gebhart/patrepeval huggingface dataset:
Expression of Multidrug Resistance Gene in Human Cancers (1989)

Many cancers have been cured by chemotherapeutic agents. However, other cancers are intrinsically drug resistant, and some acquire resistance following chemotherapy. Cloning of the cDNA for the human MDR1 gene (also known as PGY1), which encodes the multidrug efflux protein P-glycoprotein, has made it possible to measure levels of MDR1 RNA in human cancers. We report the levels of MDR1 RNA in greater than 400 human cancers. MDR1 RNA levels were usually elevated in untreated, intrinsically drug-resistant tumors, including those derived from the colon, kidney, adrenal gland, liver, and pancreas, as well as in carcinoid tumors, chronic myelogenous leukemia in blast crisis, and cell lines of non-small cell carcinoma of the lung (NSCLC) with neuroendocrine properties. MDR1 RNA levels were occasionally elevated in other untreated cancers, including neuroblastoma, acute lymphocytic leukemia (ALL) in adults, acute nonlymphocytic leukemia (ANLL) in adults, and indolent non-Hodgkin's lymphoma. MDR1 RNA levels were also increased in some cancers at relapse after chemotherapy, including ALL, ANLL, breast cancer, neuroblastoma, pheochromocytoma, and nodular, poorly differentiated lymphoma. Many types of drug-sensitive and drug-resistant tumors, including NSCLC and melanoma, contained undetectable or low levels of MDR1 RNA. The consistent association of MDR1 expression with several intrinsically resistant cancers and the increased expression of the MDR1 gene in certain cancers with acquired drug resistance indicate that the MDR1 gene contributes to multidrug resistance in many human cancers. Thus, evaluation of MDR1 gene expression may prove to be a valuable tool in the identification of individuals whose cancers are resistant to specific agents. The information may be useful in designing or altering chemotherapeutic protocols in these patients.
Comprehensive metabolic profiling of mono‐ and polyglutamated folates and their precursors in plant and animal tissue using liquid chromatography/negative ion electrospray ionisation tandem mass spectrometry (2005)

This work reports the use of reversed-phase ion-pair chromatography coupled to electrospray ionisation mass spectrometry for the simultaneous profiling of folate-based metabolites including natural folates, their polyglutamatyl derivatives and their biosynthetic precursors in plant and animal tissue. A simple sample preparation method, using 0.1% citric acid and ascorbic acid in ice-cold methanol, was used to extract and stabilise the folates, and three internal standards were used. Chromatography was on a C18 column using slow gradient elution with a mobile phase consisting of methanol/water with 5 mM dimethylhexylamine. Mass spectrometric detection was performed by multiple reaction monitoring in seven separate time windows in negative ion mode over the 25 min run time. Full, quantitative analysis was obtained for 16 folates and a 'semi-quantitative' analysis was possible for all other folates with up to eight conjugated glutamate residues by reference to structurally related calibration standards. The precision, accuracy and recovery of the method were generally within the accepted guidelines for a quantitative bioanalytical method and the method was linear over the range 0.2 to 10 ng of individual folate per sample. The method was applied to profile mono- and polyglutamated tetrahydrofolates (including subcellular analysis) in a range of plant species, including Arabidopsis, spinach, Brassica and wheat; the technique was also successfully applied to the profiling of folates in mouse tissue.
The Repulsive Guidance Molecule RGMa Is Involved in the Formation of Afferent Connections in the Dentate Gyrus (2004)

In the developing dentate gyrus, afferent fiber projections terminate in distinct laminas. This relies on an accurately regulated spatiotemporal network of guidance molecules. Here, we have analyzed the functional role of the glycosylphosphatidylinositol (GPI)-anchored repulsive guidance molecule RGMa. In situ hybridization in embryonic and postnatal brain showed expression of RGMa in the cornu ammonis and hilus of the hippocampus. In the dentate gyrus, RGM immunostaining was confined to the inner molecular layer, whereas the outer molecular layers targeted by entorhinal fibers remained free. To test the repulsive capacity of RGMa, different setups were used: the stripe and explant outgrowth assays with recombinant RGMa, and entorhino-hippocampal cocultures incubated either with a neutralizing RGMa antibody (Ab) or with the GPI anchor-digesting drug phosphatidylinositol-specific phospholipase C. Entorhinal axons were clearly repelled by RGMa in the stripe and outgrowth assays. After disrupting the RGMa function, the specific laminar termination pattern in entorhino-hippocampal cocultures was lost, and entorhinal axons entered inappropriate hippocampal areas. Our data indicate an important role of RGMa for the layer-specific termination of the perforant pathway as a repulsive signal that compels entorhinal fibers to stay in their correct target zone.
A Rudimentary Quantum Compiler (1998)

We present a new algorithm for reducing an arbitrary unitary matrix into a sequence of elementary operations (operations such as controlled-nots and qubit rotations). Such a sequence of operations can be used to manipulate an array of quantum bits (i.e., a quantum computer). We report on a C++ program called "Qubiter" that implements our algorithm. Qubiter source code is publicly available.
Elevated body swing test: a new behavioral parameter for rats with 6- hydroxydopamine-induced hemiparkinsonism (1995)

Parkinson's disease is characterized by a depletion of dopamine (DA) neurons in the nigrostriatal pathway. Stereotaxic injections of 6-hydroxydopamine (6-OHDA), a selective neurotoxin, into either the medial forebrain bundle or the substantia nigra result in a massive DA denervation of the nigrostriatal pathway. Following unilateral nigrostriatal DA depletion, hemiparkinsonian animals develop a stereotypical rotational behavior when challenged with DA agonists such as apomorphine. The drug-induced rotational behavior has been widely used as the behavioral index of hemiparkinsonian animals, but it has some limitations. Although asymmetries in the rotational behavior may indicate an imbalance of DA contents and release capacity in the bilateral nigrostriatal pathway, the behavior is a pharmacological reaction. Accordingly, the drug-induced rotation test is subject to sensitization effects. The present study proposes the elevated body swing test (EBST) as a measure of asymmetrical motor behavior of hemiparkinsonian animals in a drug-free state. The EBST simply involves elevating the animal by handling its tail and recording the frequency and direction of the swing behavior. Unilateral nigral 6-OHDA-lesioned rats exhibited significant biased swing activity with the direction contralateral to the lesioned side, corresponding to the direction of apomorphine-induced rotations. A 30 sec EBST was noted as the peak time for biased swing activity. At 7 d postlesion (the start of testing), and every week thereafter for a period of 2 months, a fairly stable biased swing activity level was observed. At 1 and 2 months postlesion, the same animals were also challenged with apomorphine.(ABSTRACT TRUNCATED AT 250 WORDS)
Endogenous Nitric Oxide and Myocardial Adaptation to Ischemia (2000)

Ischemic myocardium does not inevitably undergo necrosis but rather can survive through downregulation of contractile function, ie, "hibernate." To study the role of endogenous NO in this adaptation, 41 enflurane-anesthetized swine were subjected to 90 minutes of moderate left anterior descending coronary artery hypoperfusion and assigned to placebo (P), to 30 mg/kg N(G)-nitro-L-arginine (L-NNA) IV to inhibit NO synthase, or to aortic constriction (AO) to match the increased left ventricular pressure observed with L-NNA. During normoperfusion, a regional myocardial external work index (WI, mm Hg. mm, sonomicrometry and micromanometry) was reduced with L-NNA (from 326+/-27 [SEM] to 250+/-19, P<0.05) but increased with AO (from 321+/-16 to 363+/-19, P<0.05 versus L-NNA). At 10 minutes of ischemia, WI was lower with L-NNA (109+/-10, P<0.05) than P (180+/-22) and AO (170+/-11) and did not change further at 85 minutes of ischemia. Relationships between WI and transmural myocardial blood flow and oxygen consumption were shifted rightward by L-NNA versus P and AO at both 10 and 85 minutes of ischemia. The maximal increment in calcium-activated external work was not different during normoperfusion among groups but was decreased during ischemia with L-NNA. L-NNA transiently increased myocardial contractile calcium sensitivity along with systemic pressure but reduced it during ongoing ischemia. The free-energy change of ATP hydrolysis after an early ischemic decrease recovered toward baseline values in all groups, and necrosis was absent after 2 (triphenyltetrazolium chloride staining) or 8 (histology) hours of reperfusion. Thus, endogenous NO contributes to hibernation by reducing oxygen consumption and preserving calcium sensitivity and contractile function without an energy cost during ischemia.
Expression of GP73, a resident Golgi membrane protein, in viral and nonviral liver disease (2002)

GP73 is a novel type II Golgi membrane protein of unknown function that is expressed in the hepatocytes of patients with adult giant-cell hepatitis (Gene 2000;249:53-65). Its expression pattern in human liver disease and the regulation of its expression in hepatocytes have not been systematically studied. The aims of the present study were to compare GP73 protein levels in viral and nonviral human liver disease and in normal livers, to identify its cellular sources, and to study the regulation of its expression in hepatoma cells in vitro. GP73 protein levels were quantitated in explant livers of patients with well-defined disease etiologies and compared with the levels in normal donor livers. GP73-expressing cells were identified immunohistochemically. GP73 expression in vitro was studied by Western blotting and immunofluorescence microscopy in HepG2 and SK-Hep-1 cells and in the HepG2-derived, hepatitis B virus (HBV)-transfected HepG2215 and HepG2T14.1 cell lines. Whole organ levels of GP73 were low in normal livers. Significant increases were found in liver disease due to viral causes (HBV, HCV) or nonviral causes (alcohol-induced liver disease, autoimmune hepatitis). In normal livers, GP73 was constitutively expressed by biliary epithelial cells but not by hepatocytes. Hepatocyte expression of GP73 was dramatically up-regulated in diseased livers, regardless of the etiology, whereas biliary epithelial cell expression did not change appreciably. GP73 was present at high levels in HepG2215 cells (a cell line that supports active HBV replication), but was absent in HepG2T14.1 cells (an HBV-transfected cell line that does not support HBV replication) and in HBV-free HepG2 cells. In SK-Hep-1 cells, GP73 expression was increased in response to interferon gamma (IFN-gamma), and inhibited by tumor necrosis factor alpha (TNF-alpha). In conclusion, increased expression of GP73 in hepatocytes appears to be a general feature of advanced liver disease, and may be regulated via distinct pathways that involve hepatotropic viruses or cytokines.
Efficient live migration of virtual machines using shared storage (2013)

Live migration of virtual machines (VM) across distinct physical hosts is an important feature of virtualization technology for maintenance, load-balancing and energy reduction, especially so for data centers operators and cluster service providers. Several techniques have been proposed to reduce the downtime of the VM being transferred, often at the expense of the total migration time. In this work, we present a technique to reduce the total time required to migrate a running VM from one host to another while keeping the downtime to a minimum. Based on the observation that modern operating systems use the better part of the physical memory to cache data from secondary storage, our technique tracks the VM's I/O operations to the network-attached storage device and maintains an updated mapping of memory pages that currently reside in identical form on the storage device. During the iterative pre-copy live migration process, instead of transferring those pages from the source to the target host, the memory-to-disk mapping is sent to the target host which then fetches the contents directly from the network-attached storage device. We have implemented our approach into the Xen hypervisor and ran a series of experiments with Linux HVM guests. On average, the presented technique shows a reduction of up over 30% on average of the total transfer time for a series of benchmarks.
Onset and quality of sedation after intramuscular administration of dexmedetomidine and hydromorphone in various muscle groups in dogs (2013)

When the combination of dexmedetomidine and hydromorphone was used to induce sedation in dogs, rapid and profound sedation was achieved with IM injection into the semimembranosus muscle.
Highly conserved and disease‐specific patterns of carboxyterminally truncated Aβ peptides 1–37/38/39 in addition to 1–40/42 in Alzheimer's disease and in patients with chronic neuroinflammation (2002)

Human lumbar CSF patterns of Abeta peptides were analysed by urea-based beta-amyloid sodium dodecyl sulphate polyacrylamide gel electrophoresis with western immunoblot (Abeta-SDS-PAGE/immunoblot). A highly conserved pattern of carboxyterminally truncated Abeta1-37/38/39 was found in addition to Abeta1-40 and Abeta1-42. Remarkably, Abeta1-38 was present at a higher concentration than Abeta1-42, being the second prominent Abeta peptide species in CSF. Patients with Alzheimer's disease (AD, n = 12) and patients with chronic inflammatory CNS disease (CID, n = 10) were differentiated by unique CSF Abeta peptide patterns from patients with other neuropsychiatric diseases (OND, n = 37). This became evident only when we investigated the amount of Abeta peptides relative to their total Abeta peptide concentration (Abeta1-x%, fractional Abeta peptide pattern), which may reflect disease-specific gamma-secretase activities. Remarkably, patients with AD and CID shared elevated Abeta1-38% values, whereas otherwise the patterns were distinct, allowing separation of AD from CID or OND patients without overlap. The presence of one or two ApoE epsilon4 alleles resulted in an overall reduction of CSF Abeta peptides, which was pronounced for Abeta1-42. The severity of dementia was significantly correlated to the fractional Abeta peptide pattern but not to the absolute Abeta peptide concentrations.
The Metabolism of trans‐Cyclohexan‐1,2‐diol by an Acinetobacter Species (1977)

Acinetobacter TD63 was one of some thirty organisms isolated by elective culture with trans ‐cyclohexan‐1,2‐diol as sole source of carbon. The great majority of these isolates displayed the same growth spectrum as Nocardia globerula CL1 and Acinetobacter NCIB 9871 being capable of utilizing trans ‐cyclohexan‐1,2‐diol, 2‐hydroxycyclohexan‐1‐one, cyclohexanol, cyclohexanone, 1‐oxa‐2‐oxocycloheptane and adipate and were assumed to use well described metabolic pathways. Acinetobacter TD63 was distinctive in being incapable of growth with cyclohexanol, cyclohexanone or 1‐oxa‐2‐oxocycloheptane and because of this it was hoped that it would display an alternative pathway for the oxidation of trans ‐cyclohexan‐1,2‐diol. Studies with cell extracts have shown the presence of inducible dehydrogenase for the conversion of trans ‐cyclohexan‐1,2‐diol to 2‐hydroxycyclohexan‐1‐one and cyclohexan‐1,2‐dione and of 6‐oxohexanoate to adipate. These enzymes are linked into a metabolic sequence by the action of a monooxygenase of broad specificity but efficiently capable of converting 2‐hydroxycyclohexan‐1‐one into the lactone 1‐oxa‐2‐oxo‐7‐hydroxycycloheptane that spontaneously rearranges to yield 6‐oxohexanoate. An enzyme capable of attacking cyclohexan‐1,2‐dione (mono‐enol) in the absence of an electron donor or oxygen has also been detected. Evidence has been presented indicating that this enzyme catalyses a keto‐enol tautomerization between cyclohexan‐1,2‐dione (mono‐enol) and cyclo‐hexan‐1,2‐dione (mono‐hydrate) and is not involved in the pathway of ring cleavage. The failure of Acinetobacter TD63 to grow with cyclohexanol, cyclohexanone or 1‐oxa‐2‐oxocycloheptane is due not to this organism possessing a distinctive metabolic sequence but to a narrow inducer specificity coupled with an inability to form a lactone hydrolase enabling it to cleave the stable 1‐oxa‐2‐oxocycloheptane which is an intermediate in the established pathway of cyclohexanol and cyclohexanone oxidation.
Gefitinib Induces Apoptosis in the EGFRL858R Non–Small-Cell Lung Cancer Cell Line H3255 (2004)

Somatic mutations in the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) have recently been described in patients with non-small-cell lung cancer (NSCLC) who achieve radiographic regressions to the EGFR inhibitor gefitinib. One of these mutations, L858R (Leu-->Arg), is also found in NSCLC cell line H3255, which is very sensitive to gefitinib treatment. We characterized nine NSCLC cell lines (three isolated from patients with bronchioloalveolar carcinoma and six isolated from patients with adenocarcinoma) for their in vitro sensitivity to gefitinib. Of these, only H3255 (EGFR(L858R)) and H1666 (EGFR(WT)) are sensitive to gefitinib with IC(50) values of 40 nmol/L and 2 micromol/L, respectively. We examined the effects of gefitinib on H3255 and cell lines containing wild-type EGFR that are either sensitive (H1666) or resistant (A549 and H441) to gefitinib exposure in vitro. Gefitinib treatment (1 micromol/L) leads to significant apoptosis accompanied by increased poly(ADP-ribose) polymerase cleavage only in the H3255 cell line, leads to G(1)-S arrest in H1666, and has no effects in the A549 and H441 cell lines. Although EGFR and AKT are constitutively phosphorylated in H3255, H1666, and H441 cell lines, AKT is completely inhibited by gefitinib treatment only in the H3255 cell line. These findings further characterize a mechanism by which gefitinib treatment of NSCLC harboring EGFR(L858R) leads to a dramatic response to gefitinib.
Down-regulation of hepcidin resulting from long-term treatment with an anti–IL-6 receptor antibody (tocilizumab) improves anemia of inflammation in multicentric Castleman disease (2010)

Dysregulated production of hepcidin is implicated in anemia of inflammation, whereas interleukin-6 (IL-6) is a major inducer of hepcidin production. Overproduction of IL-6 is responsible for pathogenesis of multicentric Castleman disease (MCD), a rare lymphoproliferative disorder accompanied by systemic inflammatory responses and anemia. In this study, we investigated the roles of hepcidin and IL-6 in anemia of inflammation and the long-term effects of anti-IL-6 receptor antibody (tocilizumab) treatment on serum hepcidin and iron-related parameters in MCD patients. We found that tocilizumab treatment resulted in a rapid reduction of serum hepcidin-25 in 5 of 6 MCD patients. Long-term reductions, accompanied by progressive normalization of iron-related parameters and symptom improvement, were observed in 9 of 9 cases 1.5, 3, 6, and 12 months after the start of tocilizumab treatment. In in vitro experiments, IL-6-induced up-regulation of hepcidin mRNA in hepatoma cell lines was completely inhibited by tocilizumab but increased in the presence of patients' sera. Our results suggest that, although multiple factors affect serum hepcidin levels, IL-6 plays an essential role in the induction of hepcidin in MCD. This accounts for the long-term ameliorative effect of IL-6 blockage with tocilizumab on anemia by inhibiting hepcidin production in MCD patients.
Studies on the Chemical and Enzymatic Modification of Glycoproteins (1971)

Abstract A general method is described for the radioactive labeling of proteins containing terminal sialic acid in the carbohydrate moieties. Quantitative conversion of these residues to a radioactive 7-carbon analogue of sialic acid was achieved by sequential periodate oxidation and tritiated borohydride reduction. Evidence is presented to establish the identity of the radioactive derivative as 5-acetamido-3, 5-dideoxy-l-arabino-2-heptulosonic acid and to indicate it as the sole site of tritium incorporation in the carbohydrate chain. Upon injection into rats, labeled preparations of ceruloplasmin and orosomucoid exhibited a normal half-life in the plasma and proved suitable for metabolic studies. The data indicate that the 7-carbon sialic acid analogue mimics sialic acid with respect to hydrolysis by neuraminidase and in regulating survival of glycoproteins in the circulation.
Sequential robust design methodology and X‐ray photoelectron spectroscopy to analyze the grafting of hyaluronic acid to glass substrates (2002)

Sequential Robust Design experiments and X-ray photoelectron spectroscopic (XPS) studies were performed to examine the immobilization of hyaluronic acid (HA) on glass substrates chemisorbed with N-(2-aminoethyl)-3-aminopropyl-trimethoxysilane (EDS). Numerous reaction conditions were investigated, including the concentrations of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC), N-hydroxysulfosuccinimide (Sulfo-NHS), and HA, and the reaction buffer type, concentration, and pH. The elemental surface compositions of carbon and silicon (C/Si ratio) were used to assess the extent of HA immobilization, leading to the identification of critical HA-binding reaction conditions and the determination of an optimum surface chemistry. The optimum chemistry consisted of 200 mM EDC, 50 mM Sulfo-NHS, 10 mM N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES) buffer at a pH of 7.0, and 3 mg/mL HA. This work emphasizes the advantages of using Robust Design methods over traditional statistical experimental design, particularly when large numbers of variables are examined and costly analytical techniques are employed.
Separation of Hydrocarbons with a Microporous Metal–Organic Framework (2005)

Separating the wheat from the chaff: The microporous metal–organic framework (MMOF) of [Cu(hfipbb)(H2hfipbb)0.5] is based on a bimetallic paddle-wheel building block and comprises 1D tubular microchannels formed by the interpenetration of two identical 44 nets. The channels are hydrophobic and have the ideal size and shape to selectively adsorb C2, C3, and n-C4 olefins and alkanes (see picture).
Polymethacrylate-Based Nitric Oxide Donors with Pendant N-Diazeniumdiolated Alkyldiamine Moieties:  Synthesis, Characterization, and Preparation of Nitric Oxide Releasing Polymeric Coatings (2005)

A series of new nitric oxide (NO) releasing copolymers have been prepared by covalently anchoring alkyldiamine side chains onto a polymethacrylate-based polymer backbone, followed by NO addition to form the desired pendant diazeniumdiolate structures. The resulting diazeniumdiolated copolymers were characterized via UV spectroscopy, and their proton-driven decomposition to release NO was also examined by UV and FTIR as well as chemiluminescence. Polymers with up to 22.1 mol % of incorporated amine sites that can be converted to corresponding diazeniumdiolates could be prepared, and such polymers release up to 0.94 micromol/mg of NO. Further, novel NO releasing polymeric coatings were formulated by doping one of the new polymethacrylate-based NO donors within inert polymeric matrixes. Biodegradable poly(lactide-co-glycolide) was employed as a film additive to greatly prolong the NO release of such coatings by continuously generating protons within the organic phase of the polymeric films, thereby driving decomposition of the diazeniumdiolates.