gebhart/patrepeval huggingface dataset:
The genes for lumor necrosis factor (TNF-alpha) and lymphotoxin (TNF-beta) are tandemly arranged on chromosome 17 of the mouse (1986)

We have isolated clones containing the gene for tumor necrosis factor (TNF-alpha) from a mouse genomic library. Four out of five clones containing the TNF-alpha gene also hybridized to a human lymphotoxin (TNF-beta) probe. We constructed a restriction enzyme cleavage map of a 6.4 kb region from one of the genomic clones. From partial sequencing data and hybridizations with exon-specific oligonucleotide probes, we conclude that this region contains the mouse TNF-alpha and TNF-beta genes in a tandem arrangement, that they are separated by only about 1100 bases, and that their intron-exon structure is very similar to that seen in man. We probed genomic blots of DNA from human/mouse hybrids containing single mouse chromosomes for the presence of the mouse TNF genes. The results show that the genes are located on mouse chromosome 17, which also contains the major histocompatibility complex. Therefore, both the mouse and the human TNF genes are tandemly arranged and located on the same chromosome as the MHC.
At last, the truth about Pope John viii (1998)

It began...? He searches the dark air of his memory and finally situates the beginning as having occurred one honeyed morning after the completion of a sombre and stately mass. H e recalls the day with surprising precision. The memory is clear and pure, anew pearl. Strange, as the day itself had been cloudy and boiling with inchoate fears.
Random Walks and Electric Networks (1984)

Probability theory, like much of mathematics, is indebted to physics as a source of problems and intuition for solving these problems. Unfortunately, the level of abstraction of current mathematics often makes it difficult for anyone but an expert to appreciate this fact. Random Walks and Electric Networks looks at the interplay of physics and mathematics in terms of an example  the relation between elementary electric network theory and random walks where the mathematics involved is at the college level.
Development of the AT&T PersonaLink services online documentation system (1995)

Article Free Access Share on Development of the AT&T PersonaLink services online documentation system Author: Ronald L. Enfield Medford Software Works, Inc. Medford Software Works, Inc.View Profile Authors Info & Claims SIGDOC '95: Proceedings of the 13th annual international conference on Systems documentation: emerging from chaos: solutions for the growing complexity of our jobsFebruary 1996Pages 39–48https://doi.org/10.1145/223984.223994Published:01 February 1996Publication History 0citation226DownloadsMetricsTotal Citations0Total Downloads226Last 12 Months13Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Hyaluronic Acid-Modified DOTAP/DOPE Liposomes for the Targeted Delivery of Anti-Telomerase siRNA to CD44-Expressing Lung Cancer Cells (2009)

Cationic hyaluronic acid (HA)-modified DOTAP/DOPE liposomes were designed for the targeted delivery of anti-telomerase siRNA to CD44 receptor-expressing lung cancer cells. DOTAP/DOPE liposomes modified with 1%-20% (w/w) HA-DOPE conjugate were obtained by the ethanol injection method. Their size was below 170 nm and they exhibited zeta potentials higher than +50 mV. Lipoplexes prepared at different +/-ratios with siRNA were in the range of 200 nm and below and their zeta potentials were strongly dependent on the degree of modification and the +/-charge ratio. The presence of HA did not compromise binding, protection of siRNA from degradation, and complex stabilities in serum but rather resulted in an improvement of these properties. Liposome cytotoxicity, investigated by the MTT assay and LDH release after treatment of CD44(+) A549 cells and CD44(-) Calu-3, was demonstrated only at high concentrations. However, the addition of siRNA to HA-modified liposomes prevented cytotoxic effects compared to all other formulations. As shown by flow cytometry, transfection of siRNA into A549 cells was markedly improved with HA-modified liposomes, but not into Calu-3 cells. Using a qPCR-TRAP assay to test telomerase activity, no difference was demonstrated in the efficiency between HA-modified and nonmodified preparations. Moreover, some reduction in telomerase activity was observed with liposomes alone, lipoplexes prepared with nonsense siRNA and lipofectamine, indicative for some direct inhibitory effect of the lipids and siRNA on the expression of this enzyme. HA-modified DOTAP/DOPE liposomes represent a suitable carrier system for siRNA since properties like binding or protection of siRNA are not altered. They display an improved stability in cell culture medium and a reduced cytotoxicity. Furthermore, these novel lipoplexes could successfully be targeted to CD44-expressing A549 cells opening interesting perspectives for the treatment of lung cancer.
Controlling Morphology and Chain Aggregation in Semiconducting Conjugated Polymers: The Role of Solvent on Optical Gain in MEH-PPV (2012)

We report the results of a detailed investigation that addresses the influence of polymer morphology and chain aggregation, as controlled by the chemical nature of the solvent, on the optical gain properties of the conjugated polymer poly[2-methoxy-5-(2'-ethylhexyloxy)-p-phenylene vinylene] (MEH-PPV). Using the variable stripe length technique in the picosecond regime, we have extensively studied the optical gain performance of asymmetric planar waveguides formed with thin MEH-PPV films spin-cast from concentrated chlorobenzene (CB) and tetrahydrofuran (THF) solutions onto thermally oxidized silicon substrates. CB and THF solvents were chosen based on their known ability to promote and effectively limit aggregate formation, respectively. Very large net gain coefficients are demonstrated, reaching values of 330 and 365 cm(-1), respectively, when optically pumping the waveguides with a maximum energy density of 85 μJ/cm(2). Our results clearly demonstrate that polymer morphology, and hence, the chain conformation dependence of the degree of aggregation in the films as controlled by the solvent, has minimal impact on the net gain. Moreover, the waveguides exhibit low loss coefficients of 10-20 cm(-1) at the ASE wavelength. These results question the importance of polymer morphology and aggregate formation in polymer-based optical devices operating at high excitation densities in the stimulated emission regime as would be characteristic of lasers and optical amplifiers.
Cryptococcal meningitis (2004)

Cryptococcal meningitis is a common opportunistic infection in AIDS patients, particularly in Southeast Asia and Africa. Cases also occur in patients with other forms of immunosupression and in apparently immunocompetent individuals. Mortality from HIV-associated cryptococcal meningitis remains high (10-30%), even in developed countries, because of the inadequacy of current antifungal drugs and the complication of raised intracranial pressure. In cohorts of HIV-infected patients from sub-Saharan Africa, cryptococcosis has accounted for 13-44% of all deaths. Optimal current therapy is with amphotericin B 0.7-1 mg/kg/day plus flucytosine 100 mg/kg/day for 2 weeks, followed by fluconazole 400 mg/day for 8 weeks and 200 mg/day thereafter. Saline loading reduces amphotericin B nephrotoxicity. If there is no contraindication on CT head scan, repeat lumbar puncture with drainage of cerebrospinal fluid (CSF) is recommended for patients with very raised CSF opening pressure. Expansion of antiretroviral programmes raises the prospect of transforming the long-term prognosis of these patients, provided that they survive the acute phase of the illness. Studies are needed to define more fungicidal drug regimens and to improve the treatment of raised intracranial pressure.
Interaction of beta-lactam antibiotics with H+/peptide cotransporters in rat renal brush-border membranes. (1998)

Two H+/peptide cotransporters, PEPT1 and PEPT2, are expressed in the kidney, mediating the renal tubular reabsorption of oligopeptides and beta-lactam antibiotics. We examined the interactions of beta-lactam antibiotics with peptide transporters in rat renal brush-border membranes by evaluating the inhibitory potencies of the antibiotics against glycylsarcosine transport. Western blot analysis revealed that PEPT1 and PEPT2 were expressed in the renal brush-border membranes with the apparent molecular masses of 75 and 105 kDa, respectively. Using renal brush-border membrane vesicles, the uphill transport of glycylsarcosine was observed in the presence of an inward H+ gradient and an inside-negative membrane potential. Two transport systems with high affinity (Km of 50 microM) and low affinity (Km of 1.2 mM) appeared kinetically to mediate the glycylsarcosine uptake. The inhibition constants of the antibiotics for glycylsarcosine transport were more closely correlated with those in stable LLC-PK1 cells transfected with rat PEPT2 rather than PEPT1 cDNA. The beta-lactam antibiotics with an alpha-amino group showed trans-stimulation effects on the glycylsarcosine uptake, suggesting that these antibiotics and glycylsarcosine share a common peptide transporter. However, the antibiotics lacking an alpha-amino group failed to show the trans-stimulation effect. It is concluded that amino-beta-lactam antibiotics at therapeutic concentrations interact predominantly with PEPT2 localized in the brush-border membranes of rat kidney.
Geochemistry and microbial diversity of a trichloroethene-contaminated Superfund site undergoing intrinsic in situ reductive dechlorination (2002)

This study explored the geochemistry and microbial diversity of a Superfund site containing trichloroethene (TCE) and an unusual co-pollutant, tetrakis(2-ethylbutoxy)silane. Geochemical analysis of contaminated groundwater indicated subsurface anaerobiosis, reductive dechlorination of TCE to predominantly cis-1,2-dichloroethene, and (transient) accumulation of 2-ethylbutanol and 2-ethylbutyrate as a result of tetrakis(2-ethylbutoxy)silane breakdown. Comparative analysis of 106 16S rDNA and 61 16S-23S rDNA intergenic spacer region sequences - obtained from pristine and contaminated groundwater via DNA extraction, PCR amplification, cloning and sequencing - revealed that the contaminated groundwater featured (i) a distinct microbial community, (ii) reduced species diversity, (iii) various anaerobes, and (iv) bacteria closely related to the TCE-dechlorinating, dichloroethene-accumulating genus Dehalobacter, whereas (v) the TCE-dechlorinating, ethene-producing species Dehalococcoides ethenogenes was not detectable. Thus, geochemical and molecular biological results were in excellent agreement in this first ecological field study linking in situ reductive dechlorination of TCE to metabolism of tetraalkoxysilanes.
EnvZ-OmpR Interaction and Osmoregulation in Escherichia coli (2002)

EnvZ, a histidine kinase/phosphatase in Escherichia coli, responds to the osmolarity changes in the medium by regulating the phosphorylation state of the transcription factor OmpR, which controls the expression levels of outer membrane porin proteins OmpF and OmpC. Although both ompR and envZ genes are located on the ompB locus under the control of the ompB promoter and transcribed as a single polycistronic mRNA, the expression of envZ is known to be significantly less than ompR. However, to date no accurate estimation for the amounts of EnvZ and OmpR in the cell has been carried out. Here we examined the levels of EnvZ and OmpR in the wild-type strain MC4100 by quantitative Western blot analysis using anti-OmpR and anti-EnvZc (cytoplasmic domain of EnvZ) antisera. It was observed that during exponential growth in L-broth medium there were approximately 3500 and 100 molecules per cell of OmpR and EnvZ, respectively. The levels of OmpR and EnvZ in MC4100 cells grown in a high osmolarity medium (nutrient broth with 20% sucrose) were about the same as those grown in L-broth, whereas they were 1.7-fold higher than those in a low osmolarity medium (nutrient broth). With His10-OmpR, we also determined that the K(d) value for the EnvZc-OmpR complex formation is 1.20 +/- 0.17 microm. On the basis of these results, the molecular mechanism of osmoregulation of ompF and ompC is discussed.
Inhibition of Human Neutrophil Elastase with Peptidyl Electrophilic Ketones. 2. Orally Active PG-Val-Pro-Val Pentafluoroethyl Ketones (1994)

Valylprolyvalyl pentafluoroethyl ketones with different N-protecting groups were evaluated in vitro and in vivo as inhibitors of human neutrophil elastase (HNE). Several of these compounds were found to be orally active in HNE-induced rat and hamster lung hemorrhage models. The compound with 4-(4-morpholinylcarbonyl)benzoyl as the protecting group, 71 (MDL 101,146), was studied in greater detail. Hydration and epimerization studies were performed on 71 and related compounds in various media, including human blood serum. High-performance liquid chromatography studies on a reversed-phase system as a measure of the lipophilicity of 71 and related compounds revealed a small range of relative retention times wherein the orally active compounds fell. The Ki value determined for 71 vs HNE was 25 nM.
On the Specificity of Adaptive Mutations (1997)

Adaptive mutations are mutations that occur in nondividing or slowly dividing cells during prolonged nonlethal selection, and that appear to be specific to the challenge of the selection in the sense that the only mutations that arise are those that provide a growth advantage to the cell. The issue of the specificity has been controversial because it violates our most basic assumptions about the randomness of mutations with respect to their effect on the cell. Although a variety of experiments in several systems in both bacteria and yeast have claimed to demonstrate that specificity, those experiments have been subjected to a variety of technical criticisms suggesting that the specificity may not be real. Here I use the ebg system to provide evidence that when selection is applied to one specific nucleotide site within a gene, mutation occurs at that site but not at an alternative and equally mutable site within the same gene.
Efficient Titanium Oxide/Conjugated Polymer Photovoltaics for Solar Energy Conversion (2000)

Record high efficiencies for a polymer-based solar cell are reported here for an inorganic/organic composite photovoltaic device containing a single polymer film rather than a polymer/polymer or polymer/nanoparticle blend. The high efficiencies are reported to be due to device construction (see Figure) and the electronic properties of the phenylamino-p-phenylenevinylene-based polymer used.
Prognostic significance of p53 protein expression and DNA ploidy in surgically treated non-small cell lung carcinomas. (1993)

A series of 112 patients operated for non-small cell lung cancer was analyzed retrospectively. Nuclear suspensions were prepared from formalin-fixed, paraffin-embedded biopsies, and DNA content was measured simultaneously with p53 expression using flow cytometry. The expression of p53 protein was determined by the monoclonal antibody PAb 1801, which recognizes both wild-type (normal) and mutated forms of p53. By the level of p53 expression, four patient groups were statistically defined. Patients in the two groups with no detectable and extremely high p53 expression had a significantly better prognosis than patients in the two groups with moderately increased p53 expression. By logistic regression, p53 expression was found to be the single best predictor of 5 year survival. Patient age and tumor stage were less important prognostic factors. No difference in 5 year survival was observed between diploid and aneuploid tumors. We conclude that p53 is a useful prognostic predictor in low stage non-small cell lung carcinoma using the monoclonal antibody PAb 1801. The applicability of this antibody to archival material in flow cytometric analysis should allow a broad range of tumor types to be analyzed with respect to the prognostic significance of p53 overexpression.
A non-negative matrix tri-factorization approach to sentiment classification with lexical prior knowledge (2009)

Sentiment classification refers to the task of automatically identifying whether a given piece of text expresses positive or negative opinion towards a subject at hand. The proliferation of user-generated web content such as blogs, discussion forums and online review sites has made it possible to perform large-scale mining of public opinion. Sentiment modeling is thus becoming a critical component of market intelligence and social media technologies that aim to tap into the collective wisdom of crowds. In this paper, we consider the problem of learning high-quality sentiment models with minimal manual supervision. We propose a novel approach to learn from lexical prior knowledge in the form of domain-independent sentiment-laden terms, in conjunction with domain-dependent unlabeled data and a few labeled documents. Our model is based on a constrained non-negative tri-factorization of the term-document matrix which can be implemented using simple update rules. Extensive experimental studies demonstrate the effectiveness of our approach on a variety of real-world sentiment prediction tasks.
Gene cloning, nucleotide sequence, and expression of a cephalosporin-C deacetylase from Bacillus subtilis (1995)

The gene encoding a cephalosporin-C deacetylase (CAH) from Bacillus subtilis SHS 0133 was cloned and sequenced. The nucleotide sequence contained an open reading frame encoding a polypeptide consisting of 318 amino acids, the molecular weight of which was in good agreement with the value obtained by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The deduced amino acid sequence contained the common sequence Gly-X-Ser-X-Gly found in many esterases, lipases, and serine proteases. This indicates that CAH is a serine enzyme. A possible promoter sequence which is very similar to the consensus sequences of -35 and -10 regions recognized by B. subtilis RNA polymerase utilizing sigma factor H was found in the 5'-flanking region of the CAH structural gene. Two repeated A+T-rich blocks consisting of 24 bp were also found in the upstream region of the initiation codon. We constructed a series of expression plasmids by inserting the CAH gene into Escherichia coli ATG vectors. The degree of CAH gene expression depended on promoters and vector plasmids, which have different replication origins. The expressed CAH protein was an active form in the soluble fraction obtained after cell disruption. The highest expression level was accomplished with an expression plasmid, pCAH400, which has the trp promoter and the replication origin derived from pAT153. In the fermentation using a 30-liter jar fermentor, the transformant E. coli JM103(pCAH400) produced 440 U of CAH per ml of culture during a 24-h incubation. This value corresponded to 2.1 g of CAH protein in 1 liter of culture broth.
CMOS Image Sensors With Multi-Bucket Pixels for Computational Photography (2012)

This paper presents new image sensors with multi- bucket pixels that enable time-multiplexed exposure, an alter- native imaging approach. This approach deals nicely with scene motion, and greatly improves high dynamic range imaging, structured light illumination, motion corrected photography, etc. To implement an in-pixel memory or a bucket, the new image sensors incorporate the virtual phase CCD concept into a standard 4-transistor CMOS imager pixel. This design allows us to create a multi-bucket pixel which is compact, scalable, and supports true correlated double sampling to cancel kTC noise. Two image sensors with dual and quad-bucket pixels have been designed and fabricated. The dual-bucket sensor consists of a 640 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</sub> × 576 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</sub> array of 5.0 μm pixel in 0.11 μm CMOS technology while the quad-bucket sensor comprises 640 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</sub> × 512 <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">V</sub> array of 5.6 μm pixel in 0.13 μm CMOS technology. Some computational photography applications were implemented using the two sensors to demonstrate their values in eliminating artifacts that currently plague computational photography.
Recognition of BCR-ABL positive leukemic blasts by human CD4+ T cells elicited by primary in vitro immunization with a BCR-ABL breakpoint peptide (1996)

In chronic myeloid leukemia (CML) the classical 9;22 translocation results in a BCR-ABL fusion gene, which encodes chimeric BCR-ABL fusion 210 kD oncoproteins (p210BCR-ABL). The two main p210BCR-ABL fusion variants in CML, b2a2 and b3a2 are examples of well characterized antigens expressed by malignant cells. The possibility of an immunotherapeutic approach involving the fusion part of p210BCR-ABL in CML has previously been illustrated by observed peptide binding to major histocompatibility complex (MHC) class I alleles and by demonstrating the immunogenicity of p210BCR-ABL breakpoint peptides. In this report we show that in vitro immunization of human T cells with a 17 amino acid (aa) peptide representing the p210BCR-ABL fusion region resulted in peptide specific CD4+ T-cell lines designated P4, P6, and P7. HLA DR4 (DRB1*0401) restricted T-cell line P4 and several subsequently derived clones recognized HLA-DRB1*0401 and p210b3a2-mRNA expressing blasts from an allogeneic patient with CML in blast crisis. Recognition appeared DR expression-dependent. No responses were observed with DR4 positive p210BCR-ABL negative cells or with p210b3a2 leukemic cells with absent or insufficient expression of DR4. These observations indicate that oncoprotein p210b3a2 can be degraded and processed for presentation by MHC class II molecules at the surface of leukemic cells. The BCR-ABL fusion region is in all likelihood presented as peptides by HLA DR and thus capable to act as a distinctive tumor antigen to peptide specific CD4+ T cells.
Regulation of inflammasome activation (2015)

Inflammasome biology is one of the most exciting and rapidly growing areas in immunology. Over the past 10 years, inflammasomes have been recognized for their roles in the host defense against invading pathogens and in the development of cancer, auto-inflammatory, metabolic, and neurodegenerative diseases. Assembly of an inflammasome complex requires cytosolic sensing of pathogen-associated molecular patterns or danger-associated molecular patterns by a nucleotide-binding domain and leucine-rich repeat receptor (NLR) or absent in melanoma 2 (AIM2)-like receptors (ALR). NLRs and ALRs engage caspase-1, in most cases requiring the adapter protein apoptosis-associated speck-like protein containing a CARD (ASC), to catalyze proteolytic cleavage of pro-interleukin-1β (pro-IL-1β) and pro-IL-18 and drive pyroptosis. Recent studies indicate that caspase-8, caspase-11, IL-1R-associated kinases (IRAK), and receptor-interacting protein (RIP) kinases contribute to inflammasome functions. In addition, post-translational modifications, including ubiquitination, deubiquitination, phosphorylation, and degradation control almost every aspect of inflammasome activities. Genetic studies indicate that mutations in NLRP1, NLRP3, NLRC4, and AIM2 are linked with the development of auto-inflammatory diseases, enterocolitis, and cancer. Overall, these findings transform our understanding of the basic biology and clinical relevance of inflammasomes. In this review, we provide an overview of the latest development of inflammasome research and discuss how inflammasome activities govern health and disease.