gebhart/patrepeval huggingface dataset:
A Unidirectional DNA Walker That Moves Autonomously along a Track (2004)

There's no turning back for an autonomous DNA walker that moves along a self-assembled track, driven by the hydrolysis of ATP. The track contains three anchorages (A, B, C) at which the walker (★), a six-nucleotide DNA fragment, can be bound (see figure). The motion of the walker is unidirectional. At each step it is ligated to the next anchorage, then cut from the previous one by a restriction endonuclease. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2004/z460522_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Ethanol, marijuana, and other drug use in 600 drivers killed in single-vehicle crashes in North Carolina, 1978-1981. (1984)

Although the use of ethanol, marijuana, and other drugs may be detrimental to driving safety, this has been established by direct epidemiological evidence only for ethanol. In this study, the incidences of detection of ethanol (and other volatile substances), delta-9-tetrahydrocannabinol (THC), barbiturates, cocaine and benzoylecgonine, opiates, and phencyclidine were determined in an inclusive population of 600 verified single-vehicle operator fatalities that occurred in North Carolina in 1978 to 1981. The incidence of detection of amphetamines and methaqualone were determined for drivers accepted for study during the first two years (n = 340) and the last year (n = 260), respectively. Blood concentrations of 11-nor-deta-9-tetrahydrocannabinol-9-carboxylic acid (9-carboxy-THC) were determined in THC positive drivers. EMIT cannabinoid assays were performed on blood specimens from all drivers accepted for study during the third year, and the feasibility of using the EMIT cannabinoid assay as a screening method for cannabinoids in forensic blood specimens was investigated. The incidence of detection of ethanol (79.3%) was far greater than the incidences determined for THC (7.8%), methaqualone (6.2%), and barbiturates (3.0%). Other drugs were detected rarely, or were not detected. Blood ethanol concentrations (BECs) were usually high; 85.5% of the drivers whose bloods contained ethanol and 67.8% of all drivers had BECs greater than or equal to 1.0 g/L. Drug concentrations were usually within or were below accepted therapeutic or active ranges. Only a small number of drivers could have been impaired by drugs, and most of them had high BECs. Multiple drug use (discounting ethanol) was comparatively rare. Ethanol was the only drug tested for that appears to have a significantly adverse effect on driving safety.
Interaction of the Neisseria gonorrhoeae PilA protein with the pilE promoter involves multiple sites on the DNA (1995)

PilA is the putative DNA-binding component of a two-component system that regulates transcription of the pilin expression locus (pilE) of Neisseria gonorrhoeae. Here we report the purification of the PilA protein and characterization of its DNA-binding activity. PilA was overproduced in Escherichia coli with an isopropyl-beta-D-thiogalactopyranoside (IPTG)-inducible expression vector. Cell extracts were prepared by sonication and fractionated by anion-exchange chromotography, followed by dye affinity chromatography with Cibacron Blue. Proteins were eluted by using a gradient of KCl, and PilA-containing fractions were identified by immunoblot analysis with a polyclonal anti-PilA antiserum. Purified PilA was judged to be > 90% pure, as determined by Coomassie blue staining and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. PilA purified in this manner was used to develop a gel retardation assay with a 301-bp fragment containing the pilE promoter (PpilE) and upstream sequences as a probe. A fragment of similar size containing the E. coli aroH promoter was used as a negative control. Competition experiments using a 100- to 1,000-fold excess of unlabelled DNA fragments confirmed the specificity of PilA binding to the pilE promoter. To localize the PilA binding site within the 301-bp PpilE fragment, stepwise deletions were generated by PCR and the fragments were examined in the gel shift assay. The results of these experiments show that there are two regions upstream of PpilE that are required for binding by PilA. Taken together, these data indicate that while PilA binds specifically to the upstream region of the pilE gene, this interaction is complex and likely involves multiple regions of this DNA sequence.
Preparation of Silicon Oxycarbide Composites Toughened by Inorganic Fibers via Pyrolysis of Precursor Siloxane Composites (2011)

The optimization of silicon oxycarbide (SiOC) synthesis (sol-gel/pyrolysis) is described, starting from methyltriethoxysilane, dimethyldiethoxysilane, tetraethoxysilane, ethyltriethoxysilane and propyltriethoxysilane. Variation of final elemental composition was tested via change of monomer ratios and combinations. The main aim was to achieve low weight losses during cure and pyrolysis and high micromechanical properties. Gas chromatography and mass spectroscopy was used to analyse the by-products of cure and pyrolysis, indicating a prominent role of cyclosiloxane and polyhedral oligomeric silsesquioxane (POSS) oligomers. Best results were obtained with high contents of methyltriethoxysilane in the monomers mixture.
Mechanisms and Function of DUOX in Epithelia of the Lung (2009)

The human lung produces considerable amounts of H(2)O(2). In the normal uninflamed epithelium of both the airways and the alveoli, mucosal release of H(2)O(2) is readily detected both in cell cultures in vitro and in the exhaled breath of humans. The dual oxidases DUOX1 and DUOX2 are the H(2)O(2)-producing isoforms of the NADPH oxidase family found in epithelial cells. The DUOXs are prominently expressed at the apical cell pole of ciliated cells in the airways and in type II cells of the alveoli. Recent studies focused on the functional consequences of H(2)O(2) release by DUOX into the lung lining fluid. In the airways, a major function of DUOX is to support lactoperoxidase (LPO) to generate bactericidal OSCN(-), and there are indications that the DUOX/LPO defense system is critically dependent on the function of the CFTR Cl(-) channel, which provides both SCN(-) (for LPO function) and HCO(3)(-) (for pH adjustment) to the airway surface liquid. Although DUOX is also functional in the alveolar epithelium, no comparable heme peroxidase is present in the alveolus, and thus DUOX-mediated H(2)O(2) release by alveolar cells may have other functions, such as cellular signaling.
Bacterial capsular polysaccharide prevents the onset of asthma through T-cell activation (2014)

Over the last four decades, increases in the incidence of immune-mediated diseases in the Western world have been linked to changes in microbial exposure. It is becoming increasingly clear that the normal microbiota in the gut can profoundly alter susceptibility to a wide range of diseases, such as asthma, in which immune homeostasis is disrupted, yet the mechanisms governing this microbial influence remains poorly defined. In this study, we show that gastrointestinal exposure to PSA, a capsular polysaccharide derived from the commensal bacterium Bacteroides fragilis, significantly limits susceptibility to the induction of experimental asthma. We report that direct treatment of mice with PSA generates protection from asthma, and this effect can be given to a naïve recipient by adoptive transfer of CD4(+) T cells from PSA-exposed mice. Remarkably, we found that these PSA-induced T cells are not canonical FoxP3(+) regulatory T cells, but that they potently inhibit both Th1 and Th2 models of asthma in an IL-10-dependent fashion. These findings reveal that bacterial polysaccharides link the microbiota with the peripheral immune system by activating CD4(+)Foxp3(-) T cells upon exposure in the gut, and they facilitate resistance to unnecessary inflammatory responses via the production of IL-10.
Expression of a Single, Host-Specific, Bacterial Pathogenicity Gene in Plant Cells Elicits Division, Enlargement, and Cell Death (1999)

A fundamental question about microbial pathogens is how they elicit host-specific symptoms. We report here that expression of a single gene from a plant-pathogenic bacterium in plant cells elicits host-specific symptoms diagnostic of the disease caused by the pathogen. Expression of pthA from Xanthomonas citri in citrus cells is sufficient to cause division, enlargement, and death of host cells. Since elicitation of these symptoms depends on a functional type III protein secretion system in X. citri, we deduce that the PthA protein is a specific plant signal, its site of action is inside the plant cell, and it is a major determinant of host range.
The Molecular and Functional Characterization of a Dominant Minor H Antigen, H60 (1998)

Minor histocompatibility (H) Ags elicit T cell responses and thereby cause chronic graft rejection and graft-vs-host disease among MHC identical individuals. Although numerous independent H loci exist in mice of a given MHC haplotype, certain H Ags dominate the immune response and are thus of considerable conceptual and therapeutic importance. To identify these H Ags and their genes, lacZ-inducible CD8+ T cell hybrids were generated by immunizing C57BL/6 (B6) mice with MHC identical BALB.B spleen cells. The cDNA clones encoding the precursor for the antigenic peptide/Kb MHC class I complex were isolated by expression cloning using the BCZ39.84 T cell as a probe. The cDNAs defined a new H locus (termed H60), located on mouse chromosome 10, and encoded a novel protein that contains the naturally processed octapeptide LTFNYRNL (LYL8) presented by the Kb MHC molecule. Southern blot analysis revealed that the H60 locus was polymorphic among the BALB and the B6 strains. However, none of the H60 transcripts expressed in the donor BALB spleen were detected in the host B6 strain. The expression and immunogenicity of the LYL8/Kb complex in BALB.B and CXB recombinant inbred strains strongly suggested that the H60 locus may account for one of the previously described antigenic activity among these strains. The results establish the source of an immunodominant autosomal minor H Ag that, by its differential transcription in the donor vs the host strains, provides a novel peptide/MHC target for host CD8+ T cells.
Bend measurement using multicore optical fiber (1997)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text M. J. Gander, E. A. C. Galliot, R. McBride, J. D. C. Jones, J. G. Burnett, and A. H. Greenaway, "Bend measurement using multicore optical fiber," in 12th International Conference on Optical Fiber Sensors, Vol. 16 of 1997 OSA Technical Digest Series (Optica Publishing Group, 1997), paper OWC6. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
New markers for pancreatic islets and islet cell tumors (2002)

Islets of Langerhans account for 2 g of endocrine tissue in the pancreas, comprising approximately one million islets, with each containing 1000 endocrine cells. The major hormone secreted from the islets is insulin, which regulates blood glucose, the main fuel of the body. Islets also secrete glucagon, somatostatin and pancreatic polypeptide and all are involved in the paracrine mechanism. Islet cells can be stained immunohistochemically for the general endocrine markers, chromogranin A, synaptophysin, neuron-specific enolase and Leu7. Beta islet cells are well equipped with glucose transporter 2, which binds to glucose and regulates diffusion of glucose through the beta cell membrane. As all four islet hormones are initially synthesized as prohormones, all islet cells are equipped with prohormone convertase 1/3 and 2. In addition, islet cells also contain zinc-containing matrix metalloproteinases and their inhibitors, metallothionein, cyclin-dependent kinases and insulin-like growth factors, and many more hormones, peptides and enzymes. Thus, islets not only secrete insulin and other pancreatic hormones but are a complex organ whose major function is glucose homeostasis.
Soft tissue limb sarcomas (1999)

These findings show that HAP with doxorubicin and TNF (< or =1 mg) at a muscle temperature of < or =41.5 degrees C is a safe, active, and effective perfusional regimen for the multidisciplinary treatment of patients with advanced STLS.
Multilevel DC link inverter (2004)

This paper presents a new class of multilevel inverters based on a multilevel DC link (MLDCL) and a bridge inverter to reduce the number of switches, clamping diodes or capacitors. An MLDCL can be a diode-clamped phase leg, a flying capacitor phase leg, or cascaded half-bridge cells with each cell having its own DC source. Connecting one of the MLDCLs with a single-phase bridge inverter can form a multilevel voltage source inverter. The MLDCL provides a DC voltage with the shape of a staircase approximating the rectified shape of a commanded sinusoidal wave, with or without pulse width modulation, to the bridge inverter, which in turn alternates the polarity to produce an ac voltage. Compared with the cascaded H-bridge, diode-clamped and flying-capacitor multilevel inverters, the MLDCL inverters can significantly reduce the switch count as the number of voltage levels increases. For a given number of voltage levels, m, the required number of active switches is 2/spl times/(m-1) for the existing multilevel inverters but is m+3 for the MLDCL inverters. Simulation and experimental results are included to verify the operating principles of the MLDCL inverters.
Oncoproteomic profiling with antibody microarrays (2009)

The incidence of cancer and its associated mortality are increasing globally, indicating an urgent need to develop even more effective and sensitive sets of biomarkers that could help in early diagnosis and consequent intervention. Given that many cellular processes are carried out by proteins, cancer research has recently shifted toward an exploration of the full proteome for such discovery. Among the advanced methodologies that are being developed for analyzing the proteome, antibody microarrays have become a prominent tool for gathering the information required for a better understanding of disease biology, early detection, discrimination of tumors and monitoring of disease progression. Here, we review the technical aspects and challenges in the development and use of antibody microarray assays and examine recently reported applications in oncoproteomics.
Synthesis and Biological Activities of a New Set of Irreversibly Acting 2-(4'-Isothiocyanatobenzyl)imidazoline Analogs in Rat Thoracic Aorta (1994)

IBI [2-(4'-isothiocyanatobenzyl)imidazoline, 3] has been shown to cause slow-onset, long-lasting contractions of rat thoracic aorta through a non-alpha-adrenergic receptor (non-alpha-AR) mediated mechanism. A series of IBI-related anlogs 7-14 and 16 was prepared to determine the structural requirements for the interaction with non-alpha-AR in rat aortic strips. All IBI analogs produced concentration-dependent contractile responses on rat thoracic aorta. Whereas the actions of analogs 7, 14, and 16 were partly mediated by alpha-ARs, the stimulatory activities of the remaining IBI analogs were unaffected by phenoxybenzamine pretreatment, suggesting that a non-alpha-adrenergic mechanism is involved. We have shown that the contractile actions of IBI and analogs 10-13 were not blocked with the imidazoline/guanidinium receptive site (IGRS) ligands idazoxan, cirazoline, or clonidine. However, the calcium channel blockers nifedipine or verapamil shifted the concentration-response curve of IBI and its analogs 10-13 to the right and reduced the maximal contractile responses. The action of IBI on rat thoracic aorta was reduced by the omission of extracellular calcium in the medium. These results suggest that the stimulatory activities of IBI and analogs 10-13 are not related to the activation of alpha-AR or IGRS receptors and are likely coupled to the voltage-dependent Ca2+ channels.
Molecular cloning of the human kidney differentiation antigen gp160: human aminopeptidase A. (1993)

gp160 is a cell surface differentiation-related glycoprotein of 160 kDa expressed by epithelial cells of the glomerulus and proximal tubule cells of the human nephron but only by a subset of renal cell carcinomas (RCCs). We have reported that gp160 expression correlates with the resistance of cultured RCCs to the antiproliferative effects of alpha interferon, while lack of expression correlates with sensitivity to alpha interferon. In this study, we have purified gp160 protein, obtained partial sequences of random peptides, and isolated a full-length cDNA. The gp160 cDNA possesses 78% homology to the murine BP-1/6C3 antigen, a B-lymphocyte differentiation protein that exhibits aminopeptidase A (APA; EC 3.4.11.7) activity. Enzymatic assays on human RCC cell lines indicated a 100% concordance between APA activity and gp160 expression. APA activity of gp160-expressing RCC cells was increased or decreased by a panel of APA activators or inhibitors, respectively. Furthermore, anti-gp160 monoclonal antibodies immunoprecipitate APA activity from RCC cell lysates and selectively deplete APA activity from RCC cell extracts. These data indicate that the gp160 human kidney/RCC glycoprotein is human APA.
CD4+CD25hi regulatory T‐cell frequency correlates with persistence of human papillomavirus type 16 and T helper cell responses in patients with cervical intraepithelial neoplasia (2007)

CD4(+)CD25(hi)CTLA4(+)FoxP3(+) regulatory T cells (Treg) have been shown to maintain immune tolerance against self antigens and increased circulating frequencies have been reported in various types of cancers. Circulating invariant natural killer T-cells (iNKT) are reduced in cancer patients and low iNKT frequency is related to poor prognosis. It is not yet clear whether high Treg numbers and low iNKT cell numbers pose an increased risk for the progression of premalignant lesions or whether Treg and iNKT cell numbers are influenced by dysplasia. We therefore studied prospectively the relation between iNKT cell and Treg frequencies and the natural course of human papillomavirus type 16 (HPV16) induced pre-malignant cervical dysplasia in 82 patients who participated in a nonintervention cohort study of women with abnormal cytology. Treg frequencies were significantly increased in women who had persistent HPV16 infection. Within the HPV16 persistence group there was no difference in Treg frequencies among patients who developed a CIN3 lesion and patients who did not progress to CIN3. Furthermore, Treg frequencies were increased in patients who had detectable HPV16 E7 specific IL-2 producing T-helper cells, which suggests a causal role of HPV infection in Treg development in parallel with HPV16 specific T helper cells. No evidence was found for a role for iNKT cells in persistence of HPV16 and progression of HPV16 induced CIN lesions. However, HPV-persistence-associated Tregs may explain the inefficacy of concomitant persistence associated immunity and may contribute to subsequent progression to neoplasia.
A conotoxin from Conus textile with unusual posttranslational modifications reduces presynaptic Ca 2+ influx (1999)

Cone snails are gastropod mollusks of the genus Conus that live in tropical marine habitats. They are predators that paralyze their prey by injection of venom containing a plethora of small, conformationally constrained peptides (conotoxins). We report the identification, characterization, and structure of a gamma-carboxyglutamic acid-containing peptide, conotoxin epsilon-TxIX, isolated from the venom of the molluscivorous cone snail, Conus textile. The disulfide bonding pattern of the four cysteine residues, an unparalleled degree of posttranslational processing including bromination, hydroxylation, and glycosylation define a family of conotoxins that may target presynaptic Ca2+ channels or act on G protein-coupled presynaptic receptors via another mechanism. This conotoxin selectively reduces neurotransmitter release at an Aplysia cholinergic synapse by reducing the presynaptic influx of Ca2+ in a slow and reversible fashion. The three-dimensional structure, determined by two-dimensional 1H NMR spectroscopy, identifies an electronegative patch created by the side chains of two gamma-carboxyglutamic acid residues that extend outward from a cavernous cleft. The glycosylated threonine and hydroxylated proline enclose a localized hydrophobic region centered on the brominated tryptophan residue within the constrained intercysteine region.
CodeSearchNet Challenge: Evaluating the State of Semantic Code Search (2019)

The dataset for CodeSearchNet. See https://github.com/github/CodeSearchNet and https://arxiv.org/abs/1909.09436 for more.
Characterization of the major histocompatibility complex class II binding site on LAG-3 protein (1997)

The lymphocyte activation gene-3 (LAG-3), selectively transcribed in human activated T and NK cells, encodes a ligand for major histocompatibility complex (MHC) class II molecules. Like CD4, LAG-3 ectodomain is composed of four Ig-like domains (D1-D4). Nothing is known about the LAG-3 regions or residues required to form a stable MHC class II binding site. In contrast to CD4, soluble LAG-3 molecules stably interact with MHC class II molecules expressed on the cell surface. In addition, the first two N-terminal domains of soluble LAG-3 (D1 and D2) molecules, alone, are capable of binding MHC class II. From a LAG-3 model structure, we designed mutants and tested their ability to bind MHC class II molecules in an intercellular adhesion assay. We found residues on the membrane-distal, CDR1-2-containing top face of D1 that are essential for either binding or repulsing MHC class II proteins. Most of these residues are clustered at the base of a large extra-loop structure that is a hallmark of the LAG-3 D1 Ig-like domain. In addition, as for CD4, oligomerization of LAG-3 on the cell surface may be required to form a stable MHC binding site because mutation of three residues in the ABED beta-strands containing side of D1 results in a dominant negative effect (i.e., binding inhibition of coexpressed wild-type LAG-3).
Liposomal encapsulated anti-cancer drugs (2005)

Among several drug delivery systems, liposomal encapsulated anti-cancer agents represent an advanced and versatile technology. Several formulations of liposomal anthracyclines are approved, e.g. for the treatment of metastatic breast cancer (pegylated and non-pegylated liposomal doxorubicin) or AIDS-related Kaposi's sarcoma (pegylated liposomal doxorubicin and liposomal daunorubicin). Meanwhile, virtually all anti-cancer drugs have been encapsulated in liposomes using different technologies. This review will summarize preclinical and clinical data of approved and exemplary emerging liposomal anti-cancer agents.