gebhart/patrepeval huggingface dataset:
Multicolored pH-Tunable and Activatable Fluorescence Nanoplatform Responsive to Physiologic pH Stimuli (2012)

Tunable, ultra-pH responsive fluorescent nanoparticles with multichromatic emissions are highly valuable in a variety of biological studies, such as endocytic trafficking, endosome/lysosome maturation, and pH regulation in subcellular organelles. Small differences (e.g., <1 pH unit) and yet finely regulated physiological pH inside different endocytic compartments present a huge challenge to the design of such a system. Herein, we report a general strategy to produce pH-tunable, highly activatable multicolored fluorescent nanoparticles using commonly available pH-insensitive dyes with emission wavelengths from green to near IR range. The primary driving force of fluorescence activation between the ON (unimer) and OFF (micelle) states is the pH-induced micellization. Among three possible photochemical mechanisms, homo Förster resonance energy transfer (homoFRET)-enhanced decay was found to be the most facile strategy to render ultra-pH response over the H-dimer and photoinduced electron transfer (PeT) mechanisms. Based on this insight, we selected several fluorophores with small Stoke shifts (<40 nm) and established a panel of multicolored nanoparticles with wide emission range (500-820 nm) and different pH transitions. Each nanoparticle maintained the sharp pH response (ON/OFF < 0.25 pH unit) with corresponding pH transition point at pH 5.2, 6.4, 6.9, and 7.2. Incubation of a mixture of multicolored nanoparticles with human H2009 lung cancer cells demonstrated sequential activation of the nanoparticles inside endocytic compartments directly correlating with their pH transitions. This multicolored, pH-tunable nanoplatform offers exciting opportunities for the study of many important cell physiological processes, such as pH regulation and endocytic trafficking of subcellular organelles.
Prolonged exposure of human pancreatic islets to high glucose concentrations in vitro impairs the beta-cell function. (1992)

The aim of the present study was to clarify whether prolonged in vitro exposure of human pancreatic islets to high glucose concentrations impairs the function of these cells. For this purpose, islets isolated from adult cadaveric organ donors were cultured for seven days in RPMI 1640 medium supplemented with 10% fetal calf serum and containing either 5.6, 11, or 28 mM glucose. There was no glucose-induced decrease in islet DNA content or signs of morphological damage. However, islets cultured at 11 or 28 mM glucose showed a 45 or 60% decrease in insulin content, as compared to islets cultured at 5.6 mM glucose. Moreover, when such islets were submitted to a 60-min stimulation with a low (1.7 mM) followed by a high (16.7 mM) concentration of glucose, the islets cultured at 5.6 mM glucose showed a higher insulin response to glucose than those of the two other groups. Islets cultured at the two higher glucose concentrations showed increased rates of insulin release in the presence of low glucose, and a failure to enhance further the release in response to an elevated glucose level. Islets cultured at 28 mM glucose showed an absolute decrease in insulin release after stimulation with 16.7 mM glucose, as compared to islets cultured at 5.6 mM glucose. The rates of glucose oxidation, proinsulin biosynthesis, and total protein biosynthesis were similar in islets cultured at 5.6 or 11 mM glucose, but they were decreased in islets cultured at 28 mM glucose. These combined results suggest that lasting exposure to high glucose concentrations impairs the function of human pancreatic islets.
Overexpression of the focal adhesion kinase (p125FAK) in invasive human tumors. (1995)

The focal adhesion kinase (FAK) gene encodes a tyrosine kinase (p125FAK) thought to be involved in signal transduction pathways used in cell adhesion, motility, and anchorage-independent growth. Because alterations in these cellular processes occur in tumor invasion and metastasis, we studied the protein expression of FAK in a variety of human tumors and found that in the 119 samples studied, increased levels of p125FAK correlated with the invasive potential of a tumor. By comparing FAK expression in tumors with normal tissue from the same patient, we found that p125FAK was significantly elevated in 17 (100%) of 17 invasive and metastatic colonic lesions and in 22 (88%) of 25 invasive and metastatic breast tumors. Additional studies of FAK expression in 13 high grade sarcomas showed high levels in all samples compared to benign, noninvasive mesenchymal specimens. Furthermore, FAK protein levels were elevated in preinvasive lesions, such as large (> 2 cm) colonic villous adenomas, whereas noninvasive, yet hypercellular, neoplastic tissues such as parathyroid and hepatocellular adenomas did not overexpress FAK. These data provide evidence that both epithelial and mesenchymal tumor progression are accompanied by increased p125FAK expression and suggest that the level of FAK expression might be a marker for the invasive potential of a tumor.
Paracrine Signals from Mesenchymal Cell Populations Govern the Expansion and Differentiation of Human Hepatic Stem Cells to Adult Liver Fates (2010)

Paracrine signals from defined mesenchymal cell populations are important for the regulation of stem cell populations into specific adult fates; this finding is important for basic and clinical research as well as industrial investigations.
Insulin receptor kinase in human skeletal muscle from obese subjects with and without noninsulin dependent diabetes. (1987)

We have studied the structure and function of the insulin receptors in obese patients with and without noninsulin dependent diabetes mellitus (NIDDM) and in nonobese controls using partially purified receptors from muscle biopsies. Insulin binding was decreased in obesity due to reduced number of binding sites but no differences were observed in insulin binding between obese subjects with or without NIDDM. The structural characteristics of the receptors, as determined by affinity labeling methods and electrophoretic mobility of the beta-subunit, were not altered in obese or NIDDM compared to normal weight subjects. Furthermore, the ability of insulin to stimulate the autophosphorylation of the beta-subunit and the phosphoamino acid composition of the phosphorylated receptor were the same in all groups. However, insulin receptor kinase activity was decreased in obesity using Glu4:Tyr1 as exogenous phosphoacceptor without any appreciable additional defect when obesity was associated with NIDDM. Thus, our data are supportive of the hypothesis that in muscle of obese humans, insulin resistance is partially due to decreased insulin receptors and insulin receptor kinase activity. In NIDDM the defect(s) in muscle is probably distal to the insulin receptor kinase.
Studies of acoustic streaming in biological fluids with an ultrasound Doppler technique. (1998)

Acoustic streaming generated by diagnostic ultrasound fields is an important area for study both for safety reasons and because of its potential application as a diagnostic tool. A method of investigating streaming in biological fluids is reported. A number of fluids were insonated using a 3.5 MHz weakly focused single element transducer which was driven in pulsed mode. Streaming was detected in each fluid using an 8 MHz continuous wave Doppler system. The maximum streaming velocity was obtained by spectral analysis of the Doppler signal. Using this system longitudinal streaming profiles were measured. At an acoustic power of 150 mW the maximum streaming velocities detected were: 9.3 cm s-1 in water, 6.8 cm s-1 in 4.5% human serum albumin (HSA) solution and 4.9 cm s-1 in blood, when transmission was through a water path of approximately 10 cm into a 3 cm sample of fluid. When measurements were made in the biological fluids alone, without a water path, the maximum streaming velocities were reduced.
Ubiquinone biosynthesis Cloning of the genes coding for chorismate pyruvate‐lyase and 4‐hydroxybenzoate octaprenyl transferase from Escherichia coli (1992)

Chorismate pyruvate-lyase activity was detected in extracts of Escherichia coli. 4-Hydroxybenzoate was identified as the product of the enzymatic reaction by chemical derivatization and GC-MS analysis. The ubiC gene, coding for the chorismate pyruvate-lyase, was cloned and sequenced. The molecular weight of the gene product was calculated as 18,776 Da and confirmed by expression of the protein in E. coli minicells. The ubiA gene, coding for the 4-hydroxybenzoate octaprenyl transferase, was identified by sequence homology and complementation of a ubiA- strain. It is located directly downstream of ubiC in a typical operon structure.
Use of Molecular Beacons To Detect an Antifolate Resistance-Associated Mutation in Plasmodium falciparum (2000)

A PCR-based technique using new fluorescent probes, called molecular beacons, was developed to detect the antifolate resistance-associated S108N point mutation in Plasmodium falciparum. One hundred African clinical isolates were tested by the new method in comparison with the PCR-restriction fragment length polymorphism method. This new molecular technique appears to be a promising tool for epidemiological studies.
Development of mouse mammary gland: identification of stages in differentiation of luminal and myoepithelial cells using monoclonal antibodies and polyvalent antiserum against keratin. (1986)

The development of the mouse mammary gland was studied immunohistochemically using monoclonal antibodies against cell surface and basement membrane proteins and a polyclonal antibody against keratin. We have identified three basic cell types: basal, myoepithelial, and epithelial cells. The epithelial cells can be subdivided into three immunologically related cell types: luminal type I, luminal type II, and alveolar cells. These five cell types appear at different stages of mammary gland development and have either acquired or lost one of the antibody-defined antigens. The cytoplasmic distribution of several of these antigens varied according to the location of the cells within the mammary gland. Epithelial cells which did not line the lumen expressed antigens throughout the cytoplasm. These antigens were demonstrated on the apical site in situations where the cells lined the lumen. One antigen became increasingly basolateral as the cells became attached to the basement membrane. The basal cells synthesize laminin and deposit it at the cell base. They are present in endbuds and ducts and are probably the stem cells of the mammary gland. Transitional forms have been demonstrated which developmentally link these cells with both myoepithelial and (luminal) epithelial cells.
Rapid selective enumeration of bacteria in foods using a microcolony epifluorescence microscopy technique (1988)

The growth patterns of microcolonies of 59 different pure cultures were studied on eight selective solid media. A method of growing microcolonies on the surface of polycarbonate membrane filters, placed on the selective agar media, followed by staining and examination by epifluorescent microscopy was developed. The patterns of growth of the pure cultures as microcolonies were studied on the eight selective media. Only four media proved to be reliable for this purpose and the relationship between the microcolony count and plate count was studied on these media together with nutrient agar. Microcolony counts using three of these media (enriched lauryl sulphate aniline blue, pseudomonas selective agar (C-F-C) and Baird-Parker medium) were capable of giving reliable estimates of coliforms (r = 0.89), pseudomonads (r = 0.93) and staphylococci (r = 0.92) after incubation at 30 degrees C for 3 or 6 h (staphylococci) at contamination levels of above 10(3) bacteria/g in a variety of foods. The results are available within a working day and should allow the more efficient management of food supplies.
Protective Immunity Induced with the RTS,S/AS Vaccine Is Associated with IL-2 and TNF-α Producing Effector and Central Memory CD4+ T Cells (2011)

A phase 2a RTS,S/AS malaria vaccine trial, conducted previously at the Walter Reed Army Institute of Research, conferred sterile immunity against a primary challenge with infectious sporozoites in 40% of the 80 subjects enrolled in the study. The frequency of Plasmodium falciparum circumsporozoite protein (CSP)-specific CD4(+) T cells was significantly higher in protected subjects as compared to non-protected subjects. Intrigued by these unique vaccine-related correlates of protection, in the present study we asked whether RTS,S also induced effector/effector memory (T(E/EM)) and/or central memory (T(CM)) CD4(+) T cells and whether one or both of these sub-populations is the primary source of cytokine production. We showed for the first time that PBMC from malaria-non-exposed RTS,S-immunized subjects contain both T(E/EM) and T(CM) cells that generate strong IL-2 responses following re-stimulation in vitro with CSP peptides. Moreover, both the frequencies and the total numbers of IL-2-producing CD4(+) T(E/EM) cells and of CD4(+) T(CM) cells from protected subjects were significantly higher than those from non-protected subjects. We also demonstrated for the first time that there is a strong association between the frequency of CSP peptide-reactive CD4(+) T cells producing IL-2 and the titers of CSP-specific antibodies in the same individual, suggesting that IL-2 may be acting as a growth factor for follicular Th cells and/or B cells. The frequencies of CSP peptide-reactive, TNF-α-producing CD4(+) T(E/EM) cells and of CD4(+) T(E/EM) cells secreting both IL-2 and TNF-α were also shown to be higher in protected vs. non-protected individuals. We have, therefore, demonstrated that in addition to TNF-α, IL-2 is also a significant contributing factor to RTS,S/AS vaccine induced immunity and that both T(E/EM) and T(CM) cells are major producers of IL-2.
Biosynthesis and degradation of mammalian glycosphingolipids (2003)

Glycolipids are a large and heterogeneous family of sphingolipids that form complex patterns on eukaryotic cell surfaces. This molecular diversity is generated by only a few enzymes and is a paradigm of naturally occurring combinatorial synthesis. We report on the biosynthetic principles leading to this large molecular diversity and focus on sialic acid-containing glycolipids of the ganglio-series. These glycolipids are particularly concentrated in the plasma membrane of neuronal cells. Their de novo synthesis starts with the formation of the membrane anchor, ceramide, at the endoplasmic reticulum (ER) and is continued by glycosyltransferases of the Golgi complex. Recent findings from genetically engineered mice are discussed. The constitutive degradation of glycosphingolipids (GSLs) occurs in the acidic compartments, the endosomes and the lysosomes. Here, water-soluble glycosidases sequentially cleave off the terminal carbohydrate residues from glycolipids. For glycolipid substrates with short oligosaccharide chains, the additional presence of membrane-active sphingolipid activator proteins (SAPs) is required. A considerable part of our current knowledge about glycolipid degradation is derived from a class of human diseases, the sphingolipidoses, which are caused by inherited defects within this pathway. A new post-translational modification is the attachment of glycolipids to proteins of the human skin.
Política exterior: la ilusión del consenso (2004)

Espana como pais tiene la necesidad de preguntarse quien es y que papel quiere desempenar en la escena internacional. El nuevo gobierno necesita sabiduria, audacia y tambien fortuna.
APPLICATION OF SWINE MANURE IN DEVELOPMENT OF BIO-ADHESIVE (2012)

This paper introduces bio-binder as a partial replacement for bituminous binder on highway and airport pavements. The proposed bio-binder is produced from the thermochemical conversion of swine manure. Bio-binder is then blended with virgin binder to produce bio- modified binder (BMB). In addition to being a renewable alternative for petroleum-based binder, the production and application of bio- binder may provide a solution for the management of swine manure waste. Furthermore, the application of bio-binder will improve asphalt binder's properties while reducing asphalt pavements' construction cost, the cost of bio-binder production is $0.54/gallon compared to that of asphalt binder $2/gallon. 1. Introduction: The volatility of the world's oil market pushed oil prices to more than $70 per barrel in the summer of 2008; this resulted in asphalt binder quickly spiking to more than $400 per ton (National Asphalt Pavement, 2009). This along with high diesel fuel prices caused a significant increase in the final cost of hot-mix asphalt (HMA) pavement construction. Because of the ever increasing demand for natural petroleum and its unstable price, alternative sustainable resources for producing asphalt binder are urgently needed. This study proposes the conversion of swine manure through hydrothermal processing to a bio-based- environmentally friendly alternative for bituminous binder.
Complete nucleotide sequence and genome organization of a tobamovirus infecting cruciferae plants (1994)

Genomic RNA sequence of a tobamovirus infecting cruciferae plants (cr-TMV) was determined. The RNA is composed of 6312 nucleotides and contains four ORFs encoding the proteins of 122K (ORF1), 178K (ORF2), 29K (ORF3) and 18K (capsid protein, ORF4). ORF4 overlaps ORF3 by 74 nucleotides and the overlapping region can be folded into a stable hairpin structure. The 3'-terminal region of the cr-TMV RNA preceding the tRNA-like structure was shown to form six potentially stable pseudoknots.
Epidermal growth factor receptor--its expression and copy numbers of EGFR gene in patients with head and neck squamous cell carcinomas. (2005)

Signaling pathways activated by epidermal growth factor receptor (EGFR) are pathogenetically involved in the development of head and neck squamous cell carcinomas (HNSCC). A monoclonal antibody against the EGFR protein blocking the receptor activity (cetuximab - Erbitux - C225) is now available for therapeutic applications. The mechanisms of EGFR protein overexpression are poorly understood. Regulatory pathways, EGFR gene structural changes or its amplification may be involved. The aim of the study was to evaluate expression of the EGFR protein in patients with HNSCC, to identify EGFR gene copy numbers, and to find out whether the protein overexpression is associated with the EGFR gene amplification. In the case of a pathogenetical link of the EGFR gene amplification and the protein overexpression it would be useful to employ both diagnostic approaches to identify patients eligible for cetuximab therapy. We investigated 33 patients with HNSCC. The expression of EGFR protein was evaluated by immunohistochemistry, copy numbers of EGFR gene and the numbers of chromosome 7 centromeric signals were investigated by fluorescence in situ hybridization on interphasic nuclei (I-FISH). Histological sections from formalin fixed and paraffin embedded tissues were used. We observed three types of EGFR protein expression (homogeneous 3+ membrane positivity in 13 patients; membrane positivity varying from 1+ to 3+ in 12 patients; a strong membrane positivity at the periphery of the tumor cell clusters in 5 patients). In two cases the results were difficult to interpret. In one case single tumor cells only were positive. Numerical changes of chromosome 7 were present in 23 patients. We found the EGFR gene amplification in seven patients. The tumor cells with amplification of the EGFR gene were generally infrequent and were localized in small clusters, or they were randomly dispersed between the tumor cell population without the gene amplification. We did not find any correlation between the EGFR gene amplification and the EGFR protein overexpression. Thus, amplification of the EGFR gene is not pathogenetically involved in the EGFR protein overexpression. From the diagnostic aspect a standardized immunohistochemical assessment of the EGFR protein expression appears sufficient for detection of the EGFR status. Criteria for cetuximab treatment in patients with HNSCC may differ from those already used for patients with colorectal carcinomas and should take different patterns of the EGFR protein overexpression into consideration.
Biodegradation of atrazine in transgenic plants expressing a modified bacterial atrazine chlorohydrolase (atzA) gene (2005)

Atrazine is one of the most widely used herbicides in the USA. Atrazine chlorohydrolase (AtzA), the first enzyme in a six-step pathway leading to the mineralization of atrazine in Gram-negative soil bacteria, catalyses the hydrolytic dechlorination and detoxification of atrazine to hydroxyatrazine. In this study, we investigated the potential use of transgenic plants expressing atzA to take up, dechlorinate and detoxify atrazine. Alfalfa, Arabidopsis thaliana and tobacco were transformed with a modified bacterial atzA gene, p-atzA, under the control of the cassava vein mosaic virus promoter. All transgenic plant species actively expressed p-atzA and grew over a wide range of atrazine concentrations. Thin layer chromatography analyses indicated that in planta expression of p-atzA resulted in the production of hydroxyatrazine. Hydroponically grown transgenic tobacco and alfalfa dechlorinated atrazine to hydroxyatrazine in leaves, stems and roots. Moreover, p-atzA was found to be useful as a conditional-positive selection system to isolate alfalfa and Arabidopsis transformants following Agrobacterium-mediated transformation. Our work suggests that the in planta expression of p-atzA may be useful for the development of plants for the phytoremediation of atrazine-contaminated soils and soil water, and as a marker gene to select for the integration of exogenous DNA into the plant genome.
Natural and man-made V-gene repertoires for antibody discovery (2012)

Antibodies are the fastest-growing segment of the biologics market. The success of antibody-based drugs resides in their exquisite specificity, high potency, stability, solubility, safety, and relatively inexpensive manufacturing process in comparison with other biologics. We outline here the structural studies and fundamental principles that define how antibodies interact with diverse targets. We also describe the antibody repertoires and affinity maturation mechanisms of humans, mice, and chickens, plus the use of novel single-domain antibodies in camelids and sharks. These species all utilize diverse evolutionary solutions to generate specific and high affinity antibodies and illustrate the plasticity of natural antibody repertoires. In addition, we discuss the multiple variations of man-made antibody repertoires designed and validated in the last two decades, which have served as tools to explore how the size, diversity, and composition of a repertoire impact the antibody discovery process.