gebhart/patrepeval huggingface dataset:
Development of artificial vaccines against HIV using defined epitopes (1991)

HIV may not follow the paradigm that has been used successfully for developing most viral vaccines, namely, that the best vaccine is the one that most closely mimics natural infection. This approach is based on the premise that natural infection leads to long-lasting protective immunity, which may not be applicable to HIV. Also, some immune responses elicited by infection with HIV may enhance infection or contribute to the development of immune deficiency. To overcome these problems, an artificial vaccine could be constructed using only antigenic epitopes that elicit neutralizing antibodies, helper T cells, and CD8+ cytotoxic T cells, and avoiding epitopes that elicit deleterious responses. Progress has been made in identifying all three of these types of epitopes, in characterizing their activity in animals, and in demonstrating that at least two of these can be linked to induce neutralizing antibodies without a carrier. Methods have also been developed to induce cytotoxic T cells. It is therefore feasible to construct an artificial vaccine for HIV that should be safer and more effective than a natural whole viral or subunit vaccine.
Regulation of the expression of human ornithine decarboxylase gene and ornithine decarboxylase promoter-driven reporter gene in transgenic mice (1993)

We have studied the regulation of the expression of ornithine decarboxylase with the aid of transgenic mice harbouring either functional human ornithine decarboxylase genes or the mouse ornithine decarboxylase promoter-driven chloramphenicol acetyltransferase fusion gene in their genome. We used three different stimuli which are well known to enhance ornithine decarboxylase activity in their appropriate target tissues: (i) testosterone in female kidney, (ii) a phorbol ester in epidermis and (iii) partial hepatectomy in liver. Endogenous mouse ornithine decarboxylase activity was strikingly stimulated in response to these treatments. Even though containing the 5' flanking region of the mouse ornithine decarboxylase gene, known to possess full promoter activity, the chloramphenicol acetyltransferase reporter gene was entirely insensitive to any of these stimuli. The human transgene-derived ornithine decarboxylase activity in kidney was unaffected by testosterone treatment, but responded in skin to application of the phorbol ester and likewise was clearly enhanced in regenerating liver. Although mouse endogenous ornithine decarboxylase mRNA levels were distinctly elevated after testosterone, this treatment did not influence the accumulation of the human transgene-derived mRNA. The phorbol ester enhanced the accumulation of mouse endogenous ornithine decarboxylase mRNA and also that derived from the human transgene; however, the enzyme activity was stimulated in regenerating liver without appreciable changes in the levels of endogenous or transgene-derived message. Our present results strongly emphasize the central role of the coding sequence or ornithine decarboxylase gene in the induction of the enzyme activity.
Synthesis and structural characterization of low-valent Group V phosphine complexes (1992)

The compounds [Nb(CO)2(dmpe)2Cl] and [Ta(CO)2(dmpe)2Cl], where dmpe = 1, 2-bis(dimethylphosphino)ethane, are important precursors in chemistry leading to the reductive coupling of carbon monoxide ligands to form bis(trialkylsiloxy)acetylenes. Convenient, high-yield syntheses of these seven-coordinate niobium(I) and tantalum-(I) complexes have been devised by utilizing catalytic Mg(anthracene) to reduce either [NbCl4(dmpe)2] or [TaCl4-(dmpe)2] under an atmosphere of CO. With the use of Mg(anthracene)•3THF in the absence of CO, the complexes [TaCl2(dmpe)2] (1) and [Ta(η4-anthracene)(dmpe)2Cl] (2) were obtained, both of which have been structurally characterized by X-ray crystallography. The preparation of [V(CO)2(dmpe)2Me] and the crystal structure determinations of several related seven-coordinate [M(CO)2(dmpe)2X] complexes (M = V, X = Me (8); M = Nb, X = Cl (4), I (5); M = Ta, X = Me (7)) and [Ta(CO)2(depe)2Cl] (6), depe = 1, 2-bis(diethylphosphino)ethane, having the capped trigonal prismatic geometry, are also described. These complexes all have acute OC-M-CO angles, low vqo stretching frequencies, and close nonbonded C-C contacts, features which indicate their propensity to undergo reductive coupling reactions. The alkyl complexes [V(CO)2(dmpe)2Me] and [Ta(CO)2(dmpe)2Me] display abnormally long M-C σ bond lengths, 2.31 (1) and 2.32 (1) Å, respectively. Crystal data: (1) monoclinic, P21/n, a = 9.384 (1) Å, b = 12.863 (2) Å, c = 9.363 (1) Å, β = 95.04 (1)°, Z = 2, R = 0.030, Rw = 0.039; (2) triclinic, P1, a = 12.997 (6) Å, b = 13.495 (3) Å, c = 18.860 (4) Å, a = 75.38 (2)°, β = 84.75 (5)°, γ = 89.50 (5)°, Z = 4, R = 0.043, Rw = 0.063; (4) orthorhombic, Pna21 a = 16.106 (3) Å, b = 8.333 (1) Å, c = 33.881 (5) Å, Z = 8, R = 0.045, Rw = 0.060; (5) orthorhombic, Pnma, a = 16.571 (2) Å, b = 16.632 (2) Å, c = 8.439 (1) Å, Z = 4, R = 0.038, b = 0.046; (6) triclinic, FI, a = 11.245 (1) Å, b = 13.325 (2) Å, c = 10.881 (2) Å, α = 99.58 (1)°, β = 112.44 (1)°, γ = 70.24 (1)°, Z = 2, R = 0.018, Rw = 0.023; (7) orthorhombic, Fdd2, a = 10.615 (1) Å, b = 33.123 (7) Å, c = 12.766 (2) Å, Z = 8, R = 0.029, Fw = 0.037; (8) orthorhombic, F212121, a = 13.509 (3) Å, b = 13.777 (2) Å, c = 11.719 (2) Å, Z = 4, R = 0.050, Rw = 0.055. © 1992, American Chemical Society. All rights reserved.
Analogs of phenothiazines. 5. Synthesis and neuropharmacological activity of some piperidylidene derivatives of thioxanthenes, xanthenes, dibenzoxepins, and acridans (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAnalogs of phenothiazines. 5. Synthesis and neuropharmacological activity of some piperidylidene derivatives of thioxanthenes, xanthenes, dibenzoxepins, and acridansCarl Kaiser, Philip J. Fowler, David H. Tedeschi, Bruce M. Lester, Eleanor Garvey, Charles L. Zirkle, Edward A. Nodiff, and Andrew J. SaggiomoCite this: J. Med. Chem. 1974, 17, 1, 57–62Publication Date (Print):January 1, 1974Publication History Published online1 May 2002Published inissue 1 January 1974https://pubs.acs.org/doi/10.1021/jm00247a012https://doi.org/10.1021/jm00247a012research-articleACS PublicationsRequest reuse permissionsArticle Views599Altmetric-Citations16LEARN 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
A facile route to functionalised, protic and chiral ionic liquids based on the triaminocyclopropenium cation (2012)

Readily prepared alkoxydiaminocyclopropenium salts provide an easy access to triaminocyclopropenium (tac) ionic liquids containing functionalised, protic and chiral cations.
Human Anti-Mouse Antibodies (2000)

Human anti-mouse antibodies (HAMA) are human immunoglobulins with specificity for mouse immunoglobulins. This topic currently is of interest because of the increased use of monoclonal mouse antibodies as diagnostic reagents both for in vitro laboratory measurements and for in vivo imaging studies. Monoclonal mouse antibodies also are being used therapeutically. This short article reviews the production of HAMA in patients receiving monoclonal antibodies and illustrates the potential ways that HAMA can interfere with immunoassay measurements. Methods for measuring and neutralizing HAMA also are discussed.
DC-based cancer vaccines (2007)

Because of the large preexisting antigenic load and immunosuppressive environment within a tumor, inducing therapeutically useful antitumor immunity in cancer patients requires the development of powerful vaccination protocols. An approach gaining increasing popularity in the tumor vaccine field is to immunize cancer patients with their own DCs loaded ex vivo with tumor antigens. The underlying premise of this approach is that the efficiency and control over the vaccination process provided by ex vivo manipulation of the DCs generates an optimally potent APC and a superior method for stimulating antitumor immunity in vivo compared with the more conventional direct vaccination methods, offsetting the added cost and complexity associated with this form of customized cell therapy.
Inheritance and persistence in database programming languages (1986)

In order to represent inheritance, several recent designs for database programming languages have made use of class construct, which can be thought of as a restricted data type with an associated set of instances. Moreover, these classes are persistent they survive from one program invocation to another. This paper examines whether it is necessary to the together type, extent and persistence in order to model inheritance and suggests that they may be separated to provide more general database programming languages. In particular we shall see that it is possible to assign a generic data type to a function that extracts all the objects of a given type in the database so that the class hierarchy can be derived from the type hierarchy. We shall also examine object-level inheritance and its relationship to data types for relational databases. A final section examines how the various forms of persistence interact with inheritance at both object and type level.
Imaging Cells in Flow Cytometer Using Spatial-Temporal Transformation (2015)

Flow cytometers measure fluorescence and light scattering and analyze multiple physical characteristics of a large population of single cells as cells flow in a fluid stream through an excitation light beam. Although flow cytometers have massive statistical power due to their single cell resolution and high throughput, they produce no information about cell morphology or spatial resolution offered by microscopy, which is a much wanted feature missing in almost all flow cytometers. In this paper, we invent a method of spatial-temporal transformation to provide flow cytometers with cell imaging capabilities. The method uses mathematical algorithms and a spatial filter as the only hardware needed to give flow cytometers imaging capabilities. Instead of CCDs or any megapixel cameras found in any imaging systems, we obtain high quality image of fast moving cells in a flow cytometer using PMT detectors, thus obtaining high throughput in manners fully compatible with existing cytometers. To prove the concept, we demonstrate cell imaging for cells travelling at a velocity of 0.2 m/s in a microfluidic channel, corresponding to a throughput of approximately 1,000 cells per second.
Surface-emitting laser diode with vertical GaAs/GaAlAs quarter-wavelength multilayers and lateral buried heterostructure (1987)

Threshold current of 2 mA at room temperature cw operation is realized in a vertical distributed feedback surface-emitting laser diode with lateral buried heterostructure (LBH). In this LBH structure, the vertical distributed feedback active region (AlGaAs/GaAs multilayer) is entirely surrounded with n- and p-type AlGaAs cladding layers for minority-carrier confinement. The far-field angle is 7°. The beam shape is nearly circular. However, the lasing spectrum is broad (2–3 nm) compared with the conventional edge-emitting laser. Major differences between the surface-emitting laser diode presented here and the conventional edge-emitting laser diode are discussed.
Unique Forms of the abl Tyrosine Kinase Distinguish Ph 1 -Positive CML from Ph 1 -Positive ALL (1987)

In the Philadelphia chromosome (Ph1) of chronic myelogenous leukemia (CML), the c-abl gene on chromosome 9 is translocated to bcr on chromosome 22. This results in the expression of a chimeric bcr-abl message that encodes the P210bcr-abl tyrosine kinase. The cells of 10% of acute lymphocytic leukemia patients (ALL) carry a cytogenetically similar Ph1 translocation. We report that Ph1-positive ALL cells express unique abl-derived tyrosine kinases of 185 and 180 kilodaltons that are distinct from the bcr-abl-derived P210 protein of CML. The appearance of the 185/180-kilodalton proteins correlates with the expression of a novel 6.5-kilobase messenger RNA. Thus, similar genetic translocations in two different leukemias result in the expression of distinct c-abl-derived products.
An Encoder-Decoder Based Basecaller for Nanopore DNA Sequencing (2019)

Nanopore DNA sequencing is a method in which DNA bases are determined (basecalled) using electric current signals generated by passing DNA through nanopore sensors. The raw measured signals can be aggregated into event data presenting new bases entering the nanopore. This thesis has two contributions. First, we implemented RNN-based single- and double-strand basecallers for simulated event data to analyze the effect of signal noise. As the SNR decreased from 20 dB to 5 dB, the accuracy of the single-strand basecaller dropped 9% while the accuracy of double-strand basecaller only dropped 0.5%. Second, we implemented an end-to-end single-strand basecaller, directly processing the raw signal using an encoder-decoder model with attention instead of the CTC-style approach used in available basecallers. We achieved an accuracy of 81.9% for a viral sample and an accuracy of 90.9% for a bacterial sample. Our accuracy is comparable to state-of-the-art basecallers with a considerably smaller model.
A Hexahedral Multigrid Approach for Simulating Cuts in Deformable Objects (2010)

We present a hexahedral finite element method for simulating cuts in deformable bodies using the corotational formulation of strain at high computational efficiency. Key to our approach is a novel embedding of adaptive element refinements and topological changes of the simulation grid into a geometric multigrid solver. Starting with a coarse hexahedral simulation grid, this grid is adaptively refined at the surface of a cutting tool until a finest resolution level, and the cut is modeled by separating elements along the cell faces at this level. To represent the induced discontinuities on successive multigrid levels, the affected coarse grid cells are duplicated and the resulting connectivity components are distributed to either side of the cut. Drawing upon recent work on octree and multigrid schemes for the numerical solution of partial differential equations, we develop efficient algorithms for updating the systems of equations of the adaptive finite element discretization and the multigrid hierarchy. To construct a surface that accurately aligns with the cuts, we adapt the splitting cubes algorithm to the specific linked voxel representation of the simulation domain we use. The paper is completed by a convergence analysis of the finite element solver and a performance comparison to alternative numerical solution methods. These investigations show that our approach offers high computational efficiency and physical accuracy, and that it enables cutting of deformable bodies at very high resolutions.
Radish, a Drosophila mutant deficient in consolidated memory. (1993)

We have characterized the behavior and genetics of the Drosophila mutant radish (rsh gene). Initial learning of radish flies in two olfactory discrimination tests is high, but subsequent memory decays rapidly at both early and late times after training. Anesthesia-resistant memory (consolidated memory) is undetectable in radish flies 3 hr after training. The mutant shows normal locomotor activity and normal sensitivity to the odor cues and electric-shock reinforcement used in the learning tests. The radish gene maps within a 180-kb interval in the 11D-E region of the X chromosome.
Energy Management on Handheld Devices (2003)

Handheld devices are becoming ubiquitous and as their capabilities increase, they are starting to displace laptop computers - much as laptop computers have displaced desktop computers in many roles. Handheld devices are evolving from today’s PDAs, organizers, cellular phones, and game machines into a variety of new forms. Although partially offset by improvements in low-power electronics, this increased functionality carries a corresponding increase in energy consumption. Second, as a consequence of displacing other pieces of equipment, handheld devices are seeing more use between battery charges. Finally, battery technology is not improving at the same pace as the energy requirements of handheld electronics. Therefore, energy management, once in the realm of desired features, has become an important design requirement and one of the greatest challenges in portable computing, and it will remain so for a long time to come.
The complex bet promoters of Escherichia coli: regulation by oxygen (ArcA), choline (BetI), and osmotic stress (1996)

The bet regulon allows Escherichia coli to synthesize the osmoprotectant glycine betaine from choline. It comprises a regulatory gene, betI, and three structural genes: betT (choline porter), betA (choline dehydrogenase), and betB (betaine aldehyde dehydrogenase). The bet genes are regulated by oxygen, choline, and osmotic stress. Primer extension analysis identified two partially overlapping promoters which were responsible for the divergent expression of the betT and betIBA transcripts. The transcripts were initiated 61 bp apart. Regulation of the promoters was investigated by using cat (chloramphenicol acetyltransferase) and lacZ (beta-galactosidase) operon fusions. Mutation of betI on plasmid F'2 revealed that BetI is a repressor which regulates both promoters simultaneously in response to the inducer choline. Both promoters remained inducible by osmotic stress in a betI mutant background. On the basis of experiments with hns and hns rpoS mutants, we conclude that osmoregulation of the bet promoters was hns independent. The bet promoters were repressed by ArcA under anaerobic growth conditions. An 89-bp promoter fragment, as well as all larger fragments tested, which included both transcriptional start points, displayed osmotic induction and BetI-dependent choline regulation when linked with a cat reporter gene on plasmid pKK232-8. Flanking DNA, presumably on the betT side of the promoter region, appeared to be needed for ArcA-dependent regulation of both promoters.
cAMP-stimulated ion currents in Xenopus oocytes expressing CFTR cRNA (1992)

The cystic fibrosis transmembrane conductance regulator (CFTR) was expressed in stage V/VI Xenopus oocytes by injection of cRNA transcribed in vitro from a pBluescript vector containing 6.2-kb wild-type cDNA. This clone was also used for the preparation of antisense RNA. Double-electrode voltage clamp was employed to measure transmembrane currents. In sense RNA-injected oocytes, cAMP depolarized the membrane potential (Vm) from -52 to -31 mV and increased membrane conductance (Gm) 10-fold. However, cAMP had no effect on Vm or Gm in uninjected oocytes or in oocytes injected with antisense RNA. The endogenous Ca-activated Cl currents of control oocytes were abolished by 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid (DIDS; 50 microM) or bath Cl replacement. In contrast, the cAMP-stimulated currents of CFTR-expressing oocytes were DIDS insensitive and were inhibited only approximately 50% when bath Cl was replaced by gluconate or glutamate. In addition, the Cl channel blockers 5-nitro-2-(3-phenylpropylamino)benzoate (NPPB; 50 microM) and diphenylamine-2-carboxylic acid (DPC; 3 mM) reduced the cAMP-evoked currents by only approximately 10%. The stimulated currents of CFTR-expressing oocytes were reduced approximately 30% by 10 mM Ba, suggesting that the Cl-independent current component is due to an increase in K conductance. Our results indicate that expression of CFTR in Xenopus oocytes produces a cAMP-activated Cl current. The Cl-independent current may represent a regulatory action of CFTR on K conductance pathways or a secondary response of the oocyte membrane to the high Cl conductance induced by CFTR expression.
Enhanced Gene Delivery and Expression in Human Hepatocellular Carcinoma Cells by Cationic Immunoliposomes (1997)

A targeted vector allowing enhanced gene transfer to human hepatocellular carcinoma (HCC1) cells in vitro was developed using cationic liposomes covalently conjugated with the mAb AF-20. This high affinity antibody recognizes a rapidly internalized 180 kDa cell surface glycoprotein which is abundantly expressed on the surface of human HCC and other cancer cells. Quantitative binding analysis of liposomes with target cells by flow cytometry showed specific association of mAb-targeted liposomes with human HCC cells. Using mAb-targeted cationic liposomes containing 20% DOTAP, in the presence or absence of serum, gene expression in HuH-7 cells was enhanced up to 40-fold as compared to liposomes conjugated with an isotype-matched non-relevant control antibody. Transfection specificity was not observed in a control cell line that does not express the antigen recognized by mAb AF-20. This study demonstrates that cationic liposome formulations can be targeted with monoclonal antibodies (mAbs) to enhance specific in vitro gene delivery and expression in the presence or absence of serum.
Can N95 Respirators Be Reused after Disinfection? How Many Times? (2020)

The coronavirus disease 2019 (COVID-19) pandemic has led to a major shortage of N95 respirators, which are essential for protecting healthcare professionals and the general public who may come into contact with the virus. Thus, it is essential to determine how we can reuse respirators and other personal protective equipment in these urgent times. We investigated multiple commonly used disinfection schemes on media with particle filtration efficiency of 95%. Heating was recently found to inactivate the virus in solution within 5 min at 70 °C and is among the most scalable, user-friendly methods for viral disinfection. We found that heat (≤85 °C) under various humidities (≤100% relative humidity, RH) was the most promising, nondestructive method for the preservation of filtration properties in meltblown fabrics as well as N95-grade respirators. At 85 °C, 30% RH, we were able to perform 50 cycles of heat treatment without significant changes in the filtration efficiency. At low humidity or dry conditions, temperatures up to 100 °C were not found to alter the filtration efficiency significantly within 20 cycles of treatment. Ultraviolet (UV) irradiation was a secondary choice, which was able to withstand 10 cycles of treatment and showed small degradation by 20 cycles. However, UV can potentially impact the material strength and subsequent sealing of respirators. Finally, treatments involving liquids and vapors require caution, as steam, alcohol, and household bleach all may lead to degradation of the filtration efficiency, leaving the user vulnerable to the viral aerosols.