gebhart/patrepeval huggingface dataset:
Insertion of DNA Sequences at a Unique Restriction Enzyme Site Engineered for Vector Purposes into the Genome of Herpes Simplex Virus Type 1 (1990)

We describe the construction of a novel herpes simplex virus (HSV) vector containing a unique XbaI restriction enzyme cloning site in an intergenic position in the short unique genome region. Sequences can be inserted at this site with high efficiency by ligation with XbaI-digested vector DNA. A series of plasmids has been designed for use with this vector. These allow protein coding sequences to be placed under the control of various transcriptional regulation signals and then isolated as XbaI fragments ready for insertion into the vector. The XbaI fragments also contain the beta-galactosidase gene thereby facilitating selection of recombinant virus by screening for blue plaques. A variant of the vector has been made based on the temperature-sensitive (ts) mutant tsK, which expresses only immediate early (IE) genes at non-permissive temperatures. Chloramphenicol acetyltransferase was used as a reporter gene to assess the fidelity of expression of sequences cloned into this position. Under these circumstances IE and early HSV promoters were shown to behave as expected in both wild-type and ts vectors.
ANTIMALARIALS.1 SOME PIPERAZINE DERIVATIVES (1947)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTANTIMALARIALS.1 SOME PIPERAZINE DERIVATIVESROBERT E. LUTZ and NEWTON H. SHEARERCite this: J. Org. Chem. 1947, 12, 6, 771–775Publication Date (Print):November 1, 1947Publication History Published online1 May 2002Published inissue 1 November 1947https://pubs.acs.org/doi/10.1021/jo01170a005https://doi.org/10.1021/jo01170a005research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Blockage of polymerase-catalyzed DNA chain elongation by chemiscally modified cytosine residues in templates and the release of blockage for readthrough (1992)

The Klenow fragment-mediated in vitro DNA elongation was inhibited by the presence of a class of modified cytosines in the template DNA, i.e., the N4-amino(and -methoxy)-5,6-dihydrocytosine-6-sulfonate residues. We have studied the mechanism of the blockage, using as templates bisulfite-hydrazine (and -methoxyamine)- modified single strand phage-M13mp2 DNA and synthetic oligonucleotides. Both N4-amino-5,6-dihydrocytosine-6-sulfonate and N4-methoxy-5,6-dihydrocytosine-6-sulfonate residues blocked the elongation at one nucleotide before these sites. In this blockage, the idling of polymerase at the lesion site due to its 3'-5' exonuclease action appears not to play a major role, because Sequenase that lacks the 3'-5' exonuclease activity still could not readthrough these sites. It seems possible that conformational distortion of the template near these sites is responsible for the blockage, because on conversion of this 5,6-dihydropyrimidine-6-sulfonate structure into a planar pyrimidine, a complete restoration of polymerase-readthrough resulted. In the presence of RecA and SSB proteins, the Klenow fragment was able to partially readthrough these sites. Since there was no decrease in the 3'-5' exonuclease activity during this readthrough, it seems that the binding of these proteins relaxes the distortion in the modified template to allow the polymerase to readthrough the lesion site. These sites on phage DNA can be lethal but also are capable of inducing C-to-T transitions. This observation suggests that these sites can be read by E. coli DNA polymerases in vivo with accompanying errors.
Nanoaperture-enhanced fluorescence: Towards higher detection rates with plasmonic metals (2008)

A bare nanometric aperture milled in a metallic film forms a simple nanophotonic device that can strongly enhance the optical properties of nearby emitters such as fluorescent molecules. In this paper, we experimentally and numerically compare the properties of circular apertures milled in gold and aluminum, and discuss the influence of a noble metal holding plasmonic resonances in the visible range such as gold. We report that nanometric apertures milled in gold exhibit significantly higher fluorescence enhancement factors than apertures in aluminum. We relate this effect to a larger enhancement of the excitation intensity and radiative rate for an aperture milled in gold. A spectrally resolved analysis of the fluorescence emission from apertures is also presented. Comparison with numerical simulations shows that the enhancement factor is maximum when the photonic density of modes is maximum. Altogether, these results provide crucial knowledge for the design of nanoapertures towards high-efficiency single-molecule analysis.
Factor-independent erythropoietic progenitor cells in leukemia induced by the myeloproliferative leukemia virus (1989)

The myeloproliferative leukemia virus (MPLV), a novel murine retroviral complex that does not transform fibroblasts, has been shown to cause an acute leukemia in adult mice accompanied by a progressive polycythemia. The present study demonstrates that, on in vivo inoculation, MPLV induces a rapid suppression of growth factor requirement for in vitro colony formation by both the late and the primitive erythroid progenitor cells. CFU-e-derived erythrocytic colonies developed and differentiated in semi-solid medium without the addition of erythropoietin (Epo). In addition, the formation of CFU-e colonies was not altered by the presence of specific neutralizing Epo antibodies. In the spleen, the CFU-e pool size increased rapidly up to 30-fold. By day 6 postinfection, 100% of these progenitor cells were Epo-independent. The in vivo effects of MPLV-infection on early erythroid progenitor cell compartments were examined in cultures grown for seven days. The concentration of erythroid progenitor cells was twofold elevated in spleen from MPLV-infected mice. As early as day 4 postinfection, 50% of these progenitors produced fully hemoglobinized colonies in serum-free cultures without the addition of interleukin-3 (IL-3) and Epo. Most spontaneous colonies were large and contained up to 10(5) cells per colony. They were composed of either erythroblasts only (16%) or erythroblasts and megakaryocytes (70%); few of them were multipotential (14%). In the marrow, the total number of BFU-e was reduced and only few factor-independent bursts were observed, suggesting a rapid migration of infected progenitors from marrow to spleen. Furthermore, the data show that abnormal erythropoiesis was due to the replication defective MPLV information and was not influenced by the Fv-2 locus.
Sorbitol Dehydrogenase Inhibitors (SDIs):  A New Potent, Enantiomeric SDI, 4-[2-1R-Hydroxy-ethyl)-pyrimidin-4-yl]-piperazine-1-sulfonic Acid Dimethylamide (2001)

We report here on our medicinal chemistry and pharmacology efforts to provide a potent sorbitol dehydrogenase inhibitor (SDI) as a tool to probe a recently disclosed hypothesis centered on the role of sorbitol dehydrogenase (SDH) in the second step of the polyol pathway, under conditions of high glucose flux. Starting from a weak literature lead, 2, and through newly developed structure-activity relationships, we have designed and executed an unambiguous synthesis of enantiomeric SDI, 6, which is at least 10x more potent than 2. Also, 6 potently inhibits SDH in streptozotocin-diabetic rat sciatic nerve. We have described an expedient synthesis of a key building template, 33, for future research in the SDI area that may facilitate the discovery of even more potent SDIs with longer duration of action in vivo.
Origin and mechanisms of non-disjunction In human autosomal trisomies (1998)

Chromosomal aneuploidy is one of the major causes of pregnancy wastage. In this review we summarize the knowledge about the origin and mechanisms of non-disjunction in human autosomal trisomies 8, 13, 15, 16, 18, and 21, accumulated during the last decade by using DNA polymorphism analysis. Maternal meiosis I non-disjunction is the most important single class, but chromosome-specific patterns exist. For the acrocentric chromosomes 15 and 21, meiosis I errors predominate among the maternal errors, in contrast to trisomy 18 where meiosis II errors predominate. For trisomy 16, virtually all cases are due to maternal meiosis I non-disjunction. Postzygotic (mitotic) non-disjunction constitutes 5-15% of cases of trisomies 15, 18, and 21, whereas for trisomy 8 and trisomy 8 mosaicism the majority of cases are due to mitotic non-disjunction. For paternal non-disjunction of chromosomes 18 and 21, meiosis II or mitotic errors predominate. There is aberrant meiotic recombination associated with maternal meiotic non-disjunction in all trisomies studied in detail so far. Advanced maternal age remains the only well documented risk factor for maternal meiotic non-disjunction, but there is, however, still a surprising lack of understanding of the basic mechanism(s) behind the maternal age effect.
Air-Stable PinP(O)H as Preligand for Palladium-Catalyzed Kumada Couplings of Unactivated Tosylates (2006)

[reaction: see text] Air-stable and easily accessible PinP(O)H enables highly efficient palladium-catalyzed Kumada cross-coupling reactions of aryl tosylates. The in situ generated catalyst proved applicable not only to electron-rich and electron-poor carbocyclic tosylates but also to heterocyclic tosylates, such as pyridine and quinoline derivatives. The results described herein constitute the first use of air-stable secondary phosphine oxides as preligands for transition-metal-catalyzed coupling reactions between organometallic species and tosylates.
Defective T Cell Differentiation in the Absence of Jnk1 (1998)

The c-Jun NH2-terminal kinase (JNK) signaling pathway has been implicated in the immune response that is mediated by the activation and differentiation of CD4 helper T (TH) cells into TH1 and TH2 effector cells. JNK activity observed in wild-type activated TH cells was severely reduced in TH cells from Jnk1-/- mice. The Jnk1-/- T cells hyperproliferated, exhibited decreased activation-induced cell death, and preferentially differentiated to TH2 cells. The enhanced production of TH2 cytokines by Jnk1-/- cells was associated with increased nuclear accumulation of the transcription factor NFATc. Thus, the JNK1 signaling pathway plays a key role in T cell receptor-initiated TH cell proliferation, apoptosis, and differentiation.
Bacterial milking: A novel bioprocess for production of compatible solutes (1998)

A novel biotechnological process called “bacterial milking” has been established for the production of compatible solutes using the Gram-negative bacterium Halomonas elongata. Following a high-cell-density fermentation which provided biomass up to 48 g cell dry weight per liter, we applied alternating osmotic shocks in combination with crossflow filtration techniques to harvest the compatible solutes ectoine and hydroxyectoine. H. elongata, like other halophilic or halotolerant microorganisms, produces compatible solutes in response to the salinity of the medium. When transferred to a low salinity medium (osmotic downshock), H. elongata cells rapidly released their solutes to achieve osmotic equilibrium. Subsequent reincubation in a medium of higher salt concentration resulted in resynthesis of these compatible solutes and—after a defined regeneration time—the procedure could be repeated. By repeatedly performing this “bacterial milking” process (at least nine times) we were able to produce large amounts of ectoines with a biomass productivity of 155 mg of ectoine per cycle per gram cell dry weight. Further purification of the products was achieved by a simple two-step procedure based on cation exchange chromatography and crystallization. The principles described in this article may also be useful for the production of other low-molecular-weight compounds. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 306–313, 1998.
In vivo effects of monoclonal antibody to ICAM-1 (CD54) in nonhuman primates with renal allografts. (1990)

These studies test whether allograft rejection can be blocked by interference with leukocyte adhesion, using a murine IgG2a mAb (R6.5) reactive with monkey ICAM-1 (CD54). In 16 Cynomolgus renal allograft recipients, R6.5 was administered prophylactically as the sole immunosuppressive agent for 12 days (0.01 to 2 mg/kg/day). Survival in 14 recipients with technically successful grafts was significantly prolonged (24.2 +/- 2.4 vs 9.2 +/- 0.6 days for controls; p less than 0.001). Intercellular adhesion molecule-1 (CD54) (ICAM-1) was expressed on vascular endothelium in the kidney and other organs in the monkey in a pattern similar to that in humans. During cellular rejection in controls, ICAM-1 expression increased on endothelial cells, infiltrating mononuclear leukocytes and tubular cells. Biopsies during R6.5 administration showed decreased T cell infiltration (CD2, CD8, CD4) compared with controls and decreased arterial endothelial inflammation. No changes occurred in circulating T cells, aside from variable coating with mIgG. In six of eight other recipients R6.5 administration (0.5 to 2 mg/kg/day for 10 days) reversed preexisting rejection that resulted from taper of Cyclosporine to subtherapeutic levels. Responding grafts showed decreased edema and hemorrhage but no consistent change in the infiltrate. At 1 h after the first dose, mouse IgG deposited primarily on the graft vascular endothelium without any change in the inflammatory infiltrate. Mouse IgG also deposited on the endothelium of normal organs without eliciting an inflammatory response and was cleared from the endothelium within 4 days. Inasmuch as the principal site of binding was the vascular endothelium, we hypothesize that the antibody blocks adhesion to graft ICAM-1 molecules on the vessels. Anti-ICAM-1 also binds to recipient cells and may interfere with Ag presentation and/or T cell interactions. Whatever the mechanism(s), these studies indicate that an anti-ICAM-1 antibody inhibits T cell mediated injury in vivo, and that ICAM-1 is a critical molecule in the pathogenesis of allograft rejection.
Overview of Affinity Tags for Protein Purification (2013)

Abstract Addition of an affinity tag is a useful method for differentiating recombinant proteins expressed in bacterial and eukaryotic expression systems from the background of total cellular proteins, as well as for detecting protein‐protein interactions. This overview describes the historical basis for the development of affinity tags, affinity tags that are commonly used today, how to choose an appropriate affinity tag for a particular purpose, and several recently developed affinity tag technologies that may prove useful in the near future. Curr. Protoc. Protein Sci . 73:9.9.1‐9.9.23. © 2013 by John Wiley &amp; Sons, Inc.
A cre/loxP‐deleter transgenic line in mouse strain 129S1/SvImJ (2002)

A Cre recombinase expression cassette was inserted into the X-linked Hprt locus by gene targeting in a mouse embryonic stem (ES) cell line isogenic to strain 129S1/SvImJ (129S1), then the transgene was introduced into 129S1 mice through ES cell chimeras. When females hemizygous for this transgene were mated to males carrying a neomycin selection cassette flanked by loxP sites, the cassette was always excised regardless of Cre inheritance and without detectable mosaicism. The usefulness of this "Cre-deleter" transgenic line is in its efficiency and defined genetic status in terms of mouse strain and location of the transgene.
Novel genetic variants in Asian subjects and their influence on maintenance warfarin dose (2004)

10.1016/j.clpt.2004.05.005
Genome sequence analysis of Helicobacter pylori strains associated with gastric ulceration and gastric cancer (2009)

These data provide insight into the diversity that exists among H. pylori strains from diverse clinical and geographic origins. Highly divergent alleles and strain-specific genes identified in this study may represent useful biomarkers for analyzing geographic partitioning of H. pylori and for identifying strains capable of inducing malignant or premalignant gastric lesions.
Automatic measurement of contact angle in pore-space images (2017)

A new approach is presented to measure the in-situ contact angle (θ) between immiscible fluids, applied to segmented pore-scale X-ray images. We first identify and mesh the fluid/fluid and fluid/solid interfaces. A Gaussian smoothing is applied to this mesh to eliminate artifacts associated with the voxelized nature of the image, while preserving large-scale features of the rock surface. Then, for the fluid/fluid interface we apply an additional smoothing and adjustment of the mesh to impose a constant curvature. We then track the three-phase contact line, and the two vectors that have a direction perpendicular to both surfaces: the contact angle is found from the dot product of these vectors where they meet at the contact line. This calculation can be applied at every point on the mesh at the contact line. We automatically generate contact angle values representing each invaded pore-element in the image with high accuracy. To validate the approach, we first study synthetic three-dimensional images of a spherical droplet of oil residing on a tilted flat solid surface surrounded by brine and show that our results are accurate to within 3° if the sphere diameter is 2 or more voxels. We then apply this method to oil/brine systems imaged at ambient temperature and reservoir pressure (10MPa) using X-ray microtomography (Singh et al., 2016). We analyse an image volume of diameter approximately 4.6 mm and 10.7 mm long, obtaining hundreds of thousands of values from a dataset with around 700 million voxels. We show that in a system of altered wettability, contact angles both less than and greater than 90° can be observed. This work provides a rapid method to provide an accurate characterization of pore-scale wettability, which is important for the design and assessment of hydrocarbon recovery and carbon dioxide storage.
Three-Dimensional Quantitative Structure−Activity Relationship of Interleukin 1-β Converting Enzyme Inhibitors:  A Comparative Molecular Field Analysis Study (1999)

A three-dimensional quantitative structure-activity relationship (QSAR) study using the comparative molecular field analysis (CoMFA) method was performed on a series of interleukin 1-beta converting enzyme (ICE) inhibitors. The compounds studied have been reported to be time-dependent inhibitors of ICE. This study was performed using 49 compounds, in which the CoMFA models were developed using a training set of 39 compounds. All the compounds were modeled using the X-ray crystal structure of tetrapeptide aldehyde inhibitor/ICE complex. The inhibitor compounds were considered both as neutral species and as P1 carboxylate ionized species. Superimpositions were performed using two alignment rules, namely, an alignment of the structures based on RMS fitting of the backbone heavy atoms of each structure to compound 2 and an alignment based on SYBYL QSAR rigid body field fit of the steric and electrostatic fields of the molecules to the fields of compound 2. Use of LUMO energies or ClogP as additional descriptors in the QSAR table did not improve the significance of the CoMFA models. Steric and electrostatic fields of the inhibitors were found to be the relevant descriptors for structure-activity relationships. The predictive ability of the CoMFA model was evaluated by using a test set of 10 compounds (r2pred as high as 0.859). Further comparison of the coefficient contour maps with the steric and electrostatic properties of the receptor show a high level of compatibility.
Biodegradation of 2-nitrotoluene by Pseudomonas sp. strain JS42 (1994)

A strain of Pseudomonas spp. was isolated from nitrobenzene-contaminated soil on 4-nitrotoluene as the sole source of carbon, nitrogen, and energy. The organism also grew on 4-nitrobenzaldehyde, and 4-nitrobenzoate. 4-Nitrobenzoate and ammonia were detected in the culture fluid of glucose-grown cells after induction with 4-nitrotoluene. Washed suspensions of 4-nitrotoluene- or 4-nitrobenzoate-grown cells oxidized 4-nitrotoluene, 4-nitrobenzaldehyde, 4-nitrobenzyl alcohol, and protocatechuate. Extracts from induced cells contained 4-nitrobenzaldehyde dehydrogenase, 4-nitrobenzyl alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase activities. Under anaerobic conditions, cell extracts converted 4-nitrobenzoate or 4-hydroxylaminobenzoate to protocatechuate. Conversion of 4-nitrobenzoate to protocatechuate required NADPH. These results indicate that 4-nitrotoluene was degraded by an initial oxidation of the methyl group to form 4-nitrobenzyl alcohol, which was converted to 4-nitrobenzoate via 4-nitrobenzaldehyde. The 4-nitrobenzoate was reduced to 4-hydroxylaminobenzoate, which was converted to protocatechuate. A protocatechuate 4,5-dioxygenase catalyzed meta-ring fission of the protocatechuate. The detection of 4-nitrobenzaldehyde and 4-nitrobenzyl alcohol dehydrogenase and 4-nitrotoluene oxygenase activities in 4-nitrobenzoate-grown cells suggests that 4-nitrobenzoate is an inducer of the 4-nitrotoluene degradative pathway.
3D Stacked IC demonstrator using Hybrid Collective Die-to-Wafer bonding with copper Through Silicon Vias (TSV) (2009)

In this paper we demonstrate functional 3D circuits obtained by a 3D Stacked IC approach using Die-to-Wafer Hybrid Collective bonding with Cu Through Silicon Vias (TSV). The Cu TSV process is inserted between contact and M1 of our reference 130 nm CMOS process on 200 mm wafers. The top die is thinned down to 25 mum and bonded to the landing wafer by a combination of polymer bonding and copper to copper thermocompression bonding. Top and landing wafers contain CMOS finished with 2 levels of metal in Copper/Oxide. Ring oscillators consisting of inverters distributed over both top and bottom dies interconnected through up to 40 TSVs are used to demonstrate the process. This paper focuses on integration issues solved during process development and electrical characterization of the obtained TSVs.