gebhart/patrepeval huggingface dataset:
Phase I and Phase II Ocular Metabolic Activities and the Role of Metabolism in Ophthalmic Prodrug and Codrug Design and Delivery (2007)

While the mammalian eye is seldom considered an organ of drug metabolism, the capacity for biotransformation is present. Compared to the liver, the metabolic capabilities of the eye are minuscule; however, phase I and phase II metabolic activities have been detected in various ocular structures. The careful consideration of ocular tissue metabolic processes within the eye has important implications for controlling the detoxification of therapeutic agents and for providing the potential for site-specific bio-activation of certain drug molecules, thus enabling significant improvements in drug efficacy and the minimization of side-effect from either local or systemic drug delivery to the eye. Knowledge of these processes is important to prodrug and codrug development and to researchers involved in the design, delivery and metabolism of ophthalmic drugs. This present article reviews the progress in ocular prodrug and codrug design and delivery in light of ocular metabolic activities.
A 2D camera design with a single-pixel detector (2009)

A single-pixel camera for THz imaging has been proposed in. In this article, we propose a new design for a single-detector THz imaging system based on compressive sampling (CS), which does not need raster scanning of the object in front of the THz beam. We exploit a time-efficient and cost-effective design to acquire the CS measurements. As a result, the image acquisition time in the proposed imaging system is only limited to the speed of the THz detector. The proposed approach is applicable to other types of imaging as well.
Mapping of functional regions of Clostridium perfringens type A enterotoxin (1992)

Studies were conducted to allow construction of an initial map of the structure-versus-function relationship of the Clostridium perfringens type A enterotoxin (CPE). Removal of the N-terminal 25 amino acids of CPE increased the primary cytotoxic effect of CPE but did not affect binding. CPE sequences required for at least four epitopes were also identified.
Novel immune checkpoint targets: moving beyond PD-1 and CTLA-4 (2019)

The emergence of immune checkpoint inhibitors (ICIs), mainly including anti-programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) and anti-cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) monoclonal antibodies (mAbs), has shaped therapeutic landscape of some type of cancers. Despite some ICIs have manifested compelling clinical effectiveness in certain tumor types, the majority of patients still showed de novo or adaptive resistance. At present, the overall efficiency of immune checkpoint therapy remains unsatisfactory. Exploring additional immune checkpoint molecules is a hot research topic. Recent studies have identified several new immune checkpoint targets, like lymphocyte activation gene-3 (LAG-3), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), T cell immunoglobulin and ITIM domain (TIGIT), V-domain Ig suppressor of T cell activation (VISTA), and so on. The investigations about these molecules have generated promising results in preclinical studies and/or clinical trials. In this review, we discussed the structure and expression of these newly-characterized immune checkpoints molecules, presented the current progress and understanding of them. Moreover, we summarized the clinical data pertinent to these recent immune checkpoint molecules as well as their application prospects.
Molecular genetics and pathophysiology of 17 beta-hydroxysteroid dehydrogenase 3 deficiency. (1996)

Autosomal recessive mutations in the 17 beta-hydroxysteroid dehydrogenase 3 gene impair the formation of testosterone in the fetal testis and give rise to genetic males with female external genitalia. Such individuals are usually raised as females, but virilize at the time of expected puberty as the result of increases in serum testosterone. Here we describe mutations in 12 additional subjects/families with this disorder. The 14 mutations characterized to date include 10 missense mutations, 3 splice junction abnormalities, and 1 small deletion that results in a frame shift. Three of these mutations have occurred in more than 1 family. Complementary DNAs incorporating 9 of the 10 missense mutations have been constructed and expressed in reporter cells; 8 of the 9 missense mutations cause almost complete loss of enzymatic activity. In 2 subjects with loss of function, missense mutations testosterone levels in testicular venous blood were very low. Considered together, these findings strongly suggest that the common mechanism for testosterone formation in postpubertal subjects with this disorder is the conversion of circulating androstenedione to testosterone by one or more of the unaffected 17 beta-hydroxysteroid dehydrogenase isoenzymes.
Bacteriocins: Evolution, Ecology, and Application (2002)

Microbes produce an extraordinary array of microbial defense systems. These include classical antibiotics, metabolic by-products, lytic agents, numerous types of protein exotoxins, and bacteriocins. The abundance and diversity of this potent arsenal of weapons are clear. Less clear are their evolutionary origins and the role they play in mediating microbial interactions. The goal of this review is to explore what we know about the evolution and ecology of the most abundant and diverse family of microbial defense systems: the bacteriocins. We summarize current knowledge of how such extraordinary protein diversity arose and is maintained in microbial populations and what role these toxins play in mediating microbial population-level and community-level dynamics. In the latter half of this review we focus on the potential role bacteriocins may play in addressing human health concerns and the current role they serve in food preservation.
Circulating cell-free DNA as a promising biomarker in patients with gastric cancer: diagnostic validity and significant reduction of cfDNA after surgical resection (2014)

The changes in the levels of cfDNA can act as reliable biomarkers to detect cancer early, to predict tumor burden, estimate curative resection and even prognosis.
Evidence for a Role of IL-17 in Organ Allograft Rejection: IL-17 Promotes the Functional Differentiation of Dendritic Cell Progenitors (1999)

IL-17 is a T cell-derived cytokine that stimulates stromal cells and macrophages to secrete proinflammatory cytokines. We hypothesized that IL-17 might play a role in alloimmune responses, and that interference with its activity might suppress allograft rejection. IL-17R:Fc or control IgG was added at the start of mouse MLR or was administered i.p. (100-500 microg/day) for different durations post-transplant to murine recipients of MHC-mismatched cardiac allografts. IL-17R:Fc (50-200 microg/ml) markedly inhibited T cell proliferation in vitro and significantly prolonged nonvascularized cardiac allograft median survival time from 13 to 20 days (100 microg/day; days 0 and 1) or to 19 days (100-300 microg/day; days 0-4). Survival of vascularized grafts was also extended significantly from 10.5 to 19 days by IL-17R:Fc (500 microg/day; days 0-6). To address a possible mechanism by which IL-17 may promote alloreactivity, we examined the influence of IL-17 on the differentiation and function of bone marrow-derived cells propagated in granulocyte-macrophage CSF with or without IL-4 to promote dendritic cell (DC) growth. A minor proportion of CD11c+ DC expressed the IL-17R. IL-17 promoted the maturation of DC progenitors, as evidenced by increased cell surface expression of CD11c, costimulatory molecules (CD40, CD80, CD86), and MHC class II Ag, and allostimulatory capacity. IL-17 had a lesser effect on the phenotype and function of more fully differentiated myeloid DC. These findings suggest a role for IL-17 in allogeneic T cell proliferation that may be mediated in part via a maturation-inducing effect on DC. IL-17 appears to be a novel target for therapeutic intervention in allograft rejection.
mPPAR gamma 2: tissue-specific regulator of an adipocyte enhancer. (1994)

Previously, we have isolated and characterized an enhancer from the 5'-flanking region of the adipocyte P2 (aP2) gene that directs high-level adipocyte-specific gene expression in both cultured cells and transgenic mice. The key regulator of this enhancer is a cell type-restricted nuclear factor termed ARF6. Target sequences for ARF6 in the aP2 enhancer exhibit homology to a direct repeat of hormone response elements (HREs) spaced by one nucleotide; this motif (DR-1) has been demonstrated previously to be the preferred binding site for heterodimers of the retinoid X receptor (RXR) and the peroxisome proliferator-activated receptor (PPAR). We have cloned a novel member of the peroxisome proliferator-activated receptor family designated mPPAR gamma 2, and we demonstrate that a heterodimeric complex of mPPAR gamma 2 and RXR alpha constitute a functional ARF6 complex. Expression of mPPAR gamma 2 is induced very early during the differentiation of several cultured adipocyte cell lines and is strikingly adipose-specific in vivo. mPPAR gamma 2 and RXR alpha form heterodimers on ARF6-binding sites in vitro, and antiserum to RXR alpha specifically inhibits ARF6 activity in adipocyte nuclear extracts. Moreover, forced expression of mPPAR gamma 2 and RXR alpha activates the adipocyte-specific aP2 enhancer in cultured fibroblasts, and this activation is potentiated by peroxisome proliferators, fatty acids, and 9-cis retinoic acid. These results identify mPPAR gamma 2 as the first adipocyte-specific transcription factor and suggest mechanisms whereby fatty acids, peroxisome proliferators, 9-cis retinoic acid, and other lipids may regulate adipocyte gene expression and differentiation.
Effects of Sodium Hyaluronate on Peridural Fibrosis After Lumbar Laminotomy and Discectomy (1990)

Sodium hyaluronate, 1.9% solution, was evaluated for its ability to retard peridural fibrosis after unilateral lumbar hemilaminotomy, anular fenestration, and nuclectomy in dogs. Three materials: fat grafts, gelfoam, and sodium hyaluronate, were compared with empty controls for their ability to inhibit peridural fibrosis. Each dog served as his own internal control and the formation of fibrosis was evaluated at 2, 4, 12, and 26 weeks. Sodium hyaluronate was found to inhibit fibrosis more than the other materials on both a macroscopic and microscopic level. The area of fibrosis and tenacity of the adhesions on dissection were notably less in the sodium hyaluronate group. Microscopically, the thickness of collagen and number of fibroblasts were decreased with the use of 1.9% sodium hyaluronate. The peridural fibrosis occurred equally both anteriorly and posteriorly to the nerve roots and correlated with the area of surgical dissection. Fat grafts were not effective in preventing fibrosis anteriorly, especially in the region of the exiting nerve roots. Gelfoam did not inhibit but actually appeared to increase fibrosis formation. Interposition materials currently used in humans to prevent scar formation such as gelfoam and fat grafts have only addressed the posterior scar formation, which do little to alter the fibrosis anteriorly. The adhesions between the nerve root and the anulus fibrosus bind the nerve root down anteriorly, making it more vulnerable to recurrent disc herniation. Sodium hyaluronate, 1.9% solution, with its viscous semifluid properties, coats the nerve roots and dura anteriorly and posteriorly.(ABSTRACT TRUNCATED AT 250 WORDS)
Role of the Hyal−Cu (II) Complex on Bovine Aortic and Lymphatic Endothelial Cells Behavior on Microstructured Surfaces (2004)

The ability of micropatterned surfaces to modulate cell behavior is combined with the well-known angiogenic property of the hyaluronan-Cu (II) complex. Hyaluronan-Cu (II) microstripes 100 and 25 mum wide on aminosilanised glass substrates were fabricated by photoimmobilization following two different methods: i.e., method I consisting in the photoimmobilization of the Hyal-Cu (II) complex; and method II based on the photoimmobilization of Hyal followed by the coordination with Cu (II). The chemistry and topography of the fabricated micropatterned samples were investigated by ATR FT-IR, atomic absorption, AFM, SEM, and ToF-SIMS. ATR FT-IR analysis demonstrated that hyaluronan conjugated with a photoreactive moiety was able to coordinate Cu (II) ions and that the photoimmobilization process was successful, as indicated by the intensity decrease of the IR band of the azidic group after the photoreaction. AFM and SEM images showed that reproducible Hyal-Cu (II) microstructures with both chemical and topographical heterogeneities have been obtained by the two preparation methods. The distribution of copper on the fabricated Hyal-Cu (II) microstructures has been investigated by ToF-SIMS. In both ToF-SIMS images and spectra, on Hyal-Cu (II) microstructures prepared by method I, the Cu peak (63 m/z) was detected only on the Hyal-Cu (II) microstripes, while on Hyal-Cu (II) microstructures prepared by method II, the Cu peak showed the same intensity both on the Hyal-Cu (II) microstripes and on the aminosilanised glass substrate, in agreement with the higher amount of Cu revealed by atomic absorption. The influence of Hyal-Cu (II) micropatterned surfaces on BAEC and LEC, in terms of migration and adhesion, has been analyzed. The results obtained indicate that Hyal-Cu (II) influences BAEC behavior inducing cell migration, while it is devoid of any effect on LEC.
Deadzone compensation in nonlinear systems using neural networks (2002)

A compensation scheme is presented for general nonlinear actuator deadzones of unknown width in nonlinear systems. The compensator uses two neural networks (NN), one to estimate the unknown deadzone and another to provide adaptive compensation in the feedforward path. The compensator NN has a special augmented form containing extra neurons whose activation functions provide a 'jump function basis set' for approximating piecewise continuous functions. Closed-loop stability analysis for the deadzone compensator is provided, and yields tuning algorithms for the weights of the two NN. The technique provides a general procedure for using NN to determine the pre-inverse of an unknown right-invertible function.
Full range complex spectral optical coherence tomography technique in eye imaging (2002)

We demonstrate a new implementation of complex spectral optical coherence tomography (OCT) in biomedical imaging. By reconstruction of both amplitude and phase we are able to use the negative and positive optical path differences to get images of objects of considerable thickness. An accompanying reduction of coherent noise improves the quality of the images. The property of the complex spectral OCT that permits the measurement range to be increased and permits the simultaneous use of phase and amplitude in spectral systems was not described previously. To show the potential of this technique we measured an anterior chamber of a porcine eye in vitro.
Antigenic modulation limits the effector cell mechanisms employed by type I anti-CD20 monoclonal antibodies (2015)

Following the success of rituximab, 2 other anti-CD20 monoclonal antibodies (mAbs), ofatumumab and obinutuzumab, have entered clinical use. Ofatumumab has enhanced capacity for complement-dependent cytotoxicity, whereas obinutuzumab, a type II mAb, lacks the ability to redistribute into lipid rafts and is glycoengineered for augmented antibody-dependent cellular cytotoxicity (ADCC). We previously showed that type I mAbs such as rituximab have a propensity to undergo enhanced antigenic modulation compared with type II. Here we assessed the key effector mechanisms affected, comparing type I and II antibodies of various isotypes in ADCC and antibody-dependent cellular-phagocytosis (ADCP) assays. Rituximab and ofatumumab depleted both normal and leukemic human CD20-expressing B cells in the mouse less effectively than glycoengineered and wild-type forms of obinutuzumab, particularly when human immunoglobulin G1 (hIgG1) mAbs were compared. In contrast to mouse IgG2a, hIgG1 mAbs were ineffective in ADCC assays with murine natural killer cells as effectors, whereas ADCP was equivalent for mouse IgG2a and hIgG1. However, rituximab's ability to elicit both ADCC and ADCP was reduced by antigenic modulation, whereas type II antibodies remained unaffected. These data demonstrate that ADCP and ADCC are impaired by antigenic modulation and that ADCP is the main effector function employed in vivo.
Uncoupling protein‐3: a new member of the mitochondrial carrier family with tissue‐specific expression (1997)

Brown adipose tissue (BAT) and skeletal muscle are important sites of nonshivering thermogenesis. The uncoupling protein-1 (UCP1) is the main effector of nonshivering thermogenesis in BAT and the recently described ubiquitous UCP2 [1] has been implicated in energy balance. In an attempt to better understand the biochemical events underlying nonshivering thermogenesis in muscle, we screened a human skeletal muscle cDNA library and isolated three clones: UCP2, UCP3L and UCP3S. The novel UCP3 was 57% and 73% identical to human UCP1 and UCP2, respectively, highly skeletal muscle-specific and its expression was unaffected by cold acclimation. This new member of the UCP family is a candidate protein for the modulation of the respiratory control in skeletal muscle.
Diagnosis and treatment of impotence. (1990)

Among the common procedures used in the diagnosis of impotence, neither nocturnal penile tumescence testing nor inhome monitoring devices designed to measure tumescence or rigidity is regarded as reliable for evaluating impotence. Plethysmography as a nonspecific test of vascular competence is increasingly being supplanted by Doppler ultrasound as a safe and effective diagnostic modality. Arteriography, cavernosography, and cavernosometry are established techniques for evaluating penile vasculature. Intracavernosal injection of smooth muscle relaxing drugs, endocrine assays, and electrophysiological testing are widely used for the diagnosis of impotence. Excluding implanted devices, and intracavernosal injections. Aortoiliac reconstruction, endarterectomy, or arterial dilatations are regarded as safe and effective for the treatment of proximal occlusive lesions, and venous leakage surgery is regarded as investigational. Intracavernosal injections are widely employed in clinical environments and for self-injection at home. However, this currently represents the use of FDA-approved drugs for an unlabeled indication. The use of external vacuum devices has achieved widespread use and is regarded as being safe and effective for the treatment of impotence.
Opalescent Cholesteric Networks from Chiral Polyisocyanates in Polystyrene (1998)

The cholesteric polymer films described here, i.e., the “locked in” chiral nematic phase of polymer liquid crystals, have several advantages as materials for optical applications. The Figure shows schematically a cholesteric network based on a chiral isocyanate terpolymer in styrene in which the cholesteric liquid-crystalline structure is “locked in” by photopolymerization.
Metal bonding during sputter film deposition (1998)

We studied the bonding between two flat Si substrates with thin metal films. The bonding was accomplished during thin film sputter deposition on contamination free surfaces of metal films. In this work we used Ti and Pt. Successful bonding of these metal films (each having a thickness of 10–20 nm) occurred at room temperature over the entire bonded area (12 mm×12 mm). Self-diffusion, particularly at grain boundaries and film surface, was the mechanism for bonding. Suitable metal bonding only occurred if the film surface roughness is sufficiently smaller than the self-diffusion length of metals. Particularly in the bonding of Ti to Ti films, transmission electron microscope observation revealed that complete crystalline grains had been formed across the former interface between the single thin Ti films. The interfaceless bonding can be explained by recrystallization of the Ti lattice due to the high self-diffusion coefficient of Ti. This technique would be applied to bonding of wafers to fabricate thin film devices or microsystems. Moreover, this bonding technology can be used with many different thin film materials and various semiconductor substrates.
PlantCARE, a plant cis-acting regulatory element database (1999)

PlantCARE is a database of plant cis- acting regulatory elements, enhancers and repressors. Besides the transcription motifs found on a sequence, it also offers a link to the EMBL entry that contains the full gene sequence as well as a description of the conditions in which a motif becomes functional. The information on these sites is given by matrices, consensus and individual site sequences on particular genes, depending on the available information. PlantCARE is a relational database available via the web at the URL: http://sphinx.rug.ac.be:8080/PlantCARE/
Co-localization of sodium channel Nav1.6 and the sodium-calcium exchanger at sites of axonal injury in the spinal cord in EAE (2004)

Axonal degeneration contributes to the development of non-remitting neurological deficits and disability in multiple sclerosis, but the molecular mechanisms that underlie axonal loss in multiple sclerosis are not clearly understood. Studies of white matter axonal injury have demonstrated that voltage-gated sodium channels can provide a route for sodium influx into axons that triggers reverse operation of the Na(+)/Ca(2+) exchanger (NCX) and subsequent influx of damaging levels of intra-axonal calcium. The molecular identities of the involved sodium channels have, however, not been determined. We have previously demonstrated extensive regions of diffuse expression of Na(v)1.6 and Na(v)1.2 sodium channels along demyelinated axons in experimental allergic encephalomyelitis (EAE). Based on the hypothesis that the co-localization of Na(v)1.6 and NCX along extensive regions of demyelinated axons may predispose these axons to injury, we examined the expression of myelin basic protein, Na(v)1.2, Na(v)1.6, NCX and beta-amyloid precursor protein (beta-APP), a marker of axonal injury, in the spinal cord dorsal columns of mice with EAE. We demonstrate a significant increase in the number of demyelinated axons demonstrating diffuse Na(v)1.6 and Na(v)1.2 sodium channel immunoreactivity in EAE (92.2 +/- 2.1% of beta-APP positive axons were Na(v)1.6-positive). Only 38.0 +/- 2.9% of beta-APP positive axons were Na(v)1.2 positive, and 95% of these co-expressed Na(v)1.6 together with Na(v)1.2. Using triple-labelled fluorescent immunohistochemistry, we demonstrate that 73.5 +/- 4.3% of beta-APP positive axons co-express Na(v)1.6 and NCX, compared with 4.4 +/- 1.0% in beta-APP negative axons. Our results indicate that co-expression of Na(v)1.6 and NCX is associated with axonal injury in the spinal cord in EAE.
Novel Insights and Therapeutics in Multiple Sclerosis (2015)

The last twelve years have witnessed the development of new therapies for relapsing-remitting multiple sclerosis that demonstrate increased efficacy relative to previous therapies. Many of these new drugs target the inflammatory phase of disease by manipulating different aspects of the immune system. While these new treatments are promising, the development of therapies for patients with progressive multiple sclerosis remains a significant challenge. We discuss the distinct mechanisms that may contribute to these two types of multiple sclerosis and the implications of these differences in the development of new therapeutic targets for this debilitating disease.
Recognizing implicit discourse relations in the Penn Discourse Treebank (2009)

We present an implicit discourse relation classifier in the Penn Discourse Treebank (PDTB). Our classifier considers the context of the two arguments, word pair information, as well as the arguments' internal constituent and dependency parses. Our results on the PDTB yields a significant 14.1% improvement over the baseline. In our error analysis, we discuss four challenges in recognizing implicit relations in the PDTB.