gebhart/patrepeval huggingface dataset:
1592U89, a novel carbocyclic nucleoside analog with potent, selective anti-human immunodeficiency virus activity (1997)

1592U89, (-)-(1S,4R)-4-[2-amino-6-(cyclopropylamino)-9H-purin-9-yl]-2-cyclo pentene-1-methanol, is a carbocyclic nucleoside with a unique biological profile giving potent, selective anti-human immunodeficiency virus (HIV) activity. 1592U89 was selected after evaluation of a wide variety of analogs containing a cyclopentene substitution for the 2'-deoxyriboside of natural deoxynucleosides, optimizing in vitro anti-HIV potency, oral bioavailability, and central nervous system (CNS) penetration. 1592U89 was equivalent in potency to 3'-azido-3'-deoxythymidine (AZT) in human peripheral blood lymphocyte (PBL) cultures against clinical isolates of HIV type 1 (HIV-1) from antiretroviral drug-naive patients (average 50% inhibitory concentration [IC50], 0.26 microM for 1592U89 and 0.23 microM for AZT). 1592U89 showed minimal cross-resistance (approximately twofold) with AZT and other approved HIV reverse transcriptase (RT) inhibitors. 1592U89 was synergistic in combination with AZT, the nonnucleoside RT inhibitor nevirapine, and the protease inhibitor 141W94 in MT4 cells against HIV-1 (IIIB). 1592U89 was anabolized intracellularly to its 5'-monophosphate in CD4+ CEM cells and in PBLs, but the di- and triphosphates of 1592U89 were not detected. The only triphosphate found in cells incubated with 1592U89 was that of the guanine analog (-)-carbovir (CBV). However, the in vivo pharmacokinetic, distribution, and toxicological profiles of 1592U89 were distinct from and improved over those of CBV, probably because CBV itself was not appreciably formed from 1592U89 in cells or animals (<2%). The 5'-triphosphate of CBV was a potent, selective inhibitor of HIV-1 RT, with Ki values for DNA polymerases (alpha, beta, gamma, and epsilon which were 90-, 2,900-, 1,200-, and 1,900-fold greater, respectively, than for RT (Ki, 21 nM). 1592U89 was relatively nontoxic to human bone marrow progenitors erythroid burst-forming unit and granulocyte-macrophage CFU (IC50s, 110 microM) and human leukemic and liver tumor cell lines. 1592U89 had excellent oral bioavailability (105% in the rat) and penetrated the CNS (rat brain and monkey cerebrospinal fluid) as well as AZT. Having demonstrated an excellent preclinical profile, 1592U89 has progressed to clinical evaluation in HIV-infected patients.
β-Chemokines and neutralizing antibody titers correlate with sterilizing immunity generated in HIV-1 vaccinated macaques (1998)

One of the obstacles to AIDS vaccine development is the variability of HIV-1 within individuals and within infected populations, enabling viral escape from highly specific vaccine induced immune responses. An understanding of the different immune mechanisms capable of inhibiting HIV infection may be of benefit in the eventual design of vaccines effective against HIV-1 variants. To study this we first compared the immune responses induced in Rhesus monkeys by using two different immunization strategies based on the same vaccine strain of HIV-1. We then utilized a chimeric simian/HIV that expressed the envelope of a dual tropic HIV-1 escape variant isolated from a later time point from the same patient from which the vaccine strain was isolated. Upon challenge, one vaccine group was completely protected from infection, whereas all of the other vaccinees and controls became infected. Protected macaques developed highest titers of heterologous neutralizing antibodies, and consistently elevated HIV-1-specific T helper responses. Furthermore, only protected animals had markedly increased concentrations of RANTES, macrophage inflammatory proteins 1alpha and 1beta produced by circulating CD8(+) T cells. These results suggest that vaccine strategies that induce multiple effector mechanisms in concert with beta-chemokines may be desired in the generation of protective immune responses by HIV-1 vaccines.
Regulation of human renin expression in chorion cell primary cultures. (1990)

The human renin gene is expressed in the kidney, placenta, and several other sites. The release of renin or its precursor, prorenin, can be affected by several regulatory agents. In this study, primary cultures of human placental cells were used to examine the regulation of prorenin release and renin mRNA levels and of the transfected human renin promotor linked to chloramphenicol acetyltransferase reporter sequences. Treatment of the cultures with a calcium ionophore alone, calcium ionophore plus forskolin (that activates adenylate cyclase), or forskolin plus a phorbol ester increased prorenin release and renin mRNA levels 1.3- to 6-fold, but several classes of steroids did not affect prorenin secretion or renin RNA levels. The transfected renin promoter (584 or 100 base pairs of 5'-flanking DNA) initiated at the correct start site in these cells and forskolin increased its expression 2.5- to 4-fold. Constructs containing renin 5'-flanking DNA linked to a heterologous promoter cotransfected into HeLa cells with either glucocorticoid or estrogen receptor expression vectors were not regulated by dexamethasone or 17 beta-estradiol. These results suggest that (i) the first 584 base pairs of the renin gene 5'-flanking DNA do not contain functional glucocorticoid or estrogen response elements, (ii) placental prorenin release and renin mRNA are regulated by calcium ion and by the combinations of cAMP with either C kinase or calcium ion, and (iii) the first 100 base pairs of the human renin 5'-flanking DNA direct accurate initiation of transcription and can be regulated by cAMP. Thus, some control of renin release in the placenta (and by inference in other tissues) occurs via transcriptional influences on its promoter.
Design of a Flexible Open Platform for High Performance Active Networks (1999)

Epigallocatechin-3-gallate (EGCG), a bioactive polyphenol in green tea, exerts antiapoptotic activity and prevents tissue damage against different stimuli. Herein, we investigated the effects of EGCG treatment to simultaneously improve spermatogenesis following ionizing radiation (IR) (at a dose of 2 Gy). Mice were intraperitoneally injected with 50 mg/kg EGCG or vehicle control 3 days prior to the irradiation, and the treatment lasted intermittently for 24 days. Supplement with exogenous EGCG protected against short-term germ cell loss and attenuated IR-elicited testicular oxidative stress. Mechanistically, prosurvival effects of EGCG treatment upon IR stress were regulated, at least in part, via the mitogen-activated protein kinase/BCL2 family/caspase 3 pathway. Consistently, at post-IR Day 21, histological analyses revealed tubule damage, desquamation of germ cells, and impairment of caudal parameters in irradiated testis, which could be significantly improved by intermittent EGCG treatment. In addition, long-term EGCG application ameliorated the IR-induced blood-testicular barrier permeability and suppressed testicular steroidogenesis, thus exerting a stimulatory effect on the spermatogenic recovery. Collectively, EGCG appeared to efficiently prevent germ cells from radiation-induced cell death via multiple mechanisms. Employment of this bioactive polyphenol should be an attractive strategy to preserve fertility in males exposed to conventional radiation therapy and warrants further investigation.
Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes (2013)

We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g. pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.
Inflammation: a role for NR4A orphan nuclear receptors? (2011)

Inflammation is paradoxical; it is essential for protection following biological, chemical or physical stimuli, but inappropriate or misdirected inflammation is responsible for tissue injury in a variety of inflammatory diseases. The polarization of immune cells is critical in controlling the stages of inflammatory response. The acute phase of inflammation is characterized by a T-lymphocyte:Th2 cytokine profile and involves a co-ordinated migration of immune cells to the site of injury where production of cytokines and acute-phase proteins brings about healing. However, persistent inflammation can result in inappropriate and prolonged T-lymphocyte:Th1 cytokine-mediated action and reaction of self-molecules, leading to a chronic phase in diseases such as RA (rheumatoid arthritis), Ps (psoriasis) and atherosclerosis. The inflammatory response is also controlled by activated macrophage cells, with classically activated (M1) cells producing a wide variety of pro-inflammatory mediators, while alternatively activated (M2) macrophages participate in anti-inflammatory response. Members of the NR4A subfamily (NR4A1/NUR77, NR4A2/NURR1 and NR4A3/NOR1) of orphan NRs (nuclear receptors) have emerged as key transcriptional regulators of cytokine and growth factor action in diseases affecting our aging population. As ligand-independent and constitutively active receptors, the activity of these transcription factors is tightly controlled at the level of expression, post-translational modification and subcellular localization. NR4A subfamily members are aberrantly expressed in inflamed human synovial tissue, psoriatic skin, atherosclerotic lesions, lung and colorectal cancer cells. Significantly, prolonged or inappropriate inflammatory responses contribute to the pathogenesis of these diseases. In activated cells, NR4A receptors are rapidly and potently induced, suggesting that these receptors may act as important transcriptional mediators of inflammatory signals. NR4A receptors may contribute to the cellular processes that control inflammation, playing a critical part in the contribution of chronic inflammation or they may have a protective role, where they may mediate pro-resolution responses. Here, we will review the contribution of the NR4A orphan NRs to integration of cytokine signalling in inflammatory disorders.
RNA replication by respiratory syncytial virus (RSV) is directed by the N, P, and L proteins; transcription also occurs under these conditions but requires RSV superinfection for efficient synthesis of full-length mRNA (1995)

Previously, a cDNA was constructed so that transcription by T7 RNA polymerase yielded a approximately 1-kb negative-sense analog of genomic RNA of human respiratory syncytial virus (RSV) containing the gene for chloramphenicol acetyltransferase (CAT) under the control of putative RSV transcription motifs and flanked by the RSV genomic termini. When transfected into RSV-infected cells, this minigenome was "rescued," as evidenced by high levels of CAT expression and the production of transmissible particles which propagated and expressed high levels of CAT expression during serial passage (P.L. Collins, M. A. Mink, and D. S. Stec, Proc. Natl. Acad. Sci. USA, 88:9663-9667, 1991). Here, this cDNA, together with a second one designed to yield an exact-copy positive-sense RSV-CAT RNA antigenome, were each modified to contain a self-cleaving hammerhead ribozyme for the generation of a nearly exact 3' end. Each cDNA was transfected into cells infected with a vaccinia virus recombinant expressing T7 RNA polymerase, together with plasmids encoding the RSV N, P, and L proteins, each under the control of a T7 promoter. When the plasmid-supplied template was the mini-antigenome, the minigenome was produced. When the plasmid-supplied template was the minigenome, the products were mini-antigenome, subgenomic polyadenylated mRNA and progeny minigenome. Identification of progeny minigenome made from the plasmid-supplied minigenome template indicates that the full RSV RNA replication cycle occurred. RNA synthesis required all three RSV proteins, N, P, and L, and was ablated completely by the substitution of Asn for Asp at position 989 in the L protein. Thus, the N, P, and L proteins were sufficient for the synthesis of correct minigenome and antigenome, but this was not the case for subgenomic mRNA, indicating that the requirements for RNA replication and transcription are not identical. Complementation with N, P, and L alone yielded an mRNA pattern containing a large fraction of molecules of incomplete, heterogeneous size. In contrast, complementation with RSV (supplying all of the RSV gene products) yielded a single discrete mRNA band. Superinfection with RSV of cells staging N/P/L-based RNA synthesis yielded the single discrete mRNA species. Some additional factor supplied by RSV superinfection appeared to be involved in transcription, the most obvious possibility being one or more additional RSV gene products.
PLATEAU-WAVE PHENOMENON (I) (1991)

Plateau waves, as described by Lundberg (1960), can often be observed in patients with increased intracranial pressure (ICP) resulting from brain tumours, benign intracranial hypertension and other causes. The clinical significance of the waves, however, is still debated. In this study, the ICP was recorded continuously, the size of the ventricular system was evaluated using computerized tomography (CT), the cerebrospinal fluid (CSF) flow was studied using isotope cisternography, and the absorptive capacity of the CSF was determined by measuring the conductance to CSF outflow, in 94 patients with increased ICP. All patients who received continuous ICP monitorings had a basic ICP level of more than 200 mmHg, and these patients were assigned to two groups on the basis of the presence or absence of the plateau waves in the ICP recordings: group I comprising 17 patients without plateau waves but with a high ICP resulting from subarachnoid haemorrhage or hypertensive intracerebral haemorrhage, within 5 days after the start of bleeding; and group II consisting of 77 patients with both plateau waves and a high ICP resulting from brain tumours, meningitis carcinomatosa, benign intracranial hypertension, superior sagittal sinus thrombosis and communicating hydrocephalus. The isotope cisternography and conductance to CSF outflow studies showed that there was neither a delay in CSF circulation nor an impairment of CSF absorption in the group 1 patients and these patients showed no ventricular dilatation on CT, whereas there was a marked sluggishness in the CSF flow and a severe defect in the CSF absorption capacities of the group II patients irrespective of the presence or absence of ventricular dilatation on CT. The present observations indicate that patients with a plateau-wave phenomenon have a marked impairment of CSF absorption and CSF flow. We suggest that the phenomenon is an important sign indicating an impairment of CSF absorption capacities.
Randomized Phase III Trial of Gemcitabine Plus Cisplatin Compared With Single-Agent Gemcitabine As First-Line Treatment of Patients With Advanced Pancreatic Cancer: The GIP-1 Study (2010)

The addition of weekly cisplatin to gemcitabine failed to demonstrate any improvement as first-line treatment of advanced pancreatic cancer.
Autoimmune Diabetes Is Suppressed by Transfer of Proinsulin-Encoding Gr-1+ Myeloid Progenitor Cells That Differentiate In Vivo Into Resting Dendritic Cells (2005)

The nature of the T-cell response to antigen is governed by the activation state of the antigen-presenting dendritic cell (DC). Immature or resting DCs have been shown to induce T-cell responses that may protect against the development of autoimmune disease. Effectively harnessing this "tolerogenic" effect of resting DCs requires that it be disease-specific and that activation of DCs by manipulation ex vivo is avoided. We reasoned that this could be achieved by transferring in vivo partially differentiated myeloid progenitor cells encoding a disease-specific autoantigen. With the aim of preventing autoimmune diabetes, we transferred myeloid progenitor cells encoding proinsulin into NOD mice. Bone marrow (BM) was cultured in granulocyte macrophage colony-stimulating factor (GM-CSF) and transforming growth factor-beta1, a cytokine combination that expands myeloid cells but inhibits terminal DC differentiation, to yield Gr-1(+)/CD11b(+)/CD11c(-) myeloid progenitor cells and a minor population of CD11c(+)/CD11b(+)/CD86(lo) immature DCs. After transfer, Gr-1(+) myeloid cells acquired the characteristics of resting DCs (CD11c(+)/MHC classII(int)/CD86(lo)/CD40(lo)). Gr-1(+) myeloid cells generated from transgenic NOD mice that expressed proinsulin controlled by a major histocompatibility complex (MHC) class II promoter, but not from wild-type NOD mice, transferred into 4-week-old female NOD mice significantly suppressed diabetes development. The transfer of DC progenitors encoding a disease-specific autoantigen is, therefore, an effective immunotherapeutic strategy that could be applied to humans.
Prolonged Immunodepression after Trauma and Hemorrhagic Shock (1998)

The results indicate that a more severe and prolonged immunodepression occurs after combined trauma and hemorrhage than after trauma or hemorrhage alone.
Taq DNA polymerase blockage at pyrimidine dimers (1996)

ISSN:1362-4962
Docetaxel and Estramustine Compared with Mitoxantrone and Prednisone for Advanced Refractory Prostate Cancer (2004)

The improvement in median survival of nearly two months with docetaxel and estramustine, as compared with mitoxantrone and prednisone, provides support for this approach in men with metastatic, androgen-independent prostate cancer.
Tyrosinase Inhibitory Prenylated Flavonoids from Sophora flavescens (2003)

For the purpose of the development of a skin-whitening agent, Sophora flavescens was evaluated for tyrosinase inhibitory activity and its active principles were identified following activity-guided isolation. The ethanol extract and dichloromethane fraction from S. flavescens showed significant inhibition of mushroom tyrosinase. From the dichloromethane fraction, three known prenylated flavonoids, sophoraflavanone G, kuraridin, and kurarinone, were isolated. Compared with kojic acid (IC(50)=20.5 microM), these compounds possessed more potent tyrosinase inhibitory activity. The IC(50) values were 6.6, 0.6, and 6.2 microM for sophoraflavanone G, kuraridin, and kurarinone, respectively.
Probiotics for the Prevention of Antibiotic-associated Diarrhea and Clostridium difficile Diarrhea (2006)

Antibiotic-associated diarrhea is a common clinical problem occurring in up to 25% of patients, with diarrhea owing to Clostridium difficile accounting for up to a quarter of cases. The clinical and economic costs of antibiotic-associated diarrhea are significant and better treatments are needed. Probiotics may offer potential effective therapy for antibiotic-associated diarrhea by restoring intestinal microbial balance. A number of different probiotics have been evaluated in the prevention and treatment of antibiotic-associated diarrhea in adults and children, including the nonpathogenic yeast Saccharomyces boulardii and multiple lactic-acid fermenting bacteria such as Lactobacillus rhamnosus GG (LGG). A careful review of the literature supports the efficacy of S. boulardii in the prevention of antibiotic-associated diarrhea recurrent C. difficile infection in adults, whereas LGG is useful in the treatment of antibiotic-associated diarrhea in children. Not enough data exist to currently support the use of other probiotic preparations in these conditions. Although generally safe and well tolerated, both S. boulardii and LGG should be used cautiously in immunocompromised patients. Further study of probiotics, including large, well-designed, randomized controlled dose-ranging trials, comparative trials, and cost-benefit analyses are necessary.
The effect of surface roughness on direct wafer bonding (1999)

A theory is presented which describes the initial direct wafer bonding process. The effect of surface microroughness on the bondability is studied on the basis of the theory of contact and adhesion of elastic solids. An effective bonding energy, the maximum of which is the specific surface energy of adhesion, is proposed to describe the real binding energy of the bonding interface, including the influence of the wafer surface microroughness. Both the effective bonding energy and the real area of contact between rough surfaces depend on a dimensionless surface adhesion parameter, θ. Using the adhesion parameter as a measure, three kinds of wafer contact interfaces can be identified with respect to their bondability; viz. the nonbonding regime (θ &amp;gt;12), the bonding regime (θ &amp;lt;1), and the adherence regime (1&amp;lt;θ &amp;lt;12). Experimental data are in reasonable agreement with this theory.
Peptidyl Fluorescent Chemosensors for the Detection of Divalent Copper (2003)

Fluorescent organic chemosensors for the detection of divalent copper with high selectivity and sensitivity are the subject of intense research in the recent years. Structurally, ionophore and fluorophore are two essential parts determining the resultant performance of the chemosensor. While much work has been focused on designing highly selective ligands, little attention has been paid to the possible influence of ionophore-fluorophore interaction on their properties in metal ion binding. We studied here fluorescent chemosensors based on the Gly-His peptidyl motif and found that the functionality of the chemosensors was greatly influenced by the spatial alignment of the fluorophore in the molecules. In Gly-His-Lys(Dns) (1), the dansyl group is on a side branch and does not interact with copper, while in Dpr(Dns)-His-Lys (2), the dansyl group is also on a side branch but the close placement allows it to directly participate in the binding with copper ions. Therefore, although dansyl can signal the binding event in both molecules, the mechanisms involved are quite different, and this difference resulted in different sensing performance, e.g., the selectivity. Even more strikingly, the dansyl group in Dns-Gly-His-Gly (3) exhibited a profound effect on the molecular complexation. The binding constant decreased, and binding mode was affected since only 1:1 binding was observed while in side-branch-labeled ligands, a 2:1 binding may also be involved. In contrast to those side-chain-labeled ligands, molecule 3 is extremely simple in structure and possesses superior detecting qualities such as selectivity, molecular sensitivity, and applicability in a wide range of pH.