gebhart/patrepeval huggingface dataset:
A Transgenic Probiotic Secreting a Parasite Immunomodulator for Site-Directed Treatment of Gut Inflammation (2014)

New treatment strategies for inflammatory bowel disease are needed and parasitic nematode infections or application of helminth components improve clinical and experimental gut inflammation. We genetically modified the probiotic bacterium Escherichia coli Nissle 1917 to secrete the powerful nematode immunomodulator cystatin in the gut. This treatment was tested in a murine colitis model and on post-weaning intestinal inflammation in pigs, an outbred model with a gastrointestinal system similar to humans. Application of the transgenic probiotic significantly decreased intestinal inflammation in murine acute colitis, associated with increased frequencies of Foxp3(+) Tregs, suppressed local interleukin (IL)-6 and IL-17A production, decreased macrophage inflammatory protein-1α/β, monocyte chemoattractant protein -1/3, and regulated upon activation, normal T-cell expressed, and secreted expression and fewer inflammatory macrophages in the colon. High dosages of the transgenic probiotic were well tolerated by post-weaning piglets. Despite being recognized by T cells, secreted cystatin did not lead to changes in cytokine expression or macrophage activation in the colon. However, colon transepithelial resistance and barrier function were significantly improved in pigs receiving the transgenic probotic and post-weaning colon inflammation was reduced. Thus, the anti-inflammatory efficiency of a probiotic can be improved by a nematode-derived immunoregulatory transgene. This treatment regimen should be further investigated as a potential therapeutic option for inflammatory bowel disease.
Lambertian reflectance and linear subspaces (2003)

We prove that the set of all Lambertian reflectance functions (the mapping from surface normals to intensities) obtained with arbitrary distant light sources lies close to a 9D linear subspace. This implies that, in general, the set of images of a convex Lambertian object obtained under a wide variety of lighting conditions can be approximated accurately by a low-dimensional linear subspace, explaining prior empirical results. We also provide a simple analytic characterization of this linear space. We obtain these results by representing lighting using spherical harmonics and describing the effects of Lambertian materials as the analog of a convolution. These results allow us to construct algorithms for object recognition based on linear methods as well as algorithms that use convex optimization to enforce nonnegative lighting functions. We also show a simple way to enforce nonnegative lighting when the images of an object lie near a 4D linear space. We apply these algorithms to perform face recognition by finding the 3D model that best matches a 2D query image.
Non‐Phenolic Dicinnamamides from Pholiota Spumosa: Isolation, Synthesis and Antitumour Activity (2007)

Abstract Two new amides derived from cinnamic acid, namely,( R )‐2‐hydroxyputrescine dicinnamamide ( 4 ) and pholiotic acid {(2 R )‐2‐[( S )‐3‐hydroxy‐3‐methylglutaryloxy]putrescine dicinnamamide} ( 5 ), in addition to the known compound maytenine ( N 1 , N 8 ‐dicinnamoyl spermidine) ( 3 ) were isolated from the fruiting bodies of the Basidiomycete Pholiota spumosa . The absolute configuration of 4 was established as ( R ) by its total synthesis starting from ( S )‐dimethylmalate, whereas that of 5 was determined by conversion into the known compound methyl ( S )‐4‐[( S )‐1‐(1‐naphthalen‐1‐yl)ethylcarbamoyl]‐3‐hydroxy‐3‐methylbutanoate ( 14 ). Compounds 3 and 5 exhibited an inhibitory effect on cell growth of the androgen‐insensitive DU‐145 prostate cancer cells, which suggests that these fungal polyamine conjugates, like other polyamine analogues, might have chemotherapeutic potential against androgen‐independent prostatic cancer. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2007)
Neuronal and glial expression of the adhesion molecule TAG‐1 is regulated after peripheral nerve lesion or central neurodegeneration of adult nervous system (2005)

Expression of the cell adhesion molecule TAG-1 is down-regulated in adult brain, with the exception of certain areas exhibiting structural plasticity. Here, we present evidence that TAG-1 expression persists also in adult rat spinal cord and dorsal root ganglia (DRG), and can be up-regulated after injury. On Western blots of adult tissue, TAG-1 is detected as a 135-kDa band, with an additional specific 90-kDa band, not present in developing tissue. TAG-1 expression is found both in DRG neurons and in Schwann cells, particularly those associated with the peripherally projecting DRG processes. Quantitative in situ hybridization revealed that TAG-1 expression is significantly higher in small neurons that give rise to unmyelinated fibers, than in large DRG neurons. The regulation of TAG-1 was then examined in two different lesion paradigms. After a sciatic nerve lesion, TAG-1 expression is not up-regulated in DRG neurons, but decreases with time. At the lesion site, reactive Schwann cells up-regulate TAG-1, as demonstrated by both immunohistochemistry and in situ hybridization. In a second paradigm, we injected kainic acid into the spinal cord that kills neurons but spares glia and axons. TAG-1 is up-regulated in the spinal neuron-depleted area as well as in the corresponding dorsal and ventral roots, associated with both target-deprived afferent fibers and with the non-neuronal cells that invade the lesion site. These results demonstrate a local up-regulation of TAG-1 in the adult that is induced in response to injury, suggesting its involvement in axonal re-modelling, neuron-glia interactions, and glial cell migration.
New replication technique for the fabrication of thin polymeric microfluidic devices with tunable porosity (2005)

In this article we present a new versatile replication method to produce thin polymeric microfluidic devices with tunable porosity. This method is based on phase separation of a polymer solution on a microstructured mold. Compared to existing microfabrication techniques, such as etching and hot embossing, our technique offers four advantages: (a) simple and cheap process that can be performed at room temperature outside clean room facilities; (b) very broad range of applicable materials (including materials that could not be processed before); (c) ability to make thin flexible chips; (d) ability to introduce and tune porosity in the chip. By introducing porosity, the channel walls can be used for selective transport of gasses, liquids and solutes. A proof-of-concept will be given, by showing fast CO2 transport through the channel walls of a porous polymer chip. Furthermore, it will be demonstrated that the gas permeation performance of chips can be enhanced dramatically by a decrease in chip thickness and incorporation of porosity. We expect that the development of porous chips can lead to the on-chip integration of multiple unit operations, such as reaction, separation, gas liquid contacting and membrane emulsification.
Actually Useful Internet Security Techniques (1995)

Using a friendly, authoritative style, this book addresses security issues by examining each common Internet application used today and pulling from it the potential security problems for the reader. -- Effectively shows how to configure and maintain a computer and network against the security exposures of the Internet -- Demonstrates the potential security risks and how to overcome them with valid security techniques -- Includes real-world case studies which deal with the day-to-day security issues on a large scale basis
View management for virtual and augmented reality (2001)

We describe a view-management component for interactive 3D user interfaces. By view management, we mean maintaining visual constraints on the projections of objects on the view plane, such as locating related objects near each other, or preventing objects from occluding each other. Our view-management component accomplishes this by modifying selected object properties, including position, size, and transparency, which are tagged to indicate their constraints. For example, some objects may have geometric properties that are determined entirely by a physical simulation and which cannot be modified, while other objects may be annotations whose position and size are flexible.We introduce algorithms that use upright rectangular extents to represent on the view plane a dynamic and efficient approximation of the occupied space containing the projections of visible portions of 3D objects, as well as the unoccupied space in which objects can be placed to avoid occlusion. Layout decisions from previous frames are taken into account to reduce visual discontinuities. We present augmented reality and virtual reality examples to which we have applied our approach, including a dynamically labeled and annotated environment.
High mobility and excellent electrical stability of MOSFETs using a novel HfTaO gate dielectric (2004)

In this work, we developed a novel Hf-based gate dielectric for MOSFETs with TaN metal gate. By incorporating Ta into HfO/sub 2/ films, significant improvements were achieved in contrast to pure HfO/sub 2/: (1) the dielectric crystallization temperature is increased up to 1000/spl deg/C; (2) interface states density (D/sub it/) is reduced by one order of magnitude; (3) electron peak mobility is enhanced by more than two times; (4) charge trapping and threshold voltage shift is reduced by 20 times, greatly prolonging the device lifetime; (5) negligible sub-threshold swing and G/sub m/ variations under constant voltage stress (CVS).
Establishment of Cloned Anaplasma phagocytophilum and Analysis of p44 Gene Conversion within an Infected Horse and Infected SCID Mice (2005)

Diverse p44 alleles at the p44 expression locus (p44Es) encoding surface-exposed major membrane proteins, P44s, of Anaplasma phagocytophilum were hypothesized to be garnered by recombination to enact antigenic variation. However, this hypothesis has not been proven so far, due to inability to clone this obligate intragranulocytic rickettsia. To define the p44E recombination, we developed a novel method to clone A. phagocytophilum. This isogenic cloned population containing a defined p44E was used to infect a naive horse and severe combined immunodeficiency (SCID) mice. During a 58-day infection period in the blood of the horse, p44E conversion was evident in a total of 11 new p44Es, 48% (115/242) of the sequenced p44E population. During a 50-day infection period in the blood of SCID mice, p44E conversion was manifested in a total of 13 new p44Es, 42% (192/460) of the p44E population. Thus, similar levels of p44E convertants were detected in either the presence or absence of an acquired immune system, suggesting that T- and B-cell immune pressure was not essential for recombination and/or selection of the p44E variants. Analysis of sequentially changed p44Es revealed that the entire central hypervariable region of donor p44 pseudogenes or of donor full-length p44s replaced the same region of the resident p44E as a cassette. Putative recombination points were detected within p44 conserved regions flanking the central hypervariable region by the TOPALi analysis. Our results unambiguously demonstrated p44E recombination. The cloning method developed would facilitate precise analysis of the recombination process and the extent of diversity which the recombination creates in the antigenic repertoire.
The In Vitro Migration Capacity of Human Bone Marrow Mesenchymal Stem Cells: Comparison of Chemokine and Growth Factor Chemotactic Activities (2007)

Adult bone marrow (BM)-derived stem cells, including hematopoietic stem cells (HSCs) and MSCs, represent an important source of cells for the repair of a number of damaged tissues. In contrast to HSCs, the soluble factors able to induce MSC migration have not been extensively studied. In the present work, we compared the in vitro migration capacity of human BM-derived MSCs, preincubated or not with the inflammatory cytokines interleukin 1beta (IL1beta) and tumor necrosis factor alpha (TNFalpha), in response to 16 growth factors (GFs) and chemokines. We show that BM MSCs migrate in response to many chemotactic factors. The GFs platelet-derived growth factor-AB (PDGF-AB) and insulin-like growth factor 1 (IGF-1) are the most potent, whereas the chemokines RANTES, macrophage-derived chemokine (MDC), and stromal-derived factor-1 (SDF-1) have limited effect. Remarkably, preincubation with TNFalpha leads to increased MSC migration toward chemokines, whereas migration toward most GFs is unchanged. Consistent with these results, BM MSCs express the tyrosine kinase receptors PDGF-receptor (R) alpha, PDGF-Rbeta, and IGF-R, as well as the RANTES and MDC receptors CCR2, CCR3, and CCR4 and the SDF-1 receptor CXCR4. TNFalpha increases CCR2, CCR3, and CCR4 expression (as opposed to that of CXCR4), together with RANTES membrane binding. These data indicate that the migration capacity of BM MSCs is under the control of a large range of receptor tyrosine kinase GFs and CC and CXC chemokines. Most chemokines are more effective on TNFalpha-primed cells. Our results suggest that the mobilization of MSCs and their subsequent homing to injured tissues may depend on the systemic and local inflammatory state. Disclosure of potential conflicts of interest is found at the end of this article.
Quantitation of activated factor VII levels in plasma using a tissue factor mutant selectively deficient in promoting factor VII activation (1993)

Although the majority of factor VII (FVII) circulates in the zymogen form, low levels of activated factor VII (FVIIa) have been postulated to exist in plasma and to serve a priming function for triggering of the clotting cascade. However, direct measurement of plasma FVIIa has not previously been possible. We have quantified plasma FVIIa levels using a novel, highly sensitive assay that is free from interference by FVII. Specificity of this clot-based assay results from the use of a mutant tissue factor that is selectively deficient in promoting FVII activation, but retains FVIIa cofactor function. In normal adults, FVIIa was found to be present in plasma (mean: 3.6 ng/mL) with considerable variation between individuals (range: 0.5 to 8.4 ng/mL). FVIIa levels were only loosely correlated with FVII coagulant activity, but were elevated in pregnancy and reduced with oral anticoagulant therapy. Incubation of plasma on ice in glass containers (cold activation) resulted in substantial FVIIa generation. Measurement of plasma forms of factor VII is of potential clinical importance because elevated FVII coagulant activity has been implicated as a significant risk predictor for ischemic heart disease. Clinically, this new assay will now permit direct assessment of the role of plasma FVIIa in thrombotic disorders.
Informed consent in the Mozilla browser: implementing value-sensitive design (2003)

Reports on one of the first efforts to apply value-sensitive design (VSD) to a large-scale real-world software system. We sought to improve informed consent in Web-based interactions through the development of new technical mechanisms for cookie management. We describe our VSD methodology, explicate criteria for informed consent in online interactions and summarize how current browsers fall short with respect to those criteria. Next, we identify four goals for the redesign of current browsers. These goals, in turn, initiate an iterative design process that lies at the heart of the VSD methodology wherein we move among the design and implementation of new technical mechanisms, formative evaluation and the design goals coupled with the criteria for informed consent online. Key mechanisms include peripheral awareness of cookies and just-in-time interventions. At various phases in the design process, we implement our design improvements in the Mozilla browser (the open source for Netscape Navigator).
Antimicrobial activity of a 13 amino acid tryptophan‐rich peptide derived from a putative porcine precursor protein of a novel family of antibacterial peptides (1996)

It has long been speculated that porcine cathelin is an N-terminal fragment of a longer precursor protein which possesses antimicrobial activity. In an attempt to find such a precursor, a cDNA clone was recently isolated and sequenced by screening a cDNA library from porcine bone marrow. In order to identify the functional activity of the putative protein encoded by an open reading frame, we have synthesized various lengths of peptides that correspond to the C-terminal region of the protein and examined them for their antimicrobial activities. We found that a 13 amino acid tryptophan-rich region with the sequence of VRRFPWWWPFLRR had strong antimicrobial activity with a wide spectrum. It showed potency against Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Staphylococcus epidermidis, Proteus mirabilis, and Streptococcus group D as well as Aspergillus fumigatus. The action of this peptide is bactericidal rather than bacteriostatic and this activity is completely inhibited by 2 mM MgCl2. Our results indicate that the previously identified putative precursor encoded by the isolated cDNA indeed possesses a potent antimicrobial activity and that this 13 amino acid synthetic peptide is considered to be a potentially effective drug against various infectious agents.
Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication (2005)

Practical components for three-dimensional molecular nanofabrication must be simple to produce, stereopure, rigid, and adaptable. We report a family of DNA tetrahedra, less than 10 nanometers on a side, that can self-assemble in seconds with near-quantitative yield of one diastereomer. They can be connected by programmable DNA linkers. Their triangulated architecture confers structural stability; by compressing a DNA tetrahedron with an atomic force microscope, we have measured the axial compressibility of DNA and observed the buckling of the double helix under high loads.
Intramolecular Dimers: A New Design Strategy for Fluorescence‐Quenched Probes (2003)

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than Förster resonance energy transfer (FRET).
Depth perception in motion parallax and stereokinesis. (1993)

Perceived depth in the stereokinetic effect (SKE) illusion and in the monocular derivation of depth from motion parallax were compared. Motion parallax gradients of velocity can be decomposed into 2 components: object- and observer-relative transformations. SKE displays present only the object-relative component. Observers were asked to estimate the magnitude and near-far order of depth in motion parallax and SKE displays. Monocular derivation of depth magnitude from motion parallax is fully accounted for by the perceptual response to the SKE, and observer-relative transformations absent in the SKE are of perceptual utility only as determinants of the near-far signing of perceived sequential depth. The amount of depth and rigidity perceived in motion parallax and SKE displays covaries with the projective size of the stimuli. The monocular derivation of depth from motion is mediated by a perceptual heuristic of which the SKE is symptomatic.
Senescence-Associated Exosome Release from Human Prostate Cancer Cells (2008)

Males of advanced age represent a rapidly growing population at risk for prostate cancer. In the contemporary setting of earlier detection, a majority of prostate carcinomas are still clinically localized and often treated using radiation therapy. Our recent studies have shown that premature cellular senescence, rather than apoptosis, accounts for most of the clonogenic death induced by clinically relevant doses of irradiation in prostate cancer cells. We show here that this treatment-induced senescence was associated with a significantly increased release of exosome-like microvesicles. In premature senescence, this novel secretory phenotype was dependent on the activation of p53. In addition, the release of exosome-like microvesicles also increased during proliferative senescence in normal human diploid fibroblasts. These data support the hypothesis that senescence, initiated either by telomere attrition (e.g., aging) or DNA damage (e.g., radiotherapy), may induce a p53-dependent increase in the biogenesis of exosome-like vesicles. Ultrastructural analysis and RNA interference-mediated knockdown of Tsg101 provided significant evidence that the additional exosomes released by prematurely senescent prostate cancer cells were principally derived from multivesicular endosomes. Moreover, these exosomes were enriched in B7-H3 protein, a recently identified diagnostic marker for prostate cancer, and an abundance of what has recently been termed "exosomal shuttle RNA." Our findings are consistent with the proposal that exosomes can transfer cargos, with both immunoregulatory potential and genetic information, between cells through a novel mechanism that may be recruited to increase exosome release during accelerated and replicative cellular senescence.
Urokinase‐Type Plasminogen Activator (uPA) and Its Receptor (CD87): A New Target in Tumor Invasion and Metastasis (1995)

Extravasation and intravasation of tumor cells in solid malignant tumors is controlled by 3 steps: 1) attachment to and interaction of tumor cells with components of the basement membrane and the extracellular matrix, 2) local proteolysis, and 3) tumor cell migration. Evidence has accumulated that different types of tumor-associated proteases, their inhibitors and receptors are involved in tumor invasion and metastasis. Four different classes of proteases are known to be correlated with the malignant phenotype: 1) Matrix metalloproteases; including collagenases, gelatinases and stromelysins. 2) Cysteine proteases; including cathepsins B and L. 3) Aspartyl protease cathepsin D. 4) Serine proteases; including plasmin and tissue-type plasminogen activator (tPA) and urokinase-type plasminogen activator (uPA). A strong independent prognostic value (relapse-free and/or overall survival) has especially been demonstrated for uPA and its inhibitor PAI-1 in patients with cancer of the breast, ovary, stomach, esophagus, colon, lung, and kidney thus predicting the course of the cancer disease. The strong correlation between elevated uPA and/or PAI-1 values in primary cancer tissues and the malignant phenotype of cancer cells has prompted to explore new tumor biology-oriented concepts in order to suppress uPA or uPA receptor (CD87) expression or to abrogate interaction of uPA with CD87. Various very different approaches to interfere with the expression or reactivity of uPA or CD87 at the gene or protein level were successfully tested including antisense oligonucleotides, antibodies, inhibitors and recombinant or synthetic uPA and CD87 analogues.
Clinical Trials in Ophthalmology. A Summary and Practice Guide. (1999)

Peter J. Kertes and Mandi D. Conway, Eds. Baltimore, Williams & Wilkins, 1998. San Francisco, California