gebhart/patrepeval huggingface dataset:
Adherence and Proliferation of Endothelial Cells on Surface-Immobilized Albumin-Heparin Conjugate (1998)

Small-diameter vascular grafts rapidly fail after implantation, due to occlusion caused by thrombosis. This problem cannot be overcome using medication. A promising improvement of graft patency is the seeding of endothelial cells (EC) on the luminal surface of the vascular graft. Conjugates of albumin and heparin, which were developed to obtain nonthrombogenic coatings, could form an ideal coating for vascular grafts. Besides presenting anticoagulant function, heparin will bind proteins with cell adhesive properties, thus facilitating adherence of EC to the graft surface. EC were able to grow to confluency on CO(2) gas plasma-treated polystyrene (PS-CO(2)) coated with albumin-heparin conjugate. CO(2) gas plasma treatment resulted in the introduction of functional groups at the surface (e.g., hydroxyl, aldehyde, carboxylic acid, and epoxide groups). Addition of albumin-heparin conjugate to the functionalized surface in an aqueous solution with pH 8.2 yielded a stable monolayer of covalently bound conjugate. The number of cells adhering and proliferating on this surface was comparable to the number of cells on fibronectin-coated PS-CO(2). However, the structure and size of EC proliferating on surface-immobilized albumin-heparin was more irregular. Long-term adherence might be improved by adding fibronectin to the albumin-heparin surface, either as a mixture with albumin-heparin or in a separate incubation step.
TAP‐dependent major histocompatibility complex class I presentation of soluble proteins using listeriolysin (1997)

Immunization of mice with mixtures of listeriolysin, a pore-forming hemolysin secreted by the pathogenic bacterium Listeria monocytogenes, together with soluble ovalbumin, nucleoprotein of influenza virus, or beta-galactosidase of Escherichia coli, resulted in strong cytotoxic CD8 T cell responses to each of the respective passenger proteins in vivo. Also, the concomitant addition of either protein with listeriolysin to target cells elicited efficient sensitization of these cells which could be attributed to the pore-forming activity of listeriolysin. This response was dependent upon a functional TAP transporter and was inhibitable by brefeldin A, indicating the transfer of the soluble proteins into the cytosol and the classical major histocompatibility (MHC) class I presentation pathway. The treatment of target cells with listeriolysin under our experimental conditions did not affect cell viability and the pores generated by listeriolysin treatment were repaired within 60 min. Introduction of soluble proteins into the MHC class I presentation pathway by listeriolysin provides a powerful system to study the cytotoxic response towards intracellular pathogens and would allow for rapid screening of potential antigens in vaccine formulations.
Two-component Signal Transduction in Synechocystis sp. PCC 6803 under Phosphate Limitation: Role of Acetyl Phosphate (2007)

The two-component signal transduction, which typically consists of a histidine kinase and a response regulator, is used by bacterial cells to sense changes in their environment. Previously, the SphS-SphR histidine kinase and response regulator pair of phosphate sensing signal transduction has been identified in Synechocystis sp. PCC 6803. In addition, some response regulators in bacteria have been shown to be cross regulated by low molecular weight phosphorylated compounds in the absence of the cognate histidine kinase. The ability of an endogenous acetyl phosphate to phosphorylate the response regulator, SphR in the absence of the cognate histidine kinase, SphS was therefore tested in Synechocystis sp. PCC 6803. The mutant lacking functional SphS and acetate kinase showed no detectable alkaline phosphatase activity under phosphate-limiting growth conditions. The results suggested that the endogenous acetyl phosphate accumulated inside the mutants could not activate the SphR via phosphorylation. On the other hand, exogenous acetyl phosphate could allow the mutant lacking functional acetate kinase and phosphotransacetylase to grow under phosphate-limiting conditions suggesting the role of acetyl phosphate as an energy source. Reverse transcription PCR demonstrated that the transcripts of acetate kinase and phosphotransacetylase genes in Synechocystis sp. PCC 6803 is upregulated in response to phosphate limitation suggesting the importance of these two enzymes for energy metabolism in Synechocystis cells.
Regulation of galanin gene expression in the rat anterior pituitary gland by the somatostatin analog SMS 201-995. (1992)

In addition to inducing pituitary tumors in rats, estrogen (E2) markedly increases galanin and PRL gene expression. We previously showed that galanin secretion from pituitary cells in vitro is inhibited by dopamine and somatostatin and stimulated by TRH. The objectives of these in vivo studies were to assess whether the long-acting somatostatin analog SMS 201-995 alters 1) immunoreactive galanin or PRL levels in the anterior pituitary, neurointermediate lobe, hypothalamus, or plasma, 2) pituitary galanin and PRL mRNA levels, and 3) the development of E2-induced pituitary tumors. Ovariectomized Fischer 344 rats were implanted with E2-filled or empty Silastic capsules and treated with or without SMS 201-995 (1.5 mg) via Alzet miniosmotic pumps. Two or 6 weeks later, immunoreactive galanin and PRL levels were determined by RIA. In ovariectomized rats, the somatostatin analog lowered the anterior pituitary content of galanin by 50%, but had no effect on PRL concentrations. E2 increased galanin and PRL levels in the anterior pituitary by 220- and 4-fold, respectively. Concomitant E2 and SMS 201-995 treatment further increased galanin and PRL in the anterior pituitary by 60-80%, but decreased plasma galanin and PRL levels. Likewise, the administration of SMS 201-995 for 2 and 6 weeks inhibited the E2-induced growth of the anterior pituitary. Galanin and PRL mRNA levels were quantified by solution hybridization. Galanin mRNA levels were reduced to undetectable levels in ovariectomized rats treated with SMS 201-995. Furthermore, a 10-fold increase in galanin mRNA levels seen in the presence of E2 was inhibited 80% by SMS 201-995. PRL mRNA levels in E2-treated rats were unchanged by SMS 201-995. We conclude that SMS 201-995 1) lowers plasma galanin and PRL levels in E2-treated rats, 2) elevates the anterior pituitary contents of galanin and PRL in E2-exposed rats, probably through decreased secretion of the hormones, and 3) reduces galanin mRNA levels in E2-treated and untreated ovariectomized rats. Overall, these results establish the differential regulation of galanin and PRL gene expression in vivo by SMS 201-995. Moreover, the data demonstrate that somatostatin receptor agonists may have therapeutic potential for some prolactinomas.
An adaptive order statistics filter based on fuzzy rules for image processing (1997)

An optimal filter in terms of removing noise can be determined for any signal distribution by using an order statistics (OS) filter, a typical nonlinear filter. For restoration of signals degraded by nonstationary signals such as an image signal, nonstationary noise, and mixed noise, an adaptive process in which the filter coefficients are varied in accordance with the local information is indispensable to improving signal accuracy. From these facts, an adaptive OS filter can be considered effective for image restoration. Most of the adaptive OS filters proposed so far have several fixed coefficients which are changed in accordance with the local information. However, for the restoration of signals such as deteriorated image signals, it is ideal to have the adaptive OS filter coefficients continuously change. In this paper, filter window signals are fuzzy-clustered into five predefined typical classes using a fuzzy inference system where three types of local information are the parameters of the antecedent part. Since there is an optimal OS filter for each of the five classes, we obtain the sum of outputs of the proposed filters from the filter output value which is optimal for each class, weighted by the degree of assignment of each filter class. With the proposed adaptive OS filter, the filter coefficients are varied continuously, and improvement of image restoration accuracy is attempted. © 1997 Scripta Technica, Inc. Electron Comm Jpn Pt 3, 80(9): 70–80, 1997
Systematic microanatomical analysis of CXCL13 and CCL21 in situ production and progressive lymphoid organization in rheumatoid synovitis (2005)

CXCL13 and CCL21 have been functionally implicated in lymphoid tissue organization both in the upstream phases of lymphoid tissue embryogenesis and in ectopic lymphoid neogenesis in transgenic mice. Here, we analyzed the relationship between CXCL13 and CCL21 production and lymphoid tissue organization in rheumatoid synovitis as a model of a naturally occurring ectopic lymphoneogenesis. Through systematic analysis of mRNA and protein expression, we defined the microanatomical relationship between CXCL13 and CCL21 in progressive aggregational and structural phases of synovial inflammatory infiltrate. We provide the first direct in situ evidence that production of CXCL13 and CCL21 (rather than simply protein binding) is associated with inflammatory lymphoid tissue formation and development with the demonstration, in organized aggregates, of a secondary lymphoid organ-like compartmentalization and vascular association. Notably, the presence of CXCL13 and CCL21 (protein and mRNA) was also demonstrated in non-organized clusters and minor aggregational stages, providing evidence that their induction can take place independently and possibly upstream of T-B compartmentalization, CD21(+) follicular dendritic cell network differentiation and germinal center formation. Our data support the concept that, under inflammatory conditions, CXCL13 and CCL21 participate in lymphoid tissue microanatomical organization, attempting to recapitulate, in an aberrant lymphoid neogenetic process, their homeostatic and morphogenetic physiologic functions.
Reduced Vancomycin Susceptibility in Staphylococcus aureus , Including Vancomycin-Intermediate and Heterogeneous Vancomycin-Intermediate Strains: Resistance Mechanisms, Laboratory Detection, and Clinical Implications (2010)

The emergence of vancomycin-intermediate Staphylococcus aureus (VISA) and heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) over the past decade has provided a challenge to diagnostic microbiologists to detect these strains, clinicians treating patients with infections due to these strains, and researchers attempting to understand the resistance mechanisms. Recent data show that these strains have been detected globally and in many cases are associated with glycopeptide treatment failure; however, more rigorous clinical studies are required to clearly define the contribution of hVISA to glycopeptide treatment outcomes. It is now becoming clear that sequential point mutations in key global regulatory genes contribute to the hVISA and VISA phenotypes, which are associated predominately with cell wall thickening and restricted vancomycin access to its site of activity in the division septum; however, the phenotypic features of these strains can vary because the mutations leading to resistance can vary. Interestingly, changes in the staphylococcal surface and expression of agr are likely to impact host-pathogen interactions in hVISA and VISA infections. Given the subtleties of vancomycin susceptibility testing against S. aureus, it is imperative that diagnostic laboratories use well-standardized methods and have a framework for detecting reduced vancomycin susceptibility in S. aureus.
Deep Neural Networks for Object Detection (2013)

Deep Neural Networks (DNNs) have recently shown outstanding performance on image classification tasks [14]. In this paper we go one step further and address the problem of object detection using DNNs, that is not only classifying but also precisely localizing objects of various classes. We present a simple and yet pow-erful formulation of object detection as a regression problem to object bounding box masks. We define a multi-scale inference procedure which is able to pro-duce high-resolution object detections at a low cost by a few network applications. State-of-the-art performance of the approach is shown on Pascal VOC. 1
Isolation and expression of a gene cluster responsible for biosynthesis of the glycopeptidolipid antigens of Mycobacterium avium (1991)

Bacteria within the Mycobacterium avium complex are prominent in the environment and are a source of serious disseminated infections in patients with AIDS. Serovars of the M. avium complex are distinguished from all other mycobacteria and from one another by the presence of highly antigenic glycolipids, the glycopeptidolipids, on their surfaces. A genomic library of DNA from serovar 2 of the M. avium complex was constructed in the Escherichia coli-Mycobacterium shuttle cosmid, pYUB18, and used to clone and express in Mycobacterium smegmatis the genes responsible for the biosynthesis of the oligosaccharide segment of the M. avium serovar 2-specific glycopeptidolipid. The responsible gene cluster was mapped to a 22- to 27-kb functional region of the M. avium genome. The recombinant glycolipid was also isolated by high-pressure liquid chromatography and chemically characterized, by gas chromatography-mass spectrometry and fast atom bombardment-mass spectrometry, to demonstrate that the lipopeptide core originated in M. smegmatis, whereas the oligosaccharide segment arose from the cloned M. avium genes. This first-time demonstration of the cloning and expression, in a nonpathogenic mycobacterium, of the genes encoding complex cell wall glycoconjugates from a pathogenic mycobacterium presents a new approach for studying the role of such products in disease processes.
Anti-Transforming Growth Factor β IgG Elicits a Dual Effect on Calcium Oxalate Crystallization and Progressive Nephrocalcinosis-Related Chronic Kidney Disease (2018)

Crystallopathies are a heterogeneous group of diseases caused by intrinsic or environmental microparticles or crystals, promoting tissue inflammation and scarring. Certain proteins interfere with crystal formation and growth, e.g., with intrarenal calcium oxalate (CaOx) crystal formation, a common cause of kidney stone disease or nephrocalcinosis-related chronic kidney disease (CKD). We hypothesized that immunoglobulins can modulate CaOx microcrystal formation and crystal growth and that therefore, biological IgG-based drugs designed to specifically target disease modifying proteins would elicit a dual effect on the outcome of CaOx-related crystallopathies. Indeed, both the anti-transforming growth factor (TGF)β IgG and control IgG1 antibody impaired CaOx crystallization <i>in vitro</i>, and decreased intrarenal CaOx crystal deposition and subsequent CKD in mice on an oxalate-rich diet compared to oxalate-fed control mice. However, the TGFβ-specific IgG antibody showed nephroprotective effects beyond those of control IgG1 and substantially reduced interstitial fibrosis as indicated by magnetic resonance imaging, silver and α-smooth muscle actin staining, RT-qPCR, and flow cytometry for pro-fibrotic macrophages. Suppressing interstitial fibrosis slowed the decline of glomerular filtration rate (GFR) compared to treatment with control IgG1 [slope of <i>m</i> = -8.9 vs. <i>m</i> = -14.5 μl/min/100 g body weight (BW)/day, Δ = 38.3%], an increased GFR at the end of the study (120.4 vs. 42.6 μl/min/100 g BW, Δ = 64.6%), and prolonged end stage renal disease (ESRD)-free renal survival by 10 days (Δ = 38.5%). Delayed onset of anti-TGFβ IgG from day 7 was no longer effective. Our results suggest that biological drugs can elicit dual therapeutic effects on intrinsic crystallopathies, such as anti-TGFβ IgG antibody treatment inhibits CaOx crystallization as well as interstitial fibrosis in nephrocalcinosis-related CKD.
Human bone marrow CD34- cells engraft in vivo and undergo multilineage expression that includes giving rise to CD34+ cells. (1998)

We used the human/sheep competitive engraft model to investigate the in vivo engraftment potential of human CD34-, Lin- cells. In three separate studies, transplantation of CD34+, Lin- and CD34-, Lin- cells from the same normal human donors into preimmune fetal sheep resulted in long-term engraftment and multilineage hematopoietic cell/progenitor expression. Human cell/progenitor activities of the CD34+ group were CD3, 0.52%; CD13, 0.36%; CD45, 1.02%; glyA, 1.78%; HLA-DR, 0.99%; colony-forming units (CFU)-Mix, 7.1%; and granulocyte-macrophage CFU (CFU-GM), 13.7%; those of the CD34- group were CD3, 0.24%; CD45, 2.49%; glyA, 0.75%; HLA-DR, 0.3%; CFU-Mix, 7.1%; and CFU-GM, 4.3%. Of special interest was the detection of highly significant numbers (1 x 10[9] cells) of human CD34+ cells in animals transplanted with CD34- cells. Secondary transplantation and limiting dilution studies confirmed the presence of cells with long-term engraftment potential in CD34- populations. The results presented here demonstrate that the CD34- fraction of normal human bone marrow contains cells capable of engraftment and differentiation into CD34+ progenitors and multiple lymphohematopoietic lineages in primary and secondary hosts.
In Vivo Detection of Apoptosis in an Intracardiac Tumor (2001)

We previously demonstrated in vivo imaging of cell death in the myocardia of patients with acute myocardial infarction using technetium Tc 99m–labeled annexin-V (99mTc-p-annexin-V [Apomate], Theseus Imaging, Cambridge, Mass) and nuclear imaging.1 Because high proliferation and apoptotic indices have been reported in rapidly growing malignant tumors,2 information about the extent of apoptosis in the tumor may also provide insight into the tumor's biology and prognosis.
A Diether Phosphonolipid Surfactant Analog, DEPN-8, Is Resistant to Phospholipase-C Cleavage (1997)

Increased activities of phospholipase A2 and C (PLC) have been observed in the bronchoalveolar lavages of patients with adult respiratory distress syndrome (ARDS). DL-alpha-Di-O-hexadecylphosphonocholine [(R)(S)-DEPN-8], a surfactant analog of superior surface activity to the major lung surfactant phospholipid, dipalmitoylphosphatidylcholine (DPPC), is not a substrate for phospholipases A1, A2 and D, but is a substrate for PLC. (R)(S)-DEPN-8 was found in vitro to undergo significantly less PLC-catalyzed degradation as compared to DPPC. The results suggest that (R)(S)-DEPN-8 and structurally related analogs may be useful as components of exogenous replacement surfactant formulations for the treatment of ARDS-related lung injuries.
Reactive Thin Polymer Films as Platforms for the Immobilization of Biomolecules (2005)

Spin-coated thin films of poly(N-hydroxysuccinimidyl methacrylate) (PNHSMA) on oxidized silicon and gold surfaces were investigated as reactive layers for obtaining platforms for biomolecule immobilization with high molecular loading. The surface reactivity of PNHSMA films in coupling reactions with various primary amines, including amine-terminated poly(ethylene glycol) (PEG-NH2) and fluoresceinamine, was determined by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and ellipsometry measurements, respectively. The rate constants of PEG-NH2 attachment on the PNHSMA films were found to be significantly increased compared to the coupling on self-assembled monolayers (SAMs) of 11,11‘-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) on gold under the same conditions. More significantly, the PEG loading observed was about 3 times higher for the polymer thin films. These data indicate that the coupling reactions are not limited to the very surface of the polymer films, but proceed into the near-surface regions of the films. PNHSMA films were shown to be stable in contact with aqueous buffer; the swelling analysis, as performed by atomic force microscopy (AFM), indicated a film thickness independent swelling of ∼2 nm. An increased loading was also observed by surface plasmon resonance for the covalent immobilization of amino-functionalized probe DNA. Hybridization of fluorescently labeled target DNA was successfully detected by fluorescence microscopy and surface plasmon resonance enhanced fluorescence spectroscopy (SPFS), thereby demonstrating that thin films of PNHSMA comprise an attractive and simple platform for the immobilization of biomolecules with high densities.
Quantification and impact of nonparabolicity of the conduction band of indium tin oxide on its plasmonic properties (2014)

Doped indium tin oxide (ITO) behaves as a Drude metal with a plasma frequency that is controlled by its free carrier density. In this work, we systematically tune this frequency across the mid-infrared range by annealing treatments in a reducing environment that produce high electron concentrations (∼1021 cm−3). The changes in ITO's optical properties that result from the changes in carrier density are measured by attenuated total reflection measurements. These optical frequency measurements are complemented by Hall measurements to obtain a comprehensive picture of the Drude response of the ITO films. It was found that a complete description of the optical properties at very high carrier densities needs to account for the nonparabolicity of the conduction band of ITO and a reduced carrier mobility. More specifically, an increase in carrier concentration from 6.2 × 1019 cm−3 to 1.4 × 1021 cm−3 comes with a change of the effective electron mass from 0.35 m0 to 0.53 m0 and a decrease in the optical frequency mobility from about 20 cm2 V−1 s−1 to 9 cm2 V−1 s−1.
Small interfering RNA (siRNA) targeting of endogenous promoters induces DNA methylation, but not necessarily gene silencing, in rice (2007)

Summary Recent evidence indicates that small interfering RNA (siRNA) induces chromatin modifications and inactivation at homologous genomic sequences. A large number of endogenous siRNAs have been discovered that correspond to widely dispersed regions of the genome. We used an experimental system in which transgene‐derived siRNAs target promoter regions in rice to determine whether or not siRNAs induce chromatin modifications that result in inactivation. Our results indicate that siRNAs targeted to one transgene and seven endogenous genes induce DNA methylation at all of the target promoters, but do not induce transcriptional suppression. Chromatin immunoprecipitation (ChIP) assays indicate that reduced euchromatic histone modifications were concomitant with the silencing of one endogenous gene, but not of six other endogenous genes that were not silenced. Furthermore, heterchromatic H3K9me2 was higher only in the promoter of the transgene that was completely silenced. These findings lead us to assume that siRNA rarely induces chromatin inactivation or changes in pattern of histone modification, especially H3K9 methylation, within most regions of the genome.
Visualizing the whispering gallery modes in a cylindrical optical microcavity (1999)

Whispering gallery modes in cylindrical integrated optics microcavities have, for what is to our knowledge the first time, been mapped with a photon scanning tunneling microscope. Optical images were obtained with a spatial resolution of 50 nm. By combination of information on the spatial optical distributions with wavelength-dependent measurements, an unexpectedly rich variety of intracavity phenomena, such as polarization conversion and interference of copropagating and counterpropagating modes, could be directly observed. A quantitative comparison of the experimental data with computer simulations results in a comprehensive understanding of the various whispering gallery modes inside the microcavity.