gebhart/patrepeval huggingface dataset:
The nature of requests and commitments in email messages (2008)

It has long been established that many workplace tasks are managed through email communication, and that these tasks involve the exchange of requests and commitments. Users would be better able to manage and monitor tasks in their email if systems could identify the utterances which place responsibility for action on themselves or others. Such systems require a robust understanding of which utterances convey requests and commitments. Previous attempts to classify similar phenomena in email have mostly been at the message level and have lacked detailed and robust category definitions that allow unambiguous classification at the utterance level. To address this gap, this paper presents precise definitions for classifying requests and commitments in email, based on concepts from Speech Act Theory, and informed by the results of two independent manual annotation experiments using data from the Enron email corpus. The specific surface realisation of requests and commitments in email are also considered, with the aim of clarifying how a range of potentially difficult cases should be dealt with. This paper thus contributes a well-grounded definitional basis for the classification of task-oriented speech acts in email.
Cis-ruption mechanisms: disruption of cis-regulatory control as a cause of human genetic disease (2009)

The spatiotemporally and quantitatively correct activity of a gene requires the presence of intact coding sequence as well as properly functioning regulatory control. One of the great challenges of the post-genome era is to gain a better understanding of the mechanisms of gene control. Proper gene regulation depends not only on the required transcription factors and associated complexes being present (in the correct dosage), but also on the integrity, chromatin conformation and nuclear positioning of the gene's chromosomal segment. Thus, when either the cis-trans regulatory system of a gene or the normal context of its chromatin structure are disrupted, gene expression may be adversely affected, potentially leading to disease. As transcriptional regulation is a highly complex process depending on many factors, there are many different mechanisms that can cause aberrant gene expression. Traditionally, the term 'position effect' was used to refer to situations where the level of expression of a gene is deleteriously affected by an alteration in its chromosomal environment, while maintaining an intact transcription unit. Over the past years, an ever increasing number of such disease-related position effect cases have come to light, and detailed studies have revealed insight into the variety of causes, which can be categorized into a number of different mechanistic groups. We suggest replacing the outdated term of 'position effect disease' with the new generic name of 'cis-ruption disorder' to describe genetic disease cases that are caused by disruption of the normal cis-regulatory architecture of the disease gene locus. Here, we review these various cis-ruption mechanisms and discuss how their studies have contributed to our understanding of long- range gene regulation.
Inhibition of ICAM-I gene expression by antisense 2',4'-BNA oligonucleotides (2001)

We have previously reported that 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA) had unprecedented binding affinity towards its complementary RNA. We reported herein that the antisense 2',4'-BNA oligonucleotides showed potent inhibitory effect on gene expression of Intercellular Adhesion Molecule-1 (ICAM-1) in living cells. The contribution of RNase H to this antisense effect and adequate stability of 2',4'-BNA oligonucleotides to enzymatic degradation were also demonstrated.
Mechanisms of Magnetic Stimulation of Central Nervous System Neurons (2011)

Transcranial magnetic stimulation (TMS) is a stimulation method in which a magnetic coil generates a magnetic field in an area of interest in the brain. This magnetic field induces an electric field that modulates neuronal activity. The spatial distribution of the induced electric field is determined by the geometry and location of the coil relative to the brain. Although TMS has been used for several decades, the biophysical basis underlying the stimulation of neurons in the central nervous system (CNS) is still unknown. To address this problem we developed a numerical scheme enabling us to combine realistic magnetic stimulation (MS) with compartmental modeling of neurons with arbitrary morphology. The induced electric field for each location in space was combined with standard compartmental modeling software to calculate the membrane current generated by the electromagnetic field for each segment of the neuron. In agreement with previous studies, the simulations suggested that peripheral axons were excited by the spatial gradients of the induced electric field. In both peripheral and central neurons, MS amplitude required for action potential generation was inversely proportional to the square of the diameter of the stimulated compartment. Due to the importance of the fiber's diameter, magnetic stimulation of CNS neurons depolarized the soma followed by initiation of an action potential in the initial segment of the axon. Passive dendrites affect this process primarily as current sinks, not sources. The simulations predict that neurons with low current threshold are more susceptible to magnetic stimulation. Moreover, they suggest that MS does not directly trigger dendritic regenerative mechanisms. These insights into the mechanism of MS may be relevant for the design of multi-intensity TMS protocols, may facilitate the construction of magnetic stimulators, and may aid the interpretation of results of TMS of the CNS.
Vibrational energy relaxation of adsorbate vibrations: A theoretical study of the H/Si(111) system (1996)

The energy relaxation rate for the first excited stretching vibration of hydrogen atoms adsorbed on an Si(111) surface is calculated treating the motions of the H atoms quantum mechanically and computing the substrate phonon spectrum by molecular dynamics. The relaxation occurs through excitation of three bending modes and emission of a 188 cm−1 phonon.
Electronic media review (1997)

McMinn's Interactive Clinical Anatomy, by Peter H. Abrahams. St. Louis: Mosby, 1997. $59.95
CD3- and CD28-Dependent Induction of PDE7 Required for T Cell Activation (1999)

Costimulation of both the CD3 and CD28 receptors is essential for T cell activation. Induction of adenosine 3',5'-monophosphate (cAMP)-specific phosphodiesterase-7 (PDE7) was found to be a consequence of such costimulation. Increased PDE7 in T cells correlated with decreased cAMP, increased interleukin-2 expression, and increased proliferation. Selectively reducing PDE7 expression with a PDE7 antisense oligonucleotide inhibited T cell proliferation; inhibition was reversed by blocking the cAMP signaling pathways that operate through cAMP-dependent protein kinase (PKA). Thus, PDE7 induction and consequent suppression of PKA activity is required for T cell activation, and inhibition of PDE7 could be an approach to treating T cell-dependent disorders.
Administration of IgG Fc Fragments Prevents Glomerular Injury in Experimental Immune Complex Nephritis (2000)

Abstract Most human nephritis is due to glomerular deposition and/or formation of immune complexes (IC). In cultured mesangial cells, Fc receptor stimulation induces proliferation, matrix synthesis, and release of several mediators implicated in the initiation and progression of glomerular injury. Since Ig Fc fragments in vitro modified these phenomena, we studied the effects of systemic administration of IgG Fc fragments on the evolution of experimental IC nephritis. Fc fragment injection (1 mg/day i.p.) to rats with ongoing nephritis (proteinuria 20–50 mg/24 h vs 9 ± 0.2 mg/24 h in controls) markedly ameliorates proteinuria, renal function, and morphological renal lesions. This was accompanied by a reduction in the renal synthesis of chemokines (monocyte chemoattractant protein-1, IFN-inducible protein-10, and cytokine-induced neutrophil chemoattractant-1), matrix proteins, and growth factors (platelet-derived growth factor, and TGF-β), and in the activity of transcription factors. The treatment did not affect the glomerular deposition of IgG IC and complement C1q. In contrast, a decrease in the renal expression and production of C3 was observed without changes in serum complement levels. In vitro, very low complement consumption and no C3b covalent interaction were observed with Fc fragments, confirming that they did not modify systemic complement activity. These results indicate that the administration of Fc fragments prevents the development of glomerular damage in an aggressive model of proliferative glomerulonephritis through mechanisms involving a reduced local generation of complement, chemokines and growth factors. Modulation of IC-mesangial cell interaction by Fc fragment administration could represent a new approach to the treatment of severe immune nephritis.
Fuzzy identification of systems and its applications to modeling and control (1985)

A mathematical tool to build a fuzzy model of a system where fuzzy implications and reasoning are used is presented in this paper. The premise of an implication is the description of fuzzy subspace of inputs and its consequence is a linear input-output relation. The method of identification of a system using its input-output data is then shown. Two applications of the method to industrial processes are also discussed: a water cleaning process and a converter in a steel-making process.
Fabrication of Two-Dimensional Photonic Crystals in AlGaInP/GaInP Membranes by Inductively Coupled Plasma Etching (2006)

The fabrication process of two-dimensional photonic crystals in an AlGaInP/GaInP multi-quantum-well membrane structure is developed. The process includes high resolution electron-beam lithography, pattern transfer into SiO₂ etch mask by reactive ion etching, pattern transfer through AlGaInP/GaInP layer by inductively coupled plasma (ICP) etching and a selective undercut wet etch to create the freestanding membrane. The chlorine-based ICP etching conditions are optimized to achieve a vertical sidewall. The photonic crystal structures with periods of a=160-480nm are produced.
Enhanced Interleukin‐10 Production in Response toMycobacterium aviumProducts in Mononuclear Cells from Patients with Human Immunodeficiency Virus Infection (1998)

Patients with advanced human immunodeficiency virus (HIV) infection are susceptible to infections with Mycobacterium avium complex (MAC). Interleukin (IL)-10 may impair immunity to MAC; therefore, the effect of different MAC preparations on IL-10 production was examined in mononuclear cell cultures from HIV-infected patients. IL-10 levels in cultures for 26 patients were higher than those in 20 control cultures. The highest IL-10 levels were found in cultures from patients with the most advanced HIV disease. Monocytes were the major IL-10 producers, while little IL-10 could be attributed to Th2 lymphocytes. Cultures for patients produced reduced levels of tumor necrosis factor-alpha and normal levels of IL-12; the production of these cytokines increased after neutralization of IL-10. Circulating IL-10 was higher in HIV-infected patients than in controls, with the highest levels in the AIDS group. Elevated monocyte/macrophage-derived IL-10 production may contribute to the high susceptibility to MAC infection seen in patients with advanced HIV disease.
Coexistence of antibodies to tick-borne pathogens of babesiosis, ehrlichiosis, and Lyme borreliosis in human sera (1995)

Serum specimens from persons with or without Lyme borreliosis were analyzed by indirect fluorescent antibody staining methods for total immunoglobulins to Babesia microti, Ehrlichia chaffeensis (Arkansas strain), and Ehrlichia equi (MRK strain). There was serologic evidence of human exposure to multiple tick-borne agents in 15 (6.6%) of 227 serum samples obtained in Connecticut and Minnesota. Of these, 10 serum samples were from Connecticut patients who had erythema migrans and antibodies to Borrelia burgdorferi (range, 1:160 to 1:40, 960). A maximal antibody titer of 1:640 was noted for a B. microti infection, whereas titration end points of 1:640 and 1:1,280 were recorded for E. chaffeensis and E. equi seropositives, respectively. In specificity tests, there was no cross-reactivity among the antisera and antigens tested for the four tick-borne pathogens. On the basis of serologic testing, a small group of persons who had Lyme borreliosis had been exposed to one or more other tick-borne agents, but there was no clinical diagnosis of babesiosis or ehrlichiosis. Therefore, if the clinical picture is unclear or multiple tick-associated illnesses are suspected, more extensive laboratory testing is suggested.
Genetic applications of an inverse polymerase chain reaction. (1988)

A method is presented for the rapid in vitro amplification of DNA sequences that flank a region of known sequence. The method uses the polymerase chain reaction (PCR), but it has the primers oriented in the reverse direction of the usual orientation. The template for the reverse primers is a restriction fragment that has been ligated upon itself to form a circle. This procedure of inverse PCR (IPCR) has many applications in molecular genetics, for example, the amplification and identification of sequences flanking transposable elements. In this paper we show the feasibility of IPCR by amplifying the sequences that flank an IS1 element in the genome of a natural isolate of Escherichia coli.
Cloning and Deletion Mutagenesis of the α2δ Calcium Channel Subunit from Porcine Cerebral Cortex (1998)

The anti-epileptic, anti-hyperalgesic, and anxiolytic agent gabapentin (1-(aminomethyl)-cyclohexane acetic acid or Neurontin) has previously been shown to bind with high affinity to the alpha2delta subunit of voltage-dependent calcium channels (Gee, N. S. , Brown, J. P., Dissanayake, V. U. K., Offord, J., Thurlow, R., and Woodruff, G.N. (1996) J. Biol. Chem. 271, 5768-5776). We report here the cloning, sequencing, and deletion mutagenesis of the alpha2delta subunit from porcine brain. The deduced protein sequence has a 95.9 and 98.2% identity to the rat and human neuronal alpha2 delta sequences, respectively. [3H]Gabapentin binds with a KD of 37.5 +/- 10.4 nM to membranes prepared from COS-7 cells transfected with wild-type porcine alpha2 delta cDNA. Six deletion mutants (B-G) that lack the delta polypeptide, together with varying amounts of the alpha2 component, failed to bind [3H]gabapentin. C-terminal deletion mutagenesis of the delta polypeptide identified a segment (residues 960-994) required for correct assembly of the [3H]gabapentin binding pocket. Mutant L, which lacks the putative membrane anchor in the delta sequence, was found in both membrane-associated and soluble secreted forms. The soluble form was not proteolytically cleaved into separate alpha2 and delta chains but still retained a high affinity (KD = 30.7 +/- 8.1 nM) for [3H]gabapentin. The production of a soluble alpha2delta mutant supports the single transmembrane model of the alpha2 delta subunit and is an important step toward the large-scale recombinant expression of the protein.
B lymphocytes express and lose syndecan at specific stages of differentiation. (1989)

Lymphopoietic cells require interactions with bone marrow stroma for normal maturation and show changes in adhesion to matrix during their differentiation. Syndecan, a heparan sulfate-rich integral membrane proteoglycan, functions as a matrix receptor by binding cells to interstitial collagens, fibronectin, and thrombospondin. Therefore, we asked whether syndecan was present on the surface of lymphopoietic cells. In bone marrow, we find syndecan only on precursor B cells. Expression changes with pre-B cell maturation in the marrow and with B-lymphocyte differentiation to plasma cells in interstitial matrices. Syndecan on B cell precursors is more heterogeneous and slightly larger than on plasma cells. Syndecan 1) is lost immediately before maturation and release of B lymphocytes into the circulation, 2) is absent on circulating and peripheral B lymphocytes, and 3) is reexpressed upon their differentiation into immobilized plasma cells. Thus, syndecan is expressed only when and where B lymphocytes associate with extracellular matrix. These results indicate that B cells differentiating in vivo alter their matrix receptor expression and suggest a role for syndecan in B cell stage-specific adhesion.
Analysis of the Structural and Molecular Basis of Voltage-sensitive Sodium Channel Inhibition by the Spider Toxin Huwentoxin-IV (μ-TRTX-Hh2a) (2013)

Voltage-gated sodium channels (VGSCs) are essential to the normal function of the vertebrate nervous system. Aberrant function of VGSCs underlies a variety of disorders, including epilepsy, arrhythmia, and pain. A large number of animal toxins target these ion channels and may have significant therapeutic potential. Most of these toxins, however, have not been characterized in detail. Here, by combining patch clamp electrophysiology and radioligand binding studies with peptide mutagenesis, NMR structure determination, and molecular modeling, we have revealed key molecular determinants of the interaction between the tarantula toxin huwentoxin-IV and two VGSC isoforms, Nav1.7 and Nav1.2. Nine huwentoxin-IV residues (F6A, P11A, D14A, L22A, S25A, W30A, K32A, Y33A, and I35A) were important for block of Nav1.7 and Nav1.2. Importantly, molecular dynamics simulations and NMR studies indicated that folding was normal for several key mutants, suggesting that these amino acids probably make specific interactions with sodium channel residues. Additionally, we identified several amino acids (F6A, K18A, R26A, and K27A) that are involved in isoform-specific VGSC interactions. Our structural and functional data were used to model the docking of huwentoxin-IV into the domain II voltage sensor of Nav1.7. The model predicts that a hydrophobic patch composed of Trp-30 and Phe-6, along with the basic Lys-32 residue, docks into a groove formed by the Nav1.7 S1-S2 and S3-S4 loops. These results provide new insight into the structural and molecular basis of sodium channel block by huwentoxin-IV and may provide a basis for the rational design of toxin-based peptides with improved VGSC potency and/or selectivity.
An Early C-22 Oxidation Branch in the Brassinosteroid Biosynthetic Pathway (2002)

The natural occurrence of 22-hydroxylated steroids in cultured Catharanthus roseus cells and in Arabidopsis seedlings was investigated. Using full-scan gas chromatography-mass spectrometry analysis, (22S)-22-hydroxycampesterol (22-OHCR), (22S,24R)-22-hydroxyergost-4-en-3-one (22-OH-4-en-3-one), (22S,24R)-22-hydroxy-5alpha-ergostan-3-one (22-OH-3-one), 6-deoxocathasterone (6-deoxoCT), 3-epi-6-deoxoCT, 28-nor-22-OHCR, 28-nor-22-OH-4-en-3-one, 28-nor-22-OH-3-one, 28-nor-6-deoxoCT, and 3-epi-28-nor-6-deoxoCT were identified. Metabolic experiments with deuterium-labeled 22-OHCR were performed in cultured C. roseus cells and Arabidopsis seedlings (wild type and det2), and the metabolites were analyzed by gas chromatography-mass spectrometry. In both C. roseus cells and wild-type Arabidopsis seedlings, [(2)H(6)]22-OH-4-en-3-one, [(2)H(6)]22-OH-3-one, [(2)H(6)]6-deoxoCT, and [(2)H(6)]3-epi-6-deoxoCT were identified as metabolites of [(2)H(6)]22-OHCR, whereas the major metabolite in det2 seedlings was [(2)H(6)]22-OH-4-en-3-one. Analysis of endogenous levels of these brassinosteroids revealed that det2 accumulates 22-OH-4-en-3-one. The levels of downstream compounds were remarkably reduced compared with the wild type. Exogenously applied 22-OH-3-one and 6-deoxoCT were found to rescue det2 mutant phenotypes, whereas 22-OHCR and 22-OH-4-en-3-one did not. These results substantiate the existence of a new subpathway (22-OHCR --> 22-OH-4-en-3-one --> 22-OH-3-one --> 6-deoxoCT) and reveal that the det2 mutant is defective in the conversion of 22-OH-4-en-3-one to 22-OH-3-one, which leads to brassinolide biosynthesis.
TCR ligation on CD8+ T cells creates double-negative cells in vivo. (1998)

The lack of CD95 in mice is associated with an accumulation of TCR alphabeta+ CD4- CD8- (double-negative (DN)) cells in the lymph nodes (LNs) and other organs. To test the hypothesis that these DN cells arise from TCR alphabeta+ CD8+ cells after activation via the TCR, we have crossed an MHC class I-restricted TCR transgene (tg) onto the lpr genotype to generate two TCR-transgenic experimental groups, TCRtg+ lpr/+ (CD95-intact) and TCRtg+ lpr/lpr (CD95-deficient). Specific peptide administration resulted in peripheral deletion of TCR alphabeta cells from the LNs of CD95-intact and CD95-deficient mice. On day 3 after peptide administration in the CD95-deficient but not the CD95-intact mice, there was a ninefold increase in the percentage of DN cells in the LN; this increase returned to control levels by day 10. Peripheral deletion was associated with an accumulation of TCR alphabeta+ CD8high cells in the livers of mice of both genotypes by day 3, which returned to control levels by day 10 without an increase in the percentage or total number of DN cells. Our data show that the in vivo stimulation of TCR alphabeta+ CD8+ cells in the absence of CD95 results in an initial accumulation and an eventual loss of DN cells. This identifies a role for CD95 after TCR alphabeta stimulation in the efficient removal of TCR alphabeta+ CD8+ cells after the down-regulation of CD8. CD95 is not essential for this process, because other mechanisms can compensate, but such mechanisms are less efficient in the LN.
Holographic nanoparticle-polymer composites based on step-growth thiol-ene photopolymerization (2011)

We report on the photopolymerization kinetics and volume holographic recording characteristics of silica nanoparticle-polymer composites using thiol-ene monomers capable of step-growth polymerization. Real-time Fourier transform spectroscopy and photocalorimetry are used to characterize the visible light curing kinetics of a thiol-ene monomer system consisting of secondary dithiol with high self-life stability and low odor and triene with rigid structure and high electron density. It is shown that while the nanoparticle-(thiol-ene)polymer composites exhibit high transparency, their saturated refractive index modulation (Δnsat ) and material sensitivity (S) are as large as 1×10−2 and 1615 cm/J, respectively. The polymerization shrinkage is reduced as low as 0.4% as a result of the late gelation in conversion. These values meet the acceptable values for holographic data storage media (i.e., 5×10−3, 500 cm/J and 0.5% for Δnsat, S and shrinkage, respectively). It is also shown that because of the dispersion of inorganic silica nanoparticles and the use of the triene monomer having the rigid structure of the triazine functional group, the thermal stability of recorded holograms is much improved over our previously reported nanoparticle-polymer composites using organic nanoparticles and primary mercaptopropionate trithiol/allyl ether triene monomers [Opt. Lett. 35, 396 (2010)].
The receptor for urokinase‐plasminogen activator (1986)

Many human cells and cell lines possess a specific receptor that binds urokinase plasminogen activator (uPA) with an affinity of about 10(-10) M. Bound enzyme is not internalized, is slowly dissociated, and retains its enzymatic activity. The amino acid sequence of uPA responsible for receptor binding is located within the first 35 aminoterminal residues, ie, in the growth factor domain. Binding, however, is not competed for by other proteins that contain the growth factor domain (including epidermal growth factor). Cells that produce uPA secrete the pro-uPA form, which subsequently binds to the receptor. A431 cells, in fact, have their receptors completely saturated with pro-uPA. It is proposed that uPA:uPA-receptor interaction plays a direct role in physiological and pathological processes that require cell migration.