gebhart/patrepeval huggingface dataset:
PD-1/PD-L1 Pathway Mediates the Alleviation of Pulmonary Fibrosis by Human Mesenchymal Stem Cells in Humanized Mice (2017)

Pulmonary fibrosis is a chronic progressive lung disease with few treatments. Human mesenchymal stem cells (MSCs) have been shown to be beneficial in pulmonary fibrosis because they have immunomodulatory capacity. However, there is no reliable model to test the therapeutic effect of human MSCs in vivo. To mimic pulmonary fibrosis in humans, we established a novel bleomycin-induced pulmonary fibrosis model in humanized mice. With this model, the benefit of human MSCs in pulmonary fibrosis and the underlying mechanisms were investigated. In addition, the relevant parameters in patients with pulmonary fibrosis were examined. We demonstrate that human CD8<sup>+</sup> T cells were critical for the induction of pulmonary fibrosis in humanized mice. Human MSCs could alleviate pulmonary fibrosis and improve lung function by suppressing bleomycin-induced human T-cell infiltration and proinflammatory cytokine production in the lungs of humanized mice. Importantly, alleviation of pulmonary fibrosis by human MSCs was mediated by the PD-1/programmed death-ligand 1 pathway. Moreover, abnormal PD-1 expression was found in circulating T cells and lung tissues of patients with pulmonary fibrosis. Our study supports the potential benefit of targeting the PD-1/programmed death-ligand 1 pathway in the treatment of pulmonary fibrosis.
Differential expression of antimicrobial peptides in margins of chronic wounds (2010)

Skin wounds usually heal without major infections, although the loss of the mechanical epithelial barrier exposes the tissue to various bacteria. One reason may be the expression of antimicrobial peptides (AMP) of which some [human beta-defensins (hBD) and LL-37] were recently shown to support additionally certain steps of wound healing. There are no studies which have compared expression patterns of different classes of AMP in chronic wounds. The aim of our study was therefore to analyse the expression profile of hBD-2, hBD-3, LL-37, psoriasin and RNase 7 by immunohistochemistry from defined wound margins of chronic venous ulcers. We detected a strong induction of psoriasin and hBD-2 in chronic wounds in comparison with healthy skin. Except for stratum corneum, no expression of RNase 7 and LL-37 was detected in the epidermis while expression of hBD-3 was heterogeneous. Bacterial swabs identified Staphylococcus aureus and additional bacterial populations, but no association between colonization and AMP expression was found. The differential expression of AMP is noteworthy considering the high bacterial load of chronic ulcers. Clinically, supplementation of AMP with the capability to enhance wound healing besides restricting bacterial overgrowth could present a physiological support for treatment of disturbed wound healing.
<title>Implementing a DICOM-HL7 interface application</title> (1995)

The DICOM standard, in addition to resolving certain problems with the ACR-NEMA 2.0 standard regarding network support and the clinical data dictionary, added new capabilities, in the form of study content notification and patient, study and results management services, intended to assist in interfacing between PACS and HIS or RIS systems. We have defined and implemented a mechanism that allows a DICOM application entity (AE) to interrogate an HL7 based RIS using DICOM services. The implementation involved development of a DICOM- HL7 gateway which converted between DICOM and HL7 messages to achieve the desired retrieval capability. This mechanism, based on the DICOM query/retrieve service, was used to interface a DeJarnette Research film digitizer to an IDXrad RIS at the University of Maryland Medical Systems hospital in Baltimore, Maryland. A C++ class library was developed for both DICOM and HL7 massaging, with several constructors used to convert between the two standards.
Postrenal Transplant Non-EBV Multiple Myeloma of Donor Origin (2005)

Multiple myeloma occurring after solid organ transplantation is a rare condition, with only a few case reports found in the literature. We report a case of Epstein-Barr virus-negative, posttransplant multiple myeloma in a 67-year-old female, presenting 18 months after renal transplantation. Interestingly, fluorescence in situ hybridization analysis of the tumor revealed a Y chromosome in the majority of the cells, indicating that the neoplasm was derived from the donor kidney. To our knowledge, this represents the first reported case with these features.
Circulating Adiponectin Levels and Expression of Adiponectin Receptors in Relation to Lung Cancer: Two Case-Control Studies (2007)

Circulating adiponectin levels are not different in cases of this malignancy - which seems to be unrelated to obesity and insulin resistance - compared to their healthy controls, though hormonal levels were significantly lower in advanced versus limited lung cancer. Both adiponectin receptors were expressed in cancerous lung tissue, but not in normal control tissue and there was a differential expression by disease stage. These findings should be further explored, especially in the context of the recently reported protective effect of thiazolidinediones in diabetic patients with lung cancer.
Mutation Induction by DBD Plasma in Phosphate-solubilizing Bacteria Enterobacter Agglomerans (2012)

An efficient agar plate mutagenesis and screening technique for improving mutation frequency was established by using dielectric barrier discharge (DBD) plasma. Enterobacter agglomerans is well known as a phosphate-solubilizing plant-associated bacterium. In this study, DBD plasma was conducted toE. agglomerans mutation for improving the phosphate-soubilizing activity. The results showed that the phosphate-soubilizing activity of mutants increased compared with original strain, and the phosphate-soubilizing activity of the best mutants is 1.49-fold of original strain. It demonstrated that DBD plasma treatment has a high-efficient quality, and it will be a useful method of mutation.
Levels of empathic response (1973)

Empathic understanding is a counseling technique that receives attention in many of the training programs that are charged with producing helping personnel. Although empathic understanding is widely taught, there is very little commonality among trainers in terms of what they teach their students to be empathic to. In this article the author presents a general conceptual set that may be applied to any statement a person makes. The set is comprised of six elements to which helpers can be empathic and to which they can respond. The elements are concrete and specific and lend themselves well to systematic training.
Monodisperse Mesoporous Silica Microspheres Formed by Evaporation-Induced Self Assembly of Surfactant Templates in Aerosols (2002)

Evaporation-driven surface templating by means of a vibrating orifice aerosol generator (VOAG), a device that produces microdroplets, has been used for the synthesis of non-hollow monodisperse mesoporous silica particles (see Figure for a TEM image). Particle and pore size as well as mesoscopic order are controllable by varying the experimental conditions, precursor chemistry, and VOAG parameters.
Stochastic Optimization Methods Applied to Microwave Imaging: A Review (2007)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Stochastic methods are now very common in electromagnetics. Among the various applications, they have been recently proposed for solving inverse problems arising in radio-frequency and microwave imaging. Some of the recently proposed stochastic inversion procedures are critically discussed (e.g., genetic algorithms, differential evolution methods, memetic algorithms, particle swarm optimizations, hybrid techniques, etc.) and the way they have been applied in this area. The use of the ant colony optimization method, which is a relatively new method in electromagnetics, is also proposed. Various imaging modalities are considered (tomography, buried object detection, and borehole sensing). Finally, the main features making these approaches useful for imaging purposes are discussed and the currently considered strategies to reduce the computational load associated with stochastic optimization procedures delineated. </para>
The microfluidic palette: A diffusive gradient generator with spatio-temporal control (2009)

This paper describes a new microfluidic device called the "microfluidic palette", capable of generating multiple spatial chemical gradients simultaneously inside a microfluidic chamber. The unique aspect of this work is that chemical gradients are generated by diffusion, without convection, and can either be held constant over long periods, or modified dynamically. We characterized a representative device with a 1.5 mm circular chamber where diffusion takes place, and three access-ports for the delivery and removal of solutes. The gradient stabilizes in approximately 15 min for small molecules and can be maintained constant indefinitely. We demonstrate overlapping gradients with different spatial location and a controlled rotation of a diffusive gradient around its centre. Finally, we demonstrate the applicability of this tool to study the chemotactic response of the bacteria P. aeruginosa to glucose.
Isolation and Structures of Avicins D and G:  In Vitro Tumor-Inhibitory Saponins Derived from Acacia victoriae (2003)

Two new saponins named avicins D (1) and G (2) were isolated from the seed pods of the desert legume plant Acacia victoriae. The structures, elucidated by 1D and 2D NMR studies and by chemical means, were characterized as acacic acid-bearing oligosaccharides at C-3 and C-28 with a side chain linked to C-21 comprised of two monoterpene carboxylic acids and a quinovose moiety. Both compounds exhibited potent cytotoxicity (apoptosis) against human T-cell leukemia (Jurkat cells) in vitro.
"Post-assay" covalent labeling of phosphorothioate-containing nucleic acids with multiple fluorescent markers (1989)

A simple protocol has been developed which allows the covalent introduction of multiple fluorescent markers into DNA fragments after gel electrophoresis techniques, that is, while the nucleic acid is imbedded in the polyacrylamide gel matrix. "Post-assay" fluorescent labeling in this manner employs DNA fragments containing phosphorothioate diesters, which can be easily incorporated during chemical and enzymatic synthesis procedures, and can be alkylated with the fluorescent marker monobromobimane. Labeling the internucleotidic phosphorus residue in this manner allows the introduction of a fluorescent marker for each nucleotide residue present. Roughly a linear increase in emitted fluorescence, thus detection sensitivity, is observed with an increasing number of bimane markers. With this technique, oligodeoxynucleotides and DNA fragments can be observed in the gel matrix, without sophisticated electronic detection devices in the low femtomolar (10(-15) mol) range.
Fast Colorimetric Sensing of Adenosine and Cocaine Based on a General Sensor Design Involving Aptamers and Nanoparticles (2005)

Bereit für Farbwechsel: Mithilfe von DNA-Aptameren ließen sich aus DNA-funktionalisierten Goldnanopartikeln hoch empfindliche und selektive kolorimetrische Sensoren erzeugen, die auf die Zugabe eines Substrats mit einer sofortigen Farbantwort reagieren. Die Methode wurde für Adenosin und Kokain vorgestellt (siehe Bild), sollte sich jedoch auf jedes beliebige Aptamer anwenden lassen. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2006/z502589_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods (2006)

Prediction of the biological effect of missense substitutions has become important because they are often observed in known or candidate disease susceptibility genes. In this paper, we carried out a 3-step analysis of 1514 missense substitutions in the DNA-binding domain (DBD) of TP53, the most frequently mutated gene in human cancers. First, we calculated two types of conservation scores based on a TP53 multiple sequence alignment (MSA) for each substitution: (i) Grantham Variation (GV), which measures the degree of biochemical variation among amino acids found at a given position in the MSA; (ii) Grantham Deviation (GD), which reflects the 'biochemical distance' of the mutant amino acid from the observed amino acid at a particular position (given by GV). Second, we used a method that combines GV and GD scores, Align-GVGD, to predict the transactivation activity of each missense substitution. We compared our predictions against experimentally measured transactivation activity (yeast assays) to evaluate their accuracy. Finally, the prediction results were compared with those obtained by the program Sorting Intolerant from Tolerant (SIFT) and Dayhoff's classification. Our predictions yielded high prediction accuracy for mutants showing a loss of transactivation ( approximately 88% specificity) with lower prediction accuracy for mutants with transactivation similar to that of the wild-type (67.9 to 71.2% sensitivity). Align-GVGD results were comparable to SIFT (88.3 to 90.6% and 67.4 to 70.3% specificity and sensitivity, respectively) and outperformed Dayhoff's classification (80 and 40.9% specificity and sensitivity, respectively). These results further demonstrate the utility of the Align-GVGD method, which was previously applied to BRCA1. Align-GVGD is available online at http://agvgd.iarc.fr.
Triple-negative (basal-like) breast cancer: a new entity (2007)

Since the introduction of systemic adjuvant chemotherapy (ACT) and endocrine therapy in the early 1970s, the determination of risk of recurrence and death from breast cancer became a critical piece of information in the selection of the optimal postoperative treatment strategy. Classical histopathological prognostic factors included tumor size, regional lymph node metastases and number of axillary nodes involved, tumor grade, presence of lymphovascular invasion, and, more recently, estrogen receptor (ER) and progesterone receptor status, measurement of proliferative activity (S-phase fraction, mitotic index, Ki-67), and HER2 overexpression/amplification. As isolated factors, they have limited predictive ability in the case of individual patients. For that reason, prognostic indices were developed. The most successful is Adjuvant!Online, an online nomogram developed by Peter Ravdin. This nomogram incorporates tumor size, axillary nodal status, tumor grade, ER status, age and comorbidity. The nomogram will provide an assessment of recurrence and mortality rates at 10 years, including deaths due to comorbid conditions. In addition, the nomogram also calculates relative and absolute benefit from various adjuvant interventions: tamoxifen, aromatase inhibitors, and first-generation, secondgeneration and third-generation ACT regimens. The prognostic and predictive value of this nomogram has been externally validated, with a margin of error 1%. Over the past decade, high-throughput technologies have been developed based on gene expression profiling. These include between two and a couple of hundred genes, and have the ability to separate patients with excellent outcomes from those with higher risk. One of these prognostic profiles has been externally validated and is currently undergoing testing for clinical utility in a large, multicenter, prospective randomized trial (MINDACT). Another approach was based on prospectively identifying a set of genes from the literature and from the results of gene expression profiling. Mathematical modeling then led to the selection of 16 genes related to cell proliferation, ER-driven genes, HER2 and proteases, as well as five 'housekeeping' genes (OncotypeDx). This assay is based on RT-PCR, is reproducible and applicable to archival, paraffin-embedded material, and has been shown to predict prognosis in patients with lymph-nodenegative, ER-positive primary breast cancer. Further testing indicated that the assay might also predict sensitivity to tamoxifen, or firstgeneration adjuvant chemotherapy. This assay is also under evaluation for clinical utility in a large, multicenter, prospective randomized trial (TailoRx). Whether these multigene predictors of prognosis will have greater utility than Adjuvant!Online remains to be determined. In the meantime, exploratory analyses are ongoing to identify reliable predictors of response to individual drugs and modern combination drug regimens. These are expected to lead to individualized selection of treatment, or personalized medicine.
Consumer video retargeting (2009)

Pervasive multimedia devices require accurate video retargeting, especially in connected consumer electronics platforms. In this paper, we present a context assisted spatialtemporal grid scheme for consumer video retargeting. First, we parse consumer videos from low-level features to highlevel visual concepts, combining visual attention into a more accurate importance description. Then, a semantic importance map is built up representing the spatial importance and temporal continuity, which is incorporated with a 3D rectilinear grid scaleplate to map frames to the target display, thereby keeping the aspect ratio of semantically salient objects as well as the perceptual coherency. Extensive evaluations were done on two popular video genres, sports and advertisements. The comparison with state-of-the-art approaches on both images and videos have demonstrated the advantages of the proposed approach.
Inhibition of Mammary Carcinoma Development in HER-2/neu Transgenic Mice through Induction of Autoimmunity by Xenogeneic DNA Vaccination (2005)

Plasmid DNA vectors encoding the full-length (VR1012/HER-2-FL) or only the extracellular and transmembrane domains (VR1012/HER-2-ECD-TM) of human (h) HER-2/neu proto-oncogene were used to vaccinate HER-2/neu transgenic mice (N202) engineered to overexpress the rat (r) neu proto-oncogene product (r-p185(neu)). Both the full-length and the deleted vaccines were significantly (P = 0.0001 and P = 0.06, respectively) more active than the empty vector (VR1012/EV) in preventing and delaying HER-2/neu-driven mammary carcinogenesis. A low-level intratumoral infiltrate of dendritic cells, macrophages, CD8 T cells and polymorphonuclear granulocytes in association with low-level cytokine production was observed, which was not detected in tumors from control mice. Morphologic analyses showed that vaccination with VR1012/HER-2-FL or ECD-TM also efficiently hampered the development of terminal ductal lobular units (TDLU). Analyses of sera from vaccinated mice revealed high titers of antihuman HER-2/neu antibodies, which correlated with the delayed time of tumor onset (P = 0.002). These antibodies did not cross-react with r-p185(neu). Nontransgenic mice treated with the vaccines produced autoreactive antibodies targeting mouse (m)-p185(neu) and showed impaired function of the lactating mammary gland and accelerated involution of the gland after weaning. Together, these data indicate that xenogeneic DNA immunization breaks tolerance against the endogenous m-p185(neu), impairing the development of mammary TDLU in which m-p185(neu) expression is concentrated. The reduction in the number of TDLU decreases the number of glandular structures available for r-p185(neu)-dependent mammary carcinogenesis, resulting in a significant inhibition of mammary carcinoma development.
Transcriptional Pattern of Genes Coding for the Proteolytic System of Lactococcus lactis and Evidence for Coordinated Regulation of Key Enzymes by Peptide Supply (2001)

The transcription of 16 genes encoding 12 peptidases (pepC, pepN, pepX, pepP, pepA, pepF2, pepDA1, pepDA2, pepQ, pepT, pepM, and pepO1), P(I) and P(III) proteinases (prtP1 and prtP3), and three transport systems (dtpT, dtpP, and opp-pepO1) of Lactococcus lactis MG1363 was analyzed in response to different environmental factors. Promoter fusions with luciferase reporter genes and/or mRNA analysis were used to study the effects of sugar sources, growth at 37 degrees C, and peptide supply on the transcription of these genes. Only transcription of the pepP gene is modulated by the source of sugar. The presence of potential catabolite-responsive element (CRE) boxes in its promoter region suggests that expression of this gene is directly controlled by catabolic repression. Elevated temperature had no significant effect on the level of transcription of these genes. prtP1, prtP3, pepC, pepN, pepX, and the opp-pepO1 operon are the most highly expressed genes in chemically defined medium, and their expression is repressed 5- to 150-fold by addition of peptide sources such as Casitone in the medium. Moreover, the transcription of prtP1, prtP3, pepC, pepN, and the opp-pepO1 operon is repressed two- to eight-fold by the dipeptides leucylproline and prolylleucine. The transcription of pepDA2 might also be repressed by the peptide sources, but this effect is not observed on the regulation of dtpT, pepP, pepA, pepF2, pepDA1, pepQ, pepT, pepM, and the dtpP operon. The significance of these results with respect to the functions of different components of the proteolytic system in L. lactis are discussed.
STIMULATED EMISSION IN A PERIODIC STRUCTURE (1971)

We have investigated laser oscillation in periodic structures in which feedback is provided by backward Bragg scattering. These new laser devices are very compact and stable as the feedback mechanism is distributed throughout and integrated with the gain medium. Intrinsic to these structures is also a gratinglike spectral filtering action. We discuss periodic variations of the refractive index and of the gain and give the expression for threshold and bandwidth. Experimentally we have induced index periodicities in gelatin films into which rhodamine 6G was dissolved. The observed characteristics of laser action in these devices near 0.63 μm are reported.
A novel antibody AA98 V(H)/L directed against CD146 efficiently inhibits angiogenesis. (2008)

This newly generated AA98 V(H)/L antibody displays a therapeutic potential for tumor and other angiogenesis disorders, as well as providing a new strategy for antibody engineering for clinical applications.
MultiPLX: automatic grouping and evaluation of PCR primers (2004)

maido.remm@ut.ee.