gebhart/patrepeval huggingface dataset:
Liposomal Delivery of Purified Inhibitory-κBα Inhibits Tumor Necrosis Factor-α–Induced Human Vascular Smooth Muscle Proliferation (1999)

Vessel injury results in the elaboration of various cytokines, including tumor necrosis factor-alpha (TNF-alpha), which may influence vascular smooth muscle cell (VSMC) function and contribute to atherogenesis. We tested the hypothesis that TNF-alpha-induced VSMC proliferation requires activation of the transcription factor nuclear factor-kappaB (NF-kappaB), which could be prevented by delivery of the NF-kappaB inhibitory peptide, IkappaBalpha. TNF-alpha induced concentration-dependent human VSMC proliferation, and neutralizing antibody to interleukin-6 reduced TNF-alpha-induced VSMC proliferation by 65%. In TNF-alpha-stimulated VSMCs, there was a 3-fold increase in NF-kappaB-dependent luciferase reporter activity that was associated with degradation of IkappaBalpha. To determine an essential role for NF-kappaB in TNF-alpha-induced VSMC proliferation, recombinant IkappaBalpha was introduced into VSMCs via liposomal delivery. Under these conditions, TNF-alpha-induced NF-kappaB nuclear translocation and DNA binding were inhibited, NF-kappaB-dependent luciferase activity was reduced by 50%, there was no degradation of native IkappaBalpha detected, interleukin-6 production was reduced by 54%, and VSMC proliferation was decreased by 60%. In conclusion, the mitogenic effect of TNF-alpha on human arterial VSMCs is dependent on NF-kappaB activation and may be prevented by exogenously delivered IkappaBalpha. Furthermore, liposomal delivery of endogenous inhibitory proteins may represent a novel, therapeutically accessible method for selective transcriptional suppression in the response to vascular injury.
Modeling mouse and human development using organoid cultures (2015)

In vitro three-dimensional (3D) cultures are emerging as novel systems with which to study tissue development, organogenesis and stem cell behavior ex vivo. When grown in a 3D environment, embryonic stem cells (ESCs) self-organize into organoids and acquire the right tissue patterning to develop into several endoderm- and ectoderm-derived tissues, mimicking their in vivo counterparts. Tissue-resident adult stem cells (AdSCs) also form organoids when grown in 3D and can be propagated in vitro for long periods of time. In this Review, we discuss recent advances in the generation of pluripotent stem cell- and AdSC-derived organoids, highlighting their potential for enhancing our understanding of human development. We will also explore how this new culture system allows disease modeling and gene repair for a personalized regenerative medicine approach.
LINKER: a program to generate linker sequences for fusion proteins (2000)

The construction of functional fusion proteins often requires a linker sequence that adopts an extended conformation to allow for maximal flexibility. Linker sequences are generally selected based on intuition. Without a reliable selection criterion, the design of such linkers is often difficult, particularly in situations where longer linker sequences are required. Here we describe a program called LINKER which can automatically generate a set of linker sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. The only required input to the program is the desired linker sequence length. The program is specifically designed to assist in fusion protein construction. A number of optional input parameters have been incorporated so that users are able to enhance sequence selection based on specific applications. The program output simply contains a set of sequences with a specified length. This program should be a useful tool in both the biotechnology industry and biomedical research. It can be accessed through the Web page http://www.fccc. edu/research/labs/feng/linker.html.
The applications of PET in clinical oncology. (1991)

With the advent of a new generation of PET scanners that have introduced whole-body PET to the clinical setting, there is now more interest in developing protocols for the evaluation of both intracranial and somatic cancers. The value of PET in clinical oncology has been demonstrated with studies in a variety of cancers including colorectal carcinomas, lung tumors, head and neck tumors, primary and metastatic brain tumors, breast carcinoma, lymphoma, melanoma, bone cancers, and other soft-tissue cancers. A summary of current clinical applications of PET in oncology is presented with special attention to colorectal, lung, and intracranial neoplasms since the majority of clinical trials have focused on these cancers. A variety of radiopharmaceuticals are described that are currently included in clinical tumor-imaging protocols, including metabolic substrates such as fluorine-18-fluorodeoxyglucose and carbon-11-methionine, and analogs of chemotherapeutic agents such as fluorine-18-fluorouracil and fluoroestradiol. An attempt is also made to include examples of clinical trials that demonstrate response to therapeutic intervention. The increasing number of oncologic PET studies reflects the growing interest in functional imaging in oncology.
Toward More Secure and Reliable Access Control (2011)

Conventional access control mechanisms, relying on a single security token to authenticate remote users, introduce a single point of failure and are vulnerable to relay attacks. A threshold-based distance-bounding protocol that distributes a user's private key among various personal devices improves system security and reliability.
SYNTHETIC PEPTIDES WHICH INHIBIT THE INTERACTION BETWEEN C1q AND IMMUNOGLOBULIN AND PROLONG XENOGRAFT SURVIVAL1 (2000)

The CBP2 and WY peptides exhibit the functional activity of inhibition of complement activation. These peptides also prolong xenograft survival and thus provide reagents for the study of the importance of C1q and other complement components in transplant rejection mechanisms.
Double Strand Break DNA Repair occurs via Non-Homologous End-Joining in Mouse MII Oocytes (2018)

The unique biology of the oocyte means that accepted paradigms for DNA repair and protection are not of direct relevance to the female gamete. Instead, preservation of the integrity of the maternal genome depends on endogenous protein stores and/or mRNA transcripts accumulated during oogenesis. The aim of this study was to determine whether mature (MII) oocytes have the capacity to detect DNA damage and subsequently mount effective repair. For this purpose, DNA double strand breaks (DSB) were elicited using the topoisomerase II inhibitor, etoposide (ETP). ETP challenge led to a rapid and significant increase in DSB (P = 0.0002) and the consequential incidence of metaphase plate abnormalities (P = 0.0031). Despite this, ETP-treated MII oocytes retained their ability to participate in in vitro fertilisation, though displayed reduced developmental competence beyond the 2-cell stage (P = 0.02). To account for these findings, we analysed the efficacy of DSB resolution, revealing a significant reduction in DSB lesions 4 h post-ETP treatment. Notably, this response was completely abrogated by pharmacological inhibition of key elements (DNA-PKcs and DNA ligase IV) of the canonical non-homologous end joining DNA repair pathway, thus providing the first evidence implicating this reparative cascade in the protection of the maternal genome.
A Primer on Aspects of Cognition for Medical Informatics (2001)

As a multidisciplinary field, medical informatics draws on a range of disciplines, such as computer science, information science, and the social and cognitive sciences. The cognitive sciences can provide important insights into the nature of the processes involved in human- computer interaction and help improve the design of medical information systems by providing insight into the roles that knowledge, memory, and strategies play in a variety of cognitive activities. In this paper, the authors survey literature on aspects of medical cognition and provide a set of claims that they consider to be important in medical informatics.
Suppurative Granulomatous Lymphadenitis (1992)

The cellular composition of suppurative granulomas was investigated by the application of monoclonal and polyclonal antibodies to paraffin sections and compared with nonsuppurative, hypersensitivity-type granulomas. Macrophages, T cells, and dendritic cells showed a similar distribution in both types of granulomas. In addition to the presence of granulocytes, a major difference between suppurative granulomas and hypersensitive-type granulomas concerned their relationship with B lymphocytes. Hypersensitive-type granulomas were surrounded by small mantle B cells, but they did not contain any B lymphocytes. In contrast, variable numbers of B cells were found either at the periphery or in the center of suppurative granulomas. In view of their morphology (medium size, pale cytoplasm, irregular nuclear shape) and phenotype (L26 +/LN1 -/MB2 +/MT2 +) these B lymphocytes closely resembled monocytoid B cells. The monocytoid B cells might have a role in the recruitment of polymorphonuclear granulocytes and in the development of the necrosis, which occur within suppurative granulomas.
Microprocessor controlled movement of solid colonic content using sequential neural electrical stimulation (2002)

Microprocessor controlled electrical stimulation accelerated movement of colonic content suggesting the possibility of future implantable colonic stimulators.
Phosphato complexes of platinum(II): phosphorus-31 NMR and kinetics of formation and isomerization studies (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhosphato complexes of platinum(II): phosphorus-31 NMR and kinetics of formation and isomerization studiesRathindra N. Bose, Niranjan Goswami, and Shadi MoghaddasCite this: Inorg. Chem. 1990, 29, 18, 3461–3467Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ic00343a036https://doi.org/10.1021/ic00343a036research-articleACS PublicationsRequest reuse permissionsArticle Views146Altmetric-Citations14LEARN 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
Pharmacokinetics of amoxycillin/clavulanic acid in serum and ascitic fluid in cirrhotic patients (1989)

A combination of amoxycillin and clavulanic acid (Augmentin) might be useful for first-line treatment of spontaneous bacterial peritonitis in patients with cirrhosis. We have studied the pharmacokinetics of amoxycillin/clavulanic acid in serum and ascitic fluid of six cirrhotic patients. A total of 66 simultaneous serum and ascitic samples were analysed. Following iv injection of 1 g amoxycillin plus 0.2 g clavulanic acid, the ascites to serum AUC ratio was 1.38 for amoxycillin and 1.01 for clavulanic acid, indicating a good distribution of these drugs into the ascitic fluid. In this study, experimental data were fitted to a three compartment body model which revealed that the prolonged serum half-lives of amoxycillin (274 min) and clavulanic acid (200 min) were probably due to the slow return from the ascitic compartment.
Probability density functions for hyperbolic and isodiachronic locations (2002)

Animal locations are sometimes estimated with hyperbolic techniques by estimating the difference in distances of their sounds between pairs of receivers. Each pair specifies the animal's location to a hyperboloid because the speed of sound is assumed to be spatially homogeneous. Sufficient numbers of intersecting hyperboloids specify the location. A nonlinear method is developed for computing probability density functions for location. The method incorporates a priori probability density functions for the receiver locations, the speed of sound, winds, and the errors in the differences in travel time. The traditional linear approximation method overestimates bounds for probability density functions by one or two orders of magnitude compared with the more accurate nonlinear method. The nonlinear method incorporates a generalization of hyperbolic methods because the average speed of sound is allowed to vary between different receivers and the source. The resulting "isodiachronic" surface is the locus of points on which the difference in travel time is constant. Isodiachronic locations yield correct location errors in situations where hyperbolic methods yield incorrect results, particularly when the speed of propagation varies significantly between a source and different receivers.
Evidence for two genetic loci in Yersinia enterocolitica that can promote invasion of epithelial cells (1988)

Virulent strains of Yersinia enterocolitica cause disease syndromes ranging from mild gastroenteritis to lymphadenitis and septicemia. The ability of these bacteria to invade intestinal epithelial cells to gain access to the reticuloendothelial system is thought to be an important aspect of their virulence. We report here on the cloning of two Y. enterocolitica chromosomal loci, inv and ail, each of which confers an invasive phenotype on Escherichia coli HB101. The inv locus allows a uniformly high level of invasion in several tissue culture lines and is homologous to the inv gene of Yersinia pseudotuberculosis. The second locus, ail, shows more host specificity than inv in that it allows invasion to a variable degree of some cell lines (e.g., HEp-2, HEC1B, and CHO cells) but allows no invasion of others (e.g., Madin-Darby canine kidney cells).
Activation-dependent Conformational Changes in β-Arrestin 2 (2004)

Beta-arrestins are multifunctional adaptor proteins, which mediate desensitization, endocytosis, and alternate signaling pathways of seven membrane-spanning receptors (7MSRs). Crystal structures of the basal inactive state of visual arrestin (arrestin 1) and beta-arrestin 1 (arrestin 2) have been resolved. However, little is known about the conformational changes that occur in beta-arrestins upon binding to the activated phosphorylated receptor. Here we characterize the conformational changes in beta-arrestin 2 (arrestin 3) by comparing the limited tryptic proteolysis patterns and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) profiles of beta-arrestin 2 in the presence of a phosphopeptide (V(2)R-pp) derived from the C terminus of the vasopressin type II receptor (V(2)R) or the corresponding nonphosphopeptide (V(2)R-np). V(2)R-pp binds to beta-arrestin 2 specifically, whereas V(2)R-np does not. Activation of beta-arrestin 2 upon V(2)R-pp binding involves the release of its C terminus, as indicated by exposure of a previously inaccessible cleavage site, one of the polar core residues Arg(394), and rearrangement of its N terminus, as indicated by the shielding of a previously accessible cleavage site, residue Arg(8). Interestingly, binding of the polyanion heparin also leads to release of the C terminus of beta-arrestin 2; however, heparin and V(2)R-pp have different binding site(s) and/or induce different conformational changes in beta-arrestin 2. Release of the C terminus from the rest of beta-arrestin 2 has functional consequences in that it increases the accessibility of a clathrin binding site (previously demonstrated to lie between residues 371 and 379) thereby enhancing clathrin binding to beta-arrestin 2 by 10-fold. Thus, the V(2)R-pp can activate beta-arrestin 2 in vitro, most likely mimicking the effects of an activated phosphorylated 7MSR. These results provide the first direct evidence of conformational changes associated with the transition of beta-arrestin 2 from its basal inactive conformation to its biologically active conformation and establish a system in which receptor-beta-arrestin interactions can be modeled in vitro.
2 Retroviral Vectors (1999)

The combination of the advancements in the knowledge of gene regulation and improvements in gene delivery into cells has resulted in significant progress in the field of human gene therapy during the past 15years. In the United States alone, there were more than 50 gene therapy protocols approved by the National Institutes of Health (NIH) during 1997. The gene transfer vectors involved in these clinical trials include vectors derived from retroviruses, plasmids, adenoviruses, pox-viruses, and adeno-associated viruses (AAV). Because of their many unique properties, vectors derived from retroviruses, especially from the Moloney murine leukemia virus (Mo-MLV), have been used extensively in a majority of clinical trials for somatic gene therapy (Miller 1992; Mulligan 1993; Crystal 1995). Each retroviral particle consists of an envelope on the outside, which is derived from the host plasma membrane during virus budding, and two single-stranded RNAs encapsidated in a nucleocapsid structure. Interaction between the virus-encoded envelope protein, which is embedded in the virion envelope, with cell surface receptors allows the virus to enter into the infected cells. On infection, both RNAs serve as templates to generate one copy of a linear double-stranded DNA in the cytoplasm via reverse transcription using virion-associated reverse transcriptase. The viral genomic DNA migrates into the nucleus and integrates into the host chromosome. The integration step is mediated by the virion-associated integrase and is a highly efficient and specific reaction that results in the generation of a proviral DNA that is colinear with its unintegrated form. The unique properties that make...
Evidence that a 27-residue sequence is the actin-binding site of ABP-120 (1991)

Proteolysis experiments of ABP-120 from Dictyostelium discoideum have previously demonstrated that removal of residues 89-115 from a tryptic peptide which retains actin binding activity, abolishes actin binding (Bresnick, A. R., Warren, V., and Condeelis, J. (1990) J. Biol. Chem. 265, 9236-9240). Antibodies made against a synthetic peptide of this 27-amino acid sequence (27-mer) specifically immunoprecipitate native ABP-120 from Dictyostelium high speed supernatants, demonstrating that the 27-mer sequence is on the surface of the molecule as expected for an active site. ABP-120 is inhibited in its binding to F-actin by Fab' fragments of the anti-27-mer IgG. Half-maximal inhibition occurs at an approximate molar ratio of 7 Fab' fragments/ABP-120 monomer. Viscoelastic measurements indicate that ABP-120 forms fewer cross-links with F-actin in the presence of the 27-mer synthetic peptide than in its absence. In F-actin cosedimentation assays, the binding of ABP-120 to actin is inhibited by the 27-mer synthetic peptide. Furthermore, the 27-mer synthetic peptide cosediments with F-actin, whereas a control hydrophobic peptide and a synthetic peptide of residues 69-88 of ABP-120 do not cosediment with F-actin. These observations suggest a direct involvement of the 27-mer sequence in the actin binding activity of ABP-120.
<title>Tantalum nitride films for the absorber material of refractive-type EUVL mask</title> (2001)

Tantalum nitride (Ta<SUB>x</SUB>N) films were evaluated for use as the absorber material of masks for extreme ultraviolet lithography (EUVL). Ta<SUB>x</SUB>N films deposited by DC sputtering using an Ar+N<SUB>2</SUB> gas mixture had a low stress of less than 300 MPa, an amorphous-like structure, and a low deep ultraviolet (DUV) reflectivity. This film provides a DUV contrast of 30% with respect to the Mo/Si multilayer whose top is on Si layer. A Ta<SUB>x</SUB>N film deposited using a Xe+N<SUB>2</SUB> gas mixture was found to be better in the following ways: the stress was below 100 MPa, the change in stress was below 30 MPa, and the density was more than 1 g/cm<SUP>3</SUP> higher. Furthermore, treating the surface of Ta<SUB>x</SUB>N film with O<SUB>2</SUB> plasma or sputtering a Ta<SUB>x</SUB>O film on it using an Ar+O<SUB>2</SUB> gas mixture improved the DUV contrast because the resulting surface has a lower DUV reflectivity than Ta<SUB>x</SUB>N film. These results indicate that Ta<SUB>x</SUB>N film is one of the most suitable materials for the absorber of EUVL masks.
Rediscovering mycophenolic acid: A review of its mechanism, side effects, and potential uses (1997)

Oral mycophenolic acid (MPA) therapy has been investigated in the treatment of moderate to severe psoriasis since the early 1970s and has been found to be both safe and effective. By inhibiting de novo purine biosynthesis, it functions as an antifungal, antibacterial, antiviral, and immunosuppressive agent. The recent availability of mycophenolate mofetil (MMF), a morpholinoester of MPA, has created renewed interest in the antipsoriatic properties of MPA. MMF is currently indicated for the prevention of organ rejection in transplant recipients and is used concomitantly with cyclosporine and corticosteroids. This review focuses on the pharmacology of MPA and MMF, studies of MPA in the treatment of psoriasis, and therapy with MMF. There is a potential application of MMF in the treatment of severe psoriasis and other inflammatory dermatoses, as well as topical MPA for the treatment of psoriasis.
Defects in photorefractive CdTe:V: An electron paramagnetic resonance study (1993)

Vanadium-doped CdTe has recently been shown to have a high sensitivity for optical processing at 1.5 μm but the role of the vanadium dopant has been questioned. We present the results of an electron paramagnetic resonance study of this material, which demonstrates that vanadium is the dominant paramagnetic defect, which pins the Fermi level and gives rise to photoconductivity at 1.5 μm. The vanadium is substitutionally incorporated on a Cd site at concentrations of ≊5×1016 cm−3 and acts as a deep donor with a 2+/3+ level at Ev+0.8 eV. The defect is only observed in the 3+ charge state. The spin Hamiltonian parameters of the V3+ defect are determined as follows: electron spin S=1, Landé g-factor g=1.962±0.001, central hyperfine interaction constant A=60×10−4 cm−1, Cd Ligand hyperfine interaction constant T=4×10−4 cm−1.