gebhart/patrepeval huggingface dataset:
Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2'-deoxycytidine. (2002)

Epigenetic modifications of cytosine residues in DNA and the amino termini of histone proteins have emerged as key mechanisms in chromatin remodeling, impacting both the transcriptional regulation and the establishment of chromosomal domains. Using the chromatin immunoprecipitation (ChIP) assay, we demonstrate that aberrantly silenced genes in cancer cells exhibit a heterochromatic structure that is characterized by histone H3 lysine 9 (H3-K9) hypermethylation and histone H3 lysine 4 (H3-K4) hypomethylation. This aberrant heterochromatin is incompatible with transcriptional initiation but does not inhibit elongation by RNA polymerase II. H3-K9 methylation may, therefore, play a role in the silencing of tumor-suppressor genes in cancer. Treatment with 5-aza-2'-deoxycytidine (5-Aza-CdR), previously known for its ability to inhibit cytosine methylation, induced a rapid and substantial remodeling of the heterochromatic domains of the p14ARF/p16INK4a locus in T24 bladder cancer cells, reducing levels of dimethylated H3-K9 and increasing levels of dimethylated H3-K4 at this locus. In addition, 5-Aza-CdR increased acetylation and H3-K4 methylation at the unmethylated p14 promoter, suggesting it can induce chromatin remodeling independently of its effects on cytosine methylation.
Carotenoids: biochemistry, pharmacology and treatment (2016)

This article is part of a themed section on Principles of Pharmacological Research of Nutraceuticals. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.11/issuetoc.
Chemokine Coreceptor Signaling in HIV-1 Infection and Pathogenesis (2009)

Binding of the HIV-1 envelope to its chemokine coreceptors mediates two major biological events: membrane fusion and signaling transduction. The fusion process has been well studied, yet the role of chemokine coreceptor signaling in viral infection has remained elusive through the past decade. With the recent demonstration of the signaling requirement for HIV latent infection of resting CD4 T cells, the issue of coreceptor signaling needs to be thoroughly revisited. It is likely that virus-mediated signaling events may facilitate infection in various immunologic settings in vivo where cellular conditions need to be primed; in other words, HIV may exploit the chemokine signaling network shared among immune cells to gain access to downstream cellular components, which can then serve as effective tools to break cellular barriers. This virus-hijacked aberrant signaling process may in turn facilitate pathogenesis. In this review, we summarize past and present studies on HIV coreceptor signaling. We also discuss possible roles of coreceptor signaling in facilitating viral infection and pathogenesis.
Oral Sildenafil Is an Effective and Specific Pulmonary Vasodilator in Patients With Pulmonary Arterial Hypertension (2002)

A single oral dose of sildenafil is as effective and selective a pulmonary vasodilator as iNO. Sildenafil may be superior to iNO in that it increases cardiac output and does not increase wedge pressure. Future studies are indicated to establish whether sildenafil could be effective over a longer duration.
What factors should influence the dosage and interval of prophylactic treatment in patients with severe haemophilia A and B? (2001)

In order to prevent arthropathy, prophylaxis has to start at a young age before recurrent joint bleedings have taken place. The use of central venous lines has facilitated an early beginning to treatment, but due to side-effects, most European paediatricians prefer peripheral injections whenever possible. By starting primary prophylaxis at the age of 1--2 years with one injection weekly, the need for surgical implants may be reduced. In this study, only four of 34 boys born 1988--98 with severe haemophilia A or B needed a Port-a-Cath for primary prophylaxis. Trough levels were measured in these patients and 79% showed a trough level < 1%, while 21% reached a level > 1%. Despite this, joint bleedings during 1998 were rare in both groups [0--4] and 59% of the boys with trough levels < 1% did not report any haemartroses during that year. Mean annual joint bleedings were the same in both groups [0.70, 0.71]. The lowest effective level of factors VIII and IX must be determined individually for each patient on primary or secondary prophylaxis.
Cloning and characterization of FGF23 as a causative factor of tumor-induced osteomalacia (2001)

Tumor-induced osteomalacia (TIO) is one of the paraneoplastic diseases characterized by hypophosphatemia caused by renal phosphate wasting. Because removal of responsible tumors normalizes phosphate metabolism, an unidentified humoral phosphaturic factor is believed to be responsible for this syndrome. To identify the causative factor of TIO, we obtained cDNA clones that were abundantly expressed only in a tumor causing TIO and constructed tumor-specific cDNA contigs. Based on the sequence of one major contig, we cloned 2,270-bp cDNA, which turned out to encode fibroblast growth factor 23 (FGF23). Administration of recombinant FGF23 decreased serum phosphate in mice within 12 h. When Chinese hamster ovary cells stably expressing FGF23 were s.c. implanted into nude mice, hypophosphatemia with increased renal phosphate clearance was observed. In addition, a high level of serum alkaline phosphatase, low 1,25-dihydroxyvitamin D, deformity of bone, and impairment of body weight gain became evident. Histological examination showed marked increase of osteoid and widening of growth plate. Thus, continuous production of FGF23 reproduced clinical, biochemical, and histological features of TIO in vivo. Analyses for recombinant FGF23 products produced by Chinese hamster ovary cells indicated proteolytic cleavage of FGF23 at the RXXR motif. Recent genetic study indicates that missense mutations in this RXXR motif of FGF23 are responsible for autosomal dominant hypophosphatemic rickets, another hypophosphatemic disease with similar features to TIO. We conclude that overproduction of FGF23 causes TIO, whereas mutations in the FGF23 gene result in autosomal dominant hypophosphatemic rickets possibly by preventing proteolytic cleavage and enhancing biological activity of FGF23.
Operation of a fiber-grating compressor in the Raman regime (1988)

Compression of intense Nd:YAG laser pulses by a fiber-grating compressor is investigated experimentally and theoretically. An increased stability of compressor operation in the Raman regime and a considerable further shortening of pulses with a compression factor of 130× is reported. A complete theoretical model of pulse compression is presented, including the combined action of self-phase modulation, stimulated Raman scattering, and group-velocity dispersion in the fiber. Detailed numerical calculations show the influence of laser input power on the shape, width, and peak intensity of compressed pulses for different fiber lengths and are directly compared with measurements.
Mucosal vaccination against influenza: protection of pigs immunized with inactivated virus and ether-split vaccine. (2001)

Effective vaccinations against swine influenza reduce the economic loss of pig industries, and also may minimize the possibility of emergence of new pandemic viruses, since pigs are intermediate hosts to generate reassortant viruses among avian and mammalian influenza viruses. In this study, we showed that intranasal immunization of pigs with formalin-inactivated or ether-split influenza vaccine (A/Aichi/2/68) induced virus-specific IgG, IgM, and IgA antibodies in their nasal secretions and sera, resulting in complete protection from virus challenge. Antibody response to the challenge virus was not observed in the immunized pigs, suggesting that the replication of the virus in the primary targets, respiratory epithelial cells, was inhibited. The present results indicate that intranasal immunization of pigs with inactivated vaccines is effective to control swine influenza, and also provide a good model, as well as a mouse model, to evaluate an intranasal application of influenza vaccine for humans.
Genomic Organization and Polymorphisms of the Human C3d/Epstein-Barr Virus Receptor (1989)

The human C3d/Epstein-Barr virus receptor (CR2/CD21) is a 145-kDa protein primarily expressed on mature B lymphocytes. CR2 is a member of the regulators of complement activation (RCA) gene family found on band q32 of chromosome 1. The RCA proteins are characterized by the presence of 60-70 amino acid short consensus repeats (SCR). A full length CR2 cDNA was cloned and used to identify overlapping cosmid genomic clones. Analysis of CR2 exon-intron junctions revealed the presence of three types of exons in the short consensus repeat region of CR2. First, four exons each of which encodes two SCR are present. Five exons encode a single SCR. Six exons encode SCRs which are split in identical positions. The order of these types of exons is in a repeated array of four SCRs, indicating that the contemporary CR2 gene likely evolved from a more primitive gene containing four SCRs. The CR2 full length cDNA clone was used to find restriction fragment length polymorphisms (RFLPs). Restriction enzyme TaqI generated 2.55- and 2.10-kilobase (kb) polymorphic bands. This RFLP was mapped near the exon containing the first two SCRs. HaeIII digestion generated polymorphic bands of 1.45, 1.55, and 1.75 kb. The HaeIII 1.45-kb RFLP band maps near the exon containing the 15th SCR. The TaqI and HaeIII RFLPs will provide tools for the genetic analysis of CR2. The organization of the CR2 gene provides insights into the evolution of human CR2 and the RCA gene family.
Frequency-domain sonar processing in FPGAs and DSPs (2002)

Beamforming is a spatial filtering operation performed on data received by an array of sensors, such as antennas, microphones, or hydrophones. It provides a system with the ability to "listen" directionally even when the individual sensors in the array are omnidirectional. Over the past year we have been exploring the use of FPGA based custom computing machines for several sonar beamforming applications, including time domain beamforming (P. Graham nd B. Nelson, 1998), frequency domain beamforming, and matched field processing. In many ways sonar processing fits the criteria found by W. Mangione-Smith and B. Hutchings (1997) for good FPGA applications-the computations are data parallel, they require little control, the data sets are large (infinite streams), and the raw sensor data is at most 12 bits. However, they have three characteristics which make them challenging. First, they involve intensive arithmetic (multiply accumulates and trigonometric functions) on real and/or complex data. Second, they require significant memory support, far beyond that indicated in much previously published work. Third, the scale of the computation is large, requiring (possibly) hundreds of FPGAs and high bandwidth interconnections to meet real time constraints. We address the first issue.
Thermal Cycloreversion Reaction of a Photochromic Dithienylperfluorocyclopentene with tert-Butoxy Substituents at the Reactive Carbons (2002)

Abstract tert-Butoxy groups were introduced at 2 and 2′-positions of the thiophene rings of a dithienylperfluorocyclopentene to prepare a photochromic compound with a thermal cycloreversion reactivity and a low photocycloreversion quantum yield. The cycloreversion quantum yield was similar to the isopropyl-substituted derivative and the half-life time of the colored isomer at 100 °C was 8 s.
NADPH oxidase (CYBA) and FcγR polymorphisms as risk factors for aggressive periodontitis: A case–control association study (2006)

C242T p22phox NADPH oxidase and FcgammaR polymorphisms may predispose to AgP through a modulation of neutrophil superoxide production.
Proteolytic Processing of the C Terminus of the α1CSubunit of L-type Calcium Channels and the Role of a Proline-rich Domain in Membrane Tethering of Proteolytic Fragments (2000)

Although most L-type calcium channel alpha(1C) subunits isolated from heart or brain are approximately 190-kDa proteins that lack approximately 50 kDa of the C terminus, the C-terminal domain is present in intact cells. To test the hypothesis that the C terminus is processed but remains functionally associated with the channels, expressed, full-length alpha(1C) subunits were cleaved in vitro by chymotrypsin to generate a 190-kDa C-terminal truncated protein and C-terminal fragments of 30-56 kDa. These hydrophilic C-terminal fragments remained membrane-associated. A C-terminal proline-rich domain (PRD) was identified as the mediator of membrane association. The alpha(1C) PRD bound to SH3 domains in Src, Lyn, Hck, and the channel beta(2) subunit. Mutant alpha(1C) subunits lacking either approximately 50 kDa of the C terminus or the PRD produced increased barium currents through the channels, demonstrating that these domains participate in the previously described (Wei, X., Neely, a., Lacerda, A. E. Olcese, r., Stefani, E., Perez-Reyes, E., and Birnbaumer, L. (1994) J. Biol. Chem. 269, 1635-1640) inhibition of channel function by the C terminus.
Hypertonic Saline Lowers Raised Intracranial Pressure in Children After Head Trauma (1992)

Eighteen pediatric patients who sustained traumatic brain injury were enrolled in a double-blind, crossover study comparing the effects of 3% saline and 0.9% saline infusions on raised intracranial pressure (ICP). After resuscitation, each patient received a bolus of each saline concentration, and ICP was monitored for 2 h. Initial mean ICP before 0.9% saline infusions equaled 19.3 mm Hg and averaged 20.0 mm Hg during the subsequent 2-h trials (p = 0.32). Baseline mean ICP before 3% saline administration equaled 19.9 mm Hg and averaged 15.8 mm Hg for 2 h postinfusion (p = 0.003). Central venous pressure did not change significantly in either group, nor did measurements of renal function. Serum sodium concentrations increased in all 18 trials of 3% saline. Maximal concentrations of serum sodium occurred 30 min after bolus administration of 3% saline. Three percent saline significantly reduces raised ICP after traumatic brain injury when compared with normal saline. Intravascular dehydration, as measured by central venous pressure, did not occur during the study period.
Identification of Human Macrophage Inflammatory Proteins 1α and 1β as a Native Secreted Heterodimer (2001)

Chemokines are secreted proteins that function as chemoattractants for leukocytes. The chemokines macrophage inflammatory protein 1alpha and 1beta (MIP-1alpha and MIP-1beta) now have been shown to be secreted from activated human monocytes and peripheral blood lymphocytes (PBLs) as a heterodimer. Immunoprecipitation and immunoblot analysis revealed that antibodies to either MIP-1alpha or MIP-1beta precipitated a protein complex containing both MIP-1alpha and MIP-1beta under normal conditions from culture supernatants and lysates of these cells. Mass spectrometry of the complexes, precipitated from the culture supernatants of monocytes and PBLs, revealed the presence of NH(2)-terminal truncated MIP-1alpha (residues 5-70) together with either intact MIP-1beta or NH(2)-terminal truncated MIP-1beta (residues 3-69), respectively. The secreted MIP-1alpha/beta heterodimers were dissociated into their component monomers under acidic conditions. Exposure of monocytes or PBLs to monensin induced the accumulation of heterodimers composed of NH(2)-terminal truncated MIP-1alpha and full-length MIP-1beta in the Golgi complex. The mixing of recombinant chemokines in vitro demonstrated that heterodimerization of MIP-1alpha and MIP-1beta is specific and that it occurs at physiological conditions, pH 7.4, and in the range of nanomolar concentrations. The data presented here provide the first biochemical evidence for the existence of chemokine heterodimers under natural conditions. Formation of heterodimers of MIP-1alpha/beta may have an impact on intracellular signaling events that contribute to CCR5 and possibly to other chemokine receptor functions.
Time-domain equalization for multicarrier communication (1995)

Multicarrier communication, without time-domain equalizer (TEQ), over a channel whose impulse response duration is of the same order as the inverse carrier spacing, requires a long guard interval yielding a considerable loss in both power and bandwidth efficiency. A smaller guard interval (yielding a smaller loss) can be allowed when using at the receiver a TEQ that shortens the impulse response of the cascade of channel plus TEQ. In this contribution the impulse response of a FIR TEQ is determined according to a MMSE criterion, resulting in an eigenvalue problem. Numerical performance results as a function of TEQ complexity are presented, assuming both upstream and downstream asymmetric digital subscriber line (ADSL) communication over twisted pair cable.
A microfluidic device based on gravity and electric force driving for flow cytometry and fluorescence activated cell sorting (2004)

A novel method based on gravity and electric force driving of cells was developed for flow cytometry and fluorescence activated cell sorting in a microfluidic chip system. In the experiments cells flowed spontaneously under their own gravity in a upright microchip, passed through the detection region and then entered into the sorting electric field one by one at an average velocity of 0.55 mm s(-1) and were fluorescence activated cell sorted (FACS) by a switch-off activation program. In order to study the dynamical and kinematic characteristics of single cells in gravity and electric field of microchannels a physical and numerical module based on Newton's Law of motion was established and optimized. Hydroxylpropylmethyl cellulose (HPMC) was used to minimize cell assembling, sedimentation and adsorption to microchannels. This system was applied to estimate the necrotic and apoptotic effects of ultraviolet (UV) light on HeLa cells by exposing them to UV radiation for 10, 20 or 40 min and the results showed that UV radiation induced membrane damage contributed to the apoptosis and necrosis of HeLa cells.
Fusion Proteins Containing Androgen Receptor Sequences and Their Use in the Production of Poly- and Monoclonal Anti-Androgen Receptor Antibodies (1989)

Complementary DNA segments that encode different domains of human and rat androgen receptors were fused to the Escherichia coli trpE gene using pATH expression vectors. Fusion proteins expressed by the bacteria were used to immunize rats and rabbits to obtain polyclonal antibodies to androgen receptors. Spleen cells of immunized rats were fused with myeloma cells to obtain stable hybridomas that produced monoclonal antibodies. Gradient centrifugation and immuno-precipitation assays indicated that the antibodies interacted with androgen receptors specifically.
<title>Plasma etching of chromium films in the fabrication of photomasks</title> (1995)

To meet the advanced CD uniformity and resolution requirements of state-of-the-art maskmaking, dry chrome etch processing may be required. Dry etching is a more anisotropic process, significantly reducing etch undercut. The absence of undercutting allows the lithographer to image the resist at the iso-focal point, eliminating the need to underexpose to maintain CDs. Also, dry etch parameters can be precisely controlled via a microprocessor- controlled etch system with a highly accurate parameter-metering system that ensures greater process control. Using design-of-experiment methodologies, a chrome plasma etch process (using OCG-895i) was developed. This work proves the feasibility of plasma etching chromium patterns on photomasks. The results show an etch that has excellent uniformity, is anisotropic, and has excellent edge quality. Also, resist selectivity is high for the etching of thin chrome films. SEM results show a significant reduction in the bias needed to achieve nominal CDs. As with many dry etch processes, loading and microloading effects (i.e., localized pattern density effect on etch rates) are a concern. Initial investigations of loading and microloading effects were conducted. Results suggest that due to the high anisotropy of the etch, microloading is not an issue. However, plate loading (or the amount of chrome removed) increases etch times and can result in radial etch patterns. Loading effects must be minimized or eliminated to optimize etch uniformity.
Fecal Lactoferrin Is A Sensitive and Specific Marker in Identifying Intestinal Inflammation (2003)

Fecal lactoferrin is sensitive and specific for detecting inflammation in chronic IBD. This noninvasive test may prove useful in screening for inflammation in patients presenting with abdominal pain and diarrhea.
Interferon-inducible CXC-chemokines are crucial immune modulators and survival predictors in colorectal cancer (2017)

Tumor-infiltrating T-cells are strongly associated with prognosis in colorectal cancer, but the mechanisms governing intratumoral lymphocyte recruitment are unclear. We investigated the clinical relevance and functional contribution of interferon-regulated CXC-chemokines CXCL9, CXCL10, and CXCL11, described as T-cells attractants. Their expression was significantly elevated in tumors as compared to normal colon in 163 patients with colon cancer, represented an independent positive predictor of post-operative survival, and was highly significantly correlated with the presence of tumor-infiltrating cytotoxic CD8<sup>+</sup> T-cells and CD4<sup>+</sup> T<sub>H1</sub>-effector cells. The regulation of chemokine expression was investigated in established cell lines and in tissue explants from resected tumor specimen (n=22). All colorectal cancer cell lines tested, as well as stroma or endothelial cells, produced CXC-chemokines in response to cytokine stimulation. Moreover, resected tumor explants could be stimulated to produce CXC-chemokines, even in cases with initially low CXC-levels. Lastly, a causative role of chemokine expression was evaluated with an orthotopic mouse model, based on isogenic rectal CT26 cancer cells, engineered to express CXCL10. The orthotopic model demonstrated a protective and anti-metastatic role of intratumoral CXCL10 expression, mediated mainly by adaptive immunity.
Lithium and the brain: a psychopharmacological strategy to a molecular basis for manic depressive illness (1994)

Lithium, an effective treatment for mania and the prevention of recurrent episodes of both mania and depression in patients with manic depressive illness, exerts multiple biochemical effects. However, any clinically relevant site of action of lithium must occur at therapeutic concentrations attained in the brain of patients and must account for the lag period accompanying onset of action as well as effects persisting beyond discontinuation of treatment. This monovalent cation acts as a potent uncompetitive inhibitor in the receptor-coupled breakdown of inositol phospholipids, resulting in a relative depletion of inositol and an alteration in the generation of diacylglycerol, an endogenous activator of protein kinase C. In our laboratory, we are examining the action of chronically administered lithium on posttranslational modification of specific phosphoproteins involved in regulating signal transduction in the brain. We have found that chronic, but not acute, administration of lithium in rats markedly reduces a major phosphoprotein substrate of protein kinase C in the hippocampus, an effect that persists beyond the cessation of lithium treatment. This protein, myristoylated alanine-rich C kinase substrate ("MARCKS"), is implicated in synaptic neurotransmission, calcium regulation, and cytoskeletal restructuring. These findings have relevance for the long-term action of lithium in stabilizing an underlying dysregulation in the brain and may move us closer to formulating a molecular basis of manic depressive illness.