gebhart/patrepeval huggingface dataset:
Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3 (2017)

Thousands of long noncoding RNAs (lncRNAs) have been discovered, yet the function of the vast majority remains unclear. Here, we show that a p53-regulated lncRNA which we named <i>PINCR</i> (p53-induced noncoding RNA), is induced ~100-fold after DNA damage and exerts a prosurvival function in human colorectal cancer cells (CRC) <i>in vitro</i> and tumor growth <i>in vivo</i>. Targeted deletion of <i>PINCR</i> in CRC cells significantly impaired G1 arrest and induced hypersensitivity to chemotherapeutic drugs. <i>PINCR</i> regulates the induction of a subset of p53 targets involved in G1 arrest and apoptosis, including <i>BTG2, RRM2B</i> and <i>GPX1</i>. Using a novel RNA pulldown approach that utilized endogenous S1-tagged <i>PINCR</i>, we show that <i>PINCR</i> associates with the enhancer region of these genes by binding to RNA-binding protein Matrin 3 that, in turn, associates with p53. Our findings uncover a critical prosurvival function of a p53/<i>PINCR</i>/Matrin 3 axis in response to DNA damage in CRC cells.
Differences in CD33 Intensity Between Various Myeloid Neoplasms (2002)

We measured the concentration of CD33 antigen on the surface of cells in 315 bone marrow (BM) samples and 114 corresponding peripheral blood (PB) samples from patients with various leukemias (acute myeloid leukemia [AML], chronic myelogenous leukemia [CML], myeloproliferative disorder [MPD] other than CML, myelodysplastic syndrome [MDS]) and from control subjects. Overall CD33 intensity in total CD33+ cells was significantly higher in BM than in PB. CD33 intensity in total BM CD33+ cells differed significantly with the type of disease. The median number of CD33 molecules per cell was highest in AML, followed by MDS, CML, and control subjects and lowest in MPD. When only CD34+/CD33+ cells were examined, CD33 molecules per cell were highest in CD34+ cells in AML and lowest in MPD (P = .027). Patients with AML or MDS younger than 60 years had significantly higher intensity of CD33 expression on CD34+ cells than patients 60 years or older. Levels of CD33 intensity did not correlate with cytogenetics in patients with AML or MDS. There was no correlation between CD33 intensity and response to therapy or overall survival in 35 patients treated with protocols including Mylotarg. These data demonstrate variation in CD33 intensity between various leukemias.
Resistance to Parvovirus B19 Infection Due to Lack of Virus Receptor (Erythrocyte P Antigen) (1994)

People who do not have P antigen, which is the cellular receptor for parvovirus B19, are naturally resistant to infection with this pathogen.
Permethrin Induces Overexpression of Cytochrome c Oxidase Subunit 3 in <I>Aedes aegypti</I> (2009)

Using quantitative polymerase chain reaction (QPCR), the relative transcriptional levels of cytochrome c oxidase subunit 3 (CO3) were studied in Aedes aegypti in response to treatment with acetone, permethrin, and fipronil. The transcriptional levels of CO3 were significantly (P < 0.05) higher in acetone-treated Ae. aegypti compared with that in untreated samples. Using ribosomal L24, heat shock protein (HSP), and actin as reference genes, relative transcription levels of CO3 in acetone-treated Ae. aegypti were 2.88 +/- 0.38-, 2.60 +/- 0.60-, and 3.24 +/- 0.70-fold higher, respectively, compared with that in untreated mosquitoes. Transcriptional levels of CO3 were induced significantly higher (6.54 +/- 1.22-, 4.62 +/- 0.74-, and 9.47 +/- 3.71-fold, respectively) by permethrin at LD10 compared with acetone (P < 0.05). Taken together, our results suggest that overexpression of CO3 is tightly regulated in Ae. aegypti in response to xenobiotic treatment.
Programmed and Magnet-Induced Vagus Nerve Stimulation for Refractory Epilepsy (2001)

Vagus nerve stimulation (VNS) is an effective alternative treatment for patients with refractory epilepsy. The generator produces intermittent stimulation trains and does not require patient intervention. Using currently available technology, continuous stimulation is incompatible with a reasonable battery life. Because earlier studies have demonstrated the persistence of a stimulation effect after discontinuation of the stimulation train, we intended to evaluate the clinical efficacy of VNS in both the programmed intermittent stimulation mode and the magnet stimulation mode. Patients, companions, and caregivers were instructed on how to administer additional stimulation trains when an aura or a seizure onset occurred. We assumed that patients or caregivers could recognize habitual seizures and were able to evaluate sudden interruption of these seizures. During a mean follow-up of 35 months, 46% of patients became responders, with a reduction in seizure frequency of more than 50%. Twenty-nine percent of patients stopped having convulsive seizures. In two thirds of patients who were able to self-administer or receive additional magnet stimulation, seizures could be interrupted consistently or occasionally. More than half of the patients who reported a positive effect of magnet stimulation became responders. Only three patients were able to use the magnet themselves. In most cases, support from caregivers was necessary. This study is the first to document the efficacy of magnet-induced VNS in a larger patient population during long-term follow-up. The magnet is a useful tool that provides patients who are treated with VNS and mainly caregivers of such patients with an additional means of controlling seizures. To further confirm the self-reported results from our patients, additional studies comparing programmed stimulation and magnet-induced stimulation during monitoring conditions are needed.
Dependence of emission wavelength on cavity length and facet reflectivities in multiple quantum well semiconductor lasers (1989)

The spectral emission characteristics of multiple quantum well semiconductor lasers of the Fabry–Perot type are a strong function of laser cavity length and mirror reflectivities. 15 nm theoretically predicted wavelength shifts were validated experimentally. This has immediate applications in the development of semiconductor laser-pumped solid-state lasers, where accurate control of the semiconductor laser pump spectral emission is essential.
Identification of New Nonrandom Translocations in Multiple Myeloma With Multicolor Spectral Karyotyping (1998)

Abstract Multicolor spectral karyotyping (SKY) was performed on bone marrow samples from 50 patients with multiple myeloma (MM) in anticipation of discovering new previously unidentified translocations. All samples showed complex karyotypes with chromosome aberrations which, in most cases, were not fully characterized by G-banding. Patients of special interest were those who showed add(14)(q32), add(8)(q24) and those whose G-banding karyotypes showed poor chromosome morphology. Three new recurring chromosome translocations not previously reported in MM were identified. Two of the translocations involve recurring aberrations at band 14q32.3, the site of the IgH locus, with different exchange partners. The most frequently recurring rearrangement was a subtle translocation at 14q32.3 designated as a t(14;16)(q32;q22∼23), which was identified in six patients. A second and larger translocation at 14q32, identified in two patients, was designated as a t(9;14)(p13;q32), previously associated with Waldenstrom’s macroglobulinemia and lymphoplasmacytoid lymphoma. A third translocation, identified in two patients, involved a whole-arm t(6;8)(p10;q10) translocation. The SKY technique was able to refine the designations of over 156 aberrations not fully characterized by G-banding in this study and resolved additional chromosome aberrations in every patient studied except two. The t(14;16)(q32;q22∼23) identified by SKY in this study suggests this may be a frequent translocation in MM associated with complex karyotypes and disease progression. Therefore, the SKY technique provides a useful adjunct to routine G-banding and fluorescence in situ hybridization studies in the cytogenetic analysis of MM.
Kinetic Template‐Guided Tethering of Fragments (2012)

Birds of a tether: A tethering strategy for the site-directed discovery of low-molecular-weight fragments that bind weakly to defined protein surfaces is described. A solvent-exposed protein thiol captures acrylamide-modified fragments in a conjugate addition reaction that requires a template to produce a measureable quantity of protein-fragment adduct, which can be rapidly identified by mass spectrometry.
Associations Between Liver Histology and Severity of the Metabolic Syndrome in Subjects With Nonalcoholic Fatty Liver Disease (2005)

Nonalcoholic fatty liver disease (NAFLD) is associated with a histopathological picture resembling alcohol-induced liver injury occurring in subjects who consume insignificant amounts of alcohol. In NAFLD, steatosis alone is associated with good prognosis, whereas nonalcoholic steatohepatitis (NASH) can progress to fibrosis and cirrhosis in up to 30% of cases, potentially leading to liver failure and hepatocellular carcinoma. The prevalence of NAFLD and NASH in the U.S. is estimated at 10–20 and 2–3%, respectively (1,2,3).

The metabolic syndrome, as defined by Adult Treatment Panel (ATP) III criteria, incorporates features known to predict cardiovascular disease and type 2 diabetes (4). NAFLD has been demonstrated to be associated with features of the metabolic syndrome, including hyperglycemia (5,6), dyslipidemia (5,6), hypertension (7), and central obesity (7,8). In addition, insulin resistance, even without these other features, is almost universal in subjects with NAFLD (6). However, the factors specifically associated with hepatic inflammation, fibrosis, and thus liver disease progression are still being elucidated.

In this study of human subjects with NAFLD, we explored specific relationships between hepatic histology and markers of the metabolic syndrome.

Forty-six subjects with NAFLD were recruited from clinics. The diagnosis was based on the histological presence of macrovesicular steatosis, with or without lobular inflammation, hepatocellular degeneration, or fibrosis (8,9). All subjects …
Chemokines (2004)

Understanding the increasingly complex role of chemokines in various manifestations of atherosclerotic vascular disease and the apparent redundancy in their expression requires improved concepts defining the specialization and cooperation of chemokines in regulating the recruitment of mononuclear cells to vascular lesions. In an attempt to elaborate such models, this review highlights recent insights into the functional role of chemokines in mediating distinct steps during the atherogenic recruitment of monocytes and T cells obtained in genetically deficient mice and in suitable models. A particular focus is placed on the contribution of platelet chemokines deposited on endothelium for monocyte arrest, on differences in the involvement of chemokines between recruitment to native lesions and to neointimal lesions after arterial injury, and on closely related functions of macrophage migration inhibitory factor, a cytokine with considerable structural homology to chemokines. As an evolving aspect of atherosclerotic vascular disease, a role of chemokines, foremost stromal cell-derived factor-1alpha, in the recruitment of mononuclear progenitors of vascular cells during neointimal hyperplasia, endothelial recovery, and angiogenesis is discussed. The functional diversity and pleiotropy of chemokines in and beyond mononuclear cell recruitment awaits further elucidation to enable therapeutic targeting of atherogenesis by context-specific blockade of nonoverlapping chemokine receptor pairs.
Immunodeficient Animals: Models for Cancer Research (1996)

The classic immunodeficient mutants nude, scid and rnu have an important function in experimental cancer research: they allow unique methods of investigation and provide data of clinical relevance. This volume presents the state of the art of research work based on the use of these immunodeficient animal models. One section is dedicated to the biol
[Study of deletion of derivative chromosome 9 in patients with Ph+ chronic myeloid leukemia]. (2006)

Deletion of der(9) is seen in about 1/6 of Ph+ CML patients in our study on Chinese CML patients, Ph+ CML patients with the deletion have shorter median survival time than those without it, indicating that it is a poor prognostic index.
An mRNA Stability Complex Functions with Poly(A)-Binding Protein To Stabilize mRNA In Vitro (1999)

The stable globin mRNAs provide an ideal system for studying the mechanism governing mammalian mRNA turnover. alpha-Globin mRNA stability is dictated by sequences in the 3' untranslated region (3'UTR) which form a specific ribonucleoprotein complex (alpha-complex) whose presence correlates with mRNA stability. One of the major protein components within this complex is a family of two polycytidylate-binding proteins, alphaCP1 and alphaCP2. Using an in vitro-transcribed and polyadenylated alpha-globin 3'UTR, we have devised an in vitro mRNA decay assay which reproduces the alpha-complex-dependent mRNA stability observed in cells. Incubation of the RNA with erythroleukemia K562 cytosolic extract results in deadenylation with distinct intermediates containing a periodicity of approximately 30 nucleotides, which is consistent with the binding of poly(A)-binding protein (PABP) monomers. Disruption of the alpha-complex by sequestration of alphaCP1 and alphaCP2 enhances deadenylation and decay of the mRNA, while reconstitution of the alpha-complex stabilizes the mRNA. Similarly, PABP is also essential for the stability of mRNA in vitro, since rapid deadenylation resulted upon its depletion. An RNA-dependent interaction between alphaCP1 and alphaCP2 with PABP suggests that the alpha-complex can directly interact with PABP. Therefore, the alpha-complex is an mRNA stability complex in vitro which could function at least in part by interacting with PABP.
ChemInform Abstract: Reduction of Hydrated Ruthenium(III) Chloride with Zinc in the Presence of Cyclooctadiene: Molecular Structure of Ru(C8H10)(C8H12) and Isolation and X‐Ray Structural Characterization of Ru2Cl4(C8H12)2, RuH(C8H11)(C6H6) and Ru3Cl3(OCH3)(C8H12)3. (1990)

Abstract The (η4‐cyclooctadiene)(η6‐cyclooctatriene)‐Ru (III) (space group Pna21, Z=4) is isolated as the main product of the title reduction.
Integration of Substation Data (2007)

The paper introduces a concept for integration of substation IED data, primarily coming from digital protective relays (DPRs) and digital fault recorders (DFRs). Modern substations are equipped with different types of IEDs. DFRs are traditionally used to capture data from various events and disturbances in the power system that may need to be analyzed. Most of the modern IEDs such as digital relays, power quality meters, and sequence of event recorders can offer data recording function that is quite similar to that of DFRs. In some recent substation designs there are cases where DFR function is replaced by an equivalent function provided by DPRs. There are also cases when both DFRs and DPRs are used and configured to record the same events. In this case records from DPRs are used as a redundant source for event analysis. The paper addresses main requirements for integration of substation data: communication and automated IED data retrieval, unifying event data file formats, verification of event data content, and proper handling of the system configuration parameters. Examples of substation data integration using the proposed concept are discussed through expansion of an existing DFR data integration and analysis system and through introduction of data coming from different substation IEDs. Digital simulator was used to evaluate the concept in the example with multiple IED types
A Structural Basis for Substrate Specificities of Protein Ser/Thr Kinases: Primary Sequence Preference of Casein Kinases I and II, NIMA, Phosphorylase Kinase, Calmodulin-Dependent Kinase II, CDK5, and Erk1 (1996)

We have developed a method to study the primary sequence specificities of protein kinases by using an oriented degenerate peptide library. We report here the substrate specificities of eight protein Ser/Thr kinases. All of the kinases studied selected distinct optimal substrates. The identified substrate specificities of these kinases, together with known crystal structures of protein kinase A, CDK2, Erk2, twitchin, and casein kinase I, provide a structural basis for the substrate recognition of protein Ser/Thr kinases. In particular, the specific selection of amino acids at the +1 and -3 positions to the substrate serine/threonine can be rationalized on the basis of sequences of protein kinases. The identification of optimal peptide substrates of CDK5, casein kinases I and II, NIMA, calmodulin-dependent kinases, Erk1, and phosphorylase kinase makes it possible to predict the potential in vivo targets of these kinases.
Silicon CWDM Demultiplexers Using Contra-Directional Couplers (2013)

We experimentally demonstrate ultra-compact (&lt;0.008mm2), 4-channel CWDM demultiplexers using silicon photonic contra-directional couplers. Flat-top passbands of 10nm, insertion loss of lower than 1dB, and crosstalk of -20dB have been obtained.
Combination of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and actinomycin D induces apoptosis even in TRAIL-resistant human pancreatic cancer cells. (2001)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a novel member of the tumor necrosis factor superfamily of cytokines that induces cell death by apoptosis. TRAIL has been shown to be effective in almost two-thirds of solid tumors tested thus far, but its effect on pancreatic cancer cells is unknown. We tested the effect of TRAIL on seven human pancreatic cancer cell lines (HPAF, Panc1, Miapaca2, Bxpc3, Panc89, SW979, and Aspc1) in vitro. Of these cell lines, all but Aspc1 showed a significant dose-dependent increase in apoptosis. The apoptotic rate, as detected by a terminal deoxynucleotidyl transferase-mediated nick end labeling assay, was highest in Bxpc3 (71.5%), followed by HPAF (38.0%), Miapaca2 (24.9%), Panc1 (16.1%), Panc89 (15.8%), SW979 (13.9%), and Aspc1 (5.2%). Multiple treatments were more effective than a single treatment and caused a sustained and profound cell death in all but Aspc1 cells. There was no correlation between the effect of TRAIL and the differentiation grade of the cell lines, p53 mutation, or bcl-2 or bax expression. The resistance of Aspc1 cells to TRAIL was not related to the lack of TRAIL receptors. The combination of actinomycin D and TRAIL induced an almost complete lysis of Aspc1 cells, whereas actinomycin D alone had no effect on cell survival but inhibited the expression of the Flice inhibitory protein, which is assumed to play a role in the apoptotic pathway of TRAIL. Thus, the combination of actinomycin D and TRAIL appears to be a promising approach for the therapy of pancreatic cancers resistant to TRAIL.
Catalytic Amination of Alcohols, Aldehydes, and Ketones (1980)

Data on the catalytic amination of alcohols and carbonyl compounds are examined, the catalysts for these processes are described, and the problems of their effectiveness, selectivity, and stability are discussed. The possible mechanisms of the reactions indicated are presented. The bibliography includes 266 references.
POLARIMETRIC METHODS FOR MEASUREMENT OF INTRA OCULAR GLUCOSE CONCENTRATION (2002)

Due to the increasing lifespan in the industrialized world the number of senior Diabetes patients is growing rapidly. Using non-invasive techniques, measurements of the blood sugar level could be done more frequently and hence diagnosis as well as therapy of type II Diabetes Mellitus can be improved especially for this group of senior patients. Especially polarimetric techniques measuring at the human eye offer promising properties for non-invasive and painless measurement. This article discusses different approaches for utilizing the polarizing properties of the Aqueous Humour (AH) for quantitative glucose measurements.
Structure of the cleavage-activated prefusion form of the parainfluenza virus 5 fusion protein (2012)

The paramyxovirus parainfluenza virus 5 (PIV5) enters cells by fusion of the viral envelope with the plasma membrane through the concerted action of the fusion (F) protein and the receptor binding protein hemagglutinin-neuraminidase. The F protein folds initially to form a trimeric metastable prefusion form that is triggered to undergo large-scale irreversible conformational changes to form the trimeric postfusion conformation. It is thought that F refolding couples the energy released with membrane fusion. The F protein is synthesized as a precursor (F0) that must be cleaved by a host protease to form a biologically active molecule, F1,F2. Cleavage of F protein is a prerequisite for fusion and virus infectivity. Cleavage creates a new N terminus on F1 that contains a hydrophobic region, known as the FP, which intercalates target membranes during F protein refolding. The crystal structure of the soluble ectodomain of the uncleaved form of PIV5 F is known; here we report the crystal structure of the cleavage-activated prefusion form of PIV5 F. The structure shows minimal movement of the residues adjacent to the protease cleavage site. Most of the hydrophobic FP residues are buried in the uncleaved F protein, and only F103 at the newly created N terminus becomes more solvent-accessible after cleavage. The conformational freedom of the charged arginine residues that compose the protease recognition site increases on cleavage of F protein.
The Use of Cellulase in Inhibiting Biofilm Formation from Organisms Commonly Found on Medical Implants (2003)

A study was made of the use of cellulase to inhibit biofilm formation by a pathogenic bacterium commonly found in medical implants. A Pseudomonas aeruginosa biofilm was grown on glass slides in a parallel flow chamber for 4 d with glucose as the nutrient source. Biofilm development was assessed by measuring the colony forming units (CFU) and biomass areal density. Biofilm was grown at pH 5 and 7 in the presence of three different cellulase concentrations, 9.4, 37.6 and 75.2 units ml-1. In addition, a control study using deactivated cellulase was performed. The results show that cellulase is effective in partially inhibiting biomass and CFU formation by P. aeruginosa on glass surfaces. The effect of cellulase depended on concentration and was more effective at pH 5 than pH 7. The experiment was further extended by investigating the effect of cellulase on the apparent molecular weight of purified P. aeruginosa exopolysaccharides (EPS). The observation of EPS using size exclusion chromatography showed a decrease in apparent molecular weight when incubated with enzyme. An increase in the amount of reducing sugar with time when the purified EPS were incubated with enzyme also supports the hypothesis that cellulase degrades the EPS of P. aeruginosa. While cellulase does not provide total inhibition of biofilm formation, it is possible that the enzyme could be used in combination with other treatments or in combinations with other enzymes to increase effectiveness.
ChemInform Abstract: Synthesis and Biological Activity of Some O,O‐Diethyl Dithiophosphates/ Thiophosphates of 3‐Substituted 5‐Mercapto‐1,2,4‐triazoles. (1988)

Abstract The mercaptotriazoles (I) are coupled with the chlorophosphates (II) to form the esters (III).