gebhart/patrepeval huggingface dataset:
Opioids and human ingestive behaviour (2001)

Hydrogen sulfide (H<sub>2</sub>S) as an endogenous signaling molecule, plays an irreplaceable role in many important physiological activities. It is also closely related to sewage treatment, wine quality evaluation, and food spoilage. Herein, we have successfully synthesized a novel polymer-based probe P1 for fluorescently ratiometric sensing of H<sub>2</sub>S with a high selectivity and sensitivity. By virtue of ring-opening metathesis polymerization (ROMP), P1 was prepared with the disulfide bond linked coumarin-norbornene dyad NB-SS-COU as energy donor, the aggregation-induced emission (AIE) fluorophore anchored norbornene NB-TPE as energy receptor, and the polyethylene glycol (PEG) attached norbornene NB-PEG as a hydrophilic chain. At the 400 nm excitation, P1 displays a bright red emission at 615 nm due to the efficient fluorescence resonance energy transfer (FRET) from energy donor COU to energy acceptor TPE. Upon addition of H<sub>2</sub>S, it shows strong COU-based blue emission at 473 nm for cleavage of the disulfide bond. We also constructed a smartphone sensing platform to conduct visual quantitative detection of H<sub>2</sub>S by calculating the B/R (blue/red) emission ratio values. Moreover, P1 can be successfully employed in evaluating the level fluctuations of endogenous and exogenous H<sub>2</sub>S in living cells, testing water samples/wine samples, and monitoring food freshness.
Mupirocin and Staphylococcus aureus: a recent paradigm of emerging antibiotic resistance (2003)

We postulate that the steady rise in mupirocin resistance among S. aureus in NZ throughout the 1990s may be due, at least in part, to the over the counter availability of mupirocin from 1991 to 2000. The current patterns of mupirocin consumption need to be reviewed and its use rationalized to maximize the chances of this antibiotic retaining beneficial antistaphylococcal activity.
Targeting RNA with Small Molecules (2000)

Therapeutic targeting of RNA is not as well-developed as with DNA and proteins, and the many structures and functions of RNA suggest that it is an underutilized target. As with DNA, RNA has heterocyclic bases and base pairs with a highly anionic backbone, but as with proteins, RNA can fold into complex tertiary structures that create unique binding pockets for small molecules. Aminoglycoside targeting of ribosomal RNA is a well-known success story, and mRNAs and tRNAs have also served as therapeutic targets as well as model systems for understanding RNA-ligand interactions. The unique, species-specific structures and chemistry involved in splicing and ribozyme activity makes this RNA function an attractive target, and inhibitors of ribozyme activity have been discovered. The numerous serious human diseases caused by RNA viruses highlight the importance of developing new compounds that can target RNA structures in viral genomes. Considerable effort has been directed at finding compounds that target HIV-1 RNAs that control viral replication and frameshifting. As part of these efforts very useful new assays have been developed for small molecule-RNA interactions. The assays have led to the discovery of new inhibitors for different steps in viral replication. The next phase of research in RNA targeting will not only focus on the discovery of new compounds, but also on how to develop small molecules with high affinity and selectively for RNA that can penetrate effectively into a wide array of cell types.
Hepatitis C virus genotypes: special reference to the Indian scene. (2004)

The heterogeneity observed between different isolates of the hepatitis C virus has led to stratification of these isolates into different genotypes. Clinically the genetic diversity of the virus has important implications as genotypes respond variably to antiviral therapy and can influence disease prognosis. This article attempts to summarize current knowledge about the different biological properties of HCV genotypes, and their geographical distribution, with special reference to the Indian scenario.
N-Terminal Sequence of Human Big Gastrin: Sequence, Synthetic and Immunochemical Studies (1980)

The previously assigned structure of human big gastrin is revised as a result of sequencing and immunological studies on synthetic peptides. A nonadecapeptide has been synthesized and found to have full immunochemical potency compared with natural human G34 in a radioimmunoassay which is specific for the N-terminal sequence. Syntheses of the peptides were achieved using the stepwise procedure with benzyloxycarbonyl-amino acids and fragment couplings mediated mainly by the dicyclohexylcarbodiimide procedure in the presence of either N-hydroxysuccinimide or 1-hydroxybenzotriazole. Purification of the peptide fragments was by Sephadex LH-20 chromatography and removal of protecting groups was effected using 90% trifluoroacetic acid in the presence of scavengers. Purification of the nonadecapeptide was achieved by high performance liquid chromatography.
Expression of the Wilms' tumour gene WT1 in the developing human and in paediatric renal tumours: an immunohistochemical study. (1997)

WT1 is detected readily in formalin fixed material. There were differences in specificity between batches of the polyclonal antibodies used. The distribution of the WT1 gene product in tissues and tumours reflected previous findings with in situ hybridisation studies of WT1 mRNA.
Cliques in Neural Ensembles as Perception Carriers (2006)

Cortical ensembles of neurons perform a large class of tasks which require real-time processing of complex temporal inputs. These tasks involve identifying complex structures and relationships in massive quantities of low precision, ambiguous noisy data. To get some insights into neural mechanisms responsible for the performance of these tasks in a relatively large ensemble of cortical cells, we use a natural closed-loop computational framework. By incorporating functions of readout, reward and feedback, we apply such a framework of neural ensembles to classification and recognition tasks of real-time temporal data. This approach is inspired by neurobiological findings from ex-vivo multicellular electrical recordings and injection of dopamine to the neural culture. Analysis of this functional system provides a new insight into the structure of the spatio-temporal firing patterns, coined "Cliques", that are in a way the neurophysiological carriers of higher-level task-dependent functions and perceptual elements. Such cliques are generated by neural ensembles that interface with the external environment by means of complementary networks that serve the function of readout. Cliques are thus functions of both, network's state and computational task. To observe the cliques, a readout network must be incorporated into the computational system in a closed-loop manner. The emergence of cliques is mediated by spatio-temporal dynamical liquid-currents, through a selective process of Co-Evolutionary learning of two neural ensembles. Liquid-currents from presented inputs to cliques are the dynamic realizations by means of the neural ensembles. The definition of liquid-current intensity leads to a conclusion that the emergence of cliques occurs in cortical ensembles of cells regardless of the realizations at the cellular level and of the intrinsic dimensions of the problem.
Mutagenesis in Mammalian Cells Induced by Triple Helix Formation and Transcription-Coupled Repair (1996)

When mammalian cells were treated with triplex-forming oligonucleotides of sufficient binding affinity, mutations were specifically induced in a simian virus 40 vector contained within the cells. Triplex-induced mutagenesis was not detected in xeroderma pigmentosum group A cells nor in Cockayne's syndrome group B cells, indicating a requirement for excision repair and for transcription-coupled repair, respectively, in the process. Triplex formation was also found to stimulate DNA repair synthesis in human cell extracts, in a pattern correlating with the inhibition of transcription in such extracts. These findings may have implications for therapeutic applications of triplex DNA and raise the possibility that naturally occurring triple helices are a source of genetic instability.
Gene Transfer in Regenerating Muscle (1994)

We have compared the efficiency of direct gene transfer in normal and regenerating rat skeletal muscle. Muscle necrosis and regeneration was induced by intramuscular injection of bupivacaine in the soleus muscle of adult rats. Plasmids containing beta-galactosidase (beta-gal) or chloramphenicol acetyltransferase (CAT) genes driven by viral promoters were injected 3 days after bupivacaine treatment into the regenerating and the contralateral uninjured muscles. Expression of CAT activity was > 80-fold higher in regenerating compared to control muscles at 7 days post-transfection, but decreased at 30 and 60 days. Southern blot analysis showed that the predominant form of CAT DNA was episomal in transfected muscles; however, CAT activity measurements performed on the same transfected muscles showed no precise correlation between enzymatic activity and amount of plasmid DNA. Expression of beta-gal was detected in numerous regenerating fibers of the injured soleus muscles at 7 days post-transfection; in contrast, only rare positive fibers were found in control muscles. Focal infiltrates of mononuclear cells, which surround and invade selectively beta-gal-positive fiber segments, were observed at 30 days post-transfection, suggesting that immune mechanisms are implicated in the progressive loss of transgenes with time. The finding that regenerating muscle fibers display a higher efficiency of transfection may be relevant to gene therapy of Duchenne muscular dystrophy, because regenerating fibers are numerous in the early stages of the disease.
Normal iron metabolism and the pathophysiology of iron overload disorders. (2006)

Iron overload disorders represent a heterogenous group of conditions resulting from inherited and acquired causes. If undiagnosed they can be progressive and fatal. Early detection and phlebotomy prior to the onset of cirrhosis can reduce morbidity and normalise life expectancy. We now have greater insight into the complex mechanisms of normal and disordered iron homeostasis following the discovery of new proteins and genetic defects. Here we review the normal mechanisms and regulation of gastrointestinal iron absorption and liver iron transport and their dysregulation in iron overload states. Advances in the understanding of the natural history of iron overload disorders and new methods for clinical detection and management of hereditary haemochromatosis are also reviewed. The current screening strategies target high-risk groups such as first-degree relatives of affected individuals and those with clinical features suggestive of iron loading. Potential ethical, legal and psychosocial issues arising through application of genetic screening programs need to be resolved prior to implementation of general population screening programs.
Effective therapy for a murine model of adult T-cell leukemia with the humanized anti-CD52 monoclonal antibody, Campath-1H. (2003)

Adult T-cell leukemia (ATL) develops in a small proportion of human T-cell leukemia virus I-infected individuals. Presently, there is no effective therapy for ATL. A murine model of ATL was produced by introducing leukemic cells (MET-1) from an ATL patient into nonobese diabetic/severe combined immunodeficient mice. The MET-1 cells are activated T cells that express CD2, CD3, CD4, CD25, CD122, and CD52. We evaluated the efficacy of Campath-1H (alemtuzumab; a humanized monoclonal antibody directed to CD52), alone and in combination with humanized anti-Tac (HAT) directed to CD25 (interleukin 2 receptor alpha) or with MEDI-507 directed to CD2. We observed that four weekly treatments with 4 mg/kg HAT significantly prolonged survival of MET-1-bearing mice. However, the survival of mice receiving 4 weeks of 4 mg/kg Campath-1H was significantly longer than that of the group receiving four weekly treatments with HAT (P < 0.001). Treatment with Campath-1H for 4 weeks led to a striking prolongation of the survival of MET-1 ATL-bearing mice that was comparable with that of tumor-free nontreated controls. Using Fc receptor (FcR) gamma(-/-) mice, we found that FcRgammas on polymorphonuclear leukocytes and monocytes are required for Campath-1H-mediated tumor killing in vivo. These results demonstrate that Campath-1H has therapeutic efficacy on ATL in vivo in that the life span of the Campath-1H treatment group was comparable with that of mice that did not receive a tumor or therapy. The main tumor killing mechanism with Campath-1H in vivo involves FcRgamma-containing receptors (e.g., FcRgammaIII) on polymorphonuclear leukocytes and macrophages that mediate antibody-dependent cellular cytotoxicity and/or trigger cross-linking induced apoptosis. This study provides support for a clinical trial of Campath-1H in the treatment of patients with T-cell leukemias and lymphomas.
Information fusion and decision cascading for audio-visual speaker recognition based on time-varying stream reliability prediction (2003)

We examine the techniques for multi-modal biometric information fusion for verification and identification of speakers, where the reliability of each data stream, either audio of video, is modeled with parameters that are time-varying and depend on the context created by its local behavior. The complementary nature and the time dependent relative reliability of audio and video data is studied in the context of verification and identification, on data collected during a user's interaction with an automated system. Of significance is that this data is not corrupted artificially. Particular focus is directed to verification and its ability to refine identification decisions, by indicating a level of confidence in the system decisions. Results show more striking effects for verification, when using time-dependent fusion, than for identification.
MRC5 and QU-DB bystander cells can produce bystander factors and induce radiation bystander effect (2014)

Radiation damages initiated by radiation-induced bystander effect (RIBE) are not limited to the first or immediate neighbors of the irradiated cells, but the effects have been observed in the cells far from the irradiation site. It has been postulated that bystander cells, by producing bystander factors, are actively involved in the propagation of bystander effect in the regions beyond the initial irradiated site. Current study was planned to test the hypothesis. MRC5 and QU-DB cell lines were irradiated, and successive medium transfer technique was performed to induce bystander effects in two bystander cell groups. Conditioned medium extracted from the target cells was transferred to the bystander cells (first bystander cells). After one hour, conditioned medium was substituted by fresh medium. Two hours later, the fresh medium was transferred to a second group of non-irradiated cells (second bystander cells). Micronucleated cells (MC) were counted to quantify damages induced in the first and second bystander cell groups. Radiation effect was observed in the second bystander cells as well as in the first ones. Statistical analyses revealed that the number of MC in second bystander subgroups was significantly more than the corresponding value observed in control groups, but in most cases it was equal to the number of MC observed in the first bystander cells. MRC5 and QU-DB bystander cells can produce and release bystander signals in the culture medium and affect non-irradiated cells. Therefore, they may contribute to the RIBE propagation.
C3bi receptor (complement receptor type 3) recognizes a region of complement protein C3 containing the sequence Arg-Gly-Asp. (1987)

Human phagocytes express a receptor termed complement receptor type 3 (CR3) that recognizes the complement protein fragment C3bi. We show here that CR3 recognizes a region of C3 that contains the sequence Arg-Gly-Asp (RGD). CR3 is down-modulated upon spreading of macrophages on surfaces coated with a synthetic 21-residue peptide from C3 (residues 1383-1403). This peptide was also attached to erythrocytes by coupling myristic acid to its amino terminus and allowing the myristoylated peptide to bind to erythrocytes through hydrophobic interactions. Erythrocytes coated with this RGD-containing segment of C3 were bound by macrophages, and binding could be blocked by specific monoclonal antibodies against CR3. Since CR3 recognizes a peptide sequence that contains the RGD triplet, it appears to be a member of a larger family of adhesion-promoting receptors that recognize RGD-containing proteins. However, since CR3 does not recognize a hexapeptide containing RGD, we presume that residues beyond the RGD triplet contribute to binding. We have compared the RGD-containing region of fibronectin and vitronectin, proteins known to be recognized by means of their RGD-containing regions, with those in human and murine C3. A striking homology is observed over an approximately equal to 50 amino acid sequence present in all four proteins. We suggest that this extended region of homology contains a structure recognized by adhesion-promoting receptors.
An optical coherence microscope for 3-dimensional imaging in developmental biology (2000)

An optical coherence microscope (OCM) has been designed and constructed to acquire 3-dimensional images of highly scattering biological tissue. Volume-rendering software is used to enhance 3-D visualization of the data sets. Lateral resolution of the OCM is 5 mm (FWHM), and the depth resolution is 10 mm (FWHM) in tissue. The design trade-offs for a 3-D OCM are discussed, and the fundamental photon noise limitation is measured and compared with theory. A rotating 3-D image of a frog embryo is presented to illustrate the capabilities of the instrument.
Protein kinase CK2: an enzyme with multiple substrates and a puzzling regulation (1995)

Protein kinase CK2 (also known as casein kinase II) is a ubiquitous eukaryotic ser/thr protein kinase present in the nucleus and cytoplasm. CK2 is known to phosphorylate more than 100 substrates, many of which are involved in the control of cell division and in signal transduction. The review centers on the structure and function of CK2 alpha and beta subunits and on the regulation of its activity, a topic that remains to be elucidated. An analogy is drawn between CK2 and the cyclin-dependent kinases (cdks); both types of protein kinases share many substrates and are activated by regulatory subunits.
CARMA3 Is a Critical Mediator of G Protein-Coupled Receptor and Receptor Tyrosine Kinase-Driven Solid Tumor Pathogenesis (2018)

The CARMA-Bcl10-MALT1 (CBM) signalosome is an intracellular protein complex composed of a CARMA scaffolding protein, the Bcl10 linker protein, and the MALT1 protease. This complex was first recognized because the genes encoding its components are targeted by mutation and chromosomal translocation in lymphoid malignancy. We now know that the CBM signalosome plays a critical role in normal lymphocyte function by mediating antigen receptor-dependent activation of the pro-inflammatory, pro-survival NF-κB transcription factor, and that deregulation of this signaling complex promotes B-cell lymphomagenesis. More recently, we and others have demonstrated that a CBM signalosome also operates in cells outside of the immune system, including in several solid tumors. While CARMA1 (also referred to as CARD11) is expressed primarily within lymphoid tissues, the related scaffolding protein, CARMA3 (CARD10), is more widely expressed and participates in a CARMA3-containing CBM complex in a variety of cell types. The CARMA3-containing CBM complex operates downstream of specific G protein-coupled receptors (GPCRs) and/or growth factor receptor tyrosine kinases (RTKs). Since inappropriate expression and activation of GPCRs and/or RTKs underlies the pathogenesis of several solid tumors, there is now great interest in elucidating the contribution of CARMA3-mediated cellular signaling in these malignancies. Here, we summarize the key discoveries leading to our current understanding of the role of CARMA3 in solid tumor biology and highlight the current gaps in our knowledge.
Development of a Circulation Control Wing for UAVs (2014)

Circulation Control, which was discovered accidentally by Henry Coanda in 1935, is proven to be an efficient lift augmentation method at low Mach numbers. The objective of this research is to design and develop a Circulation Control Wing (CCW) that will provide increased lift to a fixed-wing Unmanned Aerial Vehicle (UAV). The configuration (the curvature of the trailing edge on a Clark-Y airfoil) that gives high lift augmentation ratios for reasonably low blowing rates is investigated. Wind tunnel tests are conducted on 11.7% thick circulation control airfoil with upper surface blowing capability. Different trailing edges (Coanda surfaces) have been tested at moment coefficients from 0.0 to 0.04. Test data are collected at Mach numbers of 0.021; 0.024; 0.029 and 0.030 at Reynolds numbers of 1.0 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> to 1.5 × 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> . It is found that the smaller Coanda surface configuration is more effective. At M = 0.021 and α = 13°, the (2.1) Coanda surface gave the maximum ΔC <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> = 0.42 at a C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</sub> = 0.04. The maximum lift enhancement (up to 155%) at zero angle-of-attack, is achieved by using the same Coanda surface(2.1) at C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">μ</sub> = 0.04 and M = 0.03.
Recombinant Peptides as Biomarkers for Tumor Response to Molecular Targeted Therapy (2009)

The use of recombinant peptides to assess the pharmacodynamic response of cancer holds promise in minimizing the duration of ineffective treatment regimens in patients, potentially providing a more rapid and less invasive assessment of cancer response to systemic therapy.
Uncharged stereoregular nucleic acid analogs: 2. Morpholino nucleoade otigomers with carbamate internucleoside linkages (1989)

A novel oligonucleotide analog has been prepared from ribonucleoside derived morpholine subunits linked by carbamate groups. Oxidative cleavage of the 2',3' vicinal diol of cytidine followed by reductive amination of the resulting dialdehyde afforded the morpholine subunit. Coupling of the subunits are through carbamate moieties and the oligomers were characterized by 1H NMR and FAB MS. Evidence for interaction of the hexamer 19 with p(dG6) was found, but an atypical interaction of 19 with a RNA target was observed.