gebhart/patrepeval huggingface dataset:
Intercellular adhesion molecules (ICAMs) 2 and 3 are frequently expressed in B cell chronic lymphocytic leukemia. (1996)

Using different monoclonal antibodies (moAbs) from the 5th International Workshop on Leukocyte Differentiation Antigens we studied the expression of intercellular adhesion molecules (ICAMs) 2 and 3 on a homogeneous group of 23 B cell chronic lymphocytic leukemia (CLL) patients. Our results show that either ICAM-2 or ICAM-3 are constitutively expressed on CD5+ B-CLL cells. Owing to the role of ICAM molecules in governing the migration and traffic of lymphocytes to lymph nodes, our findings need to be validated in a more consistent patient series to understand clinico-prognostic implications of such an expression.
A small-scale procedure for the rapid isolation of plant RNAs (1989)

Journal Article A small-scale procedure for the rapid isolation of plant RNAs Get access Theo C. Verwoerd, Theo C. Verwoerd MOGEN International NVEinsteinweg 97, 2333 CB Leiden, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Ben M.M. Dekker, Ben M.M. Dekker MOGEN International NVEinsteinweg 97, 2333 CB Leiden, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Andre Hoekema Andre Hoekema MOGEN International NVEinsteinweg 97, 2333 CB Leiden, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 6, 25 March 1989, Page 2362, https://doi.org/10.1093/nar/17.6.2362 Published: 25 March 1989 Article history Received: 13 February 1989 Published: 25 March 1989
Suppression of retinal neovascularization by the NF-kappaB inhibitor pyrrolidine dithiocarbamate in mice. (1999)

NF-kappaB activation appears to be required for retinal angiogenesis, given that the administration of PDTC suppressed retinal neovascularization. PDTC may prove beneficial in the treatment of ischemic neovascular diseases such as diabetic retinopathy and retinal vein occlusion.
Graph Cuts Segmentation with Geometric Shape Priors for Medical Images (2008)

In this paper, we propose a novel segmentation method that incorporates geometric shape priors, which do not require statistical training, with the graph cuts technique for robust and efficient segmentations of medical images. We introduce novel terms accounting for shape prior/segmentation and shape prior/image fit to the graph cuts representation. The latter prevents a vicious cycle of inaccurate segmentation/shape priors. We demonstrate the effectiveness of our method on cardiac images and kidney images without strong boundaries.
Así Se Van Las Lenguas Variando: Nuevas Tendencias En la Investigación del Cambio Lingüístico En Español (2012)

MONICA CASTILLO LLUCH and LOLA PONS RODRIGUEZ, Asi se van las lenguas variando: nuevas tendencias en la investigacion del cambio linguistico en espanol. Bern: Peter Lang. 2011. 435 pp. ISBN 978-3-0343- 0565-5.It is generally accepted now that linguistic change and variation are intimately connected; all changes imply a period of variation as the change spreads through the language, although not all variation necessarily implies that a change is in progress. Other realizations, though, have been adding to the complexities of this insight. For example, the understood necessity to have as large an amount of relevant data as possible is being met by the Academia's CORDE, and in a slightly different way by Mark Davies's Corpus del espanol; we need a sensitive appreciation of the relationships between spoken and written language, and several scholars have been working on this; and there is an increasing realization, spearheaded by German scholars, of the need to take genres into account (or, as they usually put it, tradiciones discursivas). The study of changes in progress in the modern world is usually undertaken by experimental sociolinguists making careful measurements of the kind of data which is inevitably unavailable for previous ages, so the study of changes in the past remains a different kind of enterprise, based on texts rather than oral recording; even so, it is generally hoped that theoretical aspects of the advances in the study of change in the present and in the past can refrain from being incompatible with each other. A further great step forward has been the importation of many of these general developments in the study of language change from diachronic linguistics in general into the analysis of the history of the Romance Languages, whose practitioners have in the past often felt that they were labouring in a different field (partly with some justification, since there are so many more data in Romance than in most of the languages chosen for study by historical linguistics). The editors of this volume convened a session at the annual conference of German Hispanists in 2009 in Tubingen, where both of them had previously studied, which has inspired this collection of fifteen studies concentrating on medieval Hispanic developments.Monica Castillo (now at Strasbourg) and Lola Pons (Sevilla) present their thoughtful introduction, but neither has a chapter of her own, which is a shame when they are both such acute investigators. After them, the chapters appear in alphabetical order of contributor, which means that thematically related studies do not appear together. …
Microarray gene expression data association rules mining based on JG-Tree (2004)

The main techniques currently employed in analyzing microarray expression data are clustering and classification. In this paper we propose to use association rules to mine the association relationships among different genes under the same experimental condition. These kinds of relations may also exist across many different experiments with various experimental conditions. In this paper, a new approach, called LIS-growth (Large ItemSet growth) tree, is proposed for mining the microarray data. Our approach uses a new data structure, JG-tree (Jiang, Gruenwald), and a new data partition format for gene expression level data. Each data value can be presented by a sign bit, fractions and exponent bits. Each bit at the same position can be organized into a JG-tree. A JG-tree is a lossless and compression tree. It can be built on fly, a kind of real-time compression for bits string. Based on these two new data structures it is possible to mine the association rules efficiently and quickly from the gene expression database. Our algorithm was tested using the real-life datasets from the gene expression database at Stanford University.
Comparison of Nebulized Particle Size Distribution with Malvern Laser Diffraction Analyzer Versus Andersen Cascade Impactor and Low-Flow Marple Personal Cascade Impactor (2000)

Particle size of nebulized aerosols can be measured directly using laser diffraction or by evaluating aerodynamic properties by cascade impaction. As of today, there are no generally accepted standards for measuring particle size distribution from nebulizers. Laser diffraction has been questioned because of potential evaporative losses of the small particles at the edge of the plume, causing an apparent shift in the particle size distribution and thus a larger mass median diameter (MMD). When particle-sizing wet aerosols, cascade impaction may give rise to an apparent shift in the distribution, resulting in a smaller mass median aerodynamic diameter (MMAD) due to evaporative losses of aerosol droplets as they enter the impactor at ambient temperature. The modified low-flow Marple 296 Personal Cascade Impactor (MPCI) is currently being proposed as the European standard for wet aerosol analysis to minimize evaporative losses during sampling. The present study compared the particle size distribution of salbutamol and sodium cromoglycate aerosols nebulized by the Pari LC Star, using laser diffraction (Malvern Mastersizer X; MMX) and cascade impaction (Andersen Cascade Impactor [ACI] and the commercially available MPCI), which was either at ambient temperature or cooled to the nebulized aerosol temperature (10 degrees C). MMDs obtained with the MMX were virtually identical to the MMADs measured with both impactors when cooled with no significant differences in geometric standard deviation (sigma(g)). When the impactors were operated at ambient temperature, MMADs were smaller (18 to 30%) with a significantly larger sigma(g) (p < 0.05) compared to the MMX. These findings suggest that droplet distribution data for wet aerosol where evaporation process has not been minimized must be viewed with caution. There was no evidence suggesting a significant evaporative loss of small droplets from the edge of the plume during laser particle sizing. The MPCI does not minimize evaporative losses of aerosol particles during sampling.
Duffy antigen modifies the chemokine response in human endotoxemia (2008)

The Duffy antigen substantially alters chemokine concentrations in blood, but it does not have a protective effect during human endotoxemia.
Anaplerotic molecules: Current and future (2005)

This review presents the concepts of anaplerosis and cataplerosis in relation to the regulation of citric acid cycle operation. Anaplerosis is the re-filling of the catalytic intermediates of the cycle that carry acetyl-CoA as it is oxidized. The main anaplerotic substrates are pyruvate, glutamine/glutamate and precursors of propionyl-CoA (odd-chain fatty acids, specific amino acids, C(5)-ketone bodies). Cataplerosis balances anaplerosis by removing excess intermediates from the citric acid cycle. The properties of the main anaplerotic substrates are reviewed from the point of view of potential clinical applications to the treatment of some inherited and acquired conditions.
The Galvactivator: A glove that senses and communicates skin conductivity (2001)

The galvactivator is a glove-like wearable device that senses the wearer's skin conductivity and maps its values to a bright LED display, making the skin conductivity level visible. Increases in skin conductivity tend to be good indicators of physiological arousal --causing the galvactivator display to glow brightly. The new form factor of this sensor frees the wearer from the traditional requirement of being tethered to a rack of equipment; thus, the device facilitates study of the skin conductivity response in everyday settings. We recently built and distributed over 1000 galvactivators to audience members at a daylong symposium. To explore the communication potential of this device, we collected and analyzed the aggregate brightness levels emitted by the devices using a video camera focused on the audience. We found that the brightness tended to be higher at the beginning of presentations and during interactive sessions, and lower during segments when a speaker spoke for long periods of time. We also collected anecdotes from participants about their interpersonal uses of the device. This paper describes the construction of the galvactivator, our experiments with the large audience, and several other potentially useful applications ranging from facilitation of conversation between two people, to new ways of aiding autistic children.
Fungal infections in bone marrow transplant patients. (1990)

In a retrospective study of over 1,500 patients who underwent bone marrow transplantation between 1980 and 1987, the incidence of invasive candidal or mold infection was 11% and 4.5%, respectively. Candidemia alone occurred in 46, candidemia and tissue infection in 56, and tissue infection alone in 69 of 1,510 patients analyzed. Aspergillus infection alone occurred in 69, other mold infections occurred in four, and Aspergillus plus other mold infections in two of 1,658 patients analyzed. Median time to onset of candidal infection was 2 weeks and of mold infections 6 weeks after transplantation. Overall mortality for patients with candidal infection was 73% and for those with Aspergillus or other mold infections, 84%. Death occurred in 39% of patients with candidemia alone, 90% of patients with candidal tissue infection with or without candidemia, and 100% of those with mixed infection. The death rate was 75% for patients infected with Aspergillus alone, 83% for those infected with other molds with or without Aspergillus, and 100% when there was coinfection with Candida or cytomegalovirus. The probability of occurrence of Aspergillus infection was influenced by patient age, donor match, type of conditioning regimen, and occurrence of acute graft-versus-host disease (GVHD), while the occurrence of candidal infection was influenced by additional factors including underlying disease and GVHD prophylactic regimen. In contrast to some published reports, the risk of Aspergillus infection was not significantly altered by infection prevention methods, including provision of a protective environment. These data confirm both the high incidence and severity of fungal infection after bone marrow transplantation and underscore the urgent need for more effective prophylaxis and treatment.
Inhibition of Human Tumor-Infiltrating Lymphocyte Effector Functions by the Homophilic Carcinoembryonic Cell Adhesion Molecule 1 Interactions (2006)

Efficient antitumor immune response requires the coordinated function of integrated immune components, but is finally exerted by the differentiated effector tumor-infiltrating lymphocytes (TIL). TIL cells comprise, therefore, an exciting platform for adoptive cell transfer (ACT) in cancer. In this study, we show that the inhibitory carcinoembryonic Ag cell adhesion molecule 1 (CEACAM1) protein is found on virtually all human TIL cells following preparation protocols of ACT treatment for melanoma. We further demonstrate that the CEACAM1 homophilic interactions inhibit the TIL effector functions, such as specific killing and IFN-gamma release. These results suggest that CEACAM1 may impair in vivo the antitumor response of the differentiated TIL. Importantly, CEACAM1 is commonly expressed by melanoma and its presence is associated with poor prognosis. Remarkably, the prolonged coincubation of reactive TIL cells with their melanoma targets results in increased functional CEACAM1 expression by the surviving tumor cells. This mechanism might be used by melanoma cells in vivo to evade ongoing destruction by tumor-reactive lymphocytes. Finally, CEACAM1-mediated inhibition may hinder in many cases the efficacy of TIL ACT treatment of melanoma. We show that the intensity of CEACAM1 expression on TIL cells constantly increases during ex vivo expansion. The implications of CEACAM1-mediated inhibition of TIL cells on the optimization of current ACT protocols and on the development of future immunotherapeutic modalities are discussed.
Fabrication of an Oriented Fc‐Fused Lectin Microarray through Boronate Formation (2008)

A stable, covalent, and highly active protein microarray was created through the formation of cyclic esters between surface boronic acids and the carbohydrate moiety of a fusion protein, Fc-dectin-1 (see picture). A biotin-labeled polysaccharide was used as a probe to investigate the binding activity of the protein. Staining of the product array with streptavidin-Cy3 revealed the effectiveness of this immobilization strategy.
Defensins: Potential Effectors in Autoimmune Rheumatic Disorders (2011)

Defensins are small cationic peptides with antimicrobial properties. They constitute a highly conserved innate immune defense mechanism across species. Based on the arrangement of disulfide-bonds, α- and β-defensins are distinguished in humans. Both types of defensin comprise several distinct molecules that are preferentially expressed at epithelial surfaces and in blood cells. In the last decade, multiple immunomodulatory functions of defensins have been recognized, including chemotactic activity, the promotion of antigen presentation, and modulations of proinflammatory cytokine secretion. These findings suggested a role for defensins not only as a first line of defense, but also as connectors of innate and adaptive immune responses. Recently, increasingly accumulating evidence has indicated that defensins may also be involved in the pathogenesis of autoimmune rheumatic disorders such as systemic lupus erythematosus and rheumatoid arthritis. The current review summarizes the data connecting defensins to autoimmunity.
Cell-Associated Plasminogen Activation: Regulation And Physiological Functions (1988)

Cells organize many of their biochemical reactions in non-membrane compartments. Recent evidence has shown that many of these compartments are liquids that form by phase separation from the cytoplasm. Here we discuss the basic physical concepts necessary ...Read More
Five Percent of Normal Cystic Fibrosis Transmembrane Conductance Regulator mRNA Ameliorates the Severity of Pulmonary Disease in Cystic Fibrosis (2002)

Estimates of the level of transcripts from the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) gene required to develop a CF phenotype range from 4-20% of normal. Due to the importance of obtaining reliable data on this issue for therapeutic strategies, we developed a novel polymerase chain reaction-based method to quantify CFTR transcripts and applied it to the analysis of nasal epithelium RNA of five patients with CF and the 3272-26A>G/F508del genotype. We calculated that 8.2 +/- 0.84% of the total CFTR RNA present in these five patients is normal full-length CFTR mRNA. We then demonstrated (in nasal samples from F508del carriers, n = 30) that the abundance of full-length F508del CFTR transcripts is reduced compared with wild-type transcripts, and estimated that the average ratio of F508del/wild-type transcripts is 0.87 +/- 0.06. To determine the amount of full-length transcripts relative to levels found in normal individuals, we corrected for the lower abundance of the F508del transcripts and calculated that the five patients with CF have, on average, 4.7 +/- 0.45% of the normal level of wild-type CFTR mRNA. Because these patients have mild CF compared with F508del homozygotes, this CFTR mRNA level appears to be sufficient to avoid the severe complications of the disease.
Mouse Model of Cervicovaginal Toxicity and Inflammation for Preclinical Evaluation of Topical Vaginal Microbicides (2004)

Clinical trials evaluating the efficacy of nonoxynol-9 (N-9) as a topical microbicide concluded that N-9 offers no in vivo protection against human immunodeficiency virus type 1 (HIV-1) infection, despite demonstrated in vitro inactivation of HIV-1 by N-9. These trials emphasize the need for better model systems to determine candidate microbicide effectiveness and safety in a preclinical setting. To that end, time-dependent in vitro cytotoxicity, as well as in vivo toxicity and inflammation, associated with N-9 exposure were characterized with the goal of validating a mouse model of microbicide toxicity. In vitro studies using submerged cell cultures indicated that human cervical epithelial cells were inherently more sensitive to N-9-mediated damage than human vaginal epithelial cells. These results correlated with in vivo findings obtained by using Swiss Webster mice in which intravaginal inoculation of 1% N-9 or Conceptrol gel (containing 4% N-9) resulted in selective and acute disruption of the cervical columnar epithelial cells 2 h postapplication accompanied by intense inflammatory infiltrates within the lamina propria. Although damage to the cervical epithelium was apparent out to 8 h postapplication, these tissues resembled control tissue by 24 h postapplication. In contrast, minimal damage and infiltration were associated with both short- and long-term exposure of the vaginal mucosa to either N-9 or Conceptrol. These analyses were extended to examine the relative toxicity of polyethylene hexamethylene biguanide (PEHMB), a polybiguanide compound under evaluation as a candidate topical microbicide. In similar studies, in vivo exposure to 1% PEHMB caused minimal damage and inflammation of the genital mucosa, a finding consistent with the demonstration that PEHMB was >350-fold less cytotoxic than N-9 in vitro. Collectively, these studies highlight the murine model of toxicity as a valuable tool for the preclinical assessment of toxicity and inflammation associated with exposure to candidate topical microbicides.
Monoclonal antibodies to rabbit sperm autoantigens. I. Inhibition of in vitro fertilization and localization on the egg (1984)

Biochemical and antigenic similarities exist among members of what can be considered a family of low molecular weight rabbit sperm autoantigens. These autoantigens are intrinsic plasma membrane glycoproteins specific to spermatogenic cells and spermatozoa. The amino acid and carbohydrate compositions of rabbit sperm autoantigen-1 (RSA-1) and RSA-2 were compared and monoclonal antibodies (mAb) were raised in mice against rabbit sperm autoantigens. The epitopes recognized by the antibodies were present on RSA-1, 2 and 3. A monoclonal anti-RSA-1, 2 and 3 (designated A.F. 1) was used to localize the antigen on spermatozoa and testis cells and investigate the epitope's tissue specificity. This mAb inhibited in vitro fertilization but did not block the sperm from dispersing the cumulus cells surrounding the egg. The mAb also demonstrated the presence of RSA-1, 2 and 3 on the plasma membrane of the egg after fertilization. It is concluded that the RSA family plays a central role in zona penetration.
Effective Anti-Hepatitis B Virus Hammerhead Ribozymes Derived from Multimeric Precursors (2007)

Endonucleolytic hammerhead ribozymes have advantages of inhibiting gene expression by acting specifically, independently of cellular pathways, and within all cell compartments. However, there are concerns about inefficient silencing because of reduced intracellular cleavage of target RNA by ribozymes. To enable production of defined single-unit ribozymes and thereby increase effectiveness, we developed self-cleaving multimeric cassettes that generate several trans-acting ribozyme units from a single transcript. cis and trans ribozyme cleavage, as assessed in vitro against three different sites within the X sequence of hepatitis B virus (HBV), occurred efficiently and precisely according to predictions deduced from the ribozyme designs. Significant knockdown of markers of viral replication in transfected cultured liver-derived cells was achieved by multiribozyme Pol II expression cassettes. To assess silencing efficacy of RNA prepared in vitro, transcription and cis cleavage reactions were carried out to prepare defined single-unit ribozymes. Transfection of ribozyme RNA was capable of inhibiting HBV surface antigen secretion from liver-derived cells without associated elevation of interferon-alpha or interferon-beta secretion into the culture upernatants. The approach described here is potentially useful for several applications, such as generation of RNA interference (RNAi) effectors, which require rapid and inexpensive generation of defined RNA sequences.