gebhart/patrepeval huggingface dataset:
Phytochemical studies on tobacco alkaloids XIV. The occurrence and properties of putrescine <italic>N</italic>-methyltransferase in tobacco roots (1971)

Putrescine N-methyltransferase, a new enzyme catalyzing the formation of N-methylputrescine from putrescine and S-adenosyl-L-methionine was found in roots of tobacco plants. The enzyme was purified 30-fold from crude extracts of tobacco roots. NMethylputrescine was identified as the reaction product by comparison with the authentic compound. The enzyme had a pH optimum between pH 8 and 9, and a molecular weight of about 60,000, as determined by gel filtration. Km values for putrescine and 5-adenosyl-L-methionine were 4.0 × 10−4 M and 1.1 × 10−4 M, respectively. Enzyme activity was inhibited by N-chloromercuribenzoate and Ag+. No cofactors were required. Of the various substrates tested, only putrescine served as a methyl acceptor. The enzyme was localized exclusively in the roots and its activity was gready enhanced by decapitation. The presence of putrescine N-methyltransferase in tobacco roots strongly suggests that N-methylputrescine participates as an intermediate in nicotine biosynthesis.
Oncogene swap as a novel mechanism of acquired resistance to epidermal growth factor receptor‐tyrosine kinase inhibitor in lung cancer (2016)

Mutant selective epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as rociletinib and AZD9291, are effective for tumors with T790M secondary mutation that become refractory to first-generation EGFR-TKI. However, acquired resistance to these prospective drugs is anticipated considering the high adaptability of cancer cells and the mechanisms remain largely obscure. Here, CNX-2006 (tool compound of rociletinib) resistant sublines were established by chronic exposure of HCC827EPR cells harboring exon 19 deletion and T790M to CNX-2006. Through the analyses of these resistant subclones, we identified two resistant mechanisms accompanied by MET amplification. One was bypass signaling by MET amplification in addition to T790M, which was inhibited by the combination of CNX-2006 and MET-TKI. Another was loss of amplified EGFR mutant allele including T790M while acquiring MET amplification. Interestingly, MET-TKI alone was able to overcome this resistance, suggesting that oncogenic dependence completely shifted from EGFR to MET. We propose describing this phenomenon as an "oncogene swap." Furthermore, we analyzed multiple lesions from a patient who died of acquired resistance to gefitinib, then found a clinical example of an oncogene swap in which the EGFR mutation was lost and a MET gene copy was gained. In conclusion, an "oncogene swap" from EGFR to MET is a novel resistant mechanism to the EGFR-TKI. This novel mechanism should be considered in order to avoid futile inhibition of the original oncogene.
Th1/Th2 type cytokines in hepatitis B patients treated with interferon-alpha. (2001)

The expression of Th2 type cytokines is predominant in patients with chronic hepatitis B. Interferon-alpha therapy can modulate the balance of Th1/Th2 type cytokines, and this is related to its clinical effect. Levels of Th1/Th2 type cytokines could be a predictor of clinical response during Interferon-alpha treatment.
Detection of antibody IgG to HIV‐1 in urine by sensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) using recombinant proteins as antigens for diagnosis of HIV‐1 infection (1993)

Anti-HIV-1 IgG in urine was detected by an ultrasensitive enzyme immunoassay (immune complex transfer enzyme immunoassay) using recombinant p24 gag protein (p24) of HIV-1 as antigen and beta-D-galactosidase from Escherichia coli as label. Anti-HIV-1 IgG in urine was reacted simultaneously with 2,4-dinitrophenyl-bovine serum albumin-recombinant p24 conjugate and recombinant p24-beta-D-galactosidase conjugate. The complex formed, consisting of the three components, was trapped onto polystyrene balls coated with affinity-purified (anti-2,4-dinitrophenyl group) IgG, eluted with epsilon N-2,4-dinitrophenyl-L-lysine, and transferred to polystyrene balls coated with affinity-purified (anti-human IgG gamma-chain) IgG. Bound beta-D-galactosidase activity was assayed by fluorometry. This assay was at least 3,000-fold more sensitive than conventional methods. The lowest signal among 49 asymptomatic carriers was 3.1-fold higher than the highest nonspecific signal among 100 seronegative subjects. The sensitivity and specificity were both 100%. The positivity could be confirmed by preincubation of urine samples with excess of the antigen. Thus, this assay would be a powerful tool for detecting IgG antibody to HIV-1 in urine.
Identification of a neurite outgrowth‐promoting domain of laminin using synthetic peptides (1989)

We have identified a synthetic peptide derived from the B2-chain of mouse laminin, Arg-Asn-Ile-Ala-Glu-Ile-Ile-Lys-Asp-Ile (p20), which stimulates the neurite outgrowth-promoting activity of the native molecule. In organotypic cultures, neurons from newborn mouse brain or embryonic peripheral nervous system responded by extensive neurite outgrowth for native laminin or the peptide p20 in the culture medium. If rat cerebellar neurons were grown on laminin, 1-5 microM (1-5 micrograms/ml) of peptide p20 in the culture medium competed with laminin and inhibited neuronal attachment and neurite outgrowth, whereas higher concentrations (greater than 50 microM; greater than 50 micrograms/ml) had a specific neurotoxic effect. When peptide p20 was used as the culture substratum, neurite outgrowth in cerebellar cultures was up to 60% of that seen on native laminin. Our results indicate that a neurite outgrowth-promoting domain of laminin is located in the alpha-helical region of the B2-chain, and is active for both central and peripheral neurons.
Uniqueness and wavelength optimization in continuous-wave multispectral diffuse optical tomography (2003)

We derive conditions for the unique and simultaneous recovery of chromophore concentrations and scattering coefficients in multispectral continuous-wave diffuse optical tomography. These conditions depend strongly on measurement wavelengths. We introduce and demonstrate a general methodology for choosing those wavelengths, which yields superior separation of scattering from absorption and superior separation of one chromophore from another. Application of these concepts should significantly improve the fidelity of continuous-wave diffuse near-infrared optical tomography in tissues.
Self-expandable stainless steel braided endoprosthesis for biliary strictures. (1990)

A new type of biliary stent was inserted in 45 patients with symptomatic biliary strictures, 40 malignant and five benign. The stent is made of stainless steel woven into a tubular mesh. It is introduced in compressed form on a 7- or 9-F delivery catheter and released at the site of the stricture. Fully open, the stent has an internal diameter of 1 cm. The 30-day mortality was 7%. The early (less than 72 hours) complication rate was 16%. Recurrent jaundice occurred in 42%; late complications of sepsis without jaundice occurred in an additional 11%. None of the stents migrated. This new design allows a large-diameter stent to be inserted percutaneously without increased risk of complications. The frequency of recurrent jaundice, however, was not less than that observed with plastic stents, but this may have reflected the spectrum of patients treated, many with hilar strictures and previous interventions.
The contact system contributes to hypotension but not disseminated intravascular coagulation in lethal bacteremia. In vivo use of a monoclonal anti-factor XII antibody to block contact activation in baboons. (1993)

The hypotension and disseminated intravascular coagulation (DIC) in bacteremia is thought to be mediated by the combined actions of cytokines, prostaglandins, and complement. The contact system, via the release of bradykinin and the activation of Factor XI, has been postulated to be contributing to the observed hypotension and DIC. Using a mAb to Factor XII (C6B7), we blocked the activation of the contact system in an established experimental baboon model in which Escherichia coli was infused to produce lethal bacteremia with hypotension. The untreated group (n = 5) displayed contact activation, manifested by a significant decrease in high molecular weight kininogen (HK) and a significant increase in alpha 2 macroglobulin-kallikrein complexes (alpha 2M-Kal). The C6B7-treated group (n = 5) showed an inactivation of Factor XII and the changes in HK and alpha 2M-Kal complexes were prevented. Both groups developed DIC manifested by a decrease in platelet, fibrinogen, and Factor V levels. The untreated group developed irreversible hypotension. The treated group experienced an initial hypotension that was reversed and extended the life of the animals. This study suggests that irreversible hypotension correlates with prolonged activation of the contact system, and specific antibody therapy can modulate both the pathophysiological and biochemical changes.
Optical Cosine Transform Using Microlens Array and Phase-Conjugate Mirror (1992)

An optical cosine transform system is designed using microlens array and phase-conjugate mirror. It can perform segmented cosine transform fulfilling the specification laid down by the CCITT H.261 recommendation on video audiovisual services. Design considerations and system sensitivity analysis will be presented.
Pervasive CpG suppression in animal mitochondrial genomes. (1994)

All available complete mitochondrial genomes (21 species) are evaluated for dinucleotide over- and under-representation. The CpG dinucleotide is pervasively under-represented in all animal mitochondria, but it is of variable relative abundance in fungal, protist, and plant mitochondrial genomes. Interpretations and hypotheses are considered relative to mitochondrial genome organization, methylation, structural specificities, directed mutation, and evolutionary events. In particular, our results support Mycoplasma capricolum or a close relative as the most likely bacterial ancestor of the mitochondria.
Induction of classical transplantation tolerance in the adult. (1989)

Transplantation tolerance across histoincompatibilities in multiple non-H-2 minors (B10.BR into CBA/Ca) and "minor" plus H-2D (B10.A into CBA/Ca) antigens has been achieved successfully by combined adult bone marrow transplantation and treatment with CD4 and CD8 mAbs. The tolerant state was confirmed by permanent acceptance of donor strain skin grafts, and in vitro unresponsiveness to donor cells. Tolerance was associated with partial donor chimerism to various degrees. Tolerance to minor transplantation antigens induced in this manner was restricted to recipient-type MHC. The possibility was raised that tolerance resulted, at least in part, from clonal anergy rather than deletion.
Enhanced in vivo delivery of antisense oligonucleotides to restore dystrophin expression in adult mdx mouse muscle (2003)

The use of antisense oligonucleotides (AOs) to induce exon skipping leading to generation of an in-frame dystrophin protein product could be of benefit in around 70% of Duchenne muscular dystrophy patients. We describe the use of hyaluronidase enhanced electrotransfer to deliver uncomplexed 2'-O-methyl modified phosphorothioate AO to adult dystrophic mouse muscle, resulting in dystrophin expression in 20-30% of fibres in tibialis anterior muscle after a single injection. Although expression was transient, many of the corrected fibres initially showed levels of dystrophin expression well above the 20% of endogenous previously shown to be necessary for phenotypic correction of the dystrophic phenotype.
Association of an Interleukin-1β Genetic Polymorphism With Altered Brain Structure in Patients With Schizophrenia (2001)

The data suggest that allele 2 within the promoter region of the interleukin-1beta gene at position -511 contributes to structural brain alterations in patients with schizophrenia.
TFSOI BiCMOS technology for low power applications (2002)

A thin film silicon on insulator BiCMOS technology has been developed for low power applications. The technology is based on a manufacturable, near-fully-depleted 0.5 /spl mu/m CMOS process with the lateral bipolar device integrated as a drop-in module for BiCMOS circuits. The bipolar device structure emphasizes use of a silicided polysilicon base contact to reduce base resistance and minimize current crowding effects. A split-oxide spacer integration is used to define the bipolar base and emitter widths independently. Low current ECL gate speeds up to 2/spl times/ faster than bulk double-polysilicon self-aligned bipolar circuits have been demonstrated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Free-Probe Fluorescence of Light-up Probes (2001)

The fluorescence enhancement of light-up probes (thiazole orange (TO) conjugated peptide nucleic acids (PNAs)) upon hybridization to target nucleic acid depends on the probe sequence, mainly due to large variations in free-probe fluorescence. Here we study three probes where the fluorescence in free state varies more than 50-fold. We find that this variation is due to a fraction that has TO intramolecularly "back-bound" to the PNA bases. The intramolecular affinity constant for this unimolecular interaction was determined by temperature titrations using absorption spectroscopy, and the fluorescence quantum yields of the probes in back-bound conformation were calculated. The molar ratio of probes in back-bound conformation was 0.70-0.96 at 30 degrees C and 0.40-0.73 at 60 degrees C, and the fluorescence quantum yield in back-bound conformation varied between 0.0020 and 0.077 at 30 degrees C, and 0.00065-0.029 at 60 degrees C. These data show that the variation in free-probe fluorescence depends mainly on the fluorescence quantum yield of the probe in back-bound conformation and to a much lesser extent on the tendency of the probe to adopt the back-bound conformation. With increasing temperature the free-probe fluorescence decreases owing to both reduced degree of back-binding and a decrease of the fluorescence quantum yield in back-bound conformation.
Can human hematopoietic stem cells be cultured ex vivo? (1994)

The factors that induce proliferation of the human hematopoietic stem cell are ill defined. Further characterization of such growth factors will be needed to develop ex vivo culture systems that induce prolonged proliferation and expansion of human hematopoietic stem cells. Human or murine hematopoietic progenitors that can initiate and sustain long-term culture systems (LTC-IC) represent a population of very primitive hematopoietic progenitors. When cultured in direct contact with stromal layers, we and others have demonstrated that a fraction of such LTC-IC can be maintained. In addition, stroma-free long-term cultures supplemented with two to nine cytokines can induce proliferation and differentiation of immature human hematopoietic progenitors. However, 70–90% of primitive LTC-IC are lost after five weeks in such cultures. We describe a “stroma-non-contact” culture system, in which progenitors are cultured separated from stroma by a 0.4 μm microporous membrane which prevents cell stroma contact but allows free passage of diffusible factors. Primitive progenitors in such cultures can not only differentiate into committed progenitors but also are maintained to a greater extent than in Dexter cultures. We will discuss the relative contribution of 1) direct contact between hematopoietic progenitors and bone marrow stroma, 2) soluble stroma-derived factors and 3) previously characterized growth promoting and presumed growth inhibitory cytokines in the in vitro maintenance and potential expansion of LTC-IC.
Global analysis of chromosome X gene expression in primary cultures of normal ovarian surface epithelial cells and epithelial ovarian cancer cell lines (2007)

The interpretation of loss of heterozygosity (LOH) in cancers is complicated as genes that map to LOH regions may be transcriptionally active (Xa) or inactive (Xi) due to X chromosome inactivation (XCI). We have analyzed the chromosome X transcriptome in four epithelial ovarian cancer (EOC) cell lines (TOV21G, TOV81D, TOV112D, and OV90) and 12 primary cultures of normal ovarian surface epithelial (NOSE) cells in relation to chromosome X integrity. Two-way comparative analysis using HuGeneFL Affymetrix GeneChips of TOV21G, TOV81D and OV90 relative to the NOSE samples was highly correlated (> 89%) in contrast to that of TOV112D (56-69%). TOV112D, followed by TOV21G, exhibited the largest number of up-regulated genes. XIST expression by RT-PCR was not detectable in TOV112D or TOV21G. Allele-specific transcription by cDNA sequence analysis of genes known to be subjected to XCI revealed maintenance of XCI in TOV81D and OV90, but not TOV21G. Biallelic expression could not be assessed in TOV112D due to reduction to hemizygosity of chromosome X. Chromosome X rearrangements were observed in FISH analysis of TOV112D and TOV21G, and both of these EOC cell lines were negative for Barr body analysis. The differentially expressed genes did not appear to map to any particular region of the X chromosome in any EOC cell line. The absence of XIST expression is consistent with Barr body loss in TOV112D and TOV21G. The combined evidence is consistent with two proposed mechanisms to account for absence of Xi in female cancers: Xi loss followed by Xa duplication (exemplified by TOV112D) and transcriptional reactivation of Xi (exemplified by TOV21G). Despite an alteration in XIST expression and differences in allelic content in the EOC cell lines, the chromosome X transcriptome was modified modestly when compared with that of NOSE samples.
Usefulness of B-Type Natriuretic Peptide Assay in the Assessment of Symptomatic State in Hypertrophic Cardiomyopathy (2004)

Plasma BNP is independently related to the presence and magnitude of heart failure symptoms in patients with HCM. As a clinical marker for heart failure, BNP is limited by considerable overlap in values between categories of heart failure severity as well as confounding variables of left ventricular wall thickness and age.
Monoubiquitylation of α-Synuclein by Seven in Absentia Homolog (SIAH) Promotes Its Aggregation in Dopaminergic Cells (2007)

alpha-Synuclein plays a major role in Parkinson disease. Unraveling the mechanisms of alpha-synuclein aggregation is essential to understand the formation of Lewy bodies and their involvement in dopaminergic cell death. alpha-Synuclein is ubiquitylated in Lewy bodies, but the role of alpha-synuclein ubiquitylation has been mysterious. We now report that the ubiquitin-protein isopeptide ligase seven in absentia homolog (SIAH) directly interacts with and monoubiquitylates alpha-synuclein and promotes its aggregation in vitro and in vivo, which is toxic to cells. Mass spectrometry analysis demonstrates that SIAH monoubiquitylates alpha-synuclein at lysines 12, 21, and 23, which were previously shown to be ubiquitylated in Lewy bodies. SIAH ubiquitylates lysines 10, 34, 43, and 96 as well. Suppression of SIAH expression by short hairpin RNA to SIAH-1 and SIAH-2 abolished alpha-synuclein monoubiquitylation in dopaminergic cells, indicating that endogenous SIAH ubiquitylates alpha-synuclein. Moreover, SIAH co-immunoprecipitated with alpha-synuclein from brain extracts. Inhibition of proteasomal, lysosomal, and autophagic pathways, as well as overexpression of a ubiquitin mutant less prone to deubiquitylation, G76A, increased monoubiquitylation of alpha-synuclein by SIAH. Monoubiquitylation increased the aggregation of alpha-synuclein in vitro. At the electron microscopy level, monoubiquitylated alpha-synuclein promoted the formation of massive amounts of amorphous aggregates. Monoubiquitylation also increased alpha-synuclein aggregation in vivo as observed by increased formation of alpha-synuclein inclusion bodies within dopaminergic cells. These inclusions are toxic to cells, and their formation was prevented when endogenous SIAH expression was suppressed. Our data suggest that monoubiquitylation represents a possible trigger event for alpha-synuclein aggregation and Lewy body formation.
Selective Changes in Thin Spine Density and Morphology in Monkey Prefrontal Cortex Correlate with Aging-Related Cognitive Impairment (2010)

Age-associated memory impairment (AAMI) occurs in many mammalian species, including humans. In contrast to Alzheimer's disease (AD), in which circuit disruption occurs through neuron death, AAMI is due to circuit and synapse disruption in the absence of significant neuron loss and thus may be more amenable to prevention or treatment. We have investigated the effects of aging on pyramidal neurons and synapse density in layer III of area 46 in dorsolateral prefrontal cortex of young and aged, male and female rhesus monkeys (Macaca mulatta) that were tested for cognitive status through the delayed non-matching-to-sample (DNMS) and delayed response tasks. Cognitive tests revealed an age-related decrement in both acquisition and performance on DNMS. Our morphometric analyses revealed both an age-related loss of spines (33%, p < 0.05) on pyramidal cells and decreased density of axospinous synapses (32%, p < 0.01) in layer III of area 46. In addition, there was an age-related shift in the distribution of spine types reflecting a selective vulnerability of small, thin spines, thought to be particularly plastic and linked to learning. While both synapse density and the overall spine size average of an animal were predictive of number of trials required for acquisition of DNMS (i.e., learning the task), the strongest correlate of behavior was found to be the head volume of thin spines, with no correlation between behavior and mushroom spine size or density. No synaptic index correlated with memory performance once the task was learned.
Characterization of Calcium Phosphate Nanoparticles Based on a PEGylated Chelator for Gene Delivery (2017)

Calcium phosphate (CaP) nanoparticles are promising gene delivery carriers due to their bioresorbability, ease of preparation, high gene loading efficacy, and endosomal escape properties. However, the rapid aggregation of the particles needs to be addressed in order to have potential in vivo. In addition, there is a need to better understand the relationship between CaP nanoparticle properties and their interactions with cells. Here, a new synthesis route involving click chemistry was developed to prepare the PEGylated chelator PEG-inositol 1,3,4,5,6-pentakisphosphate (PEG-IP5) that can coat and stabilize CaP nanoparticles. Two methods (1 and 2) differing on the time of addition of the PEGylated chelator were employed to produce stabilized particles. Method 1 yielded amorphous aggregated spheres with a particle size of about 200 nm, whereas method 2 yielded 40 nm amorphous loose aggregates of clusters, which were quickly turned into needle bundle-like crystals of about 80 nm in a few hours. Nanoparticles prepared by method 1 were internalized with significantly higher efficiency in HepG2 cells than those prepared by method 2, and the uptake was dramatically influenced by the reaction time of Ca<sup>2+</sup> and PO<sub>4</sub><sup>3-</sup> and sedimentation of the particles. Interestingly, morphological transformations were observed for both types of particles after different storage times, but this barely influenced their in vitro cellular uptake. The transfection efficiency of the particles prepared by method 1 was significantly higher, and none of the formulations tested showed signs of cytotoxicity. This study provides a better understanding of the properties (e.g., size, morphology, and crystallinity) of PEGylated CaP nanoparticles and how these influence the particles' in vitro uptake and transfection efficiency.