gebhart/patrepeval huggingface dataset:
Calcium activates two types of potassium channels in rat hippocampal neurons in culture (1991)

Several calcium-dependent potassium currents can contribute to the electrophysiological properties of neurons. In hippocampal pyramidal cells, 2 afterhyperpolarizations (AHPs) are mediated by different calcium-activated potassium currents. First, a rapidly activated current contributes to action-potential repolarization and the fast AHP following individual action potentials. In addition, a slowly developing current underlies the slow AHP, which occurs after a burst of action potentials and contributes substantially to the spike-frequency accommodation observed in these cells during a prolonged depolarizing current pulse. In order to investigate the single Ca2(+)-dependent channels that might underlie these currents, we performed patch-clamp experiments on hippocampal neurons in primary culture. When excised inside-out patches were exposed to 1 microM Ca2+, 2 types of channel activity were observed. In symmetrical bathing solutions containing 140 mM K+, the channels had conductances of 19 pS and 220 pS, and both were permeable mainly to potassium ions. The properties of these 2 channels differed in a number of ways. At negative membrane potentials, the small-conductance channels were more sensitive to Ca2+ than the large channels. At positive potentials, the small-conductance channels displayed a flickery block by Mg2+ ions on the cytoplasmic face of the membrane. Low concentrations of tetraethylammonium (TEA) on the extracellular face of the membrane specifically caused an apparent reduction of the large-channel conductance. The properties of the large- and small-conductance channels are in accord with those of the fast and slow AHP, respectively.
FDTD analysis of submillimeter-wave CPW with finite-width ground metallization (1997)

The dispersion and attenuation characteristics of conductor-backed coplanar transmission lines with finite-width ground metallizations are studied in the frequency range up to 1 THz. The finite-difference time-domain (FDTD) method is used for analysis. Open boundaries are described by means of Berenger's perfectly matched layer. The results are compared to electrooptic measurements. They show that introducing ground metallizations of finite width causes distinct changes in attenuation and dispersion characteristics.
Characterization of the cis elements involved in basal and E2-transactivated expression of the bovine papillomavirus P2443 promoter (1991)

Transcriptional transactivation and repression by the viral E2 proteins are important regulatory mechanisms for the papillomaviruses. In the bovine papillomavirus type 1 (BPV-1), several viral promoters can be transactivated by E2 through E2-dependent enhancer elements located in the viral long control region (LCR), including promoters involved in E2 expression itself. This report demonstrates that the BPV-1 P2443 promoter is transactivated by E2-responsive elements in the LCR and that this promoter is responsible for a major part of the expression of the E2 and E5 gene products. Characterization of the cis elements involved in P2443 regulation indicated that the single E2-binding site directly upstream of P2443 is not required for either the E2 transactivation or for any E2 repression of the basal or transactivated activity of this promoter. Therefore, cooperative interactions between E2 bound at the LCR and E2 bound near P2443 do not have any role in the regulation of this promoter. Further definition of the cis regulatory elements of this promoter indicated that a binding site for the transcriptional factor Sp1 exists directly upstream of the P2443 TATA box and is critical for the basal level of transcription from this promoter. Disruption of this Sp1 site eliminated P2443 promoter activity in transient expression assays for E2 and E5 and resulted in a loss of transforming activity when introduced into the full viral genome.
Phenotypic analysis of the murine CD4-related glycoprotein, CD223 (LAG-3) (2002)

CD223 (LAG-3) is an activation-induced cell surface molecule, structurally similar to the T cell coreceptor CD4, that binds MHC class II molecules with high affinity. Little is known about the expression and function of murine CD223. Here, we show that mRNA expression is restricted to the thymic medulla, splenic red pulp and sparse cells in the adult brain cortex. In contrast, surprisingly high expression was seen in defined tracts at the base of the cerebellum and in the choroid plexus of day 7 postnatal brain. mCD223:Ig, but not CD4:Ig, fusion proteins stained cells expressing MHC class II molecules. Analysis of mCD223 cell surface expression was performed with a new monoclonal antibody (mAb) that recognizes an epitope in the D2 domain. Although it blocked mCD223 function in vitro, it did not block binding of mCD223 to MHC class II molecules. While very few TCRalpha beta T cells in the spleen and thymus of naive mice express surface mCD223 (<3 %), approximately 18 % TCR gamma delta T cells and approximately 10 % NK cells are positive. This small population of TCRalpha beta T cells are cycling memory T cells (BrdU(+), CD44(hi), CD62L(lo)). In contrast, all T cells express mCD223 2-3 days post activation. This study and the anti-CD223 mAb should greatly assist in the elucidation of CD223 function.
Modeling biofilm kinetics for a low‐loaded expanded‐bed anaerobic reactor (1987)

The effect of surface coverage of biomass on biofilm kinetics in an expanded-bed, granular activated carbon an aerobic reactor was evaluated. Acetate was used as the sole organic carbon source. An assumption of 10% surface coverage of biofilm was examined and compared to 100% coverage. Best estimated values of k(a) and K(sa) did not differ significantly from one case to the other. The confidence region analysis also showed that the biofilm was fully penetrated in the expanded-bed reactor for the case of 10% coverage, as well as when 100% coverage was assumed. Because the biofilm was fully penetrated, a model having no internal diffusion resistance and using the best estimates of k(a) and K(sa) obtained from the 10 and 100% coverage assumptions was capable of giving good predictions of effluent acetate concentrations for an in dependent experiment having a reduced liquid detention time. Consideration of biofilm surface-loading criteria demonstrated how the results can be applied to other reactors for the purpose of predicting when the extent of surface coverage and internal diffusion resistance are not significant factors in biofilm modeling.
Imaging and Spectrum Analysis of Contrast Agents in the In Vivo Rabbit Eye Using Very-High–Frequency Ultrasound (1998)

We have conducted initial studies that demonstrated the feasibility of employing ultrasonic contrast agents with very-high-frequency ultrasound (VHFU), using wideband transducers with center frequencies near 40 MHz. These studies were undertaken with an ultimate objective of quantifying perfusion in vessels in the eye and other organs. We expanded the model developed by Lizzi et al. (1983) to incorporate the scattering characteristics from encapsulated bubbles, such as contrast agents. Our analysis shows how the spectral slopes and intercepts measured from contrast agents are related to factors that include the radii and concentration of contrast-agent particles. We conducted in vitro experiments to validate the theoretical predictions and obtained excellent agreement. We obtained in vivo VHFU data from the eyes of anesthetized rabbits before and after injection of Albunex and Aerosomes. Digitally computed B-mode images demonstrated echo enhancement within the ciliary body and its processes. The magnitudes of these enhancements were quantified using calibrated spectrum-analysis techniques.
Preparation of Single-cell Suspensions for Cytofluorimetric Analysis from Different Mouse Skin Regions (2016)

The skin is a barrier organ that interacts with the external environment. Being continuously exposed to potential microbial invasion, the dermis and epidermis home a variety of immune cells in both homeostatic and inflammatory conditions. Tools to obtain skin cell release for cytofluorimetric analyses are, therefore, very useful in order to study the complex network of immune cells residing in the skin and their response to microbial stimuli. Here, we describe an efficient methodology for the digestion of mouse skin to rapidly and efficiently obtain single-cell suspensions. This protocol allows maintenance of maximum cell viability without compromising surface antigen expression. We also describe how to take and digest skin samples from different anatomical locations, such as the ear, trunk, tail, and footpad. The obtained suspensions are then stained and analyzed by flow cytometry to discriminate between different leukocyte populations.
Patellofemoral replacement: Utilizing a customized femoral groove replacement (1990)

A specialized program for the computerized axial tomography (CAT) scan developed by Techmedica, Inc., allows for the creation of a titanium alloy “custom cap” as a femoral groove replacement, thus eliminating the need to remove bone stock from the femur. From 1983 to 1987, 28 custom patellofemoral replacements were performed in 25 patients with primary end-stage patellofemoral arthritis. The authors describe the surgical technique for this prosthesis. Postoperatively, there were no infections. Average range of motion was 0° to 120° indicating a 5° loss of motion. Four patients (13½%) underwent subsequent revision/removal in the early stages of the development of the component design. Improvement in manufacturing design has eliminated most of these problems.
Role of the UL25 Protein in Herpes Simplex Virus DNA Encapsidation (2008)

The herpes simplex virus protein UL25 attaches to the external vertices of herpes simplex virus type 1 capsids and is required for the stable packaging of viral DNA. To define regions of the protein important for viral replication and capsid attachment, the 580-amino-acid UL25 open reading frame was disrupted by transposon mutagenesis. The UL25 mutants were assayed for complementation of a UL25 deletion virus, and in vitro-synthesized protein was tested for binding to UL25-deficient capsids. Of the 11 mutants analyzed, 4 did not complement growth of the UL25 deletion mutant, and analysis of these and additional mutants in the capsid-binding assay demonstrated that UL25 amino acids 1 to 50 were sufficient for capsid binding. Several UL25 mutations were transferred into recombinant viruses to analyze the effect of the mutations on UL25 capsid binding and on DNA cleavage and packaging. Studies of these mutants demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids and that the C terminus is essential for DNA packaging and the production of infectious virus through its interactions with other viral packaging or tegument proteins. Analysis of viral DNA cleavage demonstrated that in the absence of a functional UL25 protein, aberrant cleavage takes place at the unique short end of the viral genome, resulting in truncated viral genomes that are not retained in capsids. Based on these observations, we propose a model where UL25 is required for the formation of DNA-containing capsids by acting to stabilize capsids that contain full-length viral genomes.
Study of Fraunhofer Diffraction From Complementary Sierpinski Carpet Grating (2005)

The Fraunhofer diffraction phenomenon on the complementary structure of Sierpinski carpet grating is discussed on the basis of Fresnel-Kirchhoff theory and Fourier analytical method. The frequency spectrum,amplitude and light-intensity functions are derived. The diffraction phenomenon of grating is simulated by use of the MATLAB software, and the curves of its frequency response characteristic are plotted. The result shows that in diffraction patterns of all-order gratings, the higher amplitude part is concentrated in the center area of the receiving screen and the lower amplitude in the area around the center, but in the further area far away from center it tends to 0. In the whole, the diffraction patterns manifest the obvious fractal characteristics as well as the basic features of the diffraction.
The Lysosomotropic Agent Monodansylcadaverine Also Acts as a Solvent Polarity Probe (2000)

The autofluorescent substance monodansylcadaverine has recently been reported as a specific in vivo marker for autophagic vacuoles. However, the mechanism for this specific labeling remained unclear. Our results reveal that the common model of ion trapping in acidic compartments cannot completely account for the observed autophagic vacuole staining. Because autophagic vacuoles are characterized by myelin-like membrane inclusions, we tested whether this lipid-rich environment is responsible for the staining properties of monodansylcadaverine. In in vitro experiments using either liposomes or solvents of different polarity, monodansylcadaverine showed an increased relative fluorescence intensity in a hydrophobic environment as well as a Stokes shift dependent on the solvent polarity. To test the effect of autophagic vacuoles or autophagic vacuole lipids on monodansylcadaverine fluorescence, we isolated autophagic vacuoles and purified autophagic vacuole lipids depleted of proteins. Entire autophagic vacuoles and autophagic vacuole lipids had the same effect on monodansylcadaverine fluorescence properties, suggesting lipids as the responsible component. Our results suggest that the in vivo fluorescence properties of monodansylcadaverine do not depend exclusively on accumulation in acidic compartments by ion trapping but also on an effective interaction of this molecule with autophagic vacuole membrane lipids. (J Histochem Cytochem 48:251-258, 2000)
Combination Chemotherapy for Influenza (2010)

The emergence of pandemic H1N1 influenza viruses in April 2009 and the continuous evolution of highly pathogenic H5N1 influenza viruses underscore the urgency of novel approaches to chemotherapy for human influenza infection. Anti-influenza drugs are currently limited to the neuraminidase inhibitors (oseltamivir and zanamivir) and to M2 ion channel blockers (amantadine and rimantadine), although resistance to the latter class develops rapidly. Potential targets for the development of new anti-influenza agents include the viral polymerase (and endonuclease), the hemagglutinin, and the non-structural protein NS1. The limitations of monotherapy and the emergence of drug-resistant variants make combination chemotherapy the logical therapeutic option. Here we review the experimental data on combination chemotherapy with currently available agents and the development of new agents and therapy targets.
A review of algorithms for segmentation of optical coherence tomography from retina. (2013)

Optical coherence tomography (OCT) is a recently established imaging technique to describe different information about the internal structures of an object and to image various aspects of biological tissues. OCT image segmentation is mostly introduced on retinal OCT to localize the intra-retinal boundaries. Here, we review some of the important image segmentation methods for processing retinal OCT images. We may classify the OCT segmentation approaches into five distinct groups according to the image domain subjected to the segmentation algorithm. Current researches in OCT segmentation are mostly based on improving the accuracy and precision, and on reducing the required processing time. There is no doubt that current 3-D imaging modalities are now moving the research projects toward volume segmentation along with 3-D rendering and visualization. It is also important to develop robust methods capable of dealing with pathologic cases in OCT imaging.
Liposomes in the Treatment of Infections (1994)

The use of liposomes in the treatment of severe infections is under investigation. Classical liposomes which localize in cells of the mononuclear phagocyte system (MPS) can be exploited in two ways. First for targeting of macrophage modulators such as muramyl peptides or IFN-gamma, to stimulate the cells of the MPS to maximal blood clearance capacity. This enhanced nonspecific anti-infectious resistance is important as in immunocompromised patients micro-organisms frequently appear in the blood from a local infection. Secondly, classical liposomes are successfully used as carriers of antibiotics in experimental intracellular parasitic-, viral-, fungal- or bacterial infections in MPS tissues. Based on these data extensive studies in patients with severe fungal infections have demonstrated successful treatment with liposomal or lipid-complexed amphotericin B. More recently, liposomal amphotericin B appeared to be effective in patients with drug-resistant visceral leishmaniasis. For the treatment of Mycobacterium avium complex infection in AIDS patients the efficacy of liposomal gentamicin is under investigation. With respect to infections in non-MPS tissues the applicability of Stealth liposomes characterized by long circulation half-lives is under investigation. Substantial localization of these liposomes in infected lung tissue of rats was demonstrated. Preliminary data in experimental bacterial lung infection showed superior efficacy of antibiotic encapsulated in Stealth liposomes.
Advanced source/drain engineering for box-shaped ultrashallow junction formation using laser annealing and pre-amorphization implantation in sub-100-nm SOI CMOS (2002)

Source/drain (S/D) engineering for ideal box-shaped junction formation using laser annealing (LA) combined with pre-amorphization implantation (PAI) is proposed and implemented in device integration for sub-100-nm CMOS on an SOI substrate. Modeling analysis for the resistance component associated with junction profile abruptness demonstrates that a noticeable reduction in parasitic series resistance with technology generation can be achieved through junction profile slope engineering. From the experimental results of LA, it is found that PAI not only controls the ultrashallow junction depth precisely, but also reduces the laser energy fluence required for impurity activation. In addition, laser annealing energy can be further reduced by use of SOI substrates in the device integration, indicating the implementation feasibility of LA to CMOS integration with an enlarged process window margin. The proposed S/D engineering is verified by the sheet resistance of junctions and the fabricated device current characteristics exhibiting substantially improved short-channel performance with higher current capability due to the box-shaped junction profile as compared with conventional rapid thermally-annealed (RTA) devices.
Treatment of metastatic urothelial cancer: opportunities for drug discovery and development (2008)

Conventional first-line platinum-based combination chemotherapy with gemcitabine/cisplatin and standard or dose-dense methotrexate, vinblastine, doxorubicin and cisplatin yields high response rates but suboptimal long-term outcomes for advanced urothelial cancer. Salvage therapy is an unmet need, with disappointing outcomes. The emergence of novel biological agents offers the promise of improved outcomes. Neoadjuvant therapy preceding cystectomy for muscle-invasive bladder cancer provides an important paradigm and an interesting approach in developing novel agents. Patients who are not candidates for cisplatin require special attention. A multidisciplinary approach and collaboration among laboratory scientists, oncologists, urologists and radiation oncologists is necessary to make therapeutic advances. Recent and ongoing trials of novel chemotherapeutic and biological agents are reviewed.
Use of vascular endothelial cell growth factor gene transfer to enhance implantable sensor function in vivo (2003)

In the current study, we developed and validated a simple, rapid and safe in vivo model to test gene transfer and sensor function in vivo. Using the model, we tested the specific hypothesis that in vivo gene transfer of angiogenic factors at sites of biosensor implantation would induce neovascularization surrounding the sensor and thereby enhance biosensor function in vivo. As the in vivo site for testing of our gene transfer cell and biosensor function systems, the developing chorioallantoic membrane (CAM) of the embryo was utilized. Vascular endothelial cell growth factor (VEGF) was used as a prototype for angiogenic factor gene transfer. A helper-independent retroviral vector derived from Rous sarcoma virus (RSV), designated RCAS, was used for gene transfer of the murine VEGF (mVEGF) gene (mVEGF:RCAS) into the DF-1 chicken cell line (designated mVEGF:DF-1). Initially, the ability of VEGF:DF-1 cells to produce VEGF and RCAS viral vectors containing the mVEGF gene (mVEGF:RCAS) was validated in vitro and in vivo, as was the ability of the mVEGF:DF-1 cells to induce neovascularization in the ex ova CAM model. Using the system, we determined the ability of mVEGF:DF-1 cells to enhance acetaminophen sensor function in vivo, by inducing neovascularization at sites of sensor implantation in the ex ova CAM model. For these studies, acetaminophen sensors were placed on 8-day-old ex ova CAMs, followed by addition of media or cells (mVEGF:DF-1 cells or GFP:DF-1 cells) at the sites of biosensor implantation on the CAM. At 4 to 10 days after sensor placement, the biosensor function was determined by measuring sensor response to an intravenous injection of acetaminophen. Sensors implanted on CAMs with buffer or control cells (GFP:DF-1 cells) displayed no induced neovascularization around the sensor and had minimal/baseline sensor responses to intravenous acetaminophen injection (media, 133.33 +/- 27.64 nA; GFP:DF-1, 187.50 +/- 55.43 nA). Alternatively, the sensors implanted with mVEGF:DF-1 cells displayed massive neovascularization and equally massive sensor response to intravenous injection of acetaminophen (VEGF:DF-1, 1387.50 +/- 276.42 nA). These data clearly demonstrate that enhancing vessel density (i.e., neovascularization) around an implanted sensor dramatically enhances sensor function in vivo.
Tear Film, Contact Lens, and Patient-Related Factors Associated with Contact Lens–Related Dry Eye (2006)

Contact lens-related dry eye may be explained mechanistically by increased tear film thinning times (evaporation or dewetting) resulting in increased tear film osmolality. Other contributing factors include the use of high-water-content lenses, which have traditionally been reported to be associated with less patient comfort than lower-water-content lenses, potentially due to spoilation and deposition. As found in other studies of dry eye, women are more likely to report contact lens-related dry eye than are men.
Expression and proinflammatory role of proteinase‐activated receptor 2 in rheumatoid synovium: Ex vivo studies using a novel proteinase‐activated receptor 2 antagonist (2007)

These findings identify PAR-2 as a novel upstream regulator of proinflammatory cytokine production in RA and indicate its potential as a novel therapeutic target in inflammatory arthritis.