gebhart/patrepeval huggingface dataset:
Use of an indirect pharmacodynamic stimulation model of MX protein induction to compare in vivo activity of interferon alfa-2a and a polyethylene glycol-modified derivative in healthy subjects (1996)

Interferon alfa-2a was chemically modified by the covalent attachment of a polyethylene glycol (PEG) moiety to enhance its circulating half-life and to reduce its immunogenicity. A comparative evaluation of the pharmacokinetics of the PEG-modified interferon alfa-2a showed a greater than twofold increase in the circulating half-life as a result of this chemical modification. An indirect physiologic response model was developed to characterize the time course of the MX protein response after subcutaneous administration of single ascending doses of either interferon alfa-2a or PEG-interferon alfa-2a in healthy volunteers. Analysis of the pharmacokinetic-pharmacodynamic relationship suggested that the PEG-modified interferon alfa-2a could not be administered less than twice weekly and therefore offered little therapeutic advantage over its unmodified counterpart, which is administered three times weekly. These results were consistent with findings in phase II trials. This study substantiates the usefulness of pharmacodynamic modeling as a tool for the development of dose recommendations and for the early selection of drug candidates in the drug development process.
Antigen unmasking on formalin‐fixed, paraffin‐embedded tissue sections (1993)

Enzymatic and non-enzymatic treatments for antigen unmasking on formalin-fixed, paraffin-embedded, dewaxed sections were optimized and compared by the use of a panel of antibodies of diagnostic relevance (anti-cytokeratins, vimentin, S-100, T- and B-cell receptors, Ki-67/MIB 1, muscle actin). Non-enzymatic unmasking was obtained by boiling the slides in a microwave oven in 0.01 M salt solution (pH 6) or in 6 M urea. Trypsin or pronase digestion was used for comparison and found to be necessary for some of the reagents. The investigation was then extended to 256 antibodies; the epitopic amino acid sequence was known for 48 of them. We found that enzymatic and non-enzymatic antigen unmasking are not dependent on the epitope sequence, but some antigens benefit selectively from one treatment but not from the other. Denaturation of proteins is the likely mechanism which leads to immunodetection on microwave oven-boiled slides; this suggestion is supported by the use of denaturating solutions and by the observation that endogenous enzymes were inactivated and a few antigens were no longer immunodetectable after boiling. Non-enzymatic methods for antigen unmasking are a powerful new tool for broadening the use of antibodies for immunostaining formalin-fixed, paraffin-embedded sections and should be used in parallel with the traditional enzymatic methods.
Myofibroblasts. II. Intestinal subepithelial myofibroblasts (1999)

Intestinal subepithelial myofibroblasts (ISEMF) and the interstitial cells of Cajal are the two types of myofibroblasts identified in the intestine. Intestinal myofibroblasts are activated and proliferate in response to various growth factors, particularly the platelet-derived growth factor (PDGF) family, which includes PDGF-BB and stem cell factor (SCF), through expression of PDGF receptors and the SCF receptor c-kit. ISEMF have been shown to play important roles in the organogenesis of the intestine, and growth factors and cytokines secreted by these cells promote epithelial restitution and proliferation, i.e., wound repair. Their role in the fibrosis of Crohn's disease and collagenous colitis is being investigated. Through cyclooxygenase (COX)-1 and COX-2 activation, ISEMF augment intestinal ion secretion in response to certain secretagogues. By forming a subepithelial barrier to Na(+) diffusion, they create a hypertonic compartment that may account for the ability of the gut to transport fluid against an adverse osmotic gradient. Through the paracrine secretion of prostaglandins and growth factors (e.g., transforming growth factor-beta), ISEMF may play a role in colonic tumorigenesis and metastasis. COX-2 in polyp ISEMF may be a target for nonsteroidal anti-inflammatory drugs (NSAIDs), which would account for the regression of the neoplasms in familial adenomatous polyposis and the preventive effect of NSAIDs in the development of sporadic colon neoplasms. More investigation is needed to clarify the functions of these pleiotropic cells.
Polyphenolic Compounds and Antioxidant Activity of New and Old Apple Varieties (2008)

There is considerable evidence to show that a greater intake of apple contributes to improved health by reducing the risk of diseases, such as cardiovascular disease and some forms of cancer. Apple fruit is a major source of phenol compounds, because its consumption is widespread in many countries and it is available on the market for the whole year. The phenolic composition of 67 varieties of apple cultivars (new and old varieties) was examined for the concentration of some important phytochemicals and antioxidant activity. For the first time, we have looked at the correlation and compared polyphenolic coumpounds in Golden Delicious variety and new varieties grown from it. Up to 18 compounds, including catechin, procyanidin, hydroxycinnamates, flavonols, anthocyanins, and dihydrochalcones, were analyzed by high-performance liquid chromatography with diode array detection analysis of crude extracts and after thiolysis and LC-MS. The mean content of total polyphenols lay between 523.02 and 2723.96 mg/100 g dw and depending upon the apples variety. Flavanols (catechin and oligomeric procyanidins) are the major class of apple polyphenols, representing more than 80%, followed by hydroxycinnamic acids (1-31%), flavonols (2-10%), dihydrochalcones (0.5-5%), and in red apples, anthocyanins (1%). In this study, the best correlation was found for the total polyphenols and ABTS method, with a lower correlation for FRAP and DPPH methods ( r = 0.871, 0.839, and 0.804, respectively). The presented data clearly demonstrated that new varieties, i.e., Ozark Gold, Julyred, and Jester, of apple had the same or higher value of bioactive compounds in comparison to the old varieties, i.e., Golden Delicious, Idared, and Jonagold.
BTBR Ob/Ob Mutant Mice Model Progressive Diabetic Nephropathy (2010)

There remains a need for robust mouse models of diabetic nephropathy (DN) that mimic key features of advanced human DN. The recently developed mouse strain BTBR with the ob/ob leptin-deficiency mutation develops severe type 2 diabetes, hypercholesterolemia, elevated triglycerides, and insulin resistance, but the renal phenotype has not been characterized. Here, we show that these obese, diabetic mice rapidly develop morphologic renal lesions characteristic of both early and advanced human DN. BTBR ob/ob mice developed progressive proteinuria beginning at 4 weeks. Glomerular hypertrophy and accumulation of mesangial matrix, characteristic of early DN, were present by 8 weeks, and glomerular lesions similar to those of advanced human DN were present by 20 weeks. By 22 weeks, we observed an approximately 20% increase in basement membrane thickness and a >50% increase in mesangial matrix. Diffuse mesangial sclerosis (focally approaching nodular glomerulosclerosis), focal arteriolar hyalinosis, mesangiolysis, and focal mild interstitial fibrosis were present. Loss of podocytes was present early and persisted. In summary, BTBR ob/ob mice develop a constellation of abnormalities that closely resemble advanced human DN more rapidly than most other murine models, making this strain particularly attractive for testing therapeutic interventions.
Lipids and Fatty Acids in <i>Artemia</i> Nauplii Enriched with Fish Oil Triacylglycerols Containing Docosahexaenoic Acid in Different Positional Distribution Patterns (1997)

Lipid profiles were compared between Artemia nauplii enriched with fish oil triacylglycerols (TG) containing docosahexaenoic acid (DHA, 22:6n-3) in different positional distribution patterns. Four fish oils were selected on the basis of the positional distribution determined by a nonenzymatic analytical method, and directly given to Artemia nauplii in the form of oil emulsions. Time-courses of the lipid contents, lipid compositions, and fatty acid compositions were not so different between the nauplii enriched with tuna orbital and bonito head oil TG, in which 22:6n-3 (22.9-24.0%) was esterified in the sn-3>sn-1_??_sn-2 positions and the sn-3_??_sn-2=sn-1 positions, respectively. In both of the enrichments, the level of 22:6n-3 initially not detected reached a plateau (3.4-3.6% of totalfatty acids) after 12h and then decreased to 1.7% (48h). Slight differences were also observed between thelipids of nauplii fed on sardine (22:6n-3, 11.5%; sn-2_??_sn-3>sn-1) and seal (22:6n-3, 7.6%; sn-3>sn-1>sn-2) oil TG. The levels of 22:6n-3 after 24h enrichment were 0.4% of total fatty acids. Such similarities of the lipid profiles in Artemia nauplii indicate that the positional distribution of 22:6n-3 in dietary TG has practically no influence to enrichment of Artemia nauplii with this fatty acid. It is probable that any TG with different positional distribution patterns of 22:6n-3 can be used for enrichment of Artemia, when 22:6n-3 is concentrated in the TG at an adequate level.
An estrogen receptor mutant with strong hormone-independent activity from a metastatic breast cancer. (1997)

Thirty tumors from metastatic breast cancer patients were screened for mutations in the estrogen receptor (ER) gene using single-strand conformation polymorphism and sequence analysis. Three missense mutations, Ser47Thr, Lys531Glu, and Tyr537Asn, were identified in these lesions. To investigate these mutated ERs or altered transcriptional activation function, expression vectors containing wild-type (wt) and mutant ERs were constructed and cotransfected with different estrogen response element reporter gene constructs into HeLa cells and MDA-MB-231 human breast cancer cells. The first two ER mutants were similar to wt ER. However, the Tyr537Asn ER mutant possessed a potent, estradiol-independent transcriptional activity, as compared to wt ER. Moreover, the constitutive activity of the Tyr537Asn ER mutant was virtually unaffected by estradiol, tamoxifen, or the pure antiestrogen ICI 164,384. Tyr537 is located at the beginning of exon 8 in the COOH-terminal portion of the hormone-binding domain of the ER, to which dimerization and transcription activation functions have also been ascribed. It has been identified as a phosphorylation site implicated in hormone binding, dimerization, and hormone-dependent transcriptional activity. Our results suggest that the Tyr537Asn substitution induces conformational changes in the ER that might mimic hormone binding, not affecting the ability of the receptor to dimerize, but conferring a constitutive transactivation function to the receptor. If present in other metastatic breast tumors, this naturally occurring ER mutant may contribute to breast cancer progression and/or hormone resistance.
Lung cancer: intermittent irradiation synchronized with respiratory motion--results of a pilot study. (1998)

Synchronized irradiation with the authors' system allowed convenient and reliable reduction of the target volume. Further study is needed to standardize the system for clinical use.
The biological and structural characterization of specific serum binding proteins for the insulin-like growth factors (1988)

The IGFs constitute an important family of skeletal growth regulatory peptides, which may play a vital autocrine and/or paracrine role in cellular growth. The role of the binding proteins in IGF physiology is quite unclear, and despite considerable progress in the past 2 years on the isolation and purification of binding proteins, many questions are still unresolved. For example, is the observed molecular heterogeneity experimentally induced, is it the result of post-translational modification of a single gene product, or are the different binding proteins products of different genes? What is the relationship between the different forms of binding proteins, and do they have different affinities for IGF-I and IGF-II? Do they have different physiological roles? It is obvious that answers to these questions are necessary in order to appreciate fully the physiological role of the binding proteins in regulating the actions of IGFs. Successful purification of different forms of IGF-binding proteins has been achieved in the last few years. This should enable the establishment of specific radioimmunoassays for each binding protein, which should allow the accurate assessment of the relative concentrations of binding proteins in various clinical or experimental states. Such studies have begun to be pursued very effectively by Baxter's group. The elucidation of the amino acid sequences of the various binding proteins will, hopefully, not only resolve the structural nature and inter-relationship of the various binding proteins, but also permit the use of recombinant DNA techniques to investigate fully, at the genetic level, the synthesis, regulation and production of the IGF-binding proteins.
Downregulation of erbB3 abrogates erbB2‐mediated tamoxifen resistance in breast cancer cells (2007)

Receptor tyrosine kinase activity is essential for erbB2 (HER2/neu) promotion of breast carcinogenesis, metastasis and therapeutic resistance. erbB2 kinase can be activated by dimerization with another erbB receptor, most of which bind ligands. Of these, the erbB2/erbB3 heterodimer is the most potent oncogenic complex. erbB2 reportedly requires erbB3 to promote cellular proliferation, although this may occur without changes in erbB2 tyrosine kinase activity in some model systems. Our investigations focus on the role(s) of erbB3 in erbB2-associated kinase activity and tamoxifen resistance. Using tumor-derived cell lines from wild type rat c-neu transgenic mice and human breast cancers, we demonstrate that erbB3 plays a critical role in the activation of erbB2 tyrosine kinase activity and erbB2-associated tumorigenesis. Mechanistically, downregulation of erbB3 by specific siRNA reduces erbB2 tyrosine phosphorylation, decreases the PI-3K/Akt signaling, and inhibits mammary/breast cancer cell proliferation and colony formation. Specific erbB3 siRNA sensitizes erbB2 transfected MCF-7 cells (MCF-7/erbB2) to tamoxifen-associated inhibition of both cell growth and colony formation and enhances tamoxifen-induced apoptosis, in contrast to control siRNA transfected MCF-7/erbB2 cells which are tamoxifen-resistant. Our data indicates that erbB2/erbB3 heterodimerization is a prerequisite for erbB2 tyrosine kinase activation in mammary/breast cancer cells and that downregulation of erbB3 inhibits erbB2-associated procarcinogenic activity via inactivation of the PI-3K/Akt pathway. Furthermore, erbB3 also contributes to erbB2-mediated tamoxifen resistance and therefore may be a clinically relevant therapeutic target in addition to erbB2.
Selective Interleukin-12 Synthesis Defect in 12/15-Lipoxygenase-deficient Macrophages Associated with Reduced Atherosclerosis in a Mouse Model of Familial Hypercholesterolemia (2002)

Targeted gene disruption or overexpression of 12/15-lipoxygenase in mice on the genetic background of apolipoprotein E or low density lipoprotein-receptor (LDL-R) deficiency has implicated 12/15-lipoxygenase in atherogenesis. The data support indirectly a role for 12/15-lipoxygenase in the oxidative modification of low density lipoprotein. In this study we set out to explore other potential mechanisms for 12/15-lipoxygenase in atherosclerosis using apolipoprotein B mRNA editing catalytic polypeptide-1/LDL-R double-deficient mice, a model highly related to the human condition of familial hypercholesterolemia. 12/15-Lipoxygenase deficiency in this strain led to approximately 50% decrease in aortic lesions in male and female mice at 8 months on a chow diet in the absence of cholesterol differences. While studying 12/15-lipoxygenase-deficient macrophages in culture, we discovered a remarkable selective defect (75-90% decrease) in interleukin-12 production but not in tumor necrosis factor-alpha or nitric oxide release, in response to lipopolysaccharide in the presence or absence of interferon-gamma priming. The lipopolysaccharide/interferon-gamma response was associated with a 33-50% decrease in nuclear interferon consensus sequence-binding protein, which is consistent with interferon consensus sequence-binding protein containing protein complex-dependent regulation of the interleukin-12 p40 gene. The decrease in interleukin-12 production was recapitulated in vivo in mouse aortas of the triple knockout group and was reflected in a marked decrease in interferon-gamma expression. The data provide support for a novel mechanism linking the 12/15-lipoxygenase pathway to a known immunomodulatory Th1 cytokine in atherogenesis.
Derivatization Methods in GC and GC/MS (2019)

The first part of this chapter presents the main objectives for performing derivatization of a sample to be analyzed by gas chromatography (GC) or gas chromatography/mass spectrometry (GC/MS). The derivatization is typically done to change the analyte properties for a better separation and also for enhancing the method sensitivity. In GC/MS, derivatization may improve the capability of compound identification. Examples illustrating such improvements are included. The second part describes several types of derivatization that are more frequently used in analytical practice. These include alkylation (e.g., methylation), formation of aryl derivatives, silylation (e.g., formation of trimethylsilyl derivatives), acylation (e.g., reactions with acyl chlorides or with chloroformates), and several other types of derivatizations. The chapter also presents typical derivatizations for analytes with specific functional groups and discusses artifact formation in certain derivatization reactions.
Large-Scale Automatic Classification of Phishing Pages (2010)

Phishing websites, fraudulent sites that impersonate a trusted third party to gain access to private data, continue to cost Internet users over a billion dollars each year. In this paper, we describe the design and performance characteristics of a scalable machine learning classifier we developed to detect phishing websites. We use this classifier to maintain Google’s phishing blacklist automatically. Our classifier analyzes millions of pages a day, examining the URL and the contents of a page to determine whether or not a page is phishing. Unlike previous work in this field, we train the classifier on a noisy dataset consisting of millionsofsamplesfrompreviously collectedliveclassification data. Despite the noise in the training data, our classifier learns a robust model for identifying phishing pages which correctly classifies more than 90 % of phishing pages several weeks after training concludes.
Poliovirus infection enhances the formation of two ribonucleoprotein complexes at the 3' end of viral negative-strand RNA (1995)

To identify proteins involved in the formation of replication complexes at the 3' end of poliovirus negative-strand RNA, a combined in vitro biochemical and in vivo genetic approach was used. Five subgenomic cDNA constructs were generated to transcribe different negative-strand RNA fragments. In UV cross-linking assays, distinct differences in binding of proteins in extracts from poliovirus-infected and uninfected cells to virus-specific, radiolabeled transcripts were observed. Two proteins present in extracts from poliovirus-infected cells with approximate molecular masses of 36 and 38 kDa were shown to cross-link to the 3' end of poliovirus negative-strand RNA. Appearance of the 36- and 38-kDa proteins in UV cross-linking assays can be detected 3 to 3.5 h after infection, and cross-linking reaches maximum levels by 5 h after infection. The binding site for the 36-kDa protein overlaps with the computer-predicted loop b region of stem-loop I, the so-called cloverleaf structure, and the RNA sequence of this region is required for efficient binding. Transfection of full-length, positive-sense RNA containing a five-nucleotide substitution (positions 20 to 25) in the loop b region of stem-loop I into tissue culture cells yielded only viral isolates with a reversion at position 24 (U-->C). This finding demonstrates that the wild-type cytidine residue at position 24 is essential for virus replication. RNA binding studies with transcripts corresponding to the 3' end of negative-strand RNA suggest that complex formation with the 36-kDa protein plays an essential role during the viral life cycle.
Role of ABCG1 and other ABCG family members in lipid metabolism (2001)

The molecular cloning and identification of mutations in ATP-binding cassette transporters in hereditary diseases have greatly expanded our knowledge of the normal physiology of intracellular lipid transport processes. In addition to the well-known ATP-binding cassette transporter A1 (ABCA1) molecule, ABC transporters belonging to the ABCG (White) subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be critically involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1, the product of a sterol-induced gene, participates in cholesterol and phospholipid efflux. The ABCG5 and ABCG8 transporters, defective in beta-sitosterolemia, are also now considered interesting targets in the control and influence of total body sterol homeostasis. In this review, advances referring to the regulation and function of ABCG half-size transporters are summarized and discussed. In addition, new implications for the transcriptional control, as well as the intracellular routing and localization, of these proteins are presented.
Thrombocytopenia in HIV-infected drug users in the HAART era (2001)

The present case-control study compared 26 HIV+ drug users having persistent thrombocytopenia (TCP<150 000/mm(3)) with 54 available age, gender and HIV CDC classification matched controls with normal platelet counts. Participants were followed longitudinally over a 2-year period (1998-2000), and hematological alterations evaluated in relationship to antiretroviral treatment, drug use and nutritional (selenium) status. Demographic information and medical history, including antiretroviral treatment were obtained. Blood was drawn for complete cell blood count, T lymphocytes and viral load. Sixty-nine percent of the individuals with persistent TCP and 49% of the controls were receiving antiretrovirals. At baseline, no significant differences in CD4 existed between the two groups. Over time, CD4 cell count declined in the cases (P = 0.05) and a significantly higher proportion of the cases (38%) developed AIDS (CD4<200 cell/mm(3)), as compared to the controls (18%, P = 0.004). A high risk for development of thrombocytopenia was observed with specific drug use (heroin 2.96 times, P = 0.0007), selenium levels below 145 microg/l (6 times, P = 0.008), and abnormal liver enzyme (SGOT) levels (2 times, P = 0.002). Together, these results indicate a number of factors that may be sensitive predictors of thrombocytopenia, which, despite antiretroviral treatment, appears to be related to more rapid disease progression in drug users.
Quetiapine in the Treatment of Focal Tardive Dystonia Induced by Other Atypical Antipsychotics (2005)

The authors report 2 patients with schizophrenia who developed focal tardive dystonia secondary to treatment with atypical antipsychotics (risperidone, olanzapine). When quetiapine was gradually introduced and other antipsychotics were discontinued, these patients experienced remarkable and sustained improvement of their dystonic symptoms, without loss of psychotic symptom control. The mechanism by which quetiapine may improve tardive dystonia caused by other atypical antipsychotics is unclear. Due to its receptor and pharmacologic profile, quetiapine is the atypical antipsychotic that is most similar to clozapine (without its hematologic side effects), which leads the authors to consider it for the treatment of tardive movement disorders.