intimate interplay between direct (interaction with the bases) and indirect (interaction with the backbone) readout. Typically approximately 15-20 hydrogen bonds are formed between a dimeric restriction enzyme and the bases of the recognition sequence, in addition to numerous van der Waals contacts to the bases and hydrogen bonds to the backbone, which may also be water mediated. The recognition process triggers large conformational changes of the enzyme and the DNA, which lead to the activation of the catalytic centers. In many restriction enzymes the catalytic centers, one in each subunit, are represented by the PD. D/EXK motif, in which the two carboxylates are responsible for Mg(2+) binding, the essential cofactor for the great majority of enzymes. The precise mechanism of cleavage has not yet been established for any enzyme, the main uncertainty concerns the number of Mg(2+) ions directly involved in cleavage. Cleavage in the two strands usually occurs in a concerted fashion and leads to inversion of configuration at the phosphorus. The products of the reaction are DNA fragments with a 3'-OH and a 5'-phosphate.
Multi-scale image harmonization (2010)

Traditional image compositing techniques, such as alpha matting and gradient domain compositing, are used to create composites that have plausible boundaries. But when applied to images taken from different sources or shot under different conditions, these techniques can produce unrealistic results. In this work, we present a framework that explicitly matches the visual appearance of images through a process we call image harmonization, before blending them. At the heart of this framework is a multi-scale technique that allows us to transfer the appearance of one image to another. We show that by carefully manipulating the scales of a pyramid decomposition of an image, we can match contrast, texture, noise, and blur, while avoiding image artifacts. The output composite can then be reconstructed from the modified pyramid coefficients while enforcing both alpha-based and seamless boundary constraints. We show how the proposed framework can be used to produce realistic composites with minimal user interaction in a number of different scenarios.
Combined Effects of IL-12 and IL-18 on the Induction of Collagen-Induced Arthritis (2000)

IL-18 expression has recently been detected in rheumatoid arthritis (RA) synovial membrane. We investigated the mechanisms by which IL-18-induced collagen-induced arthritis in DBA/1 mice primed intradermally with type II bovine collagen in IFA and boosted i.p. 21 days later with CII in saline. Mice were injected i.p. with rIL-12, rIL-18, or both (100 ng) during days -1 to 4 and again on days 20-24. Control mice received PBS. Mice treated with IL-12 or IL-18 alone developed significantly higher incidence and more severe disease compared with controls. These were elevated further by combination treatment with IL-12 and IL-18. The cytokine treatments led to markedly enhanced synovial hyperplasia, cellular infiltration, and cartilage erosion compared with controls. Cytokine-treated mice produced significantly more IFN-gamma, TNF-alpha, and IL-6 than the controls. Interestingly, IL-18-treated mice produced more TNF-alpha and IL-6, but less IFN-gamma, compared with mice treated with IL-12. Furthermore, splenic macrophages from DBA/1 mice cultured in vitro with IL-18, but not IL-12, produced substantial amounts of TNF-alpha. Mice treated with IL-18 or IL-18 plus IL-12 produced markedly more IgG1 and IgG2a anti-collagen Ab compared with controls, whereas IL-12 treatment only led to an enhanced IgG2a response. Together these results demonstrate that IL-18 can promote collagen-induced inflammatory arthritis through mechanisms that may be distinct from those induced by IL-12.
Development and assessment of aPotato virus X-based expression system with improved biosafety (2005)

Over the last decade, plant virus-based vectors have been developed and successfully exploited for high-yield production of heterologous proteins in plants. However, widespread application of recombinant viruses raises concerns about possible risks to the environment. One of the primary safety issues that must be considered is the uncontrolled spread of the genetically engineered virus from experimental plants to susceptible weeds or crops. Using a movement-deficient Potato virus X (PVX)-based transient gene expression vector which harbors the beta-glucuronidase (gus) gene, we established a plant viral expression system that provides containment of the recombinant virus and allows for safe and efficient protein production. By deletion of the viral 25k movement protein gene, systemic spread of the modified virus in non-transgenic Nicotiana benthamiana plants was successfully inhibited. In transgenic N. benthamiana plants expressing the 25K viral movement protein, this deficiency was complemented, thus resulting in systemic infection with the movement-deficient virus. While no differences in virus spread and accumulation were observed compared to infection caused by wild-type PVX in non-transgenic plants, the movement protein transgenic plants exhibited none of the normal symptoms of viral infection. Several biosafety aspects were investigated including the potential for recombination between the defective virus and the movement protein transgene, as well as complementation effects in non-transgenic plants doubly infected with the defective and the wild-type virus. Furthermore, the applicability of the safety system for the production of heterologous proteins was evaluated with gus as a model gene. With respect to the stability of the gus insert and the expression level of the GUS protein, there were no differences between the novel system developed and the conventional PVX-based expression system.
Surplus plutonium immobilization feed materials requirements and blending strategy (1998)

The Excess Fissile Materials Disposition Program`s Record of Decision (ROD) published in January 1997 by DOE/MD describes three potential pathways for the disposition of excess fissile materials: burning as MOX fuel rods, and two can-in-canister immobilization candidates: glass and ceramics. In addition, the ROD introduced processing schedules for MD disposition program. Prior to the ROD, the only acceptance specification that AMD had for incoming materials was DOE- STD-3013. However, STD-3013 is a specification aimed at maintaining safety for long term storage (approximately 100 years) and was never intended to act as an acceptance specification. An effort has begun to examine all of the technical issues associated with the processing and transfer of materials from EM to MD. Since that time, several related initiatives have begun to deal with the many issues, including the EM Material Stewardship program, the latest EM-66 sponsored trade studies, and a new storage standard. A draft of feed material requirements for the ceramic Immobilization Facility that will be used for the disposition of surplus plutonium has been developed for discussion. It established impurity limits for feed materials to the immobilization process, identifies impurities in feed materials that may have an adverse effect on the immobilization process, and indicates how these materials can be further processed and blended at the Immobilization Facility to ensure manufacture of an acceptable product.
Separation of functionally distinct human granulocyte-macrophage colony- stimulating factors (1979)

Human placental conditioned medium (HPCM) contans colony-stimulating factors (CSFs) required for the growth in vitro of neutrophilic granulocyte-macrophage (GM) and eosinophilic (EO) progenitor cells from human bone marrow. Fractionation of CSFs in HPCM was achieved by manipulation of the elution conditions on a column of phenyl-Sepharose. After equilibration of the phenyl-Sepharose column at high ionic strength (1 M ammonium sulfate), all of the CSF bound; one species of GM-CSF (alpha) and all of the elutable EO-CSF were eluted from the column simply by reducing the salt concentration, whereas the second species of GM-CSF (beta) was free of EO-CSF and was eluted only by increasing the concentration of tehylene glycol in the elution buffer. The two GM-CSFs were functionally distinct. GM-CSF alpha preferentially stimulated colony formation by day 14 of culture, and there was a decreased proportion of neutrophil colonies and increased proportion of macrophage colonies as the strength of the stimulus was decreased; GM- CSF beta, on the other hand, preferentially stimulated colony formation by day 7 of culture, and the proportion of neutrophil colonies was high (average 80%) and independent of the concentration of GM-CSF beta. GM- CSF alpha and GM-CSF beta were indistinguishable on the basis of apparent molecular size on tel filtration columns (molecular weight 30,000), charge properties on isoelectric focusing beds (isoelectric point, 4.9), and were not related to each other as a sialoglycoprotein is related to its asialo form. Adherent cell removal of the target bone marrow cells (to remove colony-stimulating cells) suggested that both GM-CSFs acted directly rather than by stimulating the production of GM- CSF. Mixing and titration experiments indicated that the differences in functional specificities of the two GM-CSFs (and the lack of EO-CSF associated with GM-CSF beta) were not due to the presence of specific inhibitory molecules or lower absolute levels of CSF in one fraction relative to the other. These two species of GM-CSF should be useful in separately enumerating subpopulations of different GM-progenitor cells inhuman hemopoietic disorders.
Targeting the indoleamine 2,3-dioxygenase pathway in cancer (2015)

Tumor cells escape the immune surveillance system of the host through a process called immune tolerance. Immunotherapy targets molecules that serve as checks and balances in the regulation of immune response. Indoleamine-2,3-dioxygenase (IDO) is an intracellular enzyme, which through the process of tryptophan depletion exerts an immunosuppressive effect, facilitating immune escape of tumors. This review summarizes our current knowledge on IDO expression in malignancies, the IDO inhibitors that are currently available and those under clinical development.
Clinical Aspects of Platelet Inhibitors and Thrombus Formation (2007)

The platelet, once thought to be solely involved in clot formation, is now known to be a key mediator in various others processes such as inflammation, thrombosis, and atherosclerosis. Supported by the wealth of evidence from clinical trials demonstrating their benefits in patient outcomes, antiplatelet agents have become paramount in the prevention and management of various diseases involving the cardiovascular, cerebrovascular, and peripheral arterial systems. Despite being among the most widely used and studied classes of medical therapies, new discoveries regarding important clinical aspects and properties of these agents continue to be made. As our understanding of platelet biology expands, more effective and safer novel therapies continue to be developed. The use of more refined agents in conjunction with a better understanding of their effects will further the ability to provide more optimized care on an individual basis.
OatA, a Peptidoglycan O-Acetyltransferase Involved in Listeria monocytogenes Immune Escape, Is Critical for Virulence (2011)

Microbial pathogens have evolved mechanisms to overcome immune responses and successfully infect their host. Here, we studied how Listeria monocytogenes evades immune detection by peptidoglycan (PGN) modification. By analyzing L. monocytogenes muropeptides, we detected O-acetylated muramic acid residues. We identified an O-acetyltransferase gene, oatA, in the L. monocytogenes genome sequence. Comparison of PGN from parental and isogenic oatA mutant strains showed that the O-acetyltransferase OatA O-acetylates Listeria PGN. We also found that PGN O-acetylation confers resistance to different types of antimicrobial compounds targeting bacterial cell wall such as lysozyme, β-lactam antibiotics, and bacteriocins and that O-acetylation is required for Listeria growth in macrophages. Moreover, oatA mutant virulence is drastically affected in mice following intravenous or oral inoculation. In addition, the oatA mutant induced early secretion of proinflammatory cytokines and chemokines in vivo. These results suggest an important role for OatA in limiting innate immune responses and promoting bacterial survival in the infected host.
Effects of glucagon, insulin, amylin and CGRP on feeding (1999)

The roles of the pancreatic peptides glucagon, insulin, and amylin in the inhibitory control of feeding are reviewed. Calcitonin gene-related peptide (CGRP) is also included because it is structurally and functionally related to amylin and because known amylin and CRRP receptors are activated by both peptides. Glucagon-like peptide 1, in contrast, is structurally distinct from pancreatic glucagon and does not cross-react with glucagon receptors, so it is not considered. Several detailed reviews of the feeding effects of these peptides have appeared recently; where appropriate, these are cited rather than the primary literature.
Pixelated spatial gene expression analysis from tissue (2018)

Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 µm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue. The on-chip reaction was validated by mRNA fluorescence in situ hybridization (mFISH) from cells in the tissue section. The entire process, from tissue loading on microchip to results from RT-LAMP can be carried out in less than 2 h. We anticipate that this technique, with its ease of use, fast turnaround, and quantitative molecular outputs, would become an invaluable tissue analysis tool for researchers and clinicians in the biomedical arena.
Transduction du signal par les récepteurs de cytokines (1994)

Les cytokines reglent la proliferation et la differenciation des cellules hematopoietiques et notamment la reponse immunitaire. Leurs recepteurs sont composes de chaines communes et de chaines specifiques portant le site de liaison de la cytokine. La fixation d'une cytokine sur son recepteur entraine la formation d'un complexe multimerique qui, a son tour, recrute des tyrosine kinases de divers types: des kinases de la famille Jak, qui phosphorylent les facteurs de transcription de type Stat dont les cibles nucleaires sont encore mal connues; d'autres kinases, dont certaines appartiennent a la famille Src, qui transmettent le signal mitogene en empruntant d'autres voies, en particulier la voie de Ras et des MAP kinases
Submicron aligned wafer bonding via capillary forces (2007)

Submicron wafer-to-wafer alignment is critical in wafer bonding for the fabrication of three-dimensional integrated circuits. In this work, the authors examine the sources of misalignment in traditional alignment methods and then examine the capabilities of an alternative alignment approach that uses capillary forces. A multiscale model was developed to investigate the potential of capillary assisted alignment. The model consists of a local model of a confined liquid droplet and a finite element model that predicts wafer-level distortions and misalignment. Using the model, the effect of pattern error and wafer nonflatness on misalignment in bonding was examined for both the traditional and capillary assisted methods. The results indicate that capillary assisted alignment has several distinct advantages over traditional methods that result primarily from the ability to align the wafers at many locations across the wafer.
Protein transduction technology: a novel therapeutic perspective. (2006)

The direct intracellular delivery of proteins has, until recently, been difficult to achieve, due primarily to the bioavailability barrier of the plasma membrane. During the past 15 years, a variety of peptides called protein transduction domains (PTDs) or cell penetrating peptides (CPPs), have been characterized for their ability to translocate into live cells. The most commonly studied are homeodomain transcription factors such as Antennapedia, the herpes simplex virus (HSV) type 1 protein VP22, and the human immunodeficiency virus (HIV-1) transactivator TAT protein. Recently, polyarginine exhibits even greater efficiency in terms of delivery of several peptides and proteins. Numerous examples of biologically active full-length proteins and peptides have been delivered to cells and tissues, both in vitro and in vivo. These studies offer new avenues for treatment of several diseases. The main mechanism of protein transduction is an electrostatic interaction with the plasma membrane, penetration into cells by macropinocytosis, and a release to cytoplasm and nuclei by retrograde transport. Moreover, the intercellular transfer of endogenous transcription factors, such as TAT and homeoproteins, seems to point to an original and important mode of signal transduction. The protein transduction systems have opened up several possibilities, not only for the development of new peptide/protein drugs but also for consideration of their physiological and developmental implications.
The Toll‐like receptor 7/8‐ligand resiquimod (R‐848) primes human neutrophils for leukotriene B 4 , prostaglandin E 2 and platelet‐activating factor biosynthesis (2007)

Toll-like receptors (TLR) recognize pathogen-associated molecular patterns and play important roles in the innate immune system. While single-stranded viral RNA is the natural ligand of TLR7/TLR8, the imidazoquinoline resiquimod (R-848) is recognized as a potent synthetic agonist of TLR7/TLR8. We investigated the effects of TLR7/8 activation on lipid mediator production in polymorphonuclear leukocytes exposed to R-848. Although R-848 had minimal effects by itself, it strongly enhanced leukotriene B4 formation on subsequent stimulation by fMLP, platelet-activating factor, and the ionophore A23187. R-848 acted via TLR8 but not TLR7 as shown by the lack of effect of the TLR7-specific ligand imiquimod. Priming with R-848 also resulted in enhanced arachidonic acid release and platelet-activating factor formation following fMLP stimulation, as well as enhanced prostaglandin E2 synthesis following the addition of arachidonic acid. Western blot analysis demonstrated that R-848 induced the phosphorylation of the cytosolic phospholipase A2alpha, promoted 5-lipoxygenase translocation and potently stimulated the expression of the type 2 cyclooxygenase. Bafilomycin A1, an inhibitor of endosomal acidification, efficiently inhibited all R-848-induced effects. These studies demonstrate that TLR8 signaling strongly promotes inflammatory lipid mediator biosynthesis and provide novel insights on innate immune response to viral infections.