gebhart/patrepeval huggingface dataset:
Determination of HER-2/neu amplification and expression in tumor tissue and cultured cells using a simple, phenol free method for nucleic acid isolation. (1990)

A rapid, simple and non-toxic procedure for the simultaneous isolation of DNA and RNA from tumor tissue and cells grown in vitro is described. Guanidinium isothiocyanate was used for homogenization of tumor tissue and for cell lysis. Separation of proteins, DNA and RNA was carried out by isopycnic centrifugation in cesium trifluoroacetate. DNA was further purified by salting out residual protein. Nucleic acids prepared by this method from 47 primary human carcinomas and 17 human cell lines were analysed for amplification and expression of the HER-2/neu proto-oncogene. 2- to 10-fold amplification of HER-2/neu was noted in 7/22 mammary carcinomas (32%) and in 4/14 ovarian carcinomas (28%). No amplification of the proto-oncogene was found in 4 laryngeal carcinomas, 1 pharyngeal carcinoma, 2 retrolingual carcinomas, 3 gastric carcinomas and 1 kidney carcinoma. HER-2/neu overexpression was observed in 6/22 of mammary carcinomas (27%) and 7/14 of ovarian carcinomas (50%). No overexpression was found in all other carcinomas studied. Concordance between amplification and overexpression was noted in 3 mammary and 4 ovarian carcinomas, respectively. 3 mammary and 3 ovarian carcinomas showed overexpression without amplification. 5 human mammary carcinoma cell lines showed both amplification and overexpression of HER-2/neu. In two mammary carcinoma cell lines (MDA MB-453 and ZR 75-1) overexpression was noted without amplification of the proto-oncogene. These data combine to suggest that mechanisms other than gene amplification may also lead to overexpression of the HER-2/neu protooncogene in cancer cells.
Cyclosporin A in Severe, Treatment-Refractory Rheumatoid Arthritis (1988)

Cyclosporin A is an effective therapy for severe, treatment-refractory rheumatoid arthritis. Side effects, particularly nephrotoxicity, are common.
Potassium Deprivation-Induced Apoptosis of Cerebellar Granule Neurons: A Sequential Requirement for New mRNA and Protein Synthesis, ICE-Like Protease Activity, and Reactive Oxygen Species (1996)

Potassium (K+) deprivation-induced apoptosis of cerebellar granule neurons requires new mRNA and protein synthesis. Using a fluorogenic substrate for interleukin-1beta converting enzyme (ICE), we show that K+ deprivation of cerebellar granule neurons induces cycloheximide-sensitive ICE-like protease activity. A peptide inhibitor of ICE-like protease activity, Ac-YVAD-chloromethylketone (Ac-YVAD-CMK), prevents K+ deprivation-induced apoptosis. Further, reactive oxygen species (ROS) are essential mediators of K+ deprivation-induced apoptosis of cerebellar granule neurons because neuronal death is also blocked by superoxide dismutase, N-acetyl-L-cysteine, and free radical spin traps. Using fluorescent assays, we show that ROS production after K+ deprivation is blocked by actinomycin D, cycloheximide, and Ac-YVAD-CMK, suggesting that ROS act downstream of gene transcription, mRNA translation, and ICE activation. Taken together, we show that new mRNA and protein synthesis, activation of ICE-like proteases, and ROS production are sequential events in K+ deprivation-induced apoptosis of cerebellar granule neurons.
Towards Blockchain-enabled Wireless Mesh Networks (2018)

Recently, mesh networking and blockchain are two of the hottest technologies in the telecommunications industry. Combining both can reformulate Internet access. While mesh networking makes connecting to the Internet easy and affordable, blockchain on top of mesh networks makes Internet access profitable by enabling bandwidth-sharing for crypto-tokens. Hyperledger Fabric (HLF) is a blockchain framework implementation and one of the Hyperledger projects hosted by The Linux Foundation. We evaluate HLF in a real production mesh network and in the laboratory. We quantify the performance, bottlenecks and limitations of the current implementation v1.0. We identify the opportunities for improvement to serve the needs of wireless mesh access networks. To the best of our knowledge, this is the first HLF deployment made in a production wireless mesh network.
Importance of CpG Dinucleotides in Activation of Natural IFN‐α‐Producing Cells by a Lupus‐Related Oligodeoxynucleotide (2001)

The oligodeoxyribonucleotide (ODN) 5'-TTTTCAATTCGAAGATGAAT-3' (ODN H), identified in systemic lupus erythematosus (SLE) serum, induced the production of interferon (IFN)-alpha in human peripheral blood mononuclear cells (PBMC) when combined with lipofectin. Flow cytometric analysis with staining for surface antigens and intracellular IFN-alpha, showed that the IFN-alpha-producing cells (IPC) were the natural IPC, also termed type 2 dendritic cell precursors (pDC2) or plasmacytoid monocytes. The importance of unmethylated CpG dinucleotides for the interferogenic activity of ODN was studied. Methylation of CpG impaired the activity of single-stranded (ss) ODN H, but increased that of the complementary ssODN I. Furthermore, CpG-methylated double-stranded (ds) ODN Hmet-Imet lost, but hemimethylated dsODN H-Imet retained interferogenic activity. Inversion of the CpG to GpC had no effect on the interferogenic activity of ssODN H, increased that of ssODN I, however abolished the activity of dsODN H-I. Alteration of the CpG in ODN H to ApG and in the ODN I to CpT destroyed their activity. The induction of IFN-alpha is therefore sequence-specific, but unmethylated CpGs are not always required, especially not in ssODNs. Interferogenic DNA sequences could therefore be more frequent in eukaryotic genomes than previously thought and their capacity to activate natural IPC may have implications for immune responses to microbial antigens and nuclear autoantigens.
AC Powder Electroluminescence Maintenance Improvement (1983)

The effects of annealing and quenching EL phosphors on their maintenance are investigated. Annealing at a temperature from 700° to 1000°C for more than 1 hr in or air, and quenching are most efficient for EL life improvement. For example, EL phosphor annealed in air at 900°C for 2 hr and quenched has a half‐life of more than 3000 hr (initial ). Sulfur vacancy density, dopant content, and phosphor particle size are not changed appreciably by annealing, but the x‐ray diffraction peak intensity changes, and the activation energy of deterioration increases from 0.3 to 0.45 eV by annealing. These results suggest that the crystal quality is changed by annealing and quenching.
Control of cell function with tunable hydrogel networks (2005)

A critical problem limiting the field of tissue engineering is the lack of engineering design rules to guide the synthesis and fabrication of artificial extracellular matrices (ECMs) or scaffolds. To address this issue, we have created artificial ECMs that are environmentally responsive and tunable with respect to mechanical properties (e.g. G*), biological ligands, tissue adhesion, and protease degradation. Our current approach is to create modular hydrogel ECMs where different properties of the matrix can be manipulated independently, thus creating a system where parametric analysis of the effect of hydrogel properties on cell proliferation and differentiation is possible. For example, we have synthesized and characterized the physical properties of semi-interpenetrating polymer networks (sIPNs) consisting of linear polyacrylic acid (pAAc) chains within a thermo-responsive N-isopropylacrylamide-co-acrylic acid network [p(NIPAAm-co-AAc)]. Studies addressing the effect of RGD ligand type and density, in the context of matrices with various mechanical properties, have indicated that G*, RGD density, and protease cross-linkers are critical for rat calvarial osteoblast adhesion and proliferation. These peptide-modified P(NIPAAm-CO-AAc) hydrogels allow for easy control of the mechanical and chemical properties of the matrix, allowing parametric analysis of the effect of these properties on cell behavior in vitro and tissue development in vivo.
Collagen and Glycosaminoglycans of Wharton’s Jelly (1997)

In this study, we report quantity, solubility and molecular polymorphism of collagen, proportional relationships between various types of collagen, ultrastructure of collagen fibres, the amounts of various glycosaminoglycans (GAGs) and proportional relationships between them in Wharton's jelly of normal umbilical cords. We compare the extracellular matrix components in Wharton's jelly with those in the umbilical cord artery. Collagen of the Wharton's jelly demonstrates some specific features. It is very insoluble in neutral salt and in a slightly acidic solution and appears to be resistant to the action of depolymerizing agent (EDTA-Na2). Only 50% of total collagen may be solubilized by pepsin digestion and fractionated by differential salt precipitation. Four collagen fractions were obtained. Three of them were identified by polyacrylamide gel electrophoresis as type I, type III, and type V collagen and proportional relationship between them was calculated. Hyaluronic acid is the most abundant component of GAGs contained in Wharton's jelly. The amounts of sulphated GAGs-keratan sulphate, heparan sulphate, chondroitin-4-sulphate, chondroitin-6-sulphate, dermatan sulphate and heparin-are distinctly lower. Each of them constitutes only a few percent of total GAGs.
THE FUNCTION OF THE VERTEBRAL VEINS AND THEIR ROLE IN THE SPREAD OF METASTASES (1940)

Philadelphia, Pa. FROM THE GRADUATE SCHOOL OF MEDICINE, UNIVERSITY OF PENNSYLVANIA, PHILADELPHIA, PA.
Role of prostaglandin E1 and copper in angiogenesis. (1982)

The interstitial fluid of MTW9A and Walker carcinomas and their ethanol extract induced strong angiogenic response in the rabbit (New Zealand White) corneal test. The fluid collected in vivo was rich in E-type prostaglandins, and prostaglandin E1 (PGE1) in particular was strongly angiogenic at the lowest dose as compared with the angiogenic responses of prostaglandins E2, I2, and F2 alpha. Neoplastic fibroblasts also induced a strong angiogenic response, but in indomethacin-treated rabbits neovascularization failed to occur. Copper was concentrated in the cornea during PGE1-induced neovascularization, and copper-deficient rabbits were unable to mount an angiogenic response in the corneal test. Ceruloplasmin, the copper carrier of plasma, was found to be angiogenic at high doses. In indomethacin-treated rabbits, however, ceruloplasmin at the same high doses failed to induce angiogenesis. The experiments are interpreted to indicate that angiogenesis is the end result of a sequence of events, two of which are PGE1 production and copper mobilization in the tissue where neovascularization occurs.
Glucocorticoid Stimulates Hepatitis B Viral Gene Expression in Cultured Human Hepatoma Cells (1992)

Glucocorticoids have been shown to influence the severity of hepatitis B virus-related chronic hepatitis in human. However, very little is known about the effects of glucocorticoids on hepatitis B virus replication in vitro. In this report, we used a well-differentiated human hepatoma cell line, Hep3B, transfected with hepatitis B virus complementary DNA as a model to show that a glucocorticoid analog, dexamethasone, can directly stimulate the production of HBsAg and HBeAg. Elevation of 3.5-kb pregenomic RNA and all other viral RNAs in the transfected Hep3B cells after dexamethasone treatment supports the hypothesis that glucocorticoids directly stimulate hepatitis B virus gene expression in vitro. The concentration of dexamethasone for its half-maximal stimulatory activity toward HBsAg, HBeAg and all viral transcripts was approximately 10(-8) mol/L, close to the affinity of glucocorticoid receptors to [3H]-triamcinolone acetonide in Hep3B cells (approximately 10(-8) mol/L). Specific glucocorticoid antagonist RU38486 completely blocked dexamethasone-induced HBV gene expression, suggesting that the stimulatory effect of dexamethasone was mediated through specific glucocorticoid receptors.
Nerve growth factor mediates hyperalgesia and cachexia in auto-immune arthritis (2005)

Pain and cachexia are two of the most debilitating aspects of rheumatoid arthritis. Despite that, the mechanisms by which they are mediated are not well understood. We provide evidence that nerve growth factor (NGF), a secreted regulatory protein that controls neuronal survival during development, is a key mediator of pain and weight loss in auto-immune arthritis. Function blocking antibodies to NGF completely reverse established pain in rats with fully developed arthritis despite continuing joint destruction and inflammation. Likewise, these antibodies reverse weight loss while not having any effect on levels of the pro-cachectic agent tumor necrosis factor (TNF). Taken together, these findings argue that pathological joint pain and joint destruction are mechanistically independent processes and that NGF regulates an alternative cachexia pathway that is independent or downstream of TNF.
Simple and Efficient Method for Heterologous Expression of Clostridial Proteins (2000)

Many clostridial proteins are poorly produced in Escherichia coli. It has been suggested that this phenomena is due to the fact that several types of codons common in clostridial coding sequences are rarely used in E. coli and the quantities of the corresponding tRNAs in E. coli are not sufficient to ensure efficient translation of the corresponding clostridial sequences. To address this issue, we amplified three E. coli genes, ileX, argU, and leuW, in E. coli; these genes encode tRNAs that are rarely used in E. coli (the tRNAs for the ATA, AGA, and CTA codons, respectively). Our data demonstrate that amplification of ileX dramatically increased the level of production of most of the clostridial proteins tested, while amplification of argU had a moderate effect and amplification of leuW had no effect. Thus, amplification of certain tRNA genes for rare codons in E. coli improves the expression of clostridial genes in E. coli, while amplification of other tRNAs for rare codons might not be needed for improved expression. We also show that amplification of a particular tRNA gene might have different effects on the level of protein production depending on the prevalence and relative positions of the corresponding codons in the coding sequence. Finally, we describe a novel approach for improving expression of recombinant clostridial proteins that are usually expressed at a very low level in E. coli.
Recent advances in nanopore sequencing (2012)

The prospect of nanopores as a next-generation sequencing platform has been a topic of growing interest and considerable government-sponsored research for more than a decade. Oxford Nanopore Technologies recently announced the first commercial nanopore sequencing devices, to be made available by the end of 2012, while other companies (Life, Roche, and IBM) are also pursuing nanopore sequencing approaches. In this paper, the state of the art in nanopore sequencing is reviewed, focusing on the most recent contributions that have or promise to have next-generation sequencing commercial potential. We consider also the scalability of the circuitry to support multichannel arrays of nanopores in future sequencing devices, which is critical to commercial viability.
Poliovirus-sensitive transgenic mice as a new animal model. (1993)

Transgenic mice susceptible to poliovirus infection were produced by introducing a human gene encoding cellular receptors for poliovirus into the mouse genome. Expression of receptor mRNAs in tissues of the transgenic mice was analysed using Northern blot hybridization. The results indicate that the human gene is expressed in many tissues of the transgenic mice just as in human tissues, and that the amount of the receptor mRNAs varies from tissue to tissue. The transgenic mice inoculated with poliovirus by any of the routes tested in this study show clinical symptoms similar to those in humans and monkeys, although the sensitivity of the mice depended on the inoculation route. In any route, the virulent Mahoney strain of type 1 poliovirus is much more virulent than the attenuated Sabin 1 strain in the transgenic mice. These observations suggest that the transgenic mice become an excellent new animal model for studying molecular mechanisms of pathogenesis of poliovirus and for assessing oral poliovirus vaccines.
Growth of Silver Colloidal Particles Obtained by Citrate Reduction To Increase the Raman Enhancement Factor (2001)

A method is reported for obtaining silver colloids with a large particle size. It is based on the growth of seed colloidal particles obtained by chemical reduction of silver nitrate with citrate. These colloids were characterized by means of UV−visible spectroscopy and transmission electron microscopy. The nucleation mechanism is discussed on the basis of the morphology and size of the resulting particles. Moreover, the surface-enhanced Raman scattering activity of the resulting colloids was evaluated in the near-infrared region by using 1,5-dimethylcytosine as adsorbate.
TabularNet (2021)

Tabular data are ubiquitous for the widespread applications of tables and hence have attracted the attention of researchers to extract underlying information. One of the critical problems in mining tabular data is how to understand their inherent semantic structures automatically. Existing studies typically adopt Convolutional Neural Network (CNN) to model the spatial information of tabular structures yet ignore more diverse relational information between cells, such as the hierarchical and paratactic relationships. To simultaneously extract spatial and relational information from tables, we propose a novel neural network architecture, TabularNet. The spatial encoder of TabularNet utilizes the row/column-level Pooling and the Bidirectional Gated Recurrent Unit (Bi-GRU) to capture statistical information and local positional correlation, respectively. For relational information, we design a new graph construction method based on the WordNet tree and adopt a Graph Convolutional Network (GCN) based encoder that focuses on the hierarchical and paratactic relationships between cells. Our neural network architecture can be a unified neural backbone for different understanding tasks and utilized in a multitask scenario. We conduct extensive experiments on three classification tasks with two real-world spreadsheet data sets, and the results demonstrate the effectiveness of our proposed TabularNet over state-of-the-art baselines.
Lipopolysaccharide-specific antibodies in plasma and stools of children with Shigella-associated leukemoid reaction and hemolytic-uremic syndrome (1996)

Antibody responses to the lipopolysaccharide (LPS) of shigellae were compared between children with uncomplicated and complicated Shigella dysenteriae 1 infection. One hundred fifteen children between 12 and 60 months of age with S. dysenteriae 1 infection were studied. Of these children, 42 had complications (leukemoid reaction and/or hemolytic-uremic syndrome [complicated shigellosis] and 73 had no complications (uncomplicated shigellosis). Antibodies to the LPS of S. dysenteriae 1 and Shigella flexneri Y were measured in plasma and stools, as were total immunoglobulin A (IgA) and IgG concentrations in plasma and the total IgA concentration in stool, on enrollment and 3 to 5 days later. In the plasma, the concentrations of homologous (IgG) and heterologous (IgA) LPS antibodies on enrollment were higher in children with complicated shigellosis than in those with uncomplicated shigellosis. In stool, the concentrations on enrollment were similar between the two groups of children. There was a rise in antibody concentrations in the plasma (homologous and heterologous) and stool (homologous) between the day of enrollment and 3 to 5 days later in children with uncomplicated shigellosis but not in those with complicated shigellosis. These findings suggest that systemic stimulation is more marked in children with complications, so that a subsequent rise in plasma antibody concentrations does not occur in these children. In contrast, the lack of a rise in stool antibody concentrations in children with complicated shigellosis is suggestive of a lower-level mucosal response. Because the duration of diarrhea before enrollment influenced the homologous antibody concentrations, children were further divided into three subgroups (short [3 to 5 days], medium [6 to 9 days], and long [> 9 days] diarrhea durations before enrollment). Comparisons of homologous antibody concentrations between the two groups of children following such subdivisions showed that in children with complicated shigellosis, antibody concentrations were higher in the plasma of children in the short diarrhea duration subgroup but lower in the stool children in the medium diarrhea duration subgroup. No differences in antibody concentrations were observed in children in the other diarrhea duration subgroups. Thus, complications in shigellosis are associated with an early and strong systemic stimulation without a concomitant stimulation of the mucosal antibody response.
Cooperative Triple-Helix Formation at Adjacent DNA Sites: Sequence Composition Dependence at the Junction (1995)

The energetics of cooperative binding by oligodeoxyribonucleotides to adjacent sites by triple helix formation have been determined as a function of sequence composition at the junction. The binding affinity of an 11-mer in the presence of a neighboring bound oligonucleotide is enhanced by factors of 12, 17, 61, and 127 when 5'-TT-3', 5'-^mC^mC-3', 5'-T^mC-3', and 5'-^mCT-3' stacks, respectively, are formed at the junction (10 mM Bis-Tris·HCl at pH 7.0, 10 mM NaCl, 250 µM spermine, 24 °C). These binding enhancements correspond to interaction energies between the two oligonucleotides of 1.5, 1.7, 2.5, and 2.9 kcal·mol^(-1), respectively. The energetic penalties for a single-base mismatch differ depending on sequence and the location of the mismatch with respect to the 5'- or 3'-side of the junction. In the case of a 5'-TT-3' stack, a T·GC mismatch on the 5'-side of the junction decreases the interaction energy from 1.5 to 0.6 kcal·mol^(-1), whereas a T·GC mismatch on the 3'-side destroys cooperativity. For a 5'-^mCT-3' stack, a ^mC·AT mismatch on the 5'-side of the junction decreases the cooperative interaction energy from 2.9 to 1.7 kcal·mol^(-1), whereas a T·GC mismatch on the 3'-side of the junction destroys cooperativity. Two 11-mer oligonucleotides interacting through a 5'-TT-3' stack binding to adjacent sites on DNA are significantly more sensitive to single-base mismatches than the corresponding 22-mer binding to the same two abutting sites.
Concurrent validity and screening efficiency of The Dyslexia Screener. (1993)

The concurrent criterion-related validity and screening efficiency of a recently developed scale, The Dyslexia Screener (TDS), was investigated by examining its relation to the Reading Cluster of the Woodcock-Johnson Psychoeducational Assessment Battery (WJ) in a sample of 100 nonreferred children participating in a longitudinal study
Effects of Simvastatin and Cholestyramine in Familial and Nonfamilial Hypercholesterolemia (1990)

Simvastatin, a potent inhibitor of 3-hydroxy-3-methylglutaryl coenzyme A reductase, was compared with cholestyramine resin in a randomized open-label 12-week multicenter study of 251 high-risk patients with familial or nonfamilial hypercholesterolemia. Simvastatin, 20 mg and 40 mg daily, produced mean reductions in total cholesterol of 26% and 33%, respectively, and reductions in low-density lipoprotein cholesterol level of 32% and 40%. Cholestyramine resin, 4 to 12 g twice daily, reduced total cholesterol and low-density lipoprotein cholesterol levels 15% and 21%, respectively. High-density lipoprotein cholesterol levels were increased 8% to 10% by all treatments. Plasma triglyceride levels were moderately decreased by simvastatin treatment, while triglyceride levels increased with cholestyramine treatment. Simvastatin was better tolerated than cholestyramine, which had numerous gastrointestinal tract side effects. No patient had a serious drug-related adverse event.