gebhart/patrepeval huggingface dataset:
Compact Biocompatible Quantum Dots via RAFT-Mediated Synthesis of Imidazole-Based Copolymer Ligand (2009)

We present a new class of polymeric ligands for quantum dot (QD) water solubilization to yield biocompatible and derivatizable QDs with compact size (∼10−12 nm diameter), high quantum yields (>50%), excellent stability across a large pH range (pH 5−10.5), and low nonspecific binding. To address the fundamental problem of thiol instability in traditional ligand exchange systems, the polymers here employ a stable multidentate imidazole binding motif to the QD surface. The polymers are synthesized via reversible addition−fragmentation chain transfer-mediated polymerization to produce molecular weight controlled monodisperse random copolymers from three types of monomers that feature imidazole groups for QD binding, polyethylene glycol (PEG) groups for water solubilization, and either primary amines or biotin groups for derivatization. The polymer architecture can be tuned by the monomer ratios to yield aqueous QDs with targeted surface functionalities. By incorporating amino-PEG monomers, we demonstrate covalent conjugation of a dye to form a highly efficient QD-dye energy transfer pair as well as covalent conjugation to streptavidin for high-affinity single molecule imaging of biotinylated receptors on live cells with minimal nonspecific binding. The small size and low serum binding of these polymer-coated QDs also allow us to demonstrate their utility for in vivo imaging of the tumor microenvironment in live mice.
Reducing Pain During Propofol Injection (1996)

We hypothesized that the concentration of propofol in the aqueous phase may be the most important variable responsible for the pain experienced during injection of the drug. The concentration of propofol in the aqueous phase (18.57 micrograms/mL) can be decreased by increasing the fat content of the solvent. To test this hypothesis, 36 patients were randomly allocated to one of three groups, each receiving a different formulation of propofol. Group A received 20 mL of propofol alone in a commercial preparation (Diprivan(R) with 10 mL of saline); Group B, 20 mL of propofol to which 5 mL of long-chain triglyceride (LCT) fat emulsion and 5 mL of saline and been added; and Group C, 20 mL of propofol and 10 mL of LCT fat emulsion. The propofol emulsion was injected over 30-60 s into a dorsal vein of the hand. Patients reported pain during injection as none, mild, moderate, or severe (almost intolerable). In Group A, 8 of 12 patients reported moderate or severe pain upon injection whereas in Group C only mild pain was reported by 6 of 12 patients. Our results suggest that a smaller concentration of propofol in the aqueous phase of the emulsion reduces pain on injection. With the addition of more lipid (10 mL), a higher percentage of propofol is absorbed by fat particles. If solvents that permit a smaller concentration of the drug in the aqueous phase of oil-in-water emulsions were used for propofol and other drugs that cause pain on injection, pain would be reduced and patient satisfaction may be increased.
Blue electroluminescence from porous silicon carbide (1994)

The possibility of a new blue light emitting diode (LED) using porous SiC as a luminescent material is described. The porous SiC is electrochemically formed on a single crystalline 6H-SiC substrate fabricated by the Acheson method. The diode structure is a Schottky-like junction between indium tin oxide (ITO) and porous SiC. The ITO/porous SiC junction shows a rectification behavior and a blue electroluminescence (EL) under the forward direction.
Artificial Chaperone-assisted Refolding of Carbonic Anhydrase B (1996)

We recently reported a new approach to protein refolding that utilizes a pair of low molecular weight folding assistants, a detergent and a cyclodextrin (Rozema, D., and Gellman, S. H. (1995) J. Am. Chem. Soc. 117, 2373-2374). Here, we provide a detailed study of carbonic anhydrase B (CAB) refolding assisted by these "artificial chaperones." When CAB is heated in the presence of a competent detergent, or when guanidinium-denatured CAB is diluted to nondenaturing guanidinium concentration in the presence of such a detergent, the detergent forms a complex with the non-native protein, thereby preventing aggregation. CAB is unable to refold from the detergent-complexed state, but folding can be induced by introduction of a cyclodextrin, which strips the detergent away from the protein. Use of artificial chaperones provides excellent yields of reactivated CAB under conditions that lead to little or no reactivation in the absence of the refolding assistants. Our studies show that the detergent can capture the unfolded protein even at submicellar concentrations, but that not all CAB-detergent complexes lead efficiently to refolded enzyme upon introduction of the stripping agent. Effective refolding appears to require that detergent stripping occur as rapidly as possible; intrinsically slow methods of detergent removal (dialysis or use of macroscopic adsorbents) are less effective than cyclodextrin at inducing renaturation upon detergent removal. The detailed characterization of artificial chaperone-assisted CAB refolding reported here should guide the application of this strategy to other proteins.
Epithelial Cell Differentiation Pathways in the Human Prostate: Identification of Intermediate Phenotypes by Keratin Expression (2001)

The prostate grows slowly throughout adult life, leading to benign prostatic hyperplasia (BPH), which often results in urethral obstruction in later years. The symptoms of BPH are the second most common reason for surgery in men over 65. The aim of this study was to determine the relationship between cell proliferation and cell differentiation in BPH tissue. Using multiple antibodies, simultaneously detected with different fluorophore-conjugated secondary antibodies, several subpopulations of epithelial cells were detected. In addition to K14, basal cells also expressed keratins 15, 17, and 19 in various combinations, and some of the luminal cells also expressed K19 together with K8 and K18. Co-staining for cytokeratins and Ki-67 indicated that 44% of proliferative cells expressed K14 and 36% K19, although the difference was not statistically significant. This report provides a detailed description of the relationship between keratin expression and cell proliferation in the prostate and indicates that K19-positive cells form the link between the basal and luminal layers of the epithelium. (J Histochem Cytochem 49:271-278, 2001)
Efficient mobile fronthaul for 24&#x00D7;20MHz LTE signals using self-seeded RSOA with adaptive crosstalk cancellation (2015)

Feedback cancellation of remodulation crosstalk for self-seeded RSOA is proposed and demonstrated. Using adaptive crosstalk cancellation, efficient mobile fronthaul for 24 20-MHz LTE channels showed about 20% improvement in the error vector magnitude of the received signal.
Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice (2017)

Knowledge of the spatial organization of the gut microbiota is important for understanding the physical and molecular interactions among its members. These interactions are thought to influence microbial succession, community stability, syntrophic relationships, and resiliency in the face of perturbations. The complexity and dynamism of the gut microbiota pose considerable challenges for quantitative analysis of its spatial organization. Here, we illustrate an approach for addressing this challenge, using (<i>i</i>) a model, defined 15-member consortium of phylogenetically diverse, sequenced human gut bacterial strains introduced into adult gnotobiotic mice fed a polysaccharide-rich diet, and (<i>ii</i>) in situ hybridization and spectral imaging analysis methods that allow simultaneous detection of multiple bacterial strains at multiple spatial scales. Differences in the binding affinities of strains for substrates such as mucus or food particles, combined with more rapid replication in a preferred microhabitat, could, in principle, lead to localized clonally expanded aggregates composed of one or a few taxa. However, our results reveal a colonic community that is mixed at micrometer scales, with distinct spatial distributions of some taxa relative to one another, notably at the border between the mucosa and the lumen. Our data suggest that lumen and mucosa in the proximal colon should be conceptualized not as stratified compartments but as components of an incompletely mixed bioreactor. Employing the experimental approaches described should allow direct tests of whether and how specified host and microbial factors influence the nature and functional contributions of "microscale" mixing to the dynamic operations of the microbiota in health and disease.
Both thermal and non-thermal stress protect against caerulein induced pancreatitis and prevent trypsinogen activation in the pancreas (2002)

These results suggest that both thermal and non-thermal stresses protect against pancreatitis by preventing intrapancreatic digestive enzyme activation and that HSP70 may mediate this protective effect.
CDK12 is a transcription elongation-associated CTD kinase, the metazoan ortholog of yeast Ctk1 (2010)

Drosophila contains one (dCDK12) and humans contain two (hCDK12 and hCDK13) proteins that are the closest evolutionary relatives of yeast Ctk1, the catalytic subunit of the major elongation-phase C-terminal repeat domain (CTD) kinase in Saccharomyces cerevisiae, CTDK-I. However, until now, neither CDK12 nor CDK13 has been demonstrated to be a bona fide CTD kinase. Using Drosophila, we demonstrate that dCDK12 (CG7597) is a transcription-associated CTD kinase, the ortholog of yCtk1. Fluorescence microscopy reveals that the distribution of dCDK12 on formaldehyde-fixed polytene chromosomes is virtually identical to that of hyperphosphorylated RNA polymerase II (RNAPII), but is distinct from that of P-TEFb (dCDK9 + dCyclin T). Chromatin immunoprecipitation (ChIP) experiments confirm that dCDK12 is present on the transcribed regions of active Drosophila genes. Compared with P-TEFb, dCDK12 amounts are lower at the 5' end and higher in the middle and at the 3' end of genes (both normalized to RNAPII). Appropriately, Drosophila dCDK12 purified from nuclear extracts manifests CTD kinase activity in vitro. Intriguingly, we find that cyclin K is associated with purified dCDK12, implicating it as the cyclin subunit of this CTD kinase. Most importantly, we demonstrate that RNAi knockdown of dCDK12 in S2 cells alters the phosphorylation state of the CTD, reducing its Ser2 phosphorylation levels. Similarly, in human HeLa cells, we show that hCDK13 purified from nuclear extracts displays CTD kinase activity in vitro, as anticipated. Also, we find that chimeric (yeast/human) versions of Ctk1 containing the kinase homology domains of hCDK12/13 (or hCDK9) are functional in yeast cells (and also in vitro); using this system, we show that a bur1(ts) mutant is rescued more efficiently by a hCDK9 chimera than by a hCDK13 chimera, suggesting the following orthology relationships: Bur1 ↔ CDK9 and Ctk1 ↔ CDK12/13. Finally, we show that siRNA knockdown of hCDK12 in HeLa cells results in alterations in the CTD phosphorylation state. Our findings demonstrate that metazoan CDK12 and CDK13 are CTD kinases, and that CDK12 is orthologous to yeast Ctk1.
Chondrocyte behavior in fibrin glue in vitro (1993)

To test fibrin glue as a vehicle in chondrocyte transplantation, chondrocytes, isolated from articular cartilage of young rabbits, were mixed with Tissucol, a highly concentrated fibrin glue, and cultured for 7 days. Histology, autoradiography (35-S) and electron microscopy were used to study chondrocyte behavior and phenotypic expression. Chondrocytes multiplied, retained their morphology, and produced matrix in fibrin glue as long as the cells were surrounded by the glue. Glue disintegration started after 3 days and was accelerated by higher cell concentrations.
Population Pharmacokinetics of Humanized Monoclonal Antibody HuCC49ΔCH2 and Murine Antibody CC49 in Colorectal Cancer Patients (2007)

To predict the optimal time for surgery after antibody administration, the population pharmacokinetics of (125)I-HuCC49deltaCH2 and (125)I-CC49 were characterized in 55 patients with colorectal cancers. A 2-compartment linear model was used to fit the pharmacokinetic data. Model stability and performance were assessed using a visual predictive check procedure. Different clinical trial designs were evaluated by simulation in combination with Bayesian estimation method to predict the optimal time for surgery. The results showed that HuCC49deltaCH2 had 65% faster clearance from blood circulation and 24% shorter mean residence time than CC49. Population pharmacokinetic analysis identified body weight as the only covariate to explain between-subject variability in clearance, intercompartmental flow rate, and volume of distribution. Model predictions indicated a wide interval for the optimal time of surgery, suggesting that it would be beneficial to individualize the time of surgery for each patient by measurement of antibody disposition. Clinical trial designs with at least 3 measurements of antibody disposition were found to be better than an empirical direct observation method for the optimal prediction of surgery time.
Cognitive and Neurophysiological Outcome of Cardiac Arrest Survivors Treated With Therapeutic Hypothermia (2007)

The use of therapeutic hypothermia was not associated with cognitive decline or neurophysiological deficits after out-of-hospital CA.
Third generation photovoltaics: Ultra‐high conversion efficiency at low cost (2001)

Abstract Since the early days of terrestrial photovoltaics, a common perception has been that ‘first generation’ silicon wafer‐based solar cells eventually would be replaced by a ‘second generation’ of lower cost thin‐film technology, probably also involving a different semiconductor. Historically, cadmium sulphide, amorphous silicon, copper indium diselenide, cadmium telluride and now thin‐film polycrystalline silicon have been regarded as key thin‐film candidates. Any mature solar cell technology seems likely to evolve to the stage where costs are dominated by those of the constituent materials, be they silicon wafers or glass sheet. It is argued, therefore, that photovoltaics is likely to evolve, in its most mature form, to a ‘third generation’ of high‐efficiency thin‐film technology. By high efficiency, what is meant is energy conversion values double or triple the 15–20% range presently targeted, closer to the thermodynamic limit of 93%. Tandem cells are the best known of such high‐efficiency approaches, where efficiency can be increased merely by adding more cells of different bandgap to a cell stack, at the expense of increased complexity and spectral sensitivity. However, a range of other more ‘paralleled’ approaches offer similar efficiency to an infinite stack of tandem cells. These options are reviewed together with possible approaches for practical implementation, likely to become more feasible with the evolution of materials technology over the next two decades. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Evaluation of respiration‐correlated digital tomosynthesis in lunga) (2010)

Digital tomosynthesis (DTS) with a linear accelerator-mounted imaging system provides a means of reconstructing tomographic images from radiographic projections over a limited gantry arc, thus requiring only a few seconds to acquire. Its application in the thorax, however, often results in blurred images from respiration-induced motion. This work evaluates the feasibility of respiration-correlated (RC) DTS for soft-tissue visualization and patient positioning. Image data acquired with a gantry-mounted kilovoltage imaging system while recording respiration were retrospectively analyzed from patients receiving radiotherapy for non-small-cell lung carcinoma. Projection images spanning an approximately 30 degrees gantry arc were sorted into four respiration phase bins prior to DTS reconstruction, which uses a backprojection, followed by a procedure to suppress structures above and below the reconstruction plane of interest. The DTS images were reconstructed in planes at different depths through the patient and normal to a user-selected angle close to the center of the arc. The localization accuracy of RC-DTS was assessed via a comparison with CBCT. Evaluation of RC-DTS in eight tumors shows visible reduction in image blur caused by the respiratory motion. It also allows the visualization of tumor motion extent. The best image quality is achieved at the end-exhalation phase of the respiratory motion. Comparison of RC-DTS with respiration-correlated cone-beam CT in determining tumor position, motion extent and displacement between treatment sessions shows agreement in most cases within 2-3 mm, comparable in magnitude to the intraobserver repeatability of the measurement. These results suggest the method's applicability for soft-tissue image guidance in lung, but must be confirmed with further studies in larger numbers of patients.
Toward an object-oriented approach to software fault tolerance (2002)

Software fault tolerance is often necessary, but can itself be dangerously error-prone because of the additional effort that must be involved in the programming process. The additional redundancy may increase size and complexity and thus adversely affect software reliability. Object-oriented programming provides an appropriate framework for controlling complexity and enforcing reliability. However, software fault tolerance cannot be achieved merely by implementing the classical fault-tolerance schemes in an object-oriented fashion. New problems arise while integrating software redundancy into object-oriented computing systems. This paper identifies a set of such problems, addresses possible solutions, and proposes an object-oriented architecture for dealing with software design faults. Both linguistic supports for the architecture and implementation issues are discussed in detail.
Induction of HIV-1-specific T cell responses by administration of cytokines in late-stage patients receiving highly active anti-retroviral therapy (1999)

Highly active anti-retroviral therapy (HAART) is associated with reduction in the morbidity and mortality of patients with advanced HIV-1 disease. The ability of such treatment to improve immune responses against HIV-1 and opportunistic pathogens is variable and limited. Addition of cytokine immunotherapy to this treatment may improve immune responses. IL-2 with or without granulocyte-macrophage colony-stimulating factor (GM-CSF) was administered to HIV-1+ individuals receiving HAART with undetectable viral loads, and CD4 counts < 100 cells/microl. In one patient presenting with Mycobacterium avium complex (MAC) infection, we evaluated the effect of cytokine immunotherapy on lymphocyte phenotype; plasma viral load; proliferative responses to mitogens, recall and HIV-1 antigens; cytokine production and message in response to non-specific and specific stimuli; and natural killer (NK) cell activity. Proliferation assays were performed in two similar patients. Before cytokine immunotherapy the predominant CD8+ population was mainly CD28-. No proliferation or IL-2 production was seen in response to mitogens, recall or HIV-1 antigens; and no HIV-1 peptide-specific interferon-gamma (IFN-gamma)-secreting cells were present. Low levels of IL-4 were detected in response to antigens to which patients had been exposed, associated with up-regulated expression of costimulatory molecules influenced by IL-4. Following IL-2 administration, loss of IL-4 was associated with increased NK cell activity and HIV-1 peptide-specific and non-specific IFN-gamma-producing cells. Proliferative responses associated with IL-2 production and responsiveness were only seen after subsequent concomitant administration of GM-CSF with IL-2. These changes mirrored clinical improvement. An imbalance of lymphocyte subsets may account for immune unresponsiveness when receiving HAART. Restoration of responses following immunotherapy suggests a shift towards a lymphocyte profile with anti-pathogen activity.
HLA-G in Transplantation: A Relevant Molecule for Inhibition of Graft Rejection? (2003)

The human MHC class I molecule HLA-G has long been known as a molecule selectively expressed by cytotrophoblastic cells. By inhibiting the cytolytic function of decidual NK cells, HLA-G protects the HLA-A and -B negative semiallogeneic embryonic tissue against the mother's immune system. In the light of this immuno-suppressive function, the role of HLA-G in transplantation was investigated. We will review here recently published data on this topic, showing that expression of HLA-G affects the responsive capacity of the immune system, might directly participate in graft acceptation, and should be taken into account for the monitoring of transplantation patients.
Inhibition of Hepatitis C Virus Replication by Arsenic Trioxide (2004)

Hepatitis C virus (HCV) is a serious global problem, and present therapeutics are inadequate to cure HCV infection. In the present study, various antiviral assays show that As2O3 at submicromolar concentrations is capable of inhibiting HCV replication. The 50% effective concentration (EC50) of As2O3 required to inhibit HCV replication was 0.35 microM when it was determined by a reporter-based HCV replication assay, and the EC50 was below 0.2 microM when it was determined by quantitative reverse transcription-PCR analysis. As2O3 did not cause cellular toxicity at this concentration, as revealed by an MTS [3-(4,5-dimethylthiozol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium, inner salt] assay. A combination of As2O3 and alpha interferon exerted synergistic effects against HCV, as revealed by a multiple linear logistic model and isobologram analysis. Furthermore, in an alternative HCV antiviral system that may recapitulate additional steps involved in HCV infection and replication, As2O3 at 0.3 microM totally abolished the HCV signal, whereas alpha interferon at a high dose (5,000 IU/ml) only partially suppressed the HCV signal. The study highlights the indications for use of a novel class of anti-HCV agent. Further elucidation of the exact antiviral mechanism of As2O3 may lead to the development of agents with potent activities against HCV or related viruses.