gebhart/patrepeval huggingface dataset:
High-power 1.5-/spl mu/m InGaAsP-InP slab-coupled optical waveguide amplifier (2005)

We report the first demonstration of a high-power semiconductor optical amplifier (SOA) based on the slab-coupled optical waveguide concept. This concept allows the realization of SOAs having large fundamental optical modes, low loss, and small optical confinement factor. These attributes support large output saturation power, long length for efficient heat removal, and direct butt-coupling to single-mode fibers. The 1.5-μm InGaAsP-InP quantum-well amplifier described here has a length of 1 cm, 1/e <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> intensity widths of 4 μm (vertical) and 8 μm (horizontal), a fiber-to-fiber gain of 13 dB, and a fiber-coupled output saturation power of 630 mW (+28 dBm). The measured butt-coupling efficiency between the amplifier and SMF-28 is 55%. Thus, the output saturation power of the amplifier itself is approximately 1.1 W (+31 dBm).
IDH1 R132H decreases proliferation of glioma cell lines in vitro and in vivo (2011)

Our results demonstrate that IDH1(R132H) dominantly reduces aggressiveness of established glioma cell lines in vitro and in vivo. In addition, the IDH1(R132H) -IDH1(wt) heterodimer has higher enzymatic activity than the IDH1(R132H) -IDH1(R132H) homodimer. Our observations in model systems of glioma might lead to a better understanding of the biology of IDH1 mutant gliomas, which are typically low grade and often slow growing.
Are P2Y12 reaction unit (PRU) and % inhibition index equivalent for the expression of P2Y12 inhibition by the VerifyNow® assay? Role of haematocrit and haemoglobin levels (2011)

The results of the whole blood VerifyNow P2Y12 assay can be expressed as platelet reaction units (PRU) or % inhibition index (%inh), but an optimal cut-off for the assessment of high on-treatment platelet reactivity (HPR) predictive of clinical events has been validated only for PRU. The aim of the study was to study the influence of haematological variables, such as platelet and leukocyte counts or haematocrit / haemoglobin, within the limits indicated by the manufacturer for assay validity, on the results of the test. We performed a comparison of PRU and %inh in a series 186 samples obtained from a clinical trial on patients under dual antiplatelet therapy. The results show that PRU significantly decreases with increasing haematocrit / haemoglobin, whereas %inh does not, due to a parallel change in PRU and iso-TRAP baseline value. PRU and % inhibition index are not equivalent for the definition of HPR, because of their different sensitivities to haematocrit / haemoglobin.
Expression capable library for studies of Neisseria gonorrhoeae, version 1.0 (2005)

This archived set of Gateway entry clones will facilitate high-throughput genomic and proteomic studies of gonococcal genes using a variety of expression and analysis systems. In addition, the DNA arrays produced will allow us to generate gene expression profiles of gonococci grown in a wide variety of conditions. Together, the resources produced in this work will facilitate experiments to dissect the molecular mechanisms of gonococcal pathogenesis on a global scale, and ultimately lead to the determination of the functions of unknown genes in the genome.
Clinical evaluation of circulating serum sialyl Tn antigen levels in patients with epithelial ovarian cancer. (1991)

Sialyl Tn antigen (NeuAc alpha 2----6GalNac alpha 1----0-Ser/Thr [STN]) with antigenic specificity in the core structure of mucin-type carbohydrate chains has been determined. In the present study, we evaluated the clinical significance of this new carbohydrate antigen, STN, in patients with epithelial ovarian cancer. With the use of a radioimmunoassay developed to detect STN antigen in serum, elevated (greater than or equal to 32.6 U/mL) antigen levels were observed in 50.0% of patients with ovarian cancer. In contrast, 3.8% of healthy individuals had STN antigen levels greater than or equal to 32.6 U/mL. In 9.6% of patients with benign gynecologic diseases and 0% of pregnant women, there were elevated levels of STN antigen. There was a significant difference (P less than .001) in STN antigen levels between patients with ovarian cancer and patients with benign gynecologic diseases, pregnant women, or the controls. The mean +/- SD for all evaluated samples of ovarian cancer was 109.2 +/- 146.8 U/mL. Both the mean values and the positive rate increased as the stage advanced. Classified according to the histologic type, the highest positive rate (61.0%) was observed in mucinous adenocarcinoma. The usefulness of STN antigen as a circulating tumor marker in ovarian cancer was estimated as follows: sensitivity 50.0%, specificity 93.5%, positive predictive value 72.2%, negative predictive value 84.7%, and diagnostic value 46.8%. Serum STN antigen levels were elevated in 12 of 33 patients with ovarian cancer who had serum CA 125 antigen levels less than 35 U/mL. While CA 125 antigen levels were elevated in 74.6% and STN antigen levels were elevated in 50.0% of the same population, the use of both assays indicated the sensitivity of detection of 83.8% in the population studied.
Gene Expression Patterns in Peripheral Blood Correlate with the Extent of Coronary Artery Disease (2009)

Systemic and local inflammation plays a prominent role in the pathogenesis of atherosclerotic coronary artery disease, but the relationship of whole blood gene expression changes with coronary disease remains unclear. We have investigated whether gene expression patterns in peripheral blood correlate with the severity of coronary disease and whether these patterns correlate with the extent of atherosclerosis in the vascular wall. Patients were selected according to their coronary artery disease index (CADi), a validated angiographical measure of the extent of coronary atherosclerosis that correlates with outcome. RNA was extracted from blood of 120 patients with at least a stenosis greater than 50% (CADi > or = 23) and from 121 controls without evidence of coronary stenosis (CADi = 0). 160 individual genes were found to correlate with CADi (rho > 0.2, P<0.003). Prominent differential expression was observed especially in genes involved in cell growth, apoptosis and inflammation. Using these 160 genes, a partial least squares multivariate regression model resulted in a highly predictive model (r(2) = 0.776, P<0.0001). The expression pattern of these 160 genes in aortic tissue also predicted the severity of atherosclerosis in human aortas, showing that peripheral blood gene expression associated with coronary atherosclerosis mirrors gene expression changes in atherosclerotic arteries. In conclusion, the simultaneous expression pattern of 160 genes in whole blood correlates with the severity of coronary artery disease and mirrors expression changes in the atherosclerotic vascular wall.
Automated array-based genomic profiling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations (2004)

B cell chronic lymphocytic leukemia (B-CLL) is characterized by a highly variable clinical course. Recurrent chromosomal imbalances provide significant prognostic markers. Risk-adapted therapy based on genomic alterations has become an option that is currently being tested in clinical trials. To supply a robust tool for such large scale studies, we developed a comprehensive DNA microarray dedicated to the automated analysis of recurrent genomic imbalances in B-CLL by array-based comparative genomic hybridization (matrix-CGH). Validation of this chip in a series of 106 B-CLL cases revealed a high specificity and sensitivity that fulfils the criteria for application in clinical oncology. This chip is immediately applicable within clinical B-CLL treatment trials that evaluate whether B-CLL cases with distinct chromosomal abnormalities should be treated with chemotherapy of different intensities and/or stem cell transplantation. Through the control set of DNA fragments equally distributed over the genome, recurrent genomic imbalances were discovered: trisomy of chromosome 19 and gain of the MYCN oncogene correlating with an elevation of MYCN mRNA expression.
Irreversible Electroporation: Treatment Effect Is Susceptible to Local Environment and Tissue Properties (2013)

IRE treatment zones are sensitive to varying electrical conductivity in tissues. Electrode location, orientation, and heterogeneities in local environment must be considered in planning ablation treatment. Online supplemental material is available for this article.
Signal Transduction in Receptor for Advanced Glycation End Products (RAGE) (2011)

The receptor for advanced glycation end products (RAGE) is a multiligand cell surface macromolecule that plays a central role in the etiology of diabetes complications, inflammation, and neurodegeneration. The cytoplasmic domain of RAGE (C-terminal RAGE; ctRAGE) is critical for RAGE-dependent signal transduction. As the most membrane-proximal event, mDia1 binds to ctRAGE, and it is essential for RAGE ligand-stimulated phosphorylation of AKT and cell proliferation/migration. We show that ctRAGE contains an unusual α-turn that mediates the mDia1-ctRAGE interaction and is required for RAGE-dependent signaling. The results establish a novel mechanism through which an extracellular signal initiated by RAGE ligands regulates RAGE signaling in a manner requiring mDia1.
Binding of HMG-I(Y) elicits structural changes in a silencer of the human ?-globin gene (1999)

Proteins involved in repression of the human beta-globin gene may be useful in the treatment of sickle cell anemia, in conjunction with therapy to reactivate fetal globin genes. If there is a reciprocal elevation of gamma-globin expression upon repression, this approach could be useful in additional hemoglobinopathies. We previously showed that repression of the beta-globin gene appears to be mediated through two DNA sequences, silencers I and II, and identified a protein termed BP1 which binds to both silencer sequences. In this study, we cloned two cDNAs encoding proteins which bind to an oligonucleotide in silencer I containing a BP1 binding site. These cDNAs correspond to HMG-I and HMG-Y, isoforms regarded as architectural proteins. We demonstrate that binding of HMG-I(Y) to this oligonucleotide causes bending/flexure of the DNA. HMG-I(Y) also binds to a second oligonucleotide containing a BP1 binding site located in a negative control region upstream of the delta-globin gene, suggesting a role for HMG-I(Y) in repression of adult globin genes. Expression studies revealed that HMG-I(Y) is ubiquitously expressed in human tissues that do not express beta-globin, being present in 48 of 50 tissues and six hematopoietic cell lines examined. Furthermore, HMG-I(Y) expression is down-regulated during differentiation of primary erythroid cells. We present a model in which HMG-I(Y) alters DNA conformation to allow binding of repressor proteins, and in which the relative amount of HMG-I(Y) helps to determine the repressive state of the beta-globin gene.
Extended Quad-Tree Partitioning for Future Video Coding (2019)

The quad-tree plus binary-tree (QTBT) coding unit (CU) partitioning structure, which has been adopted to the next generation video coding standard, shows promising coding performance when compared with the conventional quad-tree structure in HEVC. In this paper, we propose the Extended Quad-tree (EQT) partitioning, which further extends the QTBT scheme and increases the partitioning exibility. More specifcally, EQT splits a parent CU into four sub-CUs of dierent sizes, which can adequately model the local image content that cannot be elaborately characterized with QTBT. Meanwhile, EQT partitioning allows the interleaving with BT partitioning for enhanced adaptability. Experimental results on the JEM7-QTBT-Only platform show that EQT brings better coding performance with 3.17%, 3.20% and 3.06% BD-Rate gains under random access, low-delay P and low-delay B configurations, respectively.
Treatment of acute mania. (2005)

The DSM-IV criteria for mania require: a distinct period that represents a break from pre-morbid functioning, a duration of at least one week, elevated or irritable mood, at least three to four classical manic signs and symptoms and the absence of any physical factors. Although not specifically mentioned in the ICD-10 or the DSM-IV definitions, delusional, hallucinatory, even first-rank, psychotic experiences can occur in mania. Acute mania can be subdivided into classical pure mania, mania with mood-congruent or mood-incongruent psychosis, mixed state and rapid-cycling mania. One quarter to two thirds of all manic episodes are associated with delusions, while 13% to 40% are associated with hallucinations. Mixed episode is a complex syndrome which is difficult to diagnose, has the most prolonged duration of bipolar episodes and more frequent psychotic profile than pure mania with high suicidality and poor response to drugs. Mixed state mania has been well known since Kreapelin and listed in classification systems with criteria that include both a manic and a major depressive episode nearly every day for at least a one-week period. On the other hand, mixed-like episodes that are clearly caused by somatic antidepressant treatment (e.g., medication, electro-convulsive therapy or light therapy) should not contribute toward a diagnosis of Bipolar I Disorder. Although, theoretically, mania is supposed to be resolved within 1-3 months even without treatment, psychiatric hospitalization is very common in especially severe cases due to functional impairment. Current treatments for mania aim to control the agitation, impulsivity, aggression and psychotic symptoms and to help patients regain their pre-morbid functionality. However, the clinical management of mania is challenging as most patients show syndromal remission but incomplete functional recovery after the first episode of mania.
Pituitary Adenylate Cyclase-Activating Polypeptide and Its Receptors: From Structure to Functions (2000)

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a 38-amino acid peptide that was first isolated from ovine hypothalamic extracts on the basis of its ability to stimulate cAMP formation in anterior pituitary cells. PACAP belongs to the vasoactive intestinal polypeptide (VIP)-glucagon-growth hormone releasing factor-secretin superfamily. The sequence of PACAP has been remarkably well conserved during the evolution from protochordate to mammals, suggesting that PACAP is involved in the regulation of important biological functions. PACAP is widely distributed in the brain and peripheral organs, notably in the endocrine pancreas, gonads, and respiratory and urogenital tracts. Characterization of the PACAP precursor has revealed the existence of a PACAP-related peptide whose activity remains unknown. Two types of PACAP binding sites have been characterized. Type I binding sites exhibit a high affinity for PACAP and a much lower affinity for VIP whereas type II binding sites have similar affinity for PACAP and VIP. Molecular cloning of PACAP receptors has shown the existence of three distinct receptor subtypes, the PACAP-specific PAC1 receptor, which is coupled to several transduction systems, and the two PACAP/VIP-indifferent VPAC1 and VPAC2 receptors, which are primarily coupled to adenylyl cyclase. PAC1 receptors are particularly abundant in the brain and pituitary and adrenal glands whereas VPAC receptors are expressed mainly in the lung, liver, and testis. The wide distribution of PACAP and PACAP receptors has led to an explosion of studies aimed at determining the pharmacological effects and biological functions of the peptide. This report reviews the current knowledge concerning the multiple actions of PACAP in the central nervous system and in various peripheral organs including the endocrine glands, the airways, and the cardiovascular and immune systems, as well as the different effects of PACAP on a number of tumor cell types.
Glucocorticoid excess in mice results in early activation of osteoclastogenesis and adipogenesis and prolonged suppression of osteogenesis: A longitudinal study of gene expression in bone tissue from glucocorticoid‐treated mice (2008)

GC excess is associated with early activation of genes associated with osteoclastogenesis and adipogenesis and a later suppression of genes associated with osteogenesis and mineralization. Novel interventions with agents that modulate either Wnt signaling or mineralization may be effective in GC-induced osteoporosis.
Brachyury, the blastopore and the evolution of the mesoderm (2001)

The role of Brachyury and other T-box genes in the differentiation of mesoderm and endoderm of vertebrates is well established. Recently, homologues of Brachyury have been isolated from an increasing number of diverse organisms ranging from Cnidaria to vertebrates and insects. Comparative expression and function analysis allows the origin of the mesoderm and the evolution of the developmental role of Brachyury gene family in metazoans to be traced. The data suggest that an ancestral function of Brachyury was to designate a blastoporal region that had distinct properties in induction and axis elongation. A subset of blastoporal cells expressing Brachyury and other genes that convey specific mesodermal functions may have segregated as a distinct cell population from this region in the course of mesoderm evolution.
Identification of Sulfonamide-like Adverse Drug Reactions to Celecoxib in the World Health Organization Database (2001)

SummaryBackground: The selective COX-2 inhibitor celecoxib has a sulfonamide structure and is contraindicated for patients with known sulfa allergy. However, there is currently no standard available for the identification of sulfonamide-related adverse drug reactions (ADRs) and the occurrence of such ADRs with celecoxib has not been established.The aims of this study were: (1) to identify the typical pattern of sulfonamide ADRs from literature and verify this pattern in the World Health Organization (WHO) ADR database; and (2) to examine whether these sulfonamide ADRs occur more frequently with celecoxib than with the non-sulfonamide, COX-2 inhibitor rofecoxib.Methods: A sulfonamide ADR pattern was derived from the most extensive textbook source of ADRs and applied to the WHO database for the three groups of sulfonamide drugs: short- and intermediate-acting sulfonamides, and sulfasalazine. ADRs reported three or more times for each of these groups were included in a ‘sulfonamide template’ comprising 19 ADRs relating to the skin the blood the liver and anaphylaxis. This template was then applied to celecoxib and rofecoxib.Results: Overall, the relative reporting rate of a sulfonamide-type ADR with celecoxib was 80% higher than with rofecoxib, whether this was based on total number of reports (RR 1.8, 95% CI 1.6-1.9) or restricted to reports that listed coxibs as the sole suspected drugs (RR 1.8, 95% CI 1.6-1.9). There were numerically more ADRs for celecoxib than for rofecoxib in 15 of the 19 terms. Within the ADRs in the sulfonamide template, relative reporting rate of fatal reactions was 80% higher with celecoxib (RR 1.8, 95% CI 0.9-4.0). Even though serious sulfonamide reactions are rare, their clinical impact on patient safety warrants close monitoring as more data becomes available. Physicians should be aware of possible sulfonamide allergy when prescribing celecoxib.
Prevention of Apoptosis by a Baculovirus Gene During Infection of Insect Cells (1991)

Programmed cell death is an active process of self destruction that is important in both the development and maintenance of multicellular animals. The molecular mechanisms controlling activation or suppression of programmed cell death are largely unknown. Apoptosis, a morphologically and biochemically defined type of programmed cell death commonly seen in vertebrates, was found to be initiated during baculovirus replication in insect cells. A specific viral gene product, p35, was identified as being responsible for blocking the apoptotic response. Identification of the function of this gene will allow further definition of the molecular pathways involved in the regulation of programmed cell death and may identify the role of apoptosis in invertebrate viral defense systems.
Microfabricated Implantable Parylene-Based Wireless Passive Intraocular Pressure Sensors (2008)

This paper presents an implantable parylene-based wireless pressure sensor for biomedical pressure sensing applications specifically designed for continuous intraocular pressure (IOP) monitoring in glaucoma patients. It has an electrical <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LC</i> tank resonant circuit formed by an integrated capacitor and an inductor coil to facilitate passive wireless sensing using an external interrogating coil connected to a readout unit. Two surface-micromachined sensor designs incorporating variable capacitor and variable capacitor/inductor resonant circuits have been implemented to realize the pressure-sensitive components. The sensor is monolithically microfabricated by exploiting parylene as a biocompatible structural material in a suitable form factor for minimally invasive intraocular implantation. Pressure responses of the microsensor have been characterized to demonstrate its high pressure sensitivity ( > 7000 ppm/mmHg) in both sensor designs, which confirms the feasibility of pressure sensing with smaller than 1 mmHg of resolution for practical biomedical applications. A six-month animal study verifies the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">in</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">vivo</i> bioefficacy and biostability of the implant in the intraocular environment with no surgical or postoperative complications. Preliminary <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ex</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">vivo</i> experimental results verify the IOP sensing feasibility of such device. This sensor will ultimately be implanted at the pars plana or on the iris of the eye to fulfill continuous, convenient, direct, and faithful IOP monitoring.[2008-0111].
Purification and properties of the hydroxylase component of methane monooxygenase (1987)

Methane monooxygenase from Methylobacterium sp. strain CRL-26 which catalyzes the oxygenation of hydrocarbons was resolved into two components, a hydroxylase and a flavoprotein. An anaerobic procedure was developed for the purification of the hydroxylase to homogeneity. The molecular weight of the hydroxylase as determined by gel filtration was 220,000, and that determined by sedimentation equilibrium analysis was about 225,000. The purified hydroxylase contained three nonidentical subunits with molecular weights of about 55,000, 40,000, and 20,000, in equal amounts as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, indicating that it is an alpha 2 beta 2 gamma 2 protein. Optical absorption spectra revealed peaks near 408 and 280 nm, and fluorescence spectra revealed emission peaks at 490 and 630 nm. The purified hydroxylase contained 2.8 +/- 0.2 mol of iron and 0.5 +/- 0.1 mol of zinc per mol of protein but negligible amounts of acid-labile sulfide. The antisera prepared against the hydroxylase showed cross-reactivity with hydroxylase components in soluble extracts from other methanotrophs.