gebhart/patrepeval huggingface dataset:
Herbivory Rapidly Activates MAPK Signaling in Attacked and Unattacked Leaf Regions but Not between Leaves of Nicotiana attenuata (2007)

Mitogen-activated protein kinase (MAPK) signaling plays a central role in transducing extracellular stimuli into intracellular responses, but its role in mediating plant responses to herbivore attack remains largely unexplored. When Manduca sexta larvae attack their host plant, Nicotiana attenuata, the plant's wound response is reconfigured at transcriptional, phytohormonal, and defensive levels due to the introduction of oral secretions (OS) into wounds during feeding. We show that OS dramatically amplify wound-induced MAPK activity and that fatty acid-amino acid conjugates in M. sexta OS are the elicitors. Virus-induced gene silencing of salicylic acid-induced protein kinase (SIPK) and wound-induced protein kinase revealed their importance in mediating wound and OS-elicited hormonal responses and transcriptional regulation of defense-related genes. We found that after applying OS to wounds created in one portion of a leaf, SIPK is activated in both wounded and specific unwounded regions of the leaf but not in phylotactically connected adjacent leaves. We propose that M. sexta attack elicits a mobile signal that travels to nonwounded regions of the attacked leaf where it activates MAPK signaling and, thus, downstream responses; subsequently, a different signal is transported by the vascular system to systemic leaves to initiate defense responses without activating MAPKs in systemic leaves.
Caller Preferences for the Session Initiation Protocol (SIP) (2004)

This document describes a set of extensions to the Session Initiation Protocol (SIP) which allow a caller to express preferences about request handling in servers.These preferences include the ability to select which Uniform Resource Identifiers (URI) a request gets routed to, and to specify certain request handling directives in proxies and redirect servers.It does so by defining three new request header fields, Accept-Contact, Reject-Contact, and Request-Disposition, which specify the caller's preferences.
Hunting for metamorphic (2001)

As virus writers developed numerous polymorphic engines, virus scanners became stronger in their defense against them. A virus scanner which used a code emulator to detect viruses looked like it was on steroids compared to those without an emulator-based scanning engine. Nowadays, most polymorphic viruses are considered boring. Even though they can be extremely hard to detect, most of today’s products are able to deal with them relatively easily. These are the scanners that survived the DOS polymorphic days. For some of the scanners DOS polymorphic viruses meant the ‘end of days’. Other scanners died with the macro virus problem. For most products the next challenge to take is 32-bit metamorphosis. Metamorphic viruses are nothing new. We have seen them in DOS days, though some of them, like ACG, already used 32-bit instructions. The next step is 32-bit metamorphosis under Windows environments. Virus writers already took the first step in that direction. In this paper the authors will examine metamorphic engines to provide a better general understanding of the problem that we are facing. The authors also provide detection examples of some of the metamorphic viruses. VIRUS BULLETIN CONFERENCE ©2001 Virus Bulletin Ltd, The Pentagon, Abingdon, Oxfordshire, OX14 3YP, England. Tel +44 1235 555139. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form, without the prior written permission of the publishers. 124 • SZÖR &amp;amp; FERRIE, HUNTING FOR METAMORPHIC 1
Regulated Cleavage of a Contact-Mediated Axon Repellent (2000)

Contact-mediated axon repulsion by ephrins raises an unresolved question: these cell surface ligands form a high-affinity multivalent complex with their receptors present on axons, yet rather than being bound, axons can be rapidly repelled. We show here that ephrin-A2 forms a stable complex with the metalloprotease Kuzbanian, involving interactions outside the cleavage region and the protease domain. Eph receptor binding triggered ephrin-A2 cleavage in a localized reaction specific to the cognate ligand. A cleavage-inhibiting mutation in ephrin-A2 delayed axon withdrawal. These studies reveal mechanisms for protease recognition and control of cell surface proteins, and, for ephrin-A2, they may provide a means for efficient axon detachment and termination of signaling.
Using endmembers as a coordinate system in hyperspectral imagery (2002)

The linear mixing model (LMM) is a well-known and useful method for decomposing spectra in a hyperspectral image into the sum of their constituents, or endmembers. Mathematically, if the spectra are represented as n-dimensional vectors, then the LMM implies that the set of endmembers defines a basis or coordinate system for the set of spectra. Because the endmembers themselves are generally not orthogonal, the geometry (distances, difference angles, etc.) is changed by moving from band space to endmember space. We explore some of the differences between the two coordinate systems, and show in particular that the difference in angle measurements leads to an improved method for subpixel target detection.
Resistance of Glycine Species and Various Cultivated Legumes to the Soybean Aphid (Homoptera: Aphididae) (2004)

The soybean aphid, Aphis glycines Matsumura, is a new pest of soybean, Glycine max (L.) Merr., in North America. It has become widespread on soybean in North America since it was first identified in the Midwest in 2000. Species of Rhamnus L. (buckthorn) are the primary hosts of A. glycines, and soybean is known as a secondary host. There is limited information about the secondary host range of A. glycines. Aphid colonization on various legume hosts was compared in choice experiments. Aphid colonization occurred on species in the genus Glycine Wild. No colonization occurred on Lablab purpureus (L.) Sweet, Lens culinaris Medik, Phaseolus vulgaris L., Pisum sativum L., or species of Vicia L. and Vigna Savi. Colonization was limited or aphids were transient on species of Medicago L., Phaseolus L., and Trifolium L. There were significant differences in aphid colonization among Medicago truncatula accessions with numbers ranging from 7 to 97 aphids per plant. Six Glycine soja Sieb. & Zucc. accessions were as resistant as G. max accessions to A. glycines; these may represent novel sources of A. glycines resistance not found in G. max. Antibiosis was found to play a large role in the expression of resistance in three of the G. soja accessions. Results of this study indicated that G. max and G. soja were the best secondary hosts of A. glycines; however, its secondary host range may include other leguminous species. Therefore, A. glycines did not seem to have a highly restricted monophagous secondary host range.
Adherence to human small intestines of capsulatedVibrio choleraeO139 (1994)

Capsulated cells of V. cholerae O139 adhered to formalin-fixed or native mucosa of the small intestines from an adult and a child. The primary adherence target was mucus. Capsulated O139 cells adhered better to the antigen sampling cells (M cells) of ileal Peyer's patch than to the absorptive cells. O139 cells on the mucosa appeared as small aggregates. Similar organisms were found on the mucosa of duodenal biopsy samples from patients infected with V. cholerae O139. The findings indicated that capsulated cells of V. cholerae O139 tend to autoagglutinate and contribute to the effective adherence to the intestinal mucosa.
The Protective Effects of Estrogen on the Cardiovascular System (1999)

The incidence of cardiovascular disease differs significantly between men and women, in part because of differences in risk factors and hormones.1 The incidence of atherosclerotic diseases is low in premenopausal women, rises in postmenopausal women, and is reduced to premenopausal levels in postmenopausal women who receive estrogen therapy.13 Until recently, the atheroprotective effects of estrogen were attributed principally to the hormone's effects on serum lipid concentrations. However, estrogen-induced alterations in serum lipids account for only approximately one third of the observed clinical benefits of estrogen.35 Reviews of the data suggest that the direct actions of estrogen on blood . . .
Ligand-Activated Retinoic Acid Receptor Inhibits AP-1 Transactivation by Disrupting c-Jun/c-Fos Dimerization (1999)

In the presence of retinoic acid (RA), the retinoid receptors, retinoic acid receptor (RAR) and retinoid X receptor (RXR), are able to up-regulate transcription directly by binding to RA-responsive elements on the promoters of responsive genes. Liganded RARs and RXRs are also capable of down-regulating transcription, but, by contrast, this is an indirect effect, mediated by the interaction of these nuclear receptors not with DNA but the transcription factor activating protein-1 (AP-1). AP-1 is a dimeric complex of the protooncoproteins c-Jun and c-Fos and directly regulates transcription of genes important for cellular growth. Previous in vitro results have suggested that RARs can block AP-1 DNA binding. Using a mammalian two-hybrid system, we report here that human RARalpha (hRARalpha) can disrupt in a RA-dependent manner the homo- and heterodimerization properties of c-Jun and c-Fos. This inhibition of dimerization is cell specific, occurring only in those cells that exhibit RA-induced repression of AP-1 transcriptional activity. Furthermore, this mechanism appears to be specific for the RARs, since another potent inhibitor of AP-1 activity, the glucocorticoid receptor, does not affect AP-1 dimerization. Our data argue for a novel mechanism by which RARs can repress AP-1 DNA binding, in which liganded RARs are able to interfere with c-Jun/c-Jun homodimerization and c-Jun/c-Fos heterodimerization and, in this way, may prevent the formation of AP-1 complexes capable of DNA binding.
Biosensors in analytical biotechnology (1996)

Sampling modules, R. Freitag enzyme modified field-effect-transistors (EnFET) for bioprocess monitoring, T. Kullick and R. Ulber optical biosensors in bioprocess technology, O. Thorsden and R. Freitag flow injection analysis based in enzymatic reactions, B.Weigel immunoanalysis and immunosensors, R. Freitag neural networks as a tool for the evaluation of measurement signals of Bio-FET-FI-sensors, B. Hitzman et al online monitoring of animal cell cultivation, G. Kretzmer biosensors for monitoring of microbial processes, U. Bilitewski and I. Rohm.
Investigating multi-touch and pen gestures for diagram editing on interactive surfaces (2009)

Creating and editing large graphs and node-link diagrams are crucial activities in many application areas. For them, we consider multi-touch and pen input on interactive surfaces as very promising. This fundamental work presents a user study investigating how people edit node-link diagrams on an interactive tabletop. The study covers a set of basic operations, such as creating, moving, and deleting diagram elements. Participants were asked to perform spontaneous gestures for 14 given tasks. They could interact in three different ways: using one hand, both hands, as well as pen and hand together. The subjects' activities were observed and recorded in various ways, analyzed and enriched with think-aloud data. As a result, we contribute a user-elicited collection of touch and pen gestures for editing node-link diagrams. The study provides valuable insight how people would interact on interactive surfaces for this as well as other tabletop domains.
Expression of the cloned Escherichia coli O9 rfb gene in various mutant strains of Salmonella typhimurium (1991)

To investigate the effect of chromosomal mutation on the synthesis of rfe-dependent Escherichia coli O9 lipopolysaccharide (LPS), the cloned E. coli O9 rfb gene was introduced into Salmonella typhimurium strains defective in various genes involved in the synthesis of LPS. When E. coli O9 rfb was introduced into S. typhimurium strains possessing defects in rfb or rfc, they synthesized E. coli O9 LPS on their cell surfaces. The rfe-defective mutant of S. typhimurium synthesized only very small amounts of E. coli O9 LPS after the introduction of E. coli O9 rfb. These results confirmed the widely accepted idea that the biosynthesis of E. coli O9-specific polysaccharide does not require rfc but requires rfe. By using an rfbT mutant of the E. coli O9 rfb gene, the mechanism of transfer of the synthesized E. coli O9-specific polysaccharide from antigen carrier lipid to the R-core of S. typhimurium was investigated. The rfbT mutant of the E. coli O9 rfb gene failed to direct the synthesis of E. coli O9 LPS in the rfc mutant strain of S. typhimurium, in which rfaL and rfbT functions are intact, but directed the synthesis of the precursor. Because the intact E. coli O9 rfb gene directed the synthesis of E. coli O9 LPS in the same strain, it was suggested that the rfaL product of S. typhimurium and rfbT product of E. coli O9 cooperate to synthesize E. coli O9 LPS in S. typhimurium.
The use of short tandem repeat polymorphisms for monitoring chimerism following bone marrow transplantation: a short report (2008)

Following immunohaematopoietic stem cell transplantation, it is of importance to determine whether the new blood forming system is of recipient or donor origin and such phenotypic characterisation is called chimerism analysis. This is a dynamic process, which may be complete, mixed or split between compartments and in this way, plays an increasingly important role in predicting outcome for engraftment, rejection or residual disease predicating the need for pre-emptive immunotherapy. Based on recent workshop recommendations, peripheral blood cells have been used in the short tandem repeat (STR) assay to serially characterise the haematologic course and so evaluate the usefulness of this system. Forty-six patients from a single centre were followed serially for periods ranging between 3 and 60 months. The analysis was initially performed using the Applied Biosystems Profiler Plus Kit; currently, the Promega Powerplex 16 system is used. The overlap between the two assays has allowed for continuous comparison. The initial analysis was performed at 14 days post-transplant and repeated monthly. Stored DNA from the patient and donor was used to establish the pre-transplant profile. All post-transplant analyses were performed using peripheral blood. The results obtained were expressed as a percentage of the donor profile. To illustrate the ability of this technology, three representative profiles are described. In the first, stable engraftment is confirmed at 20 months with only donor pattern present. The second is intermediate, and while the patient is clinically disease free, there exists stable mixed chimerism at about 75% of donor cells. The third patient initially engrafted but the reappearance of recipient alleles presaged a haematological relapse; the latter is an indication for salvage with donor lymphocyte infusion and here this assay will be used to show the effectiveness of the intervention. These preliminary results show this to be a useful additional tool in monitoring post-transplant engraftment. As a basis for pro-active therapy, a larger study integrating the results of haematological and cytogenetic markers is planned.
Human CD34+ fetal liver stem cells differentiate to T cells in a mouse thymic microenvironment (1994)

Hematopoietic stem cells differentiate in the thymus to T cells along precisely defined intermediates. This process is thymic epithelium dependent and involves cytokines and cell-cell interactions between thymic stroma and T-cell precursors. Here we report that highly purified human CD34++ fetal liver stem cells differentiate to mature T cells, when seeded into isolated fetal thymic lobes of severe combined immunodeficient mice, and subsequently cultured in vitro. The human stem cells differentiate sequentially into CD4+CD8-CD3-, CD4+CD8+CD3-, CD4+CD8+CD3+, and finally, CD4+CD8-CD3+4 and CD4-CD8+CD3++ cells. Phenotypic analysis for additional maturation markers showed that these CD4 and CD8 single-positive thymocytes are fully maturate cells. By immunochemistry, human HLA-DR+ cells with a dendritic morphology could be detected. This novel chimeric human-mouse fetal thymus organ culture offers a tool to study human T-cell ontogeny in vitro and is a rapid and reliable test method for T-cell precursor activity of cultured or transfected human stem cells.
Oncogenic BRAFV600E Induces Expression of Neuronal Differentiation Marker MAP2 in Melanoma Cells by Promoter Demethylation and Down-regulation of Transcription Repressor HES1 (2009)

MAP2 is a neuron-specific microtubule-associated protein that binds and stabilizes dendritic microtubules. Previously, we showed that MAP2 expression is (a) activated in cutaneous primary melanoma and (b) inversely associated with melanoma tumor progression. We also showed that ectopic expression of MAP2 in metastatic melanoma cells inhibits cell growth by inducing mitotic spindle defects and apoptosis. However, molecular mechanisms of regulation of MAP2 gene expression in melanoma are not understood. Here, we show that in melanoma cells MAP2 expression is induced by the demethylating agent 5-aza-2'-cytidine, and MAP2 promoter is progressively methylated during melanoma progression, indicating that epigenetic mechanisms are involved in silencing of MAP2 in melanoma. In support of this, methylation of MAP2 promoter DNA in vitro inhibits its activity. Because MAP2 promoter activity levels in melanoma cell lines also correlated with activating mutation in BRAF, a gene that is highly expressed in neurons, we hypothesized that BRAF signaling is involved in MAP2 expression. We show that hyperactivation of BRAF-MEK signaling activates MAP2 expression in melanoma cells by two independent mechanisms, promoter demethylation or down-regulation of neuronal transcription repressor HES1. Our data suggest that BRAF oncogene levels can regulate melanoma neuronal differentiation and tumor progression.
A Class of Nonplanar Conjugated Compounds with Aggregation-Induced Emission:  Structural and Optical Properties of 2,5-Diphenyl-1,4-distyrylbenzene Derivatives with All Cis Double Bonds (2006)

We have studied the structural and optical properties of four 2,5-diphenyl-1,4-distyrylbenzene derivatives with all cis double bonds. These compounds belong to a class of nonplanar conjugated compounds possessing a typical Aggregation-Induced Emission (AIE) property that has no emission in solution but intense emission in crystal. The four molecules are packed in different stacking modes with different intermolecular interactions, resulting in different crystalline state photoluminescence (PL) efficiency. The torsional molecular configuration increases the intermolecular distances effectively in the crystalline state, which decreases the difference of the optical properties from the frozen isolated molecules to the crystalline state. The Stokes shifts of these compounds are very large and the PL spectra have only one broad emission band with poor structure, due to the relatively large configuration difference between the ground state and the first singlet excited state, and the abundant vibration energy levels of the torsional molecule with changeable conformation.
Engineered T cells directed at tumors with defined allelic loss (2020)

We describe an approach to cancer therapy based on exploitation of common losses of genetic material in tumor cells (loss of heterozygosity) (Basilion et al., 1999; Beroukhim et al., 2010). This therapeutic concept addresses the fundamental problem of discrimination between tumor and normal cells and can be applied in principle to the large majority of tumors. It utilizes modular activator/blocker elements that integrate signals related to the presence and absence of ligands displayed on the cell surface (Fedorov et al., 2013). We show that the targeting system works robustly in vitro and in a mouse cancer model where absence of the HLA-A*02 allele releases a brake on engineered T cells activated by the CD19 surface antigen. This therapeutic approach potentially opens a route toward a large, new source of cancer targets.
Enhanced Humoral and Cell-Mediated Immune Responses Generated by Cationic Polymer-Coated PLA Microspheres with Adsorbed HBsAg (2014)

Surface-engineered particulate delivery systems for vaccine administration have been widely investigated in experimental and clinical studies. However, little is known about charge-coated microspheres as potential recombinant subunit protein antigen delivery systems in terms of adsorption and related immune responses. In the present study, cationic polymers, including chitosan (CS), chitosan chloride (CSC), and polyethylenimine (PEI), were used to coat PLA microspheres to build positively charged surfaces. Antigen adsorption capacity was enhanced with increased surface charge of coated microspheres. In macrophages, HBsAg adsorbed on the surface of cationic microspheres specifically enhanced antigen uptake and augmented CD86, MHC I, and MHC II expression and IL-1β, IL-6, TNF-α, and IL-12 release. Antigens were more likely to localize independent of lysosomes after phagocytosis in antigen-attached cationic microsphere formulations. After intraperitoneal immunization, cationic microsphere-based vaccine formulations generated a rapid and efficient humoral immune response and cytokine release as compared with aluminum-adsorbed vaccine and free antigens in vivo. Moreover, microspheres coated with cationic polymers with relatively high positive charges and higher antigen adsorption exhibited strong stimulation of the Th1 response. In conclusion, PLA microspheres coated with cationic polymers may be a potential recombinant antigen delivery system to induce strong cell and humoral immune responses.
Conversion of Supramolecular Clusters to Macromolecular Objects (1999)

In a reaction proceeding within a nanoscopic volume, supramolecular clusters were transformed to polymer objects while retaining their shape and size. Spatial isolation of the cross-linkable blocks of oligobutadiene that were involved in this stitching reaction was achieved by self-assembly of the molecules that made up the clusters. Thermal activation of cross-linking yielded macromolecules (molecular weight of 70,000) with a narrow size distribution that was similar to that of the supramolecular clusters. The macromolecules obtained have an anisotropic shape (2 nanometers by 8 nanometers), as determined by electron microscopy and small-angle x-ray scattering, and form materials that exhibit a liquid crystalline state.
Effects of Daylength and Temperature on Soybean Development1 (1975)

Dates of emergence, flowering, beginning pod fill, termination of flowering, and physiological maturity were recorded for two soybean [ Glycine max (L.) Merr.] cultivars from each of the maturity groups I to V. The cultivars were planted in five dates at three Missouri locations in 1971–73; at weekly intervals from April to August at Columbia, Mo., in 1972 and 1973; and at weekly intervals from May to July at Ames, Iowa and Elora, Ont. in 1973. An iterative regression analysis (IRA) technique was used to develop mathematical equations relating the rate of development to daylength and temperature. The IRA equations predicted development more accurately than calendar days or “growing degree days” at all of the locations studied. The IRA equations were also used to assess the relative effects of daylength and temperature on soybean development. Cooler temperatures and longer daylengths encountered at northern latitudes were additive in their delaying effects on flowering. The effects of cool spring temperatures on flowering predominated in the early part of the season whereas daylength predominated in plantings after June 1. Hastening effects of short days on maturity were greater than delaying effects of cool autumn temperatures. The most obvious difference among genotypes was found for sensitivity to daylength in the flowering period; later maturing cultivars were more sensitive than early cultivars.