gebhart/patrepeval huggingface dataset:
Cigarette smoke extract induces oxidative stress and apoptosis in human lung fibroblasts (2003)

Cigarette smoke is a mixture of chemicals having direct and/or indirect toxic effects on different lung cells. We investigated the effect of cigarette smoke on human lung fibroblasts (HFL-1) oxidation and apoptosis. Cells were exposed to various concentrations (1, 5, and 10%) of cigarette smoke extract (CSE) for 3 h, and oxidative stress and apoptosis were assessed by fluorescence-activated cell sorting and confocal laser fluorescence microscopy. Both oxidative stress and apoptosis exhibited a dose-response relationship with CSE concentrations. Lung fibroblasts also showed marked DNA fragmentation at the Comet assay after exposure to 10% CSE. Coincubation of HLF-1 cells with N-acetylcysteine (1 mM) during CSE exposure significantly reduced oxidative stress, apoptosis, and DNA fragmentation, whereas preincubation (3 h) with the glutathione-depleting agent buthionine sulfoximine (125 microM) produced a significant increase of oxidative stress. Cigarette smoke is a potent source of oxidative stress, DNA damage, and apoptosis for HFL-1 cells, and we speculate that this could contribute to the development of pulmonary emphysema in the lungs of smokers.
Rapid reverse transcription-PCR detection of hepatitis C virus RNA in serum by using the TaqMan fluorogenic detection system (1996)

We describe the application of a new fluorogenic probe-based PCR assay (TaqMan; Perkin Elmer Corp./Applied Biosystems, Foster City, Calif.) for the detection of hepatitis C virus RNA in serum and plasma. This assay allows for the direct direction of specific PCR products within minutes of completion of the PCR by monitoring the increase in fluorescence of a dye-labeled oligonucleotide probe. We evaluated this assay by comparing the results obtained by nested PCR with those obtained by TaqMan PCR. Test samples included two separate dilutions series of plasma samples from experimentally infected chimpanzees and a panel of 48 serum specimens from patients with community-acquired hepatitis C virus. The quantity of HCV RNA in each chimpanzee plasma sample was determined by using branched DNA (bDNA) signal amplification assay (Quantiplex HCV RNA assay; Chiron Corp., Emeryville, Calif.). Both PCR assays demonstrated similar levels of detection and could reliably detect 13 bDNA genome equivalents per sample. We found an overall concordance of 88% between results of two PCR assays with the community-acquired panel, which resolved to 100% when discrepant samples were retested by nested PCR. TaqMan compared favorably with nested PCR with key advantages of speed, increased throughput, and decreased opportunity for false-positive results because of elimination of second-round amplification.
Therapy of experimental human brain tumors using a neuroattenuated herpes simplex virus mutant. (1995)

We conclude from these studies that strain 1716 induces regression of human neural tumors established in the brains of nude mice, resulting in their prolonged survival.
Roll Deconvolution Of Space Telescope Data: Inverse Filtering Of Two Speckle Interferograms (1985)

Roll deconvolution is a speckle method that can improve the resolution of the 2.4m Hubble Space Telescope (HST) at short UV wavelengths. A diffraction-limited image can digitally be reconstructed from two degraded images recorded at two different roll angles of the HST. The reconstruction is performed by complex inverse filtering of the two degraded images. In digital simulations we have investigated how the signal-to-noise ratio of the reconstruction depends on photon noise (104 to 50 photon counts per pixel), on the structure and size of the point spread function (caused by aberrations) and other parameters.
Non-specific Effect of Beettahistine on Cochlear Electrophysiology in Guinea Pig (1997)

Beettahistine hydrochloride (BH) is reported to be beneficial in the treatment of certain type of vestibulo-cochlear disorders. Experimentally is shown that BH inhibits vestibular firing rate and improves cochlear blood flow by dilatating the larger feeding vessels. Both these effects are weak, and hardly can explain the clinical benefits reported for the drug. We investigated the effect of BH on the organ of Corti electrophysiology in vivo. Two microliters of 1, 2, 5 and 10% saline solutions of BH was applied (in increasing order) to the round window (RW) membrane in an anesthetized guinea pig (n = 5). Summating potential (SP), action potential (AP), and cochlear microphonics (CM) were recorded at 16 kHz frequency using RW Ag wire electrode. The repeated applications of BH with increasing concentrations produced a dose-dependent threshold shift in CAP. The I/O function for 20, 30, 40, 50, 60, 70, and 80 dB at 16 kHz indicated that there was a saturation before complete blockade of the responsiveness in all measured parameters. SP and CM changes nearly followed CAP changes. The changes recover during 2 hours follow-up period. Our findings indicate that BH affects the organ of Corti electrophysiology. That the drug effect saturates before a complete blockade suggests non-specific effect of BH on the organ of Corti structures and cochlear nerve.
Synthesis of photoreactive poly(ethylene glycol) and its application to the prevention of surface‐induced platelet activation (1992)

Photoreactive poly(ethylene glycol) (PEG) was synthesized by reacting 4-fluoro-3-nitrophenyl azide (FNPA) with sodium salt of PEG. The synthesized 4-azido-2-nitrophenyl PEG (ANP-PEG) was characterized by 1H-NMR, IR, and UV spectroscopy. ANP-PEG was grafted to dimethyldichlorosilane-coated glass (DDS-glass) by photolysis without any premodification of the surface. The effects of various grafting factors, such as the polymer adsorption time, concentration of ANP-PEG, and UV irradiation time, on the PEG grafting efficiency were examined. The PEG-grafted DDS-glass was characterized by measuring surface free energies, surface-induced platelet activation, and the relative amount of PEG grafted on the surface using electron spectroscopy for chemical analysis (ESCA). Platelet adhesion and activation was analyzed by measuring the number and spread area of adherent platelets. The results showed that ANP-PEG had to be adsorbed onto DDS-glass for at least 12 h before photolysis for the maximum grafting efficiency. No platelets could adhere to the PEG-grafted DDS-glass, if the bulk concentration of ANP-PEG in the adsorption solution was between 1 mg/mL and 10 mg/mL. Above 10 mg/mL, platelet activation gradually increased and reached the maximum at 30 mg/mL. Our data indicate that the grafting of ANP-PEG requires careful control of the grafting conditions and that the grafted PEG can prevent surface-induced platelet activation.
Downy Mildew Resistance in Arabidopsis by Mutation of HOMOSERINE KINASE (2009)

Plant disease resistance is commonly triggered by early pathogen recognition and activation of immunity. An alternative form of resistance is mediated by recessive downy mildew resistant 1 (dmr1) alleles in Arabidopsis thaliana. Map-based cloning revealed that DMR1 encodes homoserine kinase (HSK). Six independent dmr1 mutants each carry a different amino acid substitution in the HSK protein. Amino acid analysis revealed that dmr1 mutants contain high levels of homoserine that is undetectable in wild-type plants. Surprisingly, the level of amino acids downstream in the aspartate (Asp) pathway was not reduced in dmr1 mutants. Exogenous homoserine does not directly affect pathogen growth but induces resistance when infiltrated in Arabidopsis. We provide evidence that homoserine accumulation in the chloroplast triggers a novel form of downy mildew resistance that is independent of known immune responses.
Social rejection shares somatosensory representations with physical pain (2011)

How similar are the experiences of social rejection and physical pain? Extant research suggests that a network of brain regions that support the affective but not the sensory components of physical pain underlie both experiences. Here we demonstrate that when rejection is powerfully elicited--by having people who recently experienced an unwanted break-up view a photograph of their ex-partner as they think about being rejected--areas that support the sensory components of physical pain (secondary somatosensory cortex; dorsal posterior insula) become active. We demonstrate the overlap between social rejection and physical pain in these areas by comparing both conditions in the same individuals using functional MRI. We further demonstrate the specificity of the secondary somatosensory cortex and dorsal posterior insula activity to physical pain by comparing activated locations in our study with a database of over 500 published studies. Activation in these regions was highly diagnostic of physical pain, with positive predictive values up to 88%. These results give new meaning to the idea that rejection "hurts." They demonstrate that rejection and physical pain are similar not only in that they are both distressing--they share a common somatosensory representation as well.
Expression cloning of an ATP receptor from mouse neuroblastoma cells. (1993)

Extracellular ATP activates cell-surface metabotropic and ionotropic nucleotide (P2) receptors in vascular, neural, connective, and immune tissues. These P2 receptors mediate a wealth of physiological processes, including nitric oxide-dependent vasodilation of vascular smooth muscle and fast excitatory neurotransmission in sensory afferents. Although ATP is now recognized as a signaling molecule, the cellular and molecular mechanisms underlying its actions have been difficult to study due to the absence of selective P2 receptor antagonists and cloned receptor genes. Nonetheless, five mammalian P2 receptor subtypes have been tentatively assigned based solely on agonist specificity and signaling properties. Here we report the cloning of a mouse cDNA encoding a P2 receptor that shares striking homology with several G protein-coupled peptide receptors. When expressed in Xenopus laevis oocytes, the cloned receptor resembles a metabotropic P2U receptor; activation by either ATP or UTP elicits the mobilization of intracellular calcium. mRNA encoding the P2U purinergic receptor is found in neural and nonneural tissues.
Spatial-filter models to describe IC lithographic behavior (1997)

Proximity correction systems require an accurate, fast way to predict how a pattern configuration will transfer to the wafer. In this paper we present an efficient method for modeling the pattern transfer process based on Dennis Gabor's `theory of communication'. This method is based on a `convolution form' where any 2D transfer process can be modeled with a set of linear, 2D spatial filters, even when the transfer process is non-linear. We will show that this form is a general case from which other well-known process simulation models can be derived. Furthermore, we will demonstrate that the convolution form can be used to model observed phenomena, even when the physical mechanisms involved are unknown.
Direct Growth ofm-plane GaN with Epitaxial Lateral Overgrowth fromc-plane Sidewall ofa-plane Sapphire (2008)

The direct growth of m-plane GaN via metal–organic vapor phase epitaxy has been demonstrated using a deep-groove-patterned a-plane sapphire substrate with a c-plane sidewall and terrace covered with a SiO2 mask. The GaN layer was laterally grown from the etched c-plane sidewall in the a-plane sapphire substrate, which means c-direction growth of GaN. According to the epitaxial relationship which m-axis of GaN layer corresponds to a-axis of c-plane sapphire when using a low-temperature buffer layer, m-plane GaN was grown with an epitaxial lateral overgrowth from the c-plane sidewall of the a-plane sapphire.
Therapeutic protein transduction of mammalian cells and mice by nucleic acid-free lentiviral nanoparticles (2006)

The straightforward production and dose-controlled administration of protein therapeutics remain major challenges for the biopharmaceutical manufacturing and gene therapy communities. Transgenes linked to HIV-1-derived vpr and pol-based protease cleavage (PC) sequences were co-produced as chimeric fusion proteins in a lentivirus production setting, encapsidated and processed to fusion peptide-free native protein in pseudotyped lentivirions for intracellular delivery and therapeutic action in target cells. Devoid of viral genome sequences, protein-transducing nanoparticles (PTNs) enabled transient and dose-dependent delivery of therapeutic proteins at functional quantities into a variety of mammalian cells in the absence of host chromosome modifications. PTNs delivering Manihot esculenta linamarase into rodent or human, tumor cell lines and spheroids mediated hydrolysis of the innocuous natural prodrug linamarin to cyanide and resulted in efficient cell killing. Following linamarin injection into nude mice, linamarase-transducing nanoparticles impacted solid tumor development through the bystander effect of cyanide.
Glycosylation Changes in Cancer (2009)

Altered glycosylation is a universal feature of cancer cells, and certain glycans are well-known markers of tumor progression. This chapter discusses glycan biosynthetic pathways that are frequently altered in cancer cells; correlations between altered glycosylation, diagnosis, and clinical prognosis; the genetic bases of some of these changes; and studies indicating their pathological importance.
Anti–B-Cell Monoclonal Antibodies in the Treatment of Severe B-Cell Lymphoproliferative Syndrome Following Bone Marrow and Organ Transplantation (1991)

Intravenous administration of anti-B-cell antibodies may be effective in controlling diffuse, severe, oligoclonal B-cell proliferation not involving the central nervous system.
Measuring Top-Quark Polarization in Top-Pair + Missing-Energy Events (2012)

The polarization of a top quark can be sensitive to new physics beyond the standard model. Since the charged lepton from top-quark decay is maximally correlated with the top-quark spin, it is common to measure the polarization from the distribution in the angle between the charged lepton and the top-quark directions. We propose a novel method based on the charged lepton energy fraction and illustrate the method with a detailed simulation of top-quark pairs produced in supersymmetric top squark pair production. We show that the lepton energy ratio distribution that we define is very sensitive to the top-quark polarization but insensitive to the precise measurement of the top-quark energy.
A Randomized, Controlled Trial of Methylprednisolone or Naloxone in the Treatment of Acute Spinal-Cord Injury (1990)

Studies in animals indicate that methylprednisolone and naloxone are both potentially beneficial in acute spinal-cord injury, but whether any treatment is clinically effective remains uncertain. We evaluated the efficacy and safety of methylprednisolone and naloxone in a multicenter randomized, double-blind, placebo-controlled trial in patients with acute spinal-cord injury, 95 percent of whom were treated within 14 hours of injury. Methylprednisolone was given to 162 patients as a bolus of 30 mg per kilogram of body weight, followed by infusion at 5.4 mg per kilogram per hour for 23 hours. Naloxone was given to 154 patients as a bolus of 5.4 mg per kilogram, followed by infusion at 4.0 mg per kilogram per hour for 23 hours. Placebos were given to 171 patients by bolus and infusion. Motor and sensory functions were assessed by systematic neurological examination on admission and six weeks and six months after injury. After six months the patients who were treated with methylprednisolone within eight hours of their injury had significant improvement as compared with those given placebo in motor function (neurologic change scores of 16.0 and 11.2, respectively; P = 0.03) and sensation to pinprick (change scores of 11.4 and 6.6; P = 0.02) and touch (change scores, 8.9 and 4.3; P = 0.03). Benefit from methylprednisolone was seen in patients whose injuries were initially evaluated as neurologically complete, as well as in those believed to have incomplete lesions. The patients treated with naloxone, or with methylprednisolone more than eight hours after their injury, did not differ in their neurologic outcomes from those given placebo. Mortality and major morbidity were similar in all three groups. We conclude that in patients with acute spinal-cord injury, treatment with methylprednisolone in the dose used in this study improves neurologic recovery when the medication is given in the first eight hours. We also conclude that treatment with naloxone in the dose used in this study does not improve neurologic recovery after acute spinal-cord injury.
Correlation between the onset age of Huntington's disease and length of the trinucleotide repeat in IT-15 (1993)

Huntington's disease (HD) is an autosomal dominant disorder with a variable age of onset that is influenced by the sex of the affected parent. The recent recognition that HD is caused by an expanded triplet repeat suggests the possibility that the onset age may be predicted by the length of the repeat. This hypothesis was tested by assaying the length of the repeat in 114 individuals who were clinically diagnosed with HD and had a known onset age. Every individual had an expanded allele. The range was from 36 to 82 repeats (mean = 48.4 +/- 9.51) and larger than the normal range (6 to 31). The size of the expanded allele was correlated with the age of onset (r = -0.65 p < .0001). Despite the highly significant correlation, the repeat size explains less than half of the variance in onset age. Furthermore, the age of onset cannot be predicted from the size of the triplet repeat, particularly if the number of repeats is in the smaller end of the expanded range. If the repeat is < or = 50 triplets, the amount of variation in the age of onset explained by the length of the triplet repeat is less than 10%. As an illustration, the onset age of individuals with 39 repeats ranges from 30 to 65 years old. The sex of the affected parent had no effect in our sample beyond the effect of the length of the repeat. Affected offspring of affected fathers had longer repeats and a larger variance in allele size than offspring of affected mothers, perhaps reflecting greater instability in paternal transmission.
Monocyte chemoattractant protein 1 is responsible for macrophage recruitment following injury to sciatic nerve (1998)

Following injury to the peripheral nervous system, circulating monocytes/macrophages are recruited to the damaged tissue, where they play vital roles during both nerve degeneration and subsequent regeneration. Monocyte chemoattractant protein-1 (MCP-1), a member of the C-C or β-chemokine family, is a powerful leukocyte recruitment/activation factor that is relatively specific for monocytes/macrophages. Because these are the predominant leukocyte type recruited by injured nerve, we hypothesized that up-regulation of MCP-1 expression is involved in recruitment of these cells. Indeed, assay of steady-state levels of MCP-1 mRNA in rat sciatic nerve during tellurium-induced primary demyelination indicated up-regulation of this chemokine with a peak after 3 days of tellurium exposure, preceding the peak of accumulation of phagocytic macrophages (assayed as lysozyme mRNA levels) by 6 days. Increasing levels of MCP-1 mRNA expression, induced by increasing levels of tellurium exposure, resulted in corresponding increases in subsequent recruitment of macrophages. In situ hybridization suggested that MCP-1 mRNA was localized in Schwann cells. No expression of MIP-2, which is a C-X-C or α-chemokine that is specific for recruitment of neutrophils, was detected, consistent with the lack of recruitment of significant numbers of these cells. In addition, we also investigated the response seen following nerve transection (axonal degeneration and secondary demyelination with no subsequent regeneration) and nerve crush (degeneration followed by regeneration). In these latter two nerve injury models, there was also a marked, early up-regulation of MCP-1 mRNA, with a time course that is compatible with a role for this chemokine in macrophage recruitment. We conclude that MCP-1 is involved in recruiting monocytes/macrophages to injured peripheral nerve and that the specificity of leukocyte types recruited results from specificity of chemokine production. J. Neurosci. Res. 53:260–267, 1998. © 1998 Wiley-Liss, Inc.
Immunologic Treatment of Alzheimer's Disease (1999)

The recent report by Schenk et al.1 raises the hope of a vaccine for Alzheimer's disease. This report has justifiably received wide attention in both the scientific and lay media. It describes an initial study in transgenic mice, which had been developed as an animal model to test potential treatments for Alzheimer's disease.Scientifically, the paper is straightforward and impressive. The authors studied transgenic mice that overexpress a mutant form of the human amyloid precursor protein. The cerebral amyloidosis that develops in these animals is similar to that in the brains of patients with Alzheimer's disease.1 Cerebral amyloidosis was largely . . .
Neonatal Sepsis and Neutrophil Insufficiencies (2010)

Sepsis has continuously been a leading cause of neonatal morbidity and mortality despite current advances in chemotherapy and patient intensive care facilities. Neonates are at high risk for developing bacterial infections due to quantitative and qualitative insufficiencies of innate immunity, particularly granulocyte lineage development and response to infection. Although antibiotics remain the mainstay of treatment, adjuvant therapies enhancing immune function have shown promise in treating sepsis in neonates. This article reviews current strategies for the clinical management of neonatal sepsis and analyzes mechanisms underlying insufficiencies of neutrophil defense in neonates with emphasis on new directions for adjuvant therapy development.
A new model for optimal routing and wavelength assignment in wavelength division multiplexed optical networks (2002)

We consider the problem of routing and assignment of wavelength (RAW) in optical networks. Given a set of requests for all-optical connections (or lightpaths), the problem is to (a) find routes from the source nodes to their respective destination nodes, and (b) assign wavelengths to these routes. Since the number of wavelengths is limited, lightpaths cannot be established between every pair of access nodes. In this paper we first consider the dynamic RAW problem where lightpath requests arrive randomly with exponentially distributed call holding times. Then, the static RAW problem is considered which assumes that all the lightpaths that are to be set-up in the network are known initially. Several heuristic algorithms have already been proposed for establishing a maximum number of lightpaths out of a given set of requests. However most of these algorithms are based an the traditional model of circuit-switched networks where routing and wavelength assignment steps are decoupled. In this paper a new graph-theoretic formulation of the RAW problem, dubbed as layered-graph, has been proposed which provides an efficient tool for solving dynamic as well as static RAW problems. The layered-graph model also provides a framework for obtaining exact optimal solution for the number of requested lightpaths as well as far the throughput that a given network can support. A dynamic and two static RAW schemes are proposed which are based on the layered-graph model. Layered-graph-based RAW schemes are shown to perform better than the existing ones.