gebhart/patrepeval huggingface dataset:
Organ specific neoantigens reactive in the leukocyte adherence inhibition assay: affinity purification of human colon carcinoma antigen and its cross-reactive protein using monoclonal antibodies. (1986)

A monoclonal antibody (mAb) was prepared against a semipurified preparation of an organ specific neoantigen (OSN) reactive in the leukocyte adherence inhibition (LAI) assay. The mAb (LC20.1) induces a positive LAI response when incubated with leukocytes of normal individuals in the presence of OSN derived from either human colon or lung carcinoma cell lines. Absorption of crude OSN preparations from these cell lines on immobilized LC20.1 mAb eliminates all the LAI reactive material suggesting that the mAb recognizes a common determinant on OSN from both colon and lung carcinomas. The LC20 mAb was used to affinity purify the colon cancer OSN as well as a cross-reactive normal protein from the urine of colon cancer patients and healthy donors, respectively. The colon cancer OSN and normal cross-reactive protein display an apparent molecular weight of 29,000, have a similar linear tryptic peptide map, and are indistinguishable by isoelectric focusing analysis. Regardless of the molecular similarity, only the colon cancer OSN preparation could induce a positive LAI when incubated with leukocytes of colon cancer patients. Seven additional anti-colon cancer OSN mAbs were prepared against purified material. These mAbs can be divided into three groups, each of which recognizes a distinct antigenic determinant that is shared by the colon cancer neoantigen and its cross-reactive normal protein.
Estrogen-induced alterations of spinal cord enkephalin gene expression (1999)

Enkephalin-synthesizing neurons in the superficial laminae of the spinal and trigeminal dorsal horn are critical components of the endogenous pain-modulatory system. We have previously demonstrated that these neurons display intracellular estrogen receptors, suggesting that estrogen can potentially influence their enkephalin expression. By using Northern blot, we now show that a bolus injection of estrogen results in a rapid increase in spinal cord enkephalin mRNA levels in ovariectomized female rats. Thus, 4 h after estrogen administration the enkephalin mRNA-expression in the lumbar spinal cord was on average 68% higher (P<0.05) than in control animals injected with vehicle only. A small increase in the amount of enkephalin mRNA was also seen after 8 h (P<0.05), whereas no difference between estrogen-injected and control animals was found after 24 h or at time periods shorter than 4 h. Taken together with the previous anatomical data, the present findings imply that estrogen has an acute effect on spinal opioid levels in areas involved in the transmission of nociceptive information.
Organometallic aspects of cytochrome P-450 metabolism (1987)

Carbeneiron porphyrins, (N,Fe)-bridged methyleneiron porphyrins, N-alkyliron porphyrins and σ-alkyliron porphyrins have all been shown to occur in nature and to be interconvertible via redox reactions. The chemistry of the naturally occurring iron porphyrins and model iron, cobalt, and ruthenium porphyrins is reviewed emphasizing their organometallic chemistry.
Beta-adrenergic receptor subtype is an intrinsic property of the receptor gene product. (1987)

The gene encoding the hamster beta-adrenergic receptor (beta AR) was expressed in mouse C6 glioma cells, a cell line which normally expressed the beta 1 subtype of the receptor. Upon transfection with the hamster beta AR gene, the cells expressed increased levels of beta AR, as assessed both by protein immunoblotting and by the binding of the radiolabeled antagonist 125I-cyanopindolol. This newly expressed receptor was of the beta 2 subtype, as determined with a variety of agonists and antagonists. These results suggest that the subtype of the beta AR is an intrinsic property of the gene product and is not the result of a post-translational modification of the receptor by the cell in which it is expressed.
Limit Distribution of Maximal Non-Aligned Two-Sequence Segmental Score (1994)

Consider two independent sequences $X_1,\ldots, X_n$ and $Y_1,\ldots, Y_n$. Suppose that $X_1,\ldots, X_n$ are i.i.d. $\mu_X$ and $Y_1,\ldots, Y_n$ are i.i.d. $\mu_Y$, where $\mu_X$ and $\mu_Y$ are distributions on finite alphabets $\sigma_X$ and $\sigma_Y$, respectively. A score $F: \sigma_X \times \sigma_Y\rightarrow \mathbb{R}$ is assigned to each pair $(X_i, Y_j)$ and the maximal nonaligned segment score is $M_n = \max_{0\leq i, j\leq n - \Delta, \Delta \geq 0} \{\sum^\Delta_{k=1} F(X_{i+k}, Y_{j+k})\}$. The limit distribution of $M_n$ is derived here when $\mu_X$ and $\mu_Y$ are not too far apart and $F$ is slightly constrained.
Medical treatment of endometriosis. (2005)

The medical treatment of endometriosis is a critical aspect of the therapeutic approach to this disease. This review will present an overview of current literature about the medical treatment of endometriosis, without referring to the surgical treatment or a combination of both. The main purpose of the current medical treatment of endometriosis is to create an amenorrheic state, in other words, to create a hypoestrogenic environment by suppressing estrogen secretion of the ovary. Current research has focused upon medications designed to attack specific aspects of the development and maintenance of endometriosis. This includes progesterone receptor modulators, gonadotropin releasing hormone (GnRH) analogs, aromatase inhibitors and, tumor necrosis factor alpha (TNFalpha) inhibitors, angiogenesis inhibitors, matrix metalloproteinase inhibitors and estrogen receptor beta agonists like inmunomodulators. These drugs show decreased spreading of lesions and reduced disease related symptoms. Medical treatment is moderately effective in reducing pain but ineffective in improving fertility; a combination of medical treatment with assisted reproductive technology may be beneficial in improving fertility.
An unnatural base pair between imidazolin-2-one and 2-amino-6-(2-thienyl)purine in replication and transcription (2002)

Nucleosides of imidazolin-2-one (designated by z) were designed and synthesized as pairing partners of 2-amino-6-(2-thienyl)purine (designated by s). Previously, we developed an unnatural base pair between s and pyridine-2-one (designated by y), and polymerases specifically incorporated the substrate of y into DNA and RNA opposite s in templates. Although s was efficiently incorporated opposite y, A was also incorporated opposite y with high efficiency. The replacement of y by z effectively improved the incorporation selectivity of s. The incorporation efficiency of A opposite z decreased, but the efficient incorporation of s opposite z was maintained as compared to that of the s-y pairing.
A monoclonal antibody to recombinant human IFN-alpha receptor inhibits biologic activity of several species of human IFN-alpha, IFN-beta, and IFN-omega. Detection of heterogeneity of the cellular type I IFN receptor (1993)

A cDNA encoding a 63-kDa human IFN-alpha R (hIFN-alpha R) has recently been cloned. Mouse cells transfected with this cDNA failed to show any signal transmission for IFN-beta, suggesting the involvement of additional chains in the receptor complex. We have expressed in Escherichia coli and COS 7 cells a soluble recombinant protein (sIFN-alpha R) comprising the extracellular domain of the hIFN-alpha R fused at the carboxyl terminus to a sequence of five histidine residues. The sIFN-alpha R was affinity purified and used to generate mAb. One mAb, 64G12, which recognized the cellular receptor as well as the recombinant proteins was found to neutralize the biologic activity of IFN-alpha, -beta, and -omega and natural type I IFN, but not IFN-gamma. To our knowledge, this is the first report of a neutralizing mAb against the human IFN-alpha R. Interestingly, we found that the affinity of this antibody for the cellular receptor depended on the cell line used. These results provide strong evidence that the cloned hIFN-alpha R chain is required for binding and signal transmission of all subspecies of type I IFN and suggest a structural heterogeneity of the receptor at the cell surface.
Cell-free DNA testing in the maternal blood in high-risk pregnancies after first-trimester combined screening (2016)

In high-risk pregnancies after combined screening, a policy of selecting a subgroup for invasive testing and another for cfDNA testing would substantially reduce the number of invasive procedures and retain the ability to diagnose most of the observed aneuploidies.
Person re-identification by Local Maximal Occurrence representation and metric learning (2015)

Person re-identification is an important technique towards automatic search of a person's presence in a surveillance video. Two fundamental problems are critical for person re-identification, feature representation and metric learning. An effective feature representation should be robust to illumination and viewpoint changes, and a discriminant metric should be learned to match various person images. In this paper, we propose an effective feature representation called Local Maximal Occurrence (LOMO), and a subspace and metric learning method called Cross-view Quadratic Discriminant Analysis (XQDA). The LOMO feature analyzes the horizontal occurrence of local features, and maximizes the occurrence to make a stable representation against viewpoint changes. Besides, to handle illumination variations, we apply the Retinex transform and a scale invariant texture operator. To learn a discriminant metric, we propose to learn a discriminant low dimensional subspace by cross-view quadratic discriminant analysis, and simultaneously, a QDA metric is learned on the derived subspace. We also present a practical computation method for XQDA, as well as its regularization. Experiments on four challenging person re-identification databases, VIPeR, QMUL GRID, CUHK Campus, and CUHK03, show that the proposed method improves the state-of-the-art rank-1 identification rates by 2.2%, 4.88%, 28.91%, and 31.55% on the four databases, respectively.
Case Report. Successful outcome of invasive nasal sinus zygomycosis in a child with relapsed acute lymphoblastic leukaemia due to liposomal amphotericin B (2001)

We report a case of life-threatening nasal sinus zygomycosis that developed during remission induction therapy for a relapsed acute lymphoblastic leukaemia. The patient was successfully treated with liposomal amphotericin B and granulocyte-colony stimulating factor followed by surgical reconstruction of the resultant cutaneous defect.
Imaging through scattering media with holography (1992)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text E. Leith, C. Chen, H. Chen, Y. Chen, D. Dilworth, J. Lopez, J. Rudd, P.-C. Sun, J. Valdmanis, and G. Vossler, "Imaging through scattering media with holography," J. Opt. Soc. Am. A 9, 1148-1153 (1992) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Intermedia: A case study of the differences between relational and object-oriented database systems (1987)

This paper compares two approaches to meeting the data handling requirements of Intermedia, a hypermedia system developed at the Institute for Research in Information and Scholarship at Brown University. Intermedia, though written using an object-oriented programming language, relies on a traditional relational database management system for data storage and retrieval. We examine the ramifications of replacing the relational database with an object-oriented database. We begin by describing the important characteristics each database system. We then describe Intermedia and give an overview of its architecture and its data handling requirements. We explain why and how we used a relational database management system and the problems that we encountered with this system. We then present the design of an object-oriented database schema for Intermedia and compare the relational and object-oriented database management system approaches .
Effect of Oral Eicosapentaenoic Acid on Weight Loss in Patients With Pancreatic Cancer (2000)

Eicosapentaenoic acid (EPA) has been shown to modulate aspects of the inflammatory response that may contribute to weight loss in cancer. This study aimed to evaluate the acceptability and effects of oral supplementation with high-purity EPA in weight-losing patients with advanced pancreatic cancer. Twenty-six patients were entered into the study. EPA (95% pure) was administered as free acid starting at 1 g/day; the dose was increased to 6 g/day over four weeks, and then a maintenance dose of 6 g/day was administered. Patients were assessed before EPA and at 4, 8, and 12 weeks while receiving EPA, for weight, body composition, hematologic and clinical chemistry variables, acute-phase protein response, and performance status. Overall survival was noted. Supplementation was well tolerated, with only five patients experiencing side effects possibly attributable to the EPA. Before starting EPA, all patients had been losing weight at a median rate of 2 kg/mo. In general, after EPA supplementation, weight was stable. After four weeks of EPA supplementation, patients had a median weight gain of 0.5 kg (p = 0.0009 vs. rate of weight loss at baseline), and this stabilization of weight persisted over the 12-week study period. Total body water as a percentage of body weight remained stable, as did the proportion of patients with an acute-phase protein response, patients' nutritional intake, and performance status. Overall median survival from diagnosis in this study was 203 days. This study suggests that EPA is well tolerated, may stabilize weight in cachectic pancreatic cancer patients, and should be tested as an anticachectic agent in controlled trials.
The sequence of the stem and flanking sequences at the 3′ end of histone mRNA are critical determinants for the binding of the stem-loop binding protein (1995)

Complexes of different electrophoretic mobility containing the stem-loop binding protein, a 45 kDa protein, bound to the stem-loop at the 3' end of histone mRNA, are present in both nuclear and cytoplasmic extracts from mammalian cells. We have determined the effect of changes in the loop, in the stem and in the flanking sequences on the affinity of the SLBP for the 3' end of histone mRNA. The sequence of the stem is particularly critical for SLBP binding. Specific sequences both 5' and 3' of the stem-loop are also required for high-affinity binding. Expanding the four base loop by one or two uridines reduced but did not abolish SLBP binding. RNA footprinting experiments show that the flanking sequences on both sides of the stem-loop are critical for efficient binding, but that cleavages in the loop do not abolish binding. Thus all three regions of the RNA sequence contribute to SLBP binding, suggesting that the 26 nt at the 3' end of histone mRNA forms a defined tertiary structure recognized by the SLBP.
Tumor necrosis factor antagonist therapy and lymphoma development: Twenty‐six cases reported to the Food and Drug Administration (2002)

Although data from a case series such as this cannot establish a clear causal relationship between exposure to these medications and the risk of lymphoproliferative disease, the known predisposition of patients with RA and CD to lymphoma, the known excess of lymphoma in other immunosuppressed populations, and the known immunosuppressive effects of the anti-TNF drugs provide a biologic basis for concern and justification for the initiation of additional epidemiologic studies to formally evaluate this possible association.
<title>Video-image-based neural network guidance system with adaptive view-angles for autonomous vehicles</title> (1991)

This paper describes the guidance function of an autonomous vehicle based on a neural network controller using video images with adaptive view angles for sensory input. The guidance function for an autonomous vehicle provides the low-level control required for maintaining the autonomous vehicle on a prescribed trajectory. Neural networks possess unique properties such as the ability to perform sensor fusion, the ability to learn, and fault tolerant architectures, qualities which are desirable for autonomous vehicle applications. To demonstrate the feasibility of using neural networks in this type of an application, an Intelledex 405 robot fitted with a video camera and vision system was used to model an autonomous vehicle with a limited range of motion. In addition to fixed-angle video images, a set of images using adaptively varied view angles based on speed are used as the input to the neural network controller. It was shown that the neural network was able to control the autonomous vehicle model along a path composed of path segments unlike the exemplars with which it was trained. This system was designed to assess only the guidance system, and it was assumed that other functions employed in autonomous vehicle control systems (mission planning, navigation, and obstacle avoidance) are to be implemented separately and are providing a desired path to the guidance system. The desired path trajectory is presented to the robot in the form of a two-dimensional path, with centerline, that is to be followed. A video camera and associated vision system provides video image data as control feedback to the guidance system. The neural network controller uses Gaussian curves for the output vector to facilitate interpolation and generalization of the output space.
The angiogenesis inhibitor SU5416 has long-lasting effects on vascular endothelial growth factor receptor phosphorylation and function. (2000)

SU5416, a selective inhibitor of the tyrosine kinase activity of the vascular endothelial growth factor (VEGF) receptor Flk-1/KDR, is currently in Phase III clinical trials for the treatment of advanced malignancies. In cellular assays, SU5416 inhibits the VEGF-dependent mitogenic/proliferative response of human umbilical vein endothelial cells (HUVECs). In tumor xenograft models, SU5416 inhibits the growth of tumors from a variety of origins by inhibiting tumor angiogenesis. In three different human tumor xenograft models, infrequent (once or twice a week) administration of SU5416 is efficacious despite the fact that it has a short plasma half-life (30 min), which suggests that SU5416 has long-lasting inhibitory activity in vivo. The goal of the present study was to determine the basis for the prolonged activity of SU5416. The results indicate that a short (3 h) exposure to 5 microM SU5416 (to mimic plasma levels of the compound as measured in patients who were receiving SU5416 therapy) produced long-lasting (at least 72 h) inhibition of the VEGF-dependent proliferation of HUVECs in culture, which indicate that SU5416 has long-lasting inhibitory activity in vitro as well as in vivo. SU5416 treatment of HUVECs did not affect surface expression of Flk-1/KDR or the affinity of the receptor for VEGF. Instead, the durability of the in vitro activity of SU5416 was shown to be attributable to its long-lasting ability to specifically inhibit VEGF-dependent phosphorylation of Flk-1/KDR and subsequent downstream signaling, although SU5416 is not an irreversible inhibitor of Flk-1/KDR tyrosine kinase activity. The long-lasting inhibition of cellular responses to VEGF was attributable to the accumulation of SU5416 in cells, as shown using radiolabeled compound, such that inhibitory cellular concentrations of SU5416 are maintained long after the removal of the compound from the medium. The long-lasting inhibitory activity of SU5416 in vitro is consistent with the finding that SU5416 has demonstrated evidence of biological activity in clinical studies when administered twice a week despite a short plasma half-life.
4. Developing an Engineered Nipah Virus Glycoprotein Based Lentiviral Vector System Retargeted To Cell Surface Receptors of Choice (2015)

Delivery of genes selectively into specific cell types is a major bottleneck in successful gene therapy. Receptor-targeted lentiviral vectors (RT-LVs) can be an effective tool to achieve selective transfer of genes to cell types of choice, ex vivo and in vivo. So far, many different target receptors specific for cell types present in many different tissue types have been successfully addressed. RT-LVs based on engineered measles virus (MV) glycoproteins are most selective but can only be produced at moderate vector titers and suffer from susceptibility towards neutralising antibodies induced by vaccination against measles. In this study, LVs have been pseudotyped with modified Nipah virus (NiV) glycoproteins in order to generate LVs with high specificity for target cell populations and enhanced titers. The glycoproteins were engineered to make them deficient for the use of EphrinB2/3, the natural NiV receptor, and truncated in their cytoplasmic tails to allow efficient incorporation into LV particles. Designed ankyrin repeat proteins (DARPins) or single chain antibodies (scFv) specific for the cell surface receptor of choice were fused to the G glycoprotein to mediate receptor binding and subsequent cell entry. All G-DARPin/-scFv fusion proteins were efficiently expressed at the cell surface and incorporated into LV particles. The particles exhibited selective entry into their particular target cells and showed stable transgene expression. Importantly, NiV-LVs were at least 250-fold less effectively neutralized than MV glycoprotein pseudotyped LVs if incubated with pooled human intravenous immunoglobulin (Intratect®). So far, EpCAM, CD4, and CD8 served as functional receptors for NiV glycoprotein based RT-LVs. The CD8-targeted vector selectively transduced CD8+ lymphocytes when added to human PBMCs in vitro. Remarkably, these NiV-based RT-LVs could be produced at 8- to 68-fold higher titers compared to the corresponding MV glycoprotein-based RT-LVs. Current efforts focus on the quantification of these observations and identification of the underlying mechanisms. In addition, the capability of NiV-based RT-LVs to transduce target cell populations in vivo is being analyzed.
Core Refinement toward Permeable β-Secretase (BACE-1) Inhibitors with Low hERG Activity (2012)

By use of iterative design aided by predictive models for target affinity, brain permeability, and hERG activity, novel and diverse compounds based on cyclic amidine and guanidine cores were synthesized with the goal of finding BACE-1 inhibitors as a treatment for Alzheimer's disease. Since synthesis feasibility had low priority in the design of the cores, an extensive synthesis effort was needed to make the relevant compounds. Syntheses of these compounds are reported, together with physicochemical properties and structure-activity relationships based on in vitro data. Four crystal structures of diverse amidines binding in the active site are deposited and discussed. Inhibitors of BACE-1 with 3 μM to 32 nM potencies in cells are shown, together with data on in vivo brain exposure levels for four compounds. The results presented show the importance of the core structure for the profile of the final compounds.