gebhart/patrepeval huggingface dataset:
High-throughput proteomics using antibody microarrays: an update (2007)

Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
Use of the DNA Flow-Thru Chip, a Three-Dimensional Biochip, for Typing and Subtyping of Influenza Viruses (2004)

Influenza A viruses, which are further subtyped on the basis of antigenic differences in external hemagglutinin and neuraminidase glycoproteins, and influenza B viruses are prominent among the viral causes of respiratory diseases and can cause a wide spectrum of illness. Each year these viruses are responsible for recurrent epidemics, frequently in association with genetic variation. There is a requirement for sensitive and rapid diagnostic techniques in order to improve both the diagnosis of infections and the quality of surveillance systems. A new three-dimensional biochip platform (Flow-Thru Chip; MetriGenix) was used to develop a rapid and reliable molecular method for the typing and subtyping of influenza viruses. Oligonucleotide probes immobilized in microchannels of a silicon wafer were selected to recognize multiple fragments of the influenza A virus matrix protein gene; the influenza B virus NS gene; the H1, H3, and H5 hemagglutinin genes; and the N1 and N2 neuraminidase genes. Biotinylated amplicons resulting from either multiplex or random reverse transcription-PCR were hybridized to arrayed oligonucleotides on the influenza virus chip before they were stained with horseradish peroxidase-streptavidin and were imaged by use of a chemiluminescent substrate. The chip analysis procedure, from the time of pipetting of the sample into the chip cartridge to the time of analysis of the results, was performed in less than 5 h. The random PCR exhibited a higher level of performance than the multiplex PCR in terms of the specificity of product hybridization to the influenza virus chip. Analysis of influenza A viruses (H1N1, H3N2, H1N2, and H5N1) and influenza B viruses showed that this microarray-based method is capable of the rapid and unambiguous identification of all types and subtypes of viruses by use of random PCR products. The redundancy of the probes designed for each gene selected yielded an additional criterion of confidence for the subtyping of viruses which are known for antigenic variations in some of their components.
Microvascular studies on the origins of perfusion-limited hypoxia. (1996)

Two forms of hypoxia are thought to exist in tumours: (1) hypoxia caused by limitations of its diffusion (chronic hypoxia); and (2) hypoxia caused by changes in perfusion (acute hypoxia). Indirect information suggests the existence of perfusion-limited hypoxia, but there is no direct proof that fluctuations in blood flow can lead to hypoxia, nor is there any information regarding potential causes of fluctuant flow. In this study, we have begun to explore these questions using R3230AC tumours transplanted into rat dorsal-flap window chambers. Two types of fluctuant flow have been observed. The first type, usually confined to single vessels, is typified by instability of flow magnitude and direction, and total vascular stasis occurs, but only for a few seconds at a time (4% incidence). The second type of fluctuation occurs in groups of vessels and is cyclic, with cycle times ranging from 20-60 min. Total vascular stasis does not necessarily occur, but the fluctuations in red cell flux are accompanied by changes in vascular oxygen content, as measured by microelectrodes. Another source of chronic hypoxia has also been identified in these experiments. Nine per cent (9%) of vessels examined had plasma flow, but very low or absent red cell flux over periods of many minutes.
Automatic navigation of an untethered device in the artery of a living animal using a conventional clinical magnetic resonance imaging system (2007)

The feasibility for in vivo navigation of untethered devices or robots is demonstrated with the control and tracking of a 1.5mm diameter ferromagnetic bead in the carotid artery of a living swine using a clinical magnetic resonance imaging (MRI) platform. Navigation is achieved by inducing displacement forces from the three orthogonal slice selection and signal encoding gradient coils of a standard MRI system. The proposed method performs automatic tracking, propulsion, and computer control sequences at a sufficient rate to allow navigation along preplanned paths in the blood circulatory system. This technique expands the range of applications in MRI-based interventions.
Thickness Dependence of the Optical Properties of Ordered Silica-Air and Air-Polymer Photonic Crystals (1999)

We report observations of the optical stop band of periodic planar arrays of submicron silica spheres, and of macroporous polymers grown from these silica templates. The stop-band width and peak attenuation depend on the number of layers and on the dielectric contrast between the spheres and the interstitial regions, both of which are experimentally controlled. The results are compared to the predictions of the scalar wave approximation. This is the first systematic study of the thickness dependence of the stop band in colloidal photonic band gap structures.
The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations (2000)

In this paper an analysis of 175 currently sequenced transport proteins that comprise the amino acid/polyamine/organocation (APC) superfamily is reported. Members of this superfamily fall into 10 well-defined families that are either prokaryote specific, eukaryote specific or ubiquitous. Most of these proteins exhibit 12 probable transmembrane spanners (TMSs), but members of two of these families deviate from this pattern, exhibiting 10 and 14 TMSs. All members of these families are tabulated, their functional properties are reviewed and phylogenetic/sequence analyses define the evolutionary relationships of the proteins to each other. Evidence is presented that the APC superfamily may include two other currently recognized families that exhibit greater degrees of sequence divergence from APC superfamily members than do the proteins of the 10 established families from each other. At least some of the protein members of these two distantly related families exhibit 11 established TMSs. Altogether, the APC superfamily probably includes 12 currently recognized families with members that exhibit exclusive specificity for amino acids and their derivatives but which can possess 10, 11, 12 or 14 TMSs per polypeptide chain.
Terminally differentiated neonatal rat myocardial cells proliferate and maintain specific differentiated functions following expression of SV40 large T antigen. (1988)

Early in neonatal development, differentiated myocardial cells lose their ability to proliferate, and further enlargement of the heart occurs through hypertrophy of existing cardiac muscle cells. To study the process of myocardial growth and hypertrophy we have recently utilized a neonatal rat myocardial cell model (Lee, H. R., Henderson, S. A., Reynolds, R., Dunnmon, P., Yuan, D., and Chien, K. R. (1988) J. Biol. Chem. 263, 7352-7538). The present study was designed to determine if the expression of SV40 large T antigen would be capable of restoring the proliferative capacity of terminally differentiated neonatal rat myocardial cells. Utilizing a replication-defective recombinant human adenovirus which contains an SV40 early T antigen insert, maximal expression of T antigen was achieved at 24-48 h postinfection, with over 85-90% of the cells displaying positive T antigen staining. Furthermore, the expression of the T antigen-induced proliferation of the myocardial cells without the loss of expression of certain differentiated properties, including myosin light chain expression and assembly into organized myofibrils, spontaneous contractile activity, and a chronotropic response to adrenergic agonists. These results demonstrate the utility of recombinant human adenoviruses to achieve high efficiency transient expression of foreign genes in differentiated myocardial cells and suggest that the expression of T antigen may provide a suitable model to study the biochemical events which are required to maintain the proliferative capacity of myocardial cells.
MALARIA PARASITE DEVELOPMENT IN MOSQUITOES (1998)

Mosquitoes of the genus Anopheles transmit malaria parasites to humans. Anopheles mosquito species vary in their vector potential because of environmental conditions and factors affecting their abundance, blood-feeding behavior, survival, and ability to support malaria parasite development. In the complex life cycle of the parasite in female mosquitoes, a process termed sporogony, mosquitoes acquire gametocyte-stage parasites from blood-feeding on an infected host. The parasites carry out fertilization in the midgut, transform to ookinetes, then oocysts, which produce sporozoites. Sporozoites invade the salivary glands and are transmitted when the mosquito feeds on another host. Most individual mosquitoes that ingest gametocytes do not support development to the sporozoite stage. Bottle-necks occur at every stage of the cycle in the mosquito. Powerful new techniques and approaches exist for evaluating malaria parasite development and for identifying mechanisms regulating malaria parasite-vector interactions. This review focuses on those interactions that are important for the development of new approaches for evaluating and blocking transmission in nature.
A Reflector Antenna for Focusing Subnanosecond Pulses in the Near Field (2010)

A prolate-spheroidal reflector antenna focusing subnanosecond pulsed electromagnetic radiation in the near field is studied. This antenna reflector is fed by a pair of balanced, conical-plate transmission lines and the radiated pulse consists of a prepulse, an impulse, and a postpulse. Whereas the prepulse amplitude decreases inversely with distance, the impulse is maximum near the geometric focus, and its power density distribution has a full-width at half-maximum (FWHM) width of 32 cm in the axial direction and 10 cm in the lateral direction.
35.2: High‐Performance Solution‐Processed Oxide TFT with Dual Channel at Low Temperature (2011)

Abstract In this study, we investigated solution‐processed oxide thin film transistors (TFTs) with dual channel (DC) at 350°C. The DC TFTs consisted of thin InZnO (IZO) channel and thick AlInZnO (AIZO) channel. The IZO could provide high carrier concentration to enhance the charge transport for high saturation mobility (μ sat ) and thick AIZO channel could also regulate the conductance for proper threshold voltage (V th ). The resistivity of front IZO thin films could be determined by composition ratio of In/Zn and thickness of IZO channel. Thus, we can demonstrate excellent device with μ sat of 5.02 cm 2 /Vs, V th of 0.35 V, and on/off ratio of over 10 6 at 350°C.
Railway timetable stability analysis using stochastic max-plus linear systems (2009)

Stability and robustness of a railway timetable are essential properties for punctual and reliable operations. Timetable performance evaluation is therefore an important aspect in the timetable design process. In particular, the stability and recoverability properties of a timetable with respect to daily process time variations must be well analysed. The timetable must be able to recover from primary delays due to stochastic process times and it must be robust against secondary delays due to train interactions. This paper presents a stability analysis approach based on stochastic max-plus linear system theory. Stochastic counter-parts of well-established concepts from the deterministic max-plus stability analysis are proposed, like timetable stability and realizability. General probability distributions can be used to model the primary stochastic behaviour of process times, while delay propagation due to timetable and infrastructure constraints are computed from the stochastic recursive system equations. Recently developed powerful algorithms can be utilized to analyse and improve large-scale stochastic systems, and to establish the amount of stochastic variations that a timetable can absorb without external control.
Radioimmunotherapy of human colon cancer xenografts using a dimeric single-chain Fv antibody construct. (1999)

Progress in the use of monoclonal antibodies (MAbs) for the treatment of solid tumors is limited by a number of factors, including poor penetration of the labeled IgG molecule into the tumors, their inability to reach the tumor in sufficient quantities without significant normal tissue toxicity, and the development of a human antimouse antibody response to the injected MAb. One possible way to alter the pharmacology of antibodies is via the use of smaller molecular weight antibody fragments called single-chain Fvs (scFvs). A divalent construct of MAb CC49, CC49 (scFv)2, composed of two noncovalently associated scFvs, was generated and shown to bind a tumor-associated antigen (TAG-72) epitope with a similar binding affinity to that of the murine IgG. The therapeutic potential of this construct after labeling with 131I was examined in athymic mice bearing established s.c. human colon carcinoma (LS-174T) xenografts. Treatment groups (n = 10) received a single dose of 131I-labeled CC49 (scFv)2 (500-2000 microCi) or 131I-labeled CC49 IgG (250 and 500 microCi). The group of mice treated with the lowest dose of 131I-(scFv)2 (500 microCi) showed statistically significant prolonged survival, compared with controls (P = 0.036). Complete tumor regression was observed in 20% of mice given 1500 microCi of labeled (scFv)2 and 30 and 60% of mice treated with 250 and 500 microCi of labeled IgG, respectively. In conclusion, the CC49 (scFv)2 construct provides a promising delivery vehicle for therapeutic applications.
Rapid preparation of giant unilamellar vesicles. (1996)

We report here a rapid evaporation method that produces in high yield giant unilamellar vesicles up to 50 microns in diameter. The vesicles are obtained after only 2 min and can be prepared from different phospholipids, including L-alpha-phosphatidylcholine (lecithin), dipalmitoleoyl L-alpha-phosphatidylcholine, and beta-arachidonoyl gamma-palmitoyl L-alpha-phosphatidylcholine. Vesicles can be produced in distilled water and in Hepes, phosphate, and borate buffers in the pH range of 7.0 to 11.5 with ionic strengths up to 50 mM. The short preparation time allows encapsulation of labile molecular targets or enzymes with high catalytic activities. Cell-sized proteoliposomes have been prepared in which gamma-glutamyltransferase (EC 2.3.2.2) was functionally incorporated into the membrane wall.
Specific excretion of Serratia marcescens protease through the outer membrane of Escherichia coli (1986)

A DNA fragment of Serratia marcescens directing an extracellular serine protease (Mr, 41,000) was cloned in Escherichia coli. The cloned fragment caused specific excretion of the protease into the extracellular medium through the outer membrane of E. coli host cells in parallel with their growth. No excretion of the periplasmic enzymes of host cells occurred. The cloned fragment contained a single open reading frame of 3,135 base pairs coding a protein of 1,045 amino acids (Mr 112,000). Comparison of the 5' nucleotide sequence with the N-terminal amino acid sequence of the protease indicated the presence of a typical signal sequence. The C-terminal amino acid of the enzyme was found at position 408, as deduced from the nucleotide sequence. Artificial frameshift mutations introduced into the coding sequence for the assumed distal polypeptide after the C terminus of the protease caused complete loss of the enzyme production. It was concluded that the Serratia serine protease is produced as a 112-kilodalton proenzyme and that its N-terminal signal peptide and a large C-terminal part are processed to cause excretion of the mature protease through the outer membrane of E. coli cells.
Weichteilveränderungen an der Hand bei der progressiven Sklerodermie (ohne Berücksichtigung der Verkalkungen) (1987)

The systemic progressive sclerosis causes numerous soft tissue changes at the hand, most often a thickening of the skin and an augmentation of the fibrous structures in the subcutis, which occur before the atrophy of the finger tip. Other soft tissue changes are the synovitic enlargement of the joint capsules and the tendon sheaths and the tendinitic enlargement of the tendons. This complex of soft tissue changes is seen in the three view low kV radiography.
Design and In Vitro Characterization of a Single Regulatory Module for Efficient Control of Gene Expression in Both Plasmid DNA and a Self-Inactivating Lentiviral Vector (2001)

These results suggest a model in which the 1Pi autoregulatory system reaches a steady state over time, the minimal amount of tetR produced by the basal activity of the CMV promoter and accumulated is adequate to replace the tetR that is lost over time. These studies also show that the inducible self-inactivating lentiviral vector can temporally and reversibly regulate transgene expression in HUVECs. The use of this transcriptional control unit in both nonviral and viral vector delivery systems will constitute an attractive technological advance for many gene therapy applications where temporal and quantitative control of gene expression is desired. The strengths and limitations of the 1Pi system are discussed.
Production of mucoid exopolysaccharide during development of Pseudomonas aeruginosa biofilms (1993)

Production of mucoid exopolysaccharide by planktonic, chemostat-derived, and adherent Pseudomonas aeruginosa 579 bacteria was separately monitored for 7 days by using a lacZ-algD promoter-reporter gene and assays of total carbohydrate and metabolic activity. Mucoid exopolysaccharide production was transiently elevated following adherence but declined to planktonic levels by day 7.
The association between androgen levels and premature coronary artery disease in men (2007)

A low level of free testosterone may be related to the development of premature coronary artery disease.
Inheritance of low-density lipoprotein subclass patterns: results of complex segregation analysis. (1988)

Heterogeneity in the size of low-density lipoprotein (LDL) particles was used to identify two distinct patterns based on gradient gel electrophoresis analysis. These two phenotypes, LDL subclass pattern A and pattern B, were characterized by a predominance of large, buoyant LDL particles and small, dense LDL particles, respectively. The inheritance of these LDL subclass patterns was investigated in a sample of 61 healthy families including 301 individuals. LDL subclass pattern B was present in 31% of the subjects, with the prevalence varying by gender, age, and (in women) menopausal status. Complex segregation analysis suggested a major locus controlling LDL subclass patterns. The model providing the best fit to the data included a dominant mode of inheritance with a frequency of .25 for the allele determining LDL subclass pattern B and reduced penetrance for men under age 20 and for premenopausal women. Thus, the allele for the LDL subclass pattern characterized by a predominance of small, dense LDL particles appears to be very common in the population, although not usually expressed until adulthood in men and until after menopause in women. The presence of a major gene controlling LDL subclass could explain much of the familial aggregation of lipid and apolipoprotein levels and may be involved in increased risk of coronary heart disease.
[Biology of papillomavirus infections. I. General characteristics]. (1998)

Papillomaviruses are pathogens which induce cutaneous and mucosal lesions in man and in many animal species. The characterization of these viruses was rather low, because viral infection cannot be fully reproduced in cell culture. The development of molecular biology techniques in the 1970s permitted to establish the remarkable plurality of the viruses, the tissue specificity and pecular pathogenicity linked to the type. Studies of the genome organization, the gene expression regulation and the protein characterization gave many informations leading to understand the mechanisms of viral-related carcinogenesis, especially the role of HPV16, the major risk factor for the development of squamous cervical carcinoma.
Leptin regulation of the immune response and the immunodeficiency of malnutrition 1 (2001)

Leptin is a 16 kDa protein mainly produced by adipose tissue in proportion to adipose tissue mass. Originally thought to be a satiety factor, leptin is a pleiotropic molecule. In addition to playing a role in energy regulation, leptin also regulates endocrine and immune functions. Both the structure of leptin and that of its receptor suggest that leptin might be classified as a cytokine. The secondary structure of leptin has similarities to the long-chain helical cytokines family, which includes interleukin 6 (IL-6), IL-11, CNTF, and LIF, and the leptin receptor is homologous to the gp-130 signal-transducing subunit of the IL-6-type cytokine receptors. Leptin plays a role in innate and acquired immunity. Leptin levels increase acutely during infection and inflammation, and may represent a protective component of the host response to inflammation. More important, leptin deficiency increases susceptibility to infectious and inflammatory stimuli and is associated with dysregulation of cytokine production. Leptin deficiency also causes a defect in hematopoiesis. Leptin regulates T cells responses, polarizing Th cells toward a Th1 phenotype. Low leptin levels occurring during starvation mediate the neuroendocrine and immune dysfunction of starvation.
Chemokine receptor CXCR4-prognostic factor for gastrointestinal tumors (2008)

To review the implication of CXCR4 for gastrointestinal cancer, a "Pubmed" analysis was performed in order to evaluate the relevance of CXCR4 and its ligands for gastrointestinal cancers. Search terms applied were "cancer, malignoma, esophageal, gastric, colon, colorectal, hepatic, pancreatic, CXCR4, SDF-1alpha, and SDF-1beta". CXCR4 expression correlated with dissemination of diverse gastrointestinal malignomas. The CXCR4 ligand SDF-1alpha might act as "chemorepellent" while SDF-1beta might act as "chemorepellent" for CTLs, inducing tumor rejection. The paracrine expression of SDF-1alpha was furthermore closely associated with neoangiogenesis. CXCR4 and its ligands influence the dissemination, immune rejection, and neoangiogenesis of human gastrointestinal cancers. Inhibition of CXCR4 might be an interesting therapeutic option.