gebhart/patrepeval huggingface dataset:
Molecular and Integrative Physiology of Intestinal Peptide Transport (2004)

Intestinal protein digestion generates a huge variety and quantity of short chain peptides that are absorbed into intestinal epithelial cells by the PEPT1 transporter in the apical membrane of enterocytes. PEPT1 operates as an electrogenic proton/peptide symporter with the ability to transport essentially every possible di- and tripeptide. Transport is enantio-selective and involves a variable proton-to-substrate stoichiometry for uptake of neutral and mono- or polyvalently charged peptides. Neither free amino acids nor peptides containing four or more amino acids are accepted as substrates. The structural similarity of a variety of drugs with the basic structure of di- or tripeptides explains the transport of aminocephalosporins and aminopenicillins, selected angiotensin-converting inhibitors, and amino acid-conjugated nucleoside-based antiviral agents by PEPT1. The high transport capacity of PEPT1 allows fast and efficient intestinal uptake of the drugs but also of amino acid nitrogen even in states of impaired mucosal functions. Transcriptional and post-transcriptional regulation of PEPT1 occurs in response to alterations in the nutritional status and in disease states, suggesting a prime role of this transporter in amino acid absorption.
Fibrinogenolysis and Fibrinolysis with Tissue Plasminogen Activator, Urokinase, Streptokinase-Activated Human Globulin, and Plasmin (1971)

SummaryIn the presence of porcine tissue plasminogen activator, fibrinolysis is greatly enhanced in comparison with fibrinogenolysis. In contrast, other activators (UK, SK-activator) and plasmin showed no, or moderate, differences between lysis of fibrinogen and fibrin. The enhanced tissue activator effect is related to the activation of plasminogen. The observations add a specific mechanism of enhancement of fibrinolysis by tissue activator to that caused by the influence of inhibitors. The process may help to enhance localized fibrinolysis following tissue injury without affecting fibrinogen.
Heteroepitaxy of Ge on (100) Si substrates (1987)

The epitaxial growth of GaAs on Si is a subject of growing interest because of the possibility of integrating high-speed and optical devices in Si-based technology. The large lattice mismatch between Si and GaAs makes the growth of high-quality epilayers very difficult. However, Ge and GaAs have similar lattice parameters and thermal expansion coefficients and thus a promising way to improve epitaxial growth of GaAs on Si is to introduce an intermediate Ge buffer layer. This technique will only be effective when the structural defects formed at the Si–Ge interface can be prevented from propagating into GaAs. A series of Ge epilayers have been grown on (100) Si by molecular-beam epitaxy and several methods to reduce dislocation propagation have been examined. These include postgrowth annealing, graded layering, growth interruption, and/or superlattice buffers. The efficiency of these methods was assessed by transmission electron microscopy, Rutherford backscattering/channeling, and double-crystal x-ray diffraction. It was found that the threading dislocation density tends to decrease with increasing thickness. The graded layering technique gave poor results. The introduction of a superlattice buffer reduced the threading dislocation density; however, the best overall quality material was obtained by depositing pure Ge on Si at 600 °C and annealing 30 min at 700 °C.
Biologic effects of 1,25-dihydroxycholecalciferol (a highly active vitamin D metabolite) in acutely uremic rats (1972)

The development of a vitamin D-resistant state in the course of renal failure may be responsible for reduced intestinal absorption of calcium and an impaired response of skeletal tissue. Moreover, the kidney has been shown to carry out the conversion of 25-hydroxycholecalciferol (25-OH-CC) to a highly biologically active metabolite, 1,25-dihydroxycholecalciferol (1,25-diOH-CC). In the present studies, vitamin D-deficient rats, made acutely uremic by either bilateral nephrectomy or urethral ligation, received physiological doses of cholecalciferol (vitamin D(3)) (CC), 25-OH-CC or 1,25-diOH-CC; 24 hr later intestinal calcium transport, in vitro, and bone calcium mobilization, in vivo, were assessed. Whereas CC and 25-OH-CC stimulated calcium transport in sham-operated controls, they were without effect in the uremic animals. In contrast, administration of 1,25-diOH-CC stimulated calcium transport in both groups of uremic animals. Administration of 1,25-diOH-CC also stimulated calcium mobilization from bone in each group of animals. However, CC and 25-OH-CC were only effective in the sham controls and the uremic group produced by urethral ligation and had little or no effect in animals without kidneys. These results indicate that renal conversion of calciferol to a more biologically active form is necessary for the stimulation of intestinal calcium absorption and calcium mobilization from bone, and that 1,25-diOH-CC may bypass a possible defect in vitamin D metabolism in uremia. From these studies it is likely that uremia, per se, may also impair intestinal calcium transport.
Replicative and Cytopathic Potential of HTLV-III/LAV with sor Gene Deletions (1986)

The genome of the human T-lymphotropic virus type III (HTLV-III/LAV) has the potential to encode at least three polypeptides in addition to those encoded by the gag, pol, and env genes. In this study, the product of the sor (short open reading frame) region, which overlaps the 3' end of the pol gene, was found to be a protein with a molecular weight of 23,000. An assay was developed for testing the ability of cloned HTLV-III proviruses to produce viruses cytopathic for T4+ lymphocytes. In the cell line used, C8166, neither the HTLV-III sor gene product nor the complete 3'-orf gene product were necessary for the replication or cytopathic effects of the HTLV-III.
Molecular mechanism for ganciclovir resistance in human T lymphocytes transduced with retroviral vectors carrying the herpes simplex virus thymidine kinase gene (2001)

The herpes simplex virus thymidine kinase gene type 1 (HSV-Tk) ganciclovir (GCV) system is a novel therapeutic strategy for the modulation of graft-versus-host disease (GVHD), a major complication of allogeneic stem cell transplantation (allo-SCT). Retroviral-mediated gene transfer of the HSV-Tk gene into donor T lymphocytes before allo-SCT may allow their in vivo selective depletion after treatment with GCV. The expression of the HSV-Tk gene was analyzed in vitro in CEM cells, a human lymphoblastoid cell line, transduced with 2 different vectors, each containing the HSV-Tk gene and a selectable marker gene. GCV-resistant clones were identified within the clones expressing the marker gene. Characterization of the molecular events leading to this resistance revealed a 227-bp deletion in the HSV-Tk gene due to the presence of cryptic splice donor and acceptor sites within the HSV-Tk gene sequence. Furthermore, it was confirmed that this deletion was present in human primary T cells transduced with either vector and in 12 patients who received transduced donor T cells, together with a T-cell-depleted allo-SCT. In vivo circulating transduced T cells containing the truncated HSV-Tk gene were identified in all patients immediately after infusion and up to 800 days after transplantation. In patients who received GCV as treatment for GVHD, a progressive increase in the proportion of transduced donor T cells carrying the deleted HSV-Tk gene was observed. These results suggest that the limitations within the HSV-Tk/GCV system can be improved by developing optimized retroviral vectors to ensure maximal killing of HSV-Tk-transduced cells.
Evaluating and comparing three text-production techniques (1996)

What are the benefits of using Natural Language Generation in an industrial application? We have attempt to answer part of this question with a description of an assessment of three techniques for producing multisentential text: semi-automatic fill-in-the-blank interfacing, automatic linguistic-and-templates hybrid generation, and human writing. This assessment used a black-box methodology, with an independent blind-tested jury that gave different quality levels in relation to a set of criteria. The texts used for the assessment were business reply letters.
Solid‐Phase Synthesis of a Tumor‐Associated Sialyl‐TN Antigen Glycopeptide with a Partial Sequence of the “Tandem Repeat” of the MUC‐1 Mucin (1997)

An allylic anchor was used for the solid-phase synthesis of glycopeptide 1 from the tandem repeat of the tumor-associated mucin MUC-1 with a sialyl-TN antigen side chain. The sialyl-TN antigen is one of the most promising of the tumor-associated antigens for the development of vaccines against epithelial tumors. Subsequent hydrolysis of the sialic acid methyl ester proceeds without epimerization in the peptide or β-elimination of the carbohydrate side chain.
Prostate Cancer: Sextant Localization with MR Imaging, MR Spectroscopy, and11C-Choline PET/CT (2007)

In localizing cancer within the prostate, comparable specificity was obtained with either 3D MR spectroscopy and MR imaging or PET/CT; however, PET/CT had lower sensitivity relative to 3D MR spectroscopy alone or combined with MR imaging.
Novel PPAR‐gamma Agonists Identified from a Natural Product Library: A Virtual Screening, Induced‐Fit Docking and Biological Assay Study (2007)

Peroxisome proliferator-activated receptor-gamma (PPAR-gamma) plays an essential role in lipid and glucose homeostasis. It is recognized as the receptor of the thiazolidinediones-a synthetic class of anti-diabetic drugs-and is the target of many drug discovery efforts because of its role in disease states, such as type II diabetes mellitus. In this study, structure-based virtual screening of the PPAR-gamma ligand binding domain against a natural product library has revealed 29 potential agonists. In vitro testing of this list identified six flavonoids to have stimulated PPAR-gamma transcriptional activity in a transcriptional factor assay. Of these, flavonoid-psi-baptigenin-was classed as the most potent PPAR-gamma agonist, possessing low micromolar affinity (EC(50) = 2.9 microM). Further in vitro testing using quantitative RT-PCR and immunoblotting experiments demonstrated that psi-baptigenin activated PPAR-gamma mRNA (4.1 +/- 0.2-fold) and protein levels (2.9 +/- 0.4-fold) in THP-1 macrophages. Moreover, psi-baptigenin's-induced PPAR-gamma enhancement was abolished in the presence of a selective PPAR-gamma antagonist, GW9662. Induced-fit docking investigations provide a detailed understanding on the ligands' mechanism of action, suggesting five of the active flavonoids induce significant conformational change in the receptor upon binding. Overall, these results offer insight into various naturally derived flavonoids as leads/templates for development of novel PPAR-gamma ligands.
The Role of Synaptic GTPase-Activating Protein in Neuronal Development and Synaptic Plasticity (2003)

Synaptic GTPase-activating protein (SynGAP) is a neuronal RasGAP (Ras GTPase-activating protein) that is selectively expressed in brain and highly enriched at excitatory synapses, where it negatively regulates Ras activity and its downstream signaling pathways. To investigate the physiological role of SynGAP in the brain, we have generated mutant mice lacking the SynGAP protein. These mice exhibit postnatal lethality, indicating that SynGAP plays a critical role during neuronal development. In addition, cell biological experiments show that neuronal cultures from mutant mice have more synaptic AMPA receptor clusters, suggesting that SynGAP regulates glutamate receptor synaptic targeting. Moreover, electrophysiological studies demonstrated that heterozygous mutant mice have a specific defect in hippocampal long-term potentiation (LTP). These studies show that the regulation of synaptic Ras signaling by SynGAP is important for proper neuronal development and glutamate receptor trafficking and is critical for the induction of LTP.
Translating Biomolecular Recognition into Nanomechanics (2000)

We report the specific transduction, via surface stress changes, of DNA hybridization and receptor-ligand binding into a direct nanomechanical response of microfabricated cantilevers. Cantilevers in an array were functionalized with a selection of biomolecules. The differential deflection of the cantilevers was found to provide a true molecular recognition signal despite large nonspecific responses of individual cantilevers. Hybridization of complementary oligonucleotides shows that a single base mismatch between two 12-mer oligonucleotides is clearly detectable. Similar experiments on protein A-immunoglobulin interactions demonstrate the wide-ranging applicability of nanomechanical transduction to detect biomolecular recognition.
A competitive enzyme-linked immunosorbent assay specific for murine hepcidin-1: correlation with hepatic mRNA expression in established and novel models of dysregulated iron homeostasis (2014)

Mice have been essential for distinguishing the role of hepcidin in iron homeostasis. Currently, investigators monitor levels of murine hepatic hepcidin-1 mRNA as a surrogate marker for the bioactive hepcidin protein itself. Here, we describe and validate a competitive, enzyme-linked immunosorbent assay that quantifies hepcidin-1 in mouse serum and urine. The assay exhibits a biologically relevant lower limit of detection, high precision, and excellent linearity and recovery. We also demonstrate correlation between serum and urine hepcidin-1 values and validate the competitive enzyme-linked immunosorbent assay by analyzing plasma hepcidin response of mice to physiological challenges, including iron deficiency, iron overload, acute blood loss, and inflammation. Furthermore, we analyze multiple murine genetic models of iron dysregulation, including β-thalassemia intermedia (Hbb(th3/+)), hereditary hemochromatosis (Hfe(-/-), Hjv(-/-), and Tfr2(Y245X/Y245X)), hypotransferrinemia (Trf(hpx/hpx)), heterozygous transferrin receptor 1 deficiency (Tfrc(+/-)) and iron refractory iron deficiency anemia (Tmprss6(-/-) and Tmprss6(hem8/hem8)). Novel compound iron metabolism mutants were also phenotypically characterized here for the first time. We demonstrate that serum hepcidin concentrations correlate with liver hepcidin mRNA expression, transferrin saturation and non-heme liver iron. In some circumstances, serum hepcidin-1 more accurately predicts iron parameters than hepcidin mRNA, and distinguishes smaller, statistically significant differences between experimental groups.
Inhibition of proliferation and induction of differentiation of pluripotent human embryonal carcinoma cells by osteogenic protein-1 (or bone morphogenetic protein-7). (1994)

Our results suggest that pluripotent human EC cells differentiate in response to OP-1 and that this factor can modulate the differentiation induced by retinoic acid. Like other members of the transforming growth factor-beta super family, OP-1 might play an inductive role in the early embryo. The results also suggest a possible therapeutic value for OP-1 in the treatment of some germ cell tumors.
Analysis of antigenic structure of Potato Virus M Ukrainian strains (2000)

Glu/Gly-Lys 3S .
Digitization requirements in mammography: Effects on computer‐aided detection of microcalcifications (1994)

We have developed a computerized method for detection of microcalcifications on digitized mammograms. The program has achieved an accuracy that can detect subtle microcalcifications which may potentially be missed by radiologists. In this study, we evaluated the dependence of the detection accuracy on the pixel size and pixel depth of the digitized mammograms. The mammograms were digitized with a laser film scanner at a pixel size of 0.035 mm x0.035 mm and 12-bit gray levels. Digitization with larger pixel sizes or fewer number of bits was simulated by averaging adjacent pixels or by eliminating the least significant bits, respectively. The SNR enhancement filter and the signal-extraction criteria in the computer program were adjusted to maximize the accuracy of signal detection for each pixel size. The overall detection accuracy was compared using the free response receiver operating characteristic curves. The results indicate that the detection accuracy decreases significantly as the pixel size increases from 0.035 mm x 0.035 mm to 0.07 mm x 0.07 mm (P < 0.007) and from 0.07 mm x 0.07 mm to 0.105 mm x 0.105 mm (P < 0.002). The detection accuracy is essentially independent of pixel depth from 12 to 9 bits and decreases significantly (P < 0.003) from 9 to 8 bits; a rapid decrease is observed as the pixel depth decreases further from 8 to 7 bits (P < 0.03) or from 7 to 6 bits (P < 0.02).(ABSTRACT TRUNCATED AT 250 WORDS)
Neutrophil-dependent acute lung injury. Requirement for P-selectin (GMP-140). (1992)

Rapid translocation of P-selectin (GMP-140) from cytoplasmic granules to the cell membrane of endothelial cells promotes adhesive interactions with neutrophils which, when activated, damage the endothelium. The role of P-selectin in lung vascular endothelial injury in rats after systemic activation of complement by intravenous infusion of cobra venom factor has been assessed. Within 5-10 min after cobra venom factor infusion, the pulmonary vasculature demonstrated immunohistochemical expression of an epitope that reacts with anti-human P-selectin. Monoclonal antibody to human P-selectin blocked in vitro adherence of rat or human platelets (activated with thrombin) to neutrophils and was demonstrated to react with thrombin-activated rat platelets. The antibody did not react with rat neutrophils. In vivo, the antibody had strongly protective effects against cobra venom factor-induced pulmonary vascular injury as determined by permeability changes and hemorrhage. In parallel, lung myeloperoxidase content was greatly reduced and, by transmission electron microscopy, there was markedly diminished adherence of neutrophils to the pulmonary vascular endothelium and much diminished injury of endothelial cells, as defined by hemorrhage. These data indicate that anti-human P-selectin reacts with a pulmonary vascular antigen in rats and that this antigen is essential for the full expression of lung injury.
Opening the Black Box: Hierarchical Sampling Optimization for Estimating Human Hand Pose (2015)

We address the problem of hand pose estimation, formulated as an inverse problem. Typical approaches optimize an energy function over pose parameters using a 'black box' image generation procedure. This procedure knows little about either the relationships between the parameters or the form of the energy function. In this paper, we show that we can significantly improving upon black box optimization by exploiting high-level knowledge of the structure of the parameters and using a local surrogate energy function. Our new framework, hierarchical sampling optimization, consists of a sequence of predictors organized into a kinematic hierarchy. Each predictor is conditioned on its ancestors, and generates a set of samples over a subset of the pose parameters. The highly-efficient surrogate energy is used to select among samples. Having evaluated the full hierarchy, the partial pose samples are concatenated to generate a full-pose hypothesis. Several hypotheses are generated using the same procedure, and finally the original full energy function selects the best result. Experimental evaluation on three publically available datasets show that our method is particularly impressive in low-compute scenarios where it significantly outperforms all other state-of-the-art methods.
Eugenol, a New Attractant for the Northern Corn Rootworm (Coleoptera: Chrysomelidae)1 (1983)

Eugenol, a component of the best commercially available, food-type lure for Japanese beetles, Popillia japonica Newman, was attractive to adults of the northern corn rootworm (NCR), Diabrotica barberi Smith and Lawrence. Captures of NCR increased significantly as concentrations of eugenol in traps increased, and more beetles were attracted to eugenol-baited traps placed outside of a cornfield than to traps placed within the field. Adult western corn rootworms, Diabrotica virgifera virgifera Le Conte, which feed almost exclusively on corn, were not attracted to eugenol. Attraction of NCR to eugenol, a compound distributed widely in the plant kingdom, may indicate the extent to which NCR is adapted to feed on hosts other than corn.
The emerging role of anti‐CD25 directed therapies as both immune modulators and targeted agents in cancer (2017)

CD25 (also termed IL2RA) forms one component of the high-affinity heterotrimeric interleukin 2 (IL2) receptor on activated T cells. Its affinity for IL2 and cellular function are tightly regulated and vary in different cell types. The high frequency of CD25 on the surface of many different haematological tumour cells is now well established and, apart from its prognostic significance, CD25 may be present on leukaemic stem cells and enable oncogenic signalling pathways in leukaemic cells. Additionally, high CD25 expression in activated circulating immune cells and Tregs is a factor that has already been exploited by IL2 immunotherapies for treatment of tumours and autoimmune disease. The relative clinical safety and efficacy of administering anti-CD25 radioimmunoconjugates and immunotoxins in various haematological tumour indications has been established and clinical trials of a novel CD25-directed antibody drug conjugate are underway.