gebhart/patrepeval huggingface dataset:
The prognostic molecular markers in hepatocellular carcinoma (2002)

The prognosis of hepatocellular carcinoma (HCC) still remains dismal, although many advances in its clinical study have been made. It is important for tumor control to identify the factors that predispose patients to death. With new discoveries in cancer biology, the pathological and biological prognostic factors of HCC have been studied quite extensively. Analyzing molecular markers (biomarkers) with prognostic significance is a complementary method. A large number of molecular factors have been shown to associate with the invasiveness of HCC, and have potential prognostic significance. One important aspect is the analysis of molecular markers for the cellular malignancy phenotype. These include alterations in DNA ploidy, cellular proliferation markers (PCNA, Ki-67, Mcm2, MIB1, MIA, and CSE1L/CAS protein), nuclear morphology, the p53 gene and its related molecule MD M2, other cell cycle regulators (cyclin A, cyclin D, cyclin E, cdc2, p27, p73), oncogenes and their receptors (such as ras, c-myc, c-fms, HGF, c-met, and erb-B receptor family members), apoptosis related factors (Fas and FasL), as well as telomerase activity. Another important aspect is the analysis of molecular markers involved in the process of cancer invasion and metastasis. Adhesion molecules (E-cadherin, catenins, serum intercellular adhesion molecule-1, CD44 variants), proteinases involved in the degradation of extracellular matrix (MMP-2, MMP-9, uPA, uPAR, PAI), as well as other molecules have been regarded as biomarkers for the malignant phenotype of HCC, and are related to prognosis and therapeutic outcomes. Tumor angiogenesis is critical to both the growth and metastasis of cancers including HCC, and has drawn much attention in recent years. Many angiogenesis-related markers, such as vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), platelet-derived endothelial cell growth factor (PD-ECGF), thrombospondin (TSP), angiogenin, pleiotrophin, and endostatin (ES) levels, as well as intratumor microvessel density (MVD) have been evaluated and found to be of prognostic significance. Body fluid (particularly blood and urinary) testing for biomarkers is easily accessible and useful in clinical patients. The prognostic significance of circulating DNA in plasma or serum, and its genetic alterations in HCC are other important trends. More attention should be paid to these two areas in future. As the progress of the human genome project advances, so does a clearer understanding of tumor biology, and more and more new prognostic markers with high sensitivity and specificity will be found and used in clinical assays. However, the combination of some items, i.e., the pathological features and some biomarkers mentioned above, seems to be more practical for now.
Studies of vitamin D (calciferol) and its analogs. 45. Studies on the A-ring diastereomers of 1.alpha.,25-dihydroxyvitamin D3 (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies of vitamin D (calciferol) and its analogs. 45. Studies on the A-ring diastereomers of 1.alpha.,25-dihydroxyvitamin D3K. Raman Muralidharan, Angel R. De Lera, Shawn D. Isaeff, Anthony W. Norman, and William H. OkamuraCite this: J. Org. Chem. 1993, 58, 7, 1895–1899Publication Date (Print):March 1, 1993Publication History Published online1 May 2002Published inissue 1 March 1993https://pubs.acs.org/doi/10.1021/jo00059a048https://doi.org/10.1021/jo00059a048research-articleACS PublicationsRequest reuse permissionsArticle Views706Altmetric-Citations53LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Inhibition of poly(adenosine diphosphate-ribose) polymerase by thymidine and thymidine analogues in L1210 cells and its relationship to the potentiation of the antitumor activity of 1,3-bis(2-chloroethyl)-1-nitrosourea but not of 3'-[3-(2-chloroethyl)-3-nitrosoureido]-3'-deoxythymidine. (1991)

The coadministration of thymidine (dThd) with either 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) or 3'-[3-(2-chloroethyl)-3-nitrosoureido]-3'-deoxythymidine (3'-CTNU) to L1210-bearing mice significantly enhanced the antitumor activity of both nitrosoureas (T-S. Lin and W. H. Prusoff, Cancer Res., 47:394-397, 1987, and T-S. Lin, P.H. Fischer, J. C. Marsh, and W. H. Prusoff, Cancer Res., 42:1624-1629, 1982). As a possible mechanism for this observed enhancement, we have investigated the role of dThd as an inhibitor of poly(ADP-ribose) polymerase (ADPRP), an enzyme which is activated in response to DNA damage. Exposure of L1210 cells in culture to 50 microM BCNU resulted in a greater than 10-fold increase in ADPRP activity within 3-4 h. The polymerase activity increased with increasing BCNU concentration after a 4-h exposure, reaching apparent saturation at 50 microM BCNU. However, this activation was abolished by 2 mM dThd. Median inhibition of the ADPRP activity elicited by 30 and 75 microM BCNU occurred at 38 and 135 microM dThd, respectively. When BCNU was replaced by 3'-CTNU, no activation of ADPRP was observed, even at or above concentration of 3'-CTNU previously shown to cause DNA damage. 3'-Amino-3'-deoxythymidine, the principal hydrolysis product of 3'-CTNU, was found to be an inhibitor of BCNU-stimulated ADPRP activity with potency similar to dThd. Furthermore, intact 3'-CTNU was found to inhibit BCNU-stimulated ADPRP activity. Although 3'-CTNU should be capable of activating ADPRP by causing DNA damage, our results suggest that no net activation is observed due to inhibition by the various thymidine species present. Thus, inhibition of ADPRP by dThd following DNA damage by BCNU is consistent with the potentiation of antitumor activity previously reported. However, the observed potentiation of 3'-CTNU activity by dThd does not appear to result from such a mechanism.
A 3-D finite-element model for computation of temperature profiles and regions of thermal damage during focused ultrasound surgery exposures (1998)

Although there have been numerous models implemented for modeling thermal diffusion effects during focused ultrasound surgery (FUS), most have limited themselves to representing simple situations for which analytical solutions and the use of cylindrical geometries sufficed. For modeling single lesion formation and the heating patterns from a single exposure, good results were achieved in comparison with experimental results for predicting lesion size, shape and location. However, these types of approaches are insufficient when considering the heating of multiple sites with FUS exposures when the time interval between exposures is short. In such cases, the heat dissipation patterns from initial exposures in the lesion array formation can play a significant role in the heating patterns for later exposures. Understanding the effects of adjacent lesion formation, such as this, requires a three-dimensional (3-D) representation of the bioheat equation. Thus, we have developed a 3-D finite-element representation for modeling the thermal diffusion effects during FUS exposures in clinically relevant tissue volumes. The strength of this approach over past methods is its ability to represent arbitrarily shaped 3-D situations. Initial simulations have allowed calculation of the temperature distribution as a function of time for adjacent FUS exposures in excised bovine liver, with the individually computed point temperatures comparing favorably with published measurements. In addition to modeling these temperature distributions, the model was implemented in conjunction with an algorithm for calculating the thermal dose as a way of predicting lesion shape. Although used extensively in conventional hyperthermia applications, this thermal dose criterion has only been applied in a limited number of simulations in FUS for comparison with experimental measurements. In this study, simulations were run for focal depths 2 and 3 cm below the surface of pig's liver, using multiple intensity levels and exposure times. The results also compare favorably to published in vitro experimental measurements, which bodes well for future application to more complex problems, such as the modeling of multiple lesion arrays within complex anatomical geometries.
Prodrugs for Gene‐Directed Enzyme‐Prodrug Therapy (Suicide Gene Therapy) (2003)

This review focuses on the prodrugs used in suicide gene therapy. These prodrugs need to satisfy a number of criteria. They must be efficient and selective substrates for the activating enzyme, and be metabolized to potent cytotoxins preferably able to kill cells at all stages of the cell cycle. Both prodrugs and their activated species should have good distributive properties, so that the resulting bystander effects can maximize the effectiveness of the therapy, since gene transduction efficiencies are generally low. A total of 42 prodrugs explored for use in suicide gene therapy with 12 different enzymes are discussed, particularly in terms of their physiocochemical properties. An important parameter in determining bystander effects generated by passive diffusion is the lipophilicity of the activated form, a property conveniently compared by diffusion coefficients (log P for nonionizable compounds and log D(7) for compounds containing an ionizable centre). Many of the early antimetabolite-based prodrugs provide very polar activated forms that have limited abilities to diffuse across cell membranes, and rely on gap junctions between cells for their bystander effects. Several later studies have shown that more lipophilic, neutral compounds have superior diffusion-based bystander effects. Prodrugs of DNA alkylating agents, that are less cell cycle-specific than antimetabolites and more effective against noncycling tumor cells, appear in general to be more active prodrugs, requiring less prolonged dosing schedules to be effective. It is expected that continued studies to optimize the bystander effects and other properties of prodrugs and the activated species they generate will contribute to improvements in the effectiveness of suicide gene therapy.
Pre-clinical validation of B cell maturation antigen (BCMA) as a target for T cell immunotherapy of multiple myeloma (2018)

Multiple myeloma has a continued need for more effective and durable therapies. B cell maturation antigen (BCMA), a plasma cell surface antigen and member of the tumor necrosis factor (TNF) receptor superfamily, is an attractive target for immunotherapy of multiple myeloma due to its high prevalence on malignant plasma cells. The current work details the pre-clinical evaluation of BCMA expression and development of a chimeric antigen receptor (CAR) targeting this antigen using a fully human single chain variable fragment (scFv). We demonstrate that BCMA is prevalently, but variably expressed by all MM with expression on 25-100% of malignant plasma cells. Extensive Immunohistochemical analysis of normal tissue expression using commercially available polyclonal antibodies demonstrated expression within B-lineage cells across a number of tissues as expected. Based upon the highly restricted expression of BCMA within normal tissues, we generated a set of novel, fully human scFv binding domains to BCMA by screening a naïve B-cell derived phage display library. Using a series of <i>in vitro</i> and pre-clinical <i>in vivo</i> studies, we identified a scFv with high specificity for BCMA and robust anti-myeloma activity when used as the binding domain of a second-generation CAR bearing a CD137 costimulatory domain. This BCMA-specific CAR is currently being evaluated in a Phase 1b clinical study in relapsed and refractory MM patients (NCT02546167).
Pyrrole‐Assisted and Easy Oxidation of Cyclic α‐Amino Acid‐ Derived Diketopiperazines under Mild Conditions (2011)

Abstract A new procedure for the aerobic oxidation of α‐amino acids acylated by pyrrole‐carboxylic acid with triplet dioxygen is introduced. The reaction is general for a variety of pyrrole‐amino acid derivatives and represents a very practical and controllable method for the selective preparation of α‐hydroperoxy‐ or α‐hydroxy‐α‐amino acid diketopiperazines with molecular dioxygen. Furthermore, the non‐catalyzed direct oxidation of amino acid derivatives at the α‐position with molecular dioxygen represents a fundamental question.
Boundary evaluation of non-convex primitives to produce parametric trimmed surfaces (1987)

To integrate a CSG-based solid modeler into an existing wireframe/surface modeling system, new boundary evaluation technology has been developed. This scheme uses exact representations for the simple quadric surfaces and both exact and approximate representations of higher-order curved surfaces. It supports parametric primitives (box, wedge, sphere, cylinder, cone, torus), procedural primitives (extrusion, revolution, tube) and a sculptured surface primitive. The output includes curves, parametric trimmed surfaces, and a data structure of adjacency information.An existing boundary evaluator (PADL-2's) has been enhanced to allow a general non-convex faceted primitive with planar and quadric facets. This new hybrid evaluator combines two techniques for curve/primitive classification. PADL-2's existing halfspace-based classification is reserved for the simple convex primitives, and a new ray firing based classification is applied to the non-convex primitives. After evaluation, approximate intersection curves (from intersections involving higher order surfaces) are refined to a specified tolerance by exploiting an exact parametric representation of the surfaces of the primitives. The refined curves and the quadric surface intersection curves are used to create a parametric trimmed surface representation of the solid. This combination of techniques and representations offers advantages in accuracy, robustness and efficiency suitable to a production environment.
Adoptive transfer of gene-engineered CD4+ helper T cells induces potent primary and secondary tumor rejection (2005)

Because CD4+ T cells play a key role in aiding cellular immune responses, we wanted to assess whether increasing numbers of gene-engineered antigen-restricted CD4+ T cells could enhance an antitumor response mediated by similarly gene-engineered CD8+ T cells. In this study, we have used retroviral transduction to generate erbB2-reactive mouse T-cell populations composed of various proportions of CD4+ and CD8+ cells and then determined the antitumor reactivity of these mixtures. Gene-modified CD4+ and CD8+ T cells were shown to specifically secrete Tc1 (T cytotoxic-1) or Tc2 cytokines, proliferate, and lyse erbB2+ tumor targets following antigen ligation in vitro. In adoptive transfer experiments using severe combined immunodeficient (scid) mice, we demonstrated that injection of equivalent numbers of antigen-specific engineered CD8+ and CD4+ T cells led to significant improvement in survival of mice bearing established lung metastases compared with transfer of unfractionated (largely CD8+) engineered T cells. Transferred CD4+ T cells had to be antigen-specific (not just activated) and secrete interferon gamma (IFN-gamma) to potentiate the antitumor effect. Importantly, antitumor responses in these mice correlated with localization and persistence of gene-engineered T cells at the tumor site. Strikingly, mice that survived primary tumor challenge could reject a subsequent rechallenge. Overall, this study has highlighted the therapeutic potential of using combined transfer of antigen-specific gene-modified CD8+ and CD4+ T cells to significantly enhance T-cell adoptive transfer strategies for cancer therapy.
Time courses of equilibration for ammonium sulfate, sodium chloride and magnesium sulfate heptahydrate in the Z/3 crystallization plate (1994)

Time courses of equilibration for three salts, sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been measured in the Z/3 crystallization plate. It is shown that by varying both the diffusant and the reservoir depth the time taken to equilibrate can be as short as 200 or as long as 1400 h. Thus, the present design of the plate should accommodate a wide variety of desired crystallization kinetics.
Life after death: targeting high mobility group box 1 in emergent cancer therapies. (2013)

High mobility group box 1 (HMGB1), an evolutionarily highly conserved and abundant nuclear protein also has roles within the cytoplasm and as an extracellular damage-associated molecular pattern (DAMP) molecule. Extracellular HMGB1 is the prototypic endogenous 'danger signal' that triggers inflammation and immunity. Recent findings suggest that posttranslational modifications dictate the cellular localization and secretion of HMGB1. HMGB1 is actively secreted from immune cells and stressed cancer cells, or passively released from necrotic cells. During cancer development or administration of therapeutic agents including chemotherapy, radiation, epigenetic drugs, oncolytic viruses, or immunotherapy, the released HMGB1 may either promote or limit cancer growth, depending on the state of progression and vascularization of the tumor. Extracellular HMGB1 enhances autophagy and promotes persistence of surviving cancer cells following initial activation. When oxidized, it chronically suppresses the immune system to promote cancer growth and progression, thereby enhancing resistance to cancer therapeutics. In its reduced form, it can facilitate and elicit innate and adaptive anti-tumor immunity, recruiting and activating immune cells, in conjunction with cytotoxic agents, particularly in early transplantable tumor models. We hypothesize that HMGB1 also functions as an epigenetic modifier, mainly through regulation of NF-kB-dependent signaling pathways, to modulate the behavior of surviving cancer cells as well as the immune cells found within the tumor microenvironment. This has significant implications for developing novel cancer therapeutics.
Recent Progress on 1.55-$\mu{\hbox {m}}$ Dilute-Nitride Lasers (2007)

We review the recent developments in GaAs-based 1.55-mum lasers grown by molecular beam epitaxy (MBE). While materials growth is challenging, the growth window appears to be relatively broad and is described in detail. The key considerations for producing high-quality GalnNAsSb material emitting at 1.55-mum regime are examined, including the nitrogen plasma conditions, ion removal from the nitrogen flux, surfactant- mediated growth, the roles of various V-II ratios, the growth temperature, the active region thermal budget, proper annealing, and composition. We find that emission may be tuned throughout the 1.55-mum communications band without penalty to the optical quality varying only one parameter - the total growth rate. This powerful result is validated by the demonstration of low-threshold edge-emitting lasers throughout the 1.55-mum regime, including threshold current densities as low as 318 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at 1.54 mum. Additional characterization by Z-parameter techniques, cavity length studies, and band offset measurements were performed to better understand the temperature stability of device performance. Lasing was extended as far as 1.63 mum under nonoptimized growth conditions. The GaAs-based dilute-nitrides are emerging as a very promising alternative to InP-based materials at 1.55-mum due to their high gain, greater range of achievable band offsets, as well as the availability of lattice-matched AlAs-GaAs materials and native oxide layers for vertical-cavity surface-emitting lasers (VCSELs). Indeed, this effort has enabled the first electrically injected C-band VCSEL on GaAs.
Insertional mutagenesis as a probe of rhodopsin's topography, stability, and activity. (1994)

This paper reports a study of rhodopsin's structure and function using insertional mutagenesis with a flexible epitope. Sixteen rhodopsin derivatives were constructed, each of which carried a 12-amino acid epitope derived from the c-Myc protein flanked by penta-glycine linkers. For eight of the insertion mutants, the membrane sideness of the epitope insert was determined by immunostaining of intact or permeabilized cells. The results confirm the sidedness of each of the six helix connecting loops and the amino and carboxyl termini as postulated by the current seven-helix models of G-protein-coupled receptors and provide the first experimental evidence for the existence of the third extracellular loop. In general, inserts that were either closer to the amino terminus or on the extracellular face were more likely to disrupt folding and/or stability than were inserts near the carboxyl terminus or on the cytosolic face. Epitope insertion at positions 139 or 239, in the second and third cytosolic loops, respectively, failed to activate transducin, whereas an insertion at position 333 in the carboxyl-terminal tail was fully functional. The experimental approach described here should prove generally useful for elucidating structural and functional properties of both membrane and globular proteins.