gebhart/patrepeval huggingface dataset:
Stat3 as a Potential Target for Cancer Immunotherapy (2007)

The abilities of tumor cells to proliferate uncontrollably, resist apoptosis, induce vasculature formation, and invade distant organs are well-recognized hallmarks of cancer. More recently, the capability of tumors to evade immune surveillance and avoid destruction by the immune system has also gained significant acceptance in the cancer research field. However, the initial explanation for the lack of antitumor immune responses was ascribed to mutations affecting tumor-associated antigen expression, antigen processing, and presentation. Although these mutations undoubtedly facilitate tumor immune evasion, they cannot account for how tumors remain undetected before the occurrence of these genetic alterations. Moreover, the tumor microenvironment, whose pivotal role in immune paralysis is gaining appreciation, does not seem to directly cause these mutations. In addition, many tumors retain intact genes encoding major histocompatibility complex, costimulatory molecules and tumor antigens, but with reduced expression levels in the presence of tumor-secreted factors. Discoveries from several recent studies support the hypothesis that oncogenesis itself, as a result of overactivity of growth factor receptors, cytokine receptors, or oncoproteins, coordinates immune evasion. In particular, signal transducer and transcription activator 3 (Stat3), which is a point of convergence for many oncogenic pathways, has emerged as a critical mediator of tumor immune evasion at multiple levels. As a result, molecules involved in the oncogenic signaling pathways, particularly Stat3, provide targets for cancer immunotherapy.
How Does Auxin Turn On Genes? (1998)

The plant hormone auxin (or IAA) plays a key role in a wide variety of growth and developmental processes. At the cellular level, auxin acts as a signal for division, extension, and differentiation during the course of the plant life cycle. At the whole-plant level, auxin plays an important role in
Identification of the Respiratory Syncytial Virus Proteins Required for Formation and Passage of Helper-Dependent Infectious Particles (1998)

We developed a system to identify the viral proteins required for the packaging and passage of human respiratory syncytial virus (RSV) by reconstructing these events with cDNA-encoded components. Plasmids encoding individual RSV proteins, each under the control of a T7 promoter, were cotransfected in various combinations together with a plasmid containing a minigenome into cells infected with a vaccinia virus recombinant expressing T7 RNA polymerase. Supernatants from these cells were passaged onto fresh cells which were then superinfected with RSV. Functional reconstitution of RSV-specific packaging and passage was detected by expression of the reporter gene carried on the minigenome. As expected, the four nucleocapsid proteins N, P, L, and M2-1 failed to direct packaging and passage of the minigenome. Passage was achieved by further addition of plasmids expressing three membrane-associated proteins, M, G, and F; inclusion of the fourth envelope- associated protein, SH, did not alter passage efficiency. Passage was reduced 10- to 20-fold by omission of G and was abrogated by omission of either M or F. Coexpression of the nonstructural NS1 or NS2 protein had little effect on packaging and passage except through indirect effects on RNA synthesis in the initial transfection. The M2-1 transcription elongation factor was not required for the generation of passage-competent particles. However, addition of increasing quantities of M2-1 to the transfection mediated a dose-dependent inhibition of passage which was alleviated by coexpression of the putative negative regulatory factor M2-2. Omission of the L plasmid reduced passage 10- to 20-fold, most likely due to reduced availability of encapsidated minigenomes for packaging. However, the residual level of passage indicated that neither L protein nor the process of RSV-specific RNA synthesis is required for the production and passage of particles. Omission of N or P from the transfection abrogated passage. Thus, the minimum RSV protein requirements for packaging and passaging a minigenome are N, P, M, and F, although the efficiency is greatly increased by addition of L and G.
Ornithine decarboxylase and polyamines in colorectal neoplasia and mucosa. (1993)

Ornithine decarboxylase (ODC) and polyamines are intimately involved in normal cellular proliferation and are likely to play a role in carcinogenesis. ODC activity and polyamine content were measured in tissue samples obtained during colonoscopy from 48 benign neoplastic polyps (20 tubular adenomas; 28 villous adenomas), 18 cancers (including 5 malignant polyps), and adjacent mucosa. ODC activity in polyp and cancer tissue specimens was higher than in adjacent mucosa in 75 and 83% of pairs, respectively. Similarly, putrescine, spermidine, and spermine contents were higher in the majority of polyps and cancers compared to adjacent mucosa. ODC activity and polyamine content in colonic mucosa from 10 patients without a history of colorectal neoplasia were not different from adjacent mucosal values in the patients with neoplasia. In conclusion, ODC and polyamines are elevated in the majority of colorectal neoplasms, but amounts in normal mucosa do not differentiate between patients with cancer, benign neoplastic polyps, and normal subjects.
Phase-resolved spectral-domain magnetomotive optical coherence tomography (2007)

We advance the magnetomotive-optical coherence tomography (MM-OCT) technique for detecting displacements of magnetic nanoparticles embedded in tissue-like phantoms by using apmplitude and phase-resolved methods with spectral-domain optical coherence tomography (SD-OCT). The magnetomotion is triggered by the external, noninvasive application of a magnetic field. We show that both amplitude and phase data are indicative of the presence and motion of light scatterers, and could potentially be used for studying the dynamics of magnetomotion. The magnetic field modulation is synchronized with data acquisition in a controlled, integrated system that includes a console for monitoring and initiating data acquisition, scanning devices, an electromagnet power supply, and the detection system. Using Fourier analysis, we show that the amplitude and phase modulations in the samples that contain magnetic contrast agents match the frequency of the applied magnetic field, while control samples do not respond to magnetic field activity. We vary the strength of the magnetic field and show that the amplitude and phase steps between regions of zero-magnetic field and regions with non-zero magnetic field change accordingly. The phase is shown to be more sensitive.
<title>Bayesian framework for semantic classification of outdoor vacation images</title> (1998)

Grouping images into (semantically) meaningful categories using low-level visual features is still a challenging and important problem in content-based image retrieval. Based on these groupings, effective indices can be built for an image database. In this paper, we cast the image classification problem in a Bayesian framework. Specifically, we consider city vs. landscape classification, and further, classification of landscape into sunset, forest, and mountain classes. We demonstrate how high-level concepts can be understood from specific low-level image features, under the constraint that the test images do belong to one of the delineated classes. We further demonstrate that a small codebook (the optimal size is selected using the MDL principle) extracted from a vector quantizer, can be used to estimate the class-conditional densities needed for the Bayesian methodology. Classification based on color histograms, color coherence vectors, edge direction histograms, and edge-direction coherence vectors as features shows promising results. On a database of 2,716 city and landscape images, our system achieved an accuracy of 95.3 percent for city vs. landscape classification. On a subset of 528 landscape images, our system achieves an accuracy of 94.9 percent for sunset vs. forest and mountain classification, and 93.6 percent for forest vs. mountain classification. Our final goal is to combine multiple 2- class classifiers into a single hierarchical classifier.
Interactive watercolor rendering with temporal coherence and abstraction (2006)

This paper presents an interactive watercolor rendering technique that recreates the specific visual effects of lavis watercolor. Our method allows the user to easily process images and 3d models and is organized in two steps: an abstraction step that recreates the uniform color regions of watercolor and an effect step that filters the resulting abstracted image to obtain watercolor-like images. In the case of 3d environments we also propose two methods to produce temporally coherent animations that keep a uniform pigment repartition while avoiding the shower door effect.
IL-17 Contributes to Cell-Mediated Defense against Pulmonary Yersinia pestis Infection (2010)

Pneumonic plague is one of the world's most deadly infectious diseases. The causative bacterium, Yersinia pestis, has the potential to be exploited as a biological weapon, and no vaccine is available. Vaccinating B cell-deficient mice with D27-pLpxL, a live attenuated Y. pestis strain, induces cell-mediated protection against lethal pulmonary Y. pestis challenge. In this article, we demonstrate that prime/boost vaccination with D27-pLpxL confers better protection than prime-only vaccination. The improved survival does not result from enhanced bacterial clearance but is associated with increased levels of IL-17 mRNA and protein in the lungs of challenged mice. The boost also increases pulmonary numbers of IL-17-producing CD4 T cells. Interestingly, most of these cells simultaneously produce canonical type 1 and type 17 cytokines; most produce IL-17 and TNF-α, and many produce IL-17, TNF-α, and IFN-γ. Neutralizing IL-17 counteracts the improved survival associated with prime/boost vaccination without significantly impacting bacterial burden. Thus, IL-17 appears to mediate the enhanced protection conferred by booster immunization. Although neutralizing IL-17 significantly reduces neutrophil recruitment to the lungs of mice challenged with Y. pestis, this impact is equally evident in mice that receive one or two immunizations with D27-pLpxL, suggesting it cannot suffice to account for the improved survival that results from booster immunization. We conclude that IL-17 plays a yet to be identified role in host defense that enhances protection against pulmonary Y. pestis challenge, and we suggest that pneumonic plague vaccines should aim to induce mixed type 1 and type 17 cellular responses.
Antigen Specificity and High Affinity Binding Provided by One Single Loop of a Camel Single-domain Antibody (2001)

Detailed knowledge on antibody-antigen recognition is scarce given the unlimited antibody specificities of which only few have been investigated at an atomic level. We report the crystal structures of an antibody fragment derived from a camel heavy chain antibody against carbonic anhydrase, free and in complex with antigen. Surprisingly, this single-domain antibody interacts with nanomolar affinity with the antigen through its third hypervariable loop (19 amino acids long), providing a flat interacting surface of 620 A(2). For the first time, a single-domain antibody is observed with its first hypervariable loop adopting a type-1 canonical structure. The second hypervariable loop, of unique size due to a somatic mutation, reveals a regular beta-turn. The third hypervariable loop covers the remaining hypervariable loops and the side of the domain that normally interacts with the variable domain of the light chain. Specific amino acid substitutions and reoriented side chains reshape this side of the domain and increase its hydrophilicity. Of interest is the substitution of the conserved Trp-103 by Arg because it opens new perspectives to 'humanize' a camel variable domain of heavy chain of heavy chain antibody (VHH) or to 'camelize' a human or a mouse variable domain of heavy chain of conventional antibody (VH).
Robust omniphobic surfaces (2008)

Superhydrophobic surfaces display water contact angles greater than 150 degrees in conjunction with low contact angle hysteresis. Microscopic pockets of air trapped beneath the water droplets placed on these surfaces lead to a composite solid-liquid-air interface in thermodynamic equilibrium. Previous experimental and theoretical studies suggest that it may not be possible to form similar fully-equilibrated, composite interfaces with drops of liquids, such as alkanes or alcohols, that possess significantly lower surface tension than water (gamma(lv) = 72.1 mN/m). In this work we develop surfaces possessing re-entrant texture that can support strongly metastable composite solid-liquid-air interfaces, even with very low surface tension liquids such as pentane (gamma(lv) = 15.7 mN/m). Furthermore, we propose four design parameters that predict the measured contact angles for a liquid droplet on a textured surface, as well as the robustness of the composite interface, based on the properties of the solid surface and the contacting liquid. These design parameters allow us to produce two different families of re-entrant surfaces- randomly-deposited electrospun fiber mats and precisely fabricated microhoodoo surfaces-that can each support a robust composite interface with essentially any liquid. These omniphobic surfaces display contact angles greater than 150 degrees and low contact angle hysteresis with both polar and nonpolar liquids possessing a wide range of surface tensions.
A Survey on Transfer Learning (2009)

A major assumption in many machine learning and data mining algorithms is that the training and future data must be in the same feature space and have the same distribution. However, in many real-world applications, this assumption may not hold. For example, we sometimes have a classification task in one domain of interest, but we only have sufficient training data in another domain of interest, where the latter data may be in a different feature space or follow a different data distribution. In such cases, knowledge transfer, if done successfully, would greatly improve the performance of learning by avoiding much expensive data-labeling efforts. In recent years, transfer learning has emerged as a new learning framework to address this problem. This survey focuses on categorizing and reviewing the current progress on transfer learning for classification, regression, and clustering problems. In this survey, we discuss the relationship between transfer learning and other related machine learning techniques such as domain adaptation, multitask learning and sample selection bias, as well as covariate shift. We also explore some potential future issues in transfer learning research.
Cancer Serum Index and Prostatic Acid Phosphatase for Detection of Progressive Prostatic Cancer (1985)

The ratio of alpha 1 acid glycoprotein/prealbumin, referred to as a cancer serum index, has been proposed as a marker for neoplastic disease. In a series of 130 patients with prostate cancer, the cancer serum index was measured along with serum prostatic acid phosphatase. A significant difference for both the cancer serum index and serum prostatic acid phosphatase was detected between those patients with no evidence of active disease after treatment and those with progressive disease after treatment.
An isolated, surface-expressed I domain of the integrin αLβ2 is sufficient for strong adhesive function when locked in the open conformation with a disulfide bond (2001)

We introduced disulfide bonds to lock the integrin alphaLbeta2 I domain in predicted open, ligand binding or closed, nonbinding conformations. Transfectants expressing alphaLbeta2 heterodimers containing locked-open but not locked-closed or wild-type I domains constitutively adhered to intercellular adhesion molecule-1 (ICAM-1) substrates. Locking the I domain closed abolished constitutive and activatable adhesion. The isolated locked-open I domain bound as well as the activated alphaLbeta2 heterodimer, and binding was abolished by reduction of the disulfide. Lovastatin, which binds under the conformationally mobile C-terminal alpha-helix of the I domain, inhibited binding to ICAM-1 by alphaLbeta2 with wild-type, but not locked-open I domains. These data establish the importance of conformational change in the alphaL I domain for adhesive function and show that this domain is sufficient for full adhesive activity.
RETRACTED: The cytokine interleukin-33 mediates anaphylactic shock (2009)

Anaphylactic shock is characterized by elevated immunoglobulin-E (IgE) antibodies that signal via the high affinity Fc epsilon receptor (Fc epsilonRI) to release inflammatory mediators. Here we report that the novel cytokine interleukin-33 (IL-33) potently induces anaphylactic shock in mice and is associated with the symptom in humans. IL-33 is a new member of the IL-1 family and the ligand for the orphan receptor ST2. In humans, the levels of IL-33 are substantially elevated in the blood of atopic patients during anaphylactic shock, and in inflamed skin tissue of atopic dermatitis patients. In murine experimental atopic models, IL-33 induced antigen-independent passive cutaneous and systemic anaphylaxis, in a T cell-independent, mast cell-dependent manner. In vitro, IL-33 directly induced degranulation, strong eicosanoid and cytokine production in IgE-sensitized mast cells. The molecular mechanisms triggering these responses include the activation of phospholipase D1 and sphingosine kinase1 to mediate calcium mobilization, Nuclear factor-kappaB activation, cytokine and eicosanoid secretion, and degranulation. This report therefore reveals a hitherto unrecognized pathophysiological role of IL-33 and suggests that IL-33 may be a potential therapeutic target for anaphylaxis, a disease of considerable unmet medical need.
Multi-field surface electrode for selective electrical stimulation (2004)

Udgivelsesdato: JUN
Development and implementation of a robust deammonification process (2007)

Deammonification represents a short-cut in the N-metabolism pathway and comprises 2 steps: about half the amount of ammonia is oxidised to nitrite and then residual ammonia and nitrite is anaerobically transformed to elementary nitrogen. Implementation of the pH-controlled DEMON process for deammonification of reject water in a single-sludge SBR system at the WWTP Strass (Austria) contributed essentially to energy self-sufficiency of the plant. The specific energy demand of the side-stream process equals 1.16 kWh per kg ammonia nitrogen removed comparing to about 6.5 kWh of mainstream treatment. Has this resource saving technology already approached state of the art? Deammonification has been operated in full-scale now for almost 3 years without interruption reaching annual ammonia removal rates beyond 90%. Biomass enrichment and DEMON-start-up in Strass took a period of 2.5 years whereas start-up period at the WWTP Glarnerland (Switzerland) was reduced to 50 days due to transfer of substantial amounts of seed sludge.
Multinuclear nuclear magnetic resonance studies of Na cation-stabilized complex formed by d(G-G-T-T-T-T-C-G-G) in solution (1991)

There has been much recent interest in the self-association of short deoxyguanosine-rich motifs within single-stranded DNAs to generate monovalent cation modulated four-stranded helical segments called G-quadruplexes stabilized by hydrogen-bonded G-tetrad alignments. We have addressed structural aspects of this novel alignment and report on multinuclear 1H, 31P and 13C nuclear magnetic resonance studies on the d(G2T4CG2) deoxynonanucleotide with Na cation as counterion in aqueous solution at low temperature. This sequence forms stable structures even though it cannot align by Watson-Crick hydrogen bond formation (see the paper on d(G2T5G2) describing optical and calorimetric measurements by Jin, R., Breslauer, K. J., Jones, R. A. & Gaffney, B. L. (1990), Science, 250, 543-546). The four narrow exchangeable protons detected between 11.5 and 12.0 parts per million (p.p.m.), which are common to the d(G2T4CG2) deoxynonanucleotide and the d(G2TCG2) deoxyhexanucleotide sequences, are assigned to deoxyguanosine imino protons hydrogen-bonded to carbonyl acceptor groups. These narrow imino protons are not detected for d(IGN5IG) and d(I2N5G2), where two deoxyguanosine residues are replaced by two deoxyinosine residues in the deoxynonanucleotide sequences. This implies that the 2-amino protons of deoxyguanosine must also participate in hydrogen bond formation and stabilize the structured conformation of d(G2T4CG2) in Na cation-containing solution. We have completely assigned the base and sugar H1', H2',2'', H3', and H4' protons of the d(G2T4CG2) oligomer following analysis of two-dimensional nuclear Overhauser enhancement spectroscopy and two-dimensional correlated spectroscopy data sets in 0.1 M-NaCl, 10 mM-sodium phosphate, 2H2O solution at 0 degree C. The relative magnitude of the nuclear Overhauser enhancements (NOEs) between the base H8 and its own sugar H1' protons of individual deoxyguanosine residues establishes that G1 and G8 adopt syn orientations while G2 and G9 adopt anti orientations about the glycosidic bond in the d(G1-G2-T3-T4-T5-T6-C7-G8-G9) sequence in both Na and K cation-containing aqueous solution. Consequently, any structure proposed for the tetramolecular complex of d(G2T4CG2) must exhibit alternating G(syn) and G(anti) glycosidic torsion angles within each strand. The directionality and magnitude of the observed NOEs are consistent with the G(syn)-G(anti) steps adopting right-handed helical conformations in solution. We also note that the H8 protons of G1 and G8 (7.35 to 7.45 p.p.m.) in a syn alignment are shifted significantly upfield from the H8 protons of G2 and G9 (8.0 to 8.3 p.p.m.) in an anti alignment.(ABSTRACT TRUNCATED AT 400 WORDS)
Comparative Reactivities of Phosphate Ester Cleavages by Metallomicelles (1996)

The hydrolytic efficiency of the hydrophilic Cu(II) complex of tetramethylethylenediamine (TMED C1· Cu(II)) and the amphiphilic N-n-hexadecyl-N,N‘,N‘-trimethylethylenediamine complex (TMED C16·Cu(II)) in comicelles with CTANO3 was studied toward a series of phosphate triesters and diesters that were either neutral (1−7) or cationic and amphiphilic (8−10). While the pseudo-first-order rate constants at [catalyst] = 1 × 10-3 M are larger (ca. one order of magnitude) for the micellar catalyst, the second-order rate constants are higher for the hydrophilic catalyst. With phosphate triesters, regardless of the structure of the substrate, TMED C1·Cu(II)-bound OH- is a better nucleophile than free OH-, while TMED C16· Cu(II)-bound OH- is poorer. This is explained by electrophilic assistance of the metal center which greatly diminishes in micelles. With phosphate diesters the OH- bound to both TMED C1·Cu(II) and TMED C16·Cu(II) is a better nucleophile than free OH-. Partial neutralization of the negative charge of the substrate may explain this behavior. In all cases the amphiphilic substrates are intrinsically more reactive than the neutral ones. Comparison with an iodosobenzoate-based catalyst shows that this is ineffective with phosphate diesters while it is a better reagent than the metallomicellar one with phosphate triesters. Its higher effectiveness, however, seems to vanish as the substrate becomes less reactive.