gebhart/patrepeval huggingface dataset:
MicroRNA-21 Targets the Tumor Suppressor Gene Tropomyosin 1 (TPM1) (2007)

MicroRNAs are small noncoding RNA molecules that control expression of target genes. Our previous studies show that mir-21 is overexpressed in tumor tissues compared with the matched normal tissues. Moreover, suppression of mir-21 by antisense oligonucleotides inhibits tumor cell growth both in vitro and in vivo. However, it remains largely unclear as to how mir-21 affects tumor growth, because our understanding of mir-21 targets is limited. In this study, we performed two-dimensional differentiation in-gel electrophoresis of tumors treated with anti-mir-21 and identified the tumor suppressor tropomyosin 1 (TPM1) as a potential mir-21 target. In agreement with this, there is a putative mir-21 binding site at the 3'-untranslated region (3'-UTR) of TPM1 variants V1 and V5. Thus, we cloned the 3'-UTR of TPM1 into a luciferase reporter and found that although mir-21 down-regulated the luciferase activity, anti-mir-21 up-regulated it. Moreover, deletion of the mir-21 binding site abolished the effect of mir-21 on the luciferase activity, suggesting that this mir-21 binding site is critical. Western blot with the cloned TPM1-V1 plus the 3'-UTR indicated that TPM1 protein level was also regulated by mir-21, whereas real-time quantitative reverse transcription-PCR revealed no difference at the mRNA level, suggesting translational regulation. Finally, overexpression of TPM1 in breast cancer MCF-7 cells suppressed anchorage-independent growth. Thus, down-regulation of TPM1 by mir-21 may explain, at least in part, why suppression of mir-21 can inhibit tumor growth, further supporting the notion that mir-21 functions as an oncogene.
Rates of hippocampal atrophy correlate with change in clinical status in aging and AD (2000)

Rates of hippocampal atrophy match both baseline cognitive status and the change in cognitive status over time in elderly persons who lie along the cognitive continuum from normal to MCI to AD.
Correlations and interactions in the production of interleukin-6 (IL- 6), IL-1, and tumor necrosis factor (TNF) in human blood mononuclear cells: IL-6 suppresses IL-1 and TNF (1990)

Interleukin-6 (IL-6) shares several biologic properties with IL-1, including hematopoietin-1 activity and stimulation of T cells. Because many of their biologic activities overlap, we developed and used a specific radioimmunoassay (RIA) for IL-6 to compare production of this cytokine on a molar basis with that of IL-1 alpha, IL-1 beta, and tumor necrosis factor (TNF)alpha. The RIA correlated well with the hybridoma bioassay for IL-6 (r = .87, P less than .001). Freshly isolated human peripheral blood mononuclear cells (PBMC) cultured in the absence of stimuli did not produce IL-6 in most cases. Kinetics of secretion and cell-association of IL-6 were studied. In contrast to IL-1 alpha but similar to TNF, IL-6 was almost entirely secreted into the extracellular fluid. Incubation with different stimuli (lipopolysaccharide [LPS], phytohemagglutinin [PHA], Staphylococcus epidermidis, or IL-1 alpha) resulted in production of IL-6. However, on a molar basis PBMC produced approximately two to three times less IL-6 than IL-1 alpha, IL-1 beta, or TNF, regardless of the stimulus. The amount of IL-6 produced from PBMC was consistent when measured in the same subjects six time during a 12-week period. In a cohort of 38 donors, the coefficient of variation for IL-6 production was .32, compared with .92 for IL-1 beta and .96 for TNF. Comparing cytokine production by PBMC, there was a significant correlation between IL-6 and IL-1 beta (r = .72) and between IL-6 and TNF (r = .66). IL-6 did not stimulate IL-1 beta or TNF production, but suppressed IL-1 beta and TNF production induced by LPS or PHA by 30% (P less than .01). This suppression of IL-1 beta and TNF by IL-6 appears to be on the level of transcription.
Purification and identification of the functional sodium- and chloride-coupled gamma-aminobutyric acid transport glycoprotein from rat brain. (1986)

Using the reconstitution conditions developed recently (Radian, R., and Kanner, B. I. (1985) J. Biol. Chem. 260, 11859-11865) we have now purified the sodium- and chloride-coupled gamma-aminobutyric acid transporter from rat brain to apparent homogeneity. A partially purified transporter preparation was passed over wheat germ agglutinin-Sepharose 6MB and non-bound proteins were washed away. The transport activity, as expressed upon reconstitution of the protein into liposomes, was eluted by a solution containing Triton X-100 and N-acetylglucosamine. The specific transport activity was increased almost 400-fold over that of the crude extract. Taking into account an approximately 2.5-fold inactivation during the lectin column chromatography, the actual purification is about 1000-fold. Sodium dodecyl sulfate-polyacrylamide electrophoresis of the active fractions revealed one band of 80 kDa and small amounts of a band which ran at an apparent molecular mass of 160 kDa. The ratio between the two could be experimentally changed such as, for instance, by lyophilization. Polyclonal antibodies were prepared against the 80-kDa band which also cross-reacted with the 160-kDa band, indicating that the latter apparently represents a dimer form of the first. Using Protein A-Sepharose Cl-4B and the antibody against the 80-kDa band, we were able to quantitatively immunoprecipitate the potential gamma-aminobutyric acid transport activity from a crude transporter preparation. The pure transporter preparation exhibited the same features of the transporter in synaptic plasma membrane vesicles, namely dependence on sodium and chloride, electrogeneity, affinity, and efflux and exchange properties. We conclude that the 80-kDa band represents the gamma-aminobutyric acid transporter.
Performance evaluation of loop‐type ground radiation antenna based on its optimum impedance level (2017)

The performance of a loop‐type ground radiation antenna was analysed based on its impedance level for an arbitrary location on the ground plane. At the corner of the ground plane, the open capacitor configuration (i.e. the PIFA type antenna) shows better performance, whereas the loop‐type antenna with a capacitor and shorted inductor is a better choice at the middle of the ground plane. The optimum value of the impedance level of the antenna determines the antenna performance for an arbitrary location on the ground plane is proposed. The idea was demonstrated using a 10 × 4.5 mm loop‐type antenna, which was fabricated on the 50 × 25 mm ground plane. The design is intended for mobile device applications operating in the Bluetooth band.
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation (2016)

Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50-60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability.
A 32 × 32 optical phased array using polysilicon sub-wavelength high-contrast-grating mirrors (2014)

We report on microelectromechanical systems (MEMS)-actuated 32 × 32 optical phased arrays (OPAs) with high fill-factors and microsecond response time. To reduce the mirror weight and temperature-dependent curvature, we use high-contrast-grating (HCG) mirrors comprising a single layer of sub-wavelength polysilicon gratings with 400 nm thickness, 1250 nm pitch, and 570 nm grating bar width. The mirror has a broad reflection band and a peak reflectivity of 99.9% at 1550 nm wavelength. With 20 × 20 μm2 pixels and 2 μm, the OPA has a total aperture of 702 × 702 μm2 and a fill factor of 85%. The OPA is electrostatically controlled by voltage and has a total field of view of ± 2°, an instantaneous field of view (beam width) of 0.14°, and a response time of 3.8 μs. The latter agrees well with the mechanical resonance frequency of the HCG mirror (0.42 MHz).
PERP regulates enamel formation via effects on cell–cell adhesion and gene expression (2011)

Little is known about the role of cell-cell adhesion in the development of mineralized tissues. Here we report that PERP, a tetraspan membrane protein essential for epithelial integrity, regulates enamel formation. PERP is necessary for proper cell attachment and gene expression during tooth development, and its expression is controlled by P63, a master regulator of stratified epithelial development. During enamel formation, PERP is localized to the interface between the enamel-producing ameloblasts and the stratum intermedium (SI), a layer of cells subjacent to the ameloblasts. Perp-null mice display dramatic enamel defects, which are caused, in part, by the detachment of ameloblasts from the SI. Microarray analysis comparing gene expression in teeth of wild-type and Perp-null mice identified several differentially expressed genes during enamel formation. Analysis of these genes in ameloblast-derived LS8 cells upon knockdown of PERP confirmed the role for PERP in the regulation of gene expression. Together, our data show that PERP is necessary for the integrity of the ameloblast-SI interface and that a lack of Perp causes downregulation of genes that are required for proper enamel formation.
Monoclonal Antibody Protocols (1995)

Since the initial description of techniques to immortalize anti­ body-producing B-lymphocytes by fusion with tissue culture-adapted myeloma cells, methods have been developed to produce monoclonal antibodies of defined specificity in multiple animal species. Stable hybrids can be readily produced in mice using a number of myeloma and hybridoma cell lines. To obviate the problem of identifying fusion partners in other animal species, xenohybrids have been produced using B-lymphocytes from the relevant species and mouse myeloma cells. The use of xenohybrids has minimized the problem of obtain­ ing stable antibody-producing hybrids in all species examined thus far. Although alternative techniques are being developed to produce monoclonal antibodies by molecular methods, hybridoma technol­ ogy will remain the technology of choice for producing monoclonal antibodies for a variety of applications in research and industry. The objective of Monoclonal Antibody Protocols is to provide investigators with a set of methods for producing and using mono­ clonal antibodies in biomedical, agricultural, and biological sciences. The book is not intended to provide methodology for all possible applications, but rather a series of methods presented in an easy-- follow format that can be used by new and established investiga­ tors, graduate and postgraduate fellows, and technical staff
Effect of altered CH2-associated carbohydrate structure on the functional properties and in vivo fate of chimeric mouse-human immunoglobulin G1. (1994)

Immunoglobulin G (IgG) molecules are glycosylated in CH2 at Asn297; the N-linked carbohydrates attached there have been shown to contribute to antibody (Ab) stability and various effector functions. The carbohydrate attached to the IgG constant region is a complex biantennary structure. Alterations in the structure of oligosaccharide have been associated with human diseases such as rheumatoid arthritis and osteoarthritis. To study the effects of altered carbohydrate structure on Ab effector function, we have used gene transfection techniques to produce mouse-human chimeric IgG1 Abs in the Chinese hamster ovary (CHO) cell line Lec 1, which is incapable of processing the high-mannose intermediate through the terminal glycosylation steps. We also produced IgG1 Abs in Pro-5, the wild-type CHO cell line that is the parent of Lec 1. The Pro-5-produced Ab (IgG1-Pro-5) was similar to IgG1-My 1, a myeloma-produced IgG1 Ab of the same specificity, in its biologic properties such as serum half-life, ability to effect complement-mediated cytolysis, and affinity for Fc gamma RI. Although the Lec 1-produced Ab, IgG1-Lec 1, was properly assembled and retained antigen specificity, it was incapable of complement-mediated hemolysis and was substantially deficient in complement consumption, C1q binding, and C1 activation. IgG1-Lec 1 also showed reduced but significant affinity for Fc gamma R1 receptors. The in vivo half-life of IgG1-Lec 1 was shorter than that of either the myeloma- or Pro-5-produced counterpart, with more being cleared during the alpha-phase and with more rapid clearance during the beta-phase. Clearance of IgG1-Lec 1 could be inhibited by the administration of yeast-derived mannan. Thus the uptake of IgG1-Lec 1 appears to be accelerated by the presence of terminally mannosylated oligosaccharide. Therefore, certain Ab functions as well as the in vivo fate of the protein are dramatically affected by altered carbohydrate structure. Expression of Igs in cell lines with defined glycosylation mutations is shown to be a useful technique for investigating the contribution of carbohydrate structure to Ab function.
Effects of Testosterone on Coronary Vasomotor Regulation in Men With Coronary Heart Disease (1999)

Short-term intracoronary administration of testosterone, at physiological concentrations, induces coronary artery dilatation and increases coronary blood flow in men with established coronary artery disease.
Augmentation of the human immune response by cyclophosphamide. (1982)

Abstract Pretreatment of experimental animals with cyclophosphamide (CY) markedly potentiates the acquisition of T-cell-mediated immunity to an antigen given 1 to 4 days later. We have examined the primary induction of delayed-type hypersensitivity (DTH) and antibody to keyhole limpet hemocyanin (KLH) and DTH to 1-chloro-2,4-dinitrobenzene (DNCB) in 22 patients receiving CY for metastatic cancer, 12 with melanoma and 10 with colorectal carcinoma. Sixteen days before CY, one-half of the patients received KLH and one-half received DNCB; 3 days after CY, they received KLH or DNCB, whichever they had not received initially. Blood was drawn for antibody titer and/or skin testing was performed 14 days after administration of antigen. For each antigen, the responses of pre-CY patients were compared with those of post-CY patients. We found that pretreatment of patients with CY significantly augmented the development of DTH to KLH. The DTH reactions of the group of patients given KLH 3 days after CY were significantly greater than those of the group of patients given KLH without CY (medians: KLH alone, 0; KLH after CY, 18 mm; p = 0.025). With CY pretreatment, 11 of 11 patients developed a DTH response of greater than 5 mm compared with 4 of 11 patients without CY (p = 0.002). No patient developed DTH to DNCB when it was given without CY whereas 3 of 11 patients developed DTH when DNCB was given 3 days after CY (p = 0.082). CY pretreatment neither augmented nor suppressed the antibody response to KLH; the proportion of patients with antibody 14 days after antigen was 2 of 11 without CY and 4 of 11 with CY pretreatment (p = 0.24). It appears that CY pretreatment resulted in the development of DTH responses in otherwise unreactive patients. Reversal of the T-cell anergy of advanced cancer could lead to augmentation of the immune response to tumor-associated antigens.
Tumorigenic 3T3 cells maintain an alkaline intracellular pH under physiological conditions. (1990)

One of the earliest events in the response of mammalian cells to mitogens is activation of Na+/H+ exchange, which increases intracellular pH (pHin) in the absence of HCO3- or at external pH values below 7.2. The proliferative response can be blocked by preventing the pHin increase; yet, the proliferative response cannot be stimulated by artificially raising pHin with weak bases or high medium pH. These observations support the hypothesis that optimal pHin is a necessary, but not sufficient, component of the proliferative-response sequence. This hypothesis has recently been challenged by the observation that transfection of NIH 3T3 cells with yeast H(+)-ATPase renders them tumorigenic. Although previous measurements indicated that these transfected cells maintain a higher pHin in the absence of HCO3-, whether H(+)-ATPase transfection raised the pHin under physiologically relevant conditions was not known. The current report shows that these transfected cells do maintain a higher pHin than control cells in the presence of HCO3-, supporting the possibility that elevated pHin is a proliferative trigger in situ. We also show that these cells are serum-independent for growth and that they glycolyze much more rapidly than phenotypically normal cells.
Platelet Aggregation Inhibiting and Anticoagulant Effects of Oligoamines, Part 32 Antimicrobial Effects of Oligoamines (1996)

Twenty-four oligoamines belonging to six (1-6) structurally different types were tested in vitro for their antibacterial activity against 14 different bacterial species comprising a total of 187 strains. Ten compounds were able to inhibit growth of at least one strain at concentrations < or = 10 mumol/L. For three compounds, minimum inhibitory concentrations for some strains were even below 1 mumol/L. Clear structure-activity relationships showed that the inhibitory effect depended on the bridge connecting the nitrogen atoms, the substitution of the nitrogens, and the number of nitrogen atoms present in one molecule. Substitutions like N-4-phenylbutyl, N-octyl, and N-nonyl were most active, while short (butyl) and long (dodecyl) substituents diminished or abolished the activity. The antimicrobial spectrum of the oligoamines tested here covered gram-positive (e.g. Staphylococcus aureus, Listeria monocytogenes, Bacillus subtilis) and gram-negative (e.g. Escherichia coli, Citrobacter spp., Acinetobacter spp.) microorganisms. The type of action was classified as bactericidal. As the inhibition of growth is complete immediately after the addition of the oligoamines, an interaction with the bacterial cell-membrane is probable.
Three‐dimensionally resolved NAD(P)H cellular metabolic redox imaging of the in situ cornea with two‐photon excitation laser scanning microscopy (1995)

Three-dimensional maps of cellular metabolic oxidation/reduction states of rabbit cornea in situ were obtained by imaging the fluorescence of the naturally occurring reduced pyridine nucleotides (both reduced nicotinamide-adenine dinucleotide, NADH, and reduced nicotinamide-adenine dinucleotide phosphate, NADPH, denoted here as NAD(P)H). Autofluorescence images with submicrometre lateral resolution were obtained throughout the entire 400 microns thickness of the cornea. Two-photon excitation scanning laser microscopy with near-infrared excitation provided high fluorescence collection efficiency, reduced photodamage, and eliminated ultraviolet chromatic aberration, all of which have previously degraded the visualization of pyridine nucleotide fluorescence. Sharp autofluorescence images of the basal epithelium (40 microns within the cornea) show substantial subcellular detail, providing the ability to monitor autofluorescence intensity changes over time, which reflect changes in oxidative metabolism and cellular dynamics necessary for maintenance of the ocular surface. The autofluorescence was confirmed to be mostly of NAD(P)H origin by cyanide exposure, which increased the fluorescence from all cell types in the cornea by about a factor of two. Autofluorescence images of individual keratocytes in the stroma were observed only after cyanide treatment, while in the predominant extracellular collagen (> 90% of the stromal volume), fluorescence was not distinguished from the background. Observation of keratocyte metabolism demonstrates the sensitivity made available by two-photon microscopy for future redox fluorescence imaging of cellular metabolic states.
Biological control of phytophagous ladybird beetles Epilachna vigintioctopunctata (Col., Coccinellidae) by chitinolytic phylloplane bacteria Alcaligenes paradoxus entrapped in alginate beads (2003)

Abstract: The chitinase secreting strain KPM‐012A of Alcaligenes paradoxus was isolated from tomato leaves and vitally entrapped in sodium alginate gel beads to provide a new method for biocontrol of phytophagous ladybird beetles Epilachna vigintioctopunctata . First, the peritrophic membrane was dissected from the adult ladybird beetles that ingested the suspension of KPM‐012A after starvation to observe degradation of the midgut surface by the bacteria under electron microscopy. The peritrophic membrane around the bacteria was degraded, suggesting the release of chitinase from the ingested bacteria. Large amounts of chitinase were successfully released from KPM‐012A‐entrapped calcium alginate beads. This chitinase release from the microbial beads was sustained for 1 week and was sufficient to digest the peritrophic membrane. Daily supply of tomato leaves treated with the microbial beads caused considerable suppression of leaf feeding and oviposition by the adult ladybird beetles, indicating that this method is effective for decreasing population of insect pests in the subsequent generation. Thus, the present study provided an experimental basis for the biocontrol measures of herbivorous insect pests by the chitinolytic bacteria entrapped in alginate beads.
Myotubes differentiate optimally on substrates with tissue-like stiffness (2004)

Contractile myocytes provide a test of the hypothesis that cells sense their mechanical as well as molecular microenvironment, altering expression, organization, and/or morphology accordingly. Here, myoblasts were cultured on collagen strips attached to glass or polymer gels of varied elasticity. Subsequent fusion into myotubes occurs independent of substrate flexibility. However, myosin/actin striations emerge later only on gels with stiffness typical of normal muscle (passive Young's modulus, E approximately 12 kPa). On glass and much softer or stiffer gels, including gels emulating stiff dystrophic muscle, cells do not striate. In addition, myotubes grown on top of a compliant bottom layer of glass-attached myotubes (but not softer fibroblasts) will striate, whereas the bottom cells will only assemble stress fibers and vinculin-rich adhesions. Unlike sarcomere formation, adhesion strength increases monotonically versus substrate stiffness with strongest adhesion on glass. These findings have major implications for in vivo introduction of stem cells into diseased or damaged striated muscle of altered mechanical composition.