gebhart/patrepeval huggingface dataset:
Role of Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand in Interferon-Induced Apoptosis in Human Bladder Cancer Cells (2004)

Immunomodulators such as Bacillus Calmette-Guerin and interferon are clinically active in transitional cell carcinoma of the bladder, but their mechanisms of action remain unclear. Here we investigated the effects of IFNalpha on tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) expression and apoptosis in a panel of 20 human bladder cancer cell lines. Six (30%) displayed significant DNA fragmentation in response to increasing concentrations of IFNalpha (10-100,000 units/mL). In these lines IFNalpha induced early activation of caspase-8, and DNA fragmentation was blocked by a caspase-8-selective inhibitor (IETDfmk), consistent with the involvement of death receptor(s) in cell death. IFNalpha stimulated marked increases in TRAIL mRNA and protein in the majority of IFN-sensitive and IFN-resistant cell lines. A blocking anti-TRAIL antibody significantly inhibited IFN-induced DNA fragmentation in four of six IFN-sensitive cell lines, confirming that TRAIL played a direct role in cell death. Bortezomib (PS-341, Velcade), a potent TRAIL-sensitizing agent, increased sensitivity to IFNalpha in two of the IFN-resistant cell lines that produced large amounts of TRAIL in response to IFN treatment. Our data show that IFN-induced apoptosis in bladder cancer cells frequently involves autocrine TRAIL production. Combination therapy strategies aimed at overcoming TRAIL resistance may be very effective in restoring IFN sensitivity in a subset of human bladder tumors.
Identification and Characterization of a Novel Testosterone-Regulated Prominin-Like Gene in the Rat Ventral Prostate (2002)

More than two dozen androgen-responsive genes were identified from the castrated rat ventral prostate on the basis of their induction by exogenous testosterone. One of the identified genes encodes a novel 886-amino-acid protein that was named prominin-like protein 2 (PROML2) because it shares 32% identity to prominin and prominin-like protein 1, a family of important plasma membrane proteins with five transmembrane domains. The rat PROML2 gene is expressed abundantly in the glandular epithelial cells of the rat ventral prostate. The PROML2 gene is expressed in the human prostate and human prostate cancer cell lines with the highest level in less aggressive LNCaP cells and low expression in highly aggressive PC3 and DU145 cells, suggesting a correlation between PROML2 down-regulation and aggressiveness of prostate cancer cells. Transient transfection of green fluorescent protein-tagged rat PROML2 expression vector into prostate cancer cell lines showed that PROML2 protein is localized to the nuclear envelope and perinuclear region and induces cell death in all of the transfected prostate cancer cells. Taken together, our results argue that PROML2 is a novel proapoptotic membrane protein and its down-regulation may associate with aggressive phenotype of prostate cancer cells.
International recommendations for consumption of long-chain omega-3 fatty acids (2007)

As an appreciation of the cardioprotective properties of the long-chain, fish-oil-derived omega-3 fatty acids (eicosapentaenoic and docosahexaenoic acids) has grown, so too have official dietary guidelines. Health organizations and government agencies are typically recommending intakes that either maintain the status quo (about 100-200 mg/day in most western countries) or are intended to actively reduce risk for cardiovascular disease. The latter are around usually 400-600 mg/day, an amount likely to stimulate commercial interests to fortify foods with omega-3 fatty acids. Fortification is perhaps the best long-term solution to the chronically-low intake of omega-3 fatty acids that plagues western cultures.
Restoration of Ig Secretion: Mutation of Germline-Encoded Residues in T15L Chains Leads to Secretion of Free Light Chains and Assembled Antibody Complexes Bearing Secretion-Impaired Heavy Chains (2003)

We previously described T15H chain mutants that were impaired in assembly with L chain and in ability to be secreted from the cell. The unmutated T15L chain is unusual in that it is secretion-impaired in the absence of assembly with H chain. The T15L chain preferentially pairs with T15H in vivo, suggesting that if we introduced mutations that would allow secretion of free T15L chain, they might also lead to the secretion of the complex with the defective H chain. We mutated four positions in the germline T15L that had amino acids infrequently found in other kappa-chains. Mutation to the most frequently occurring amino acid at three of the four positions allowed secretion of free L chain, while the combination of two secretion-restoring mutations was synergistic. Coexpression of secretion-restored mutant L chains with the secretion-defective mutant H chains rescued secretion of the assembled H(2)L(2) complex, suggesting that during somatic hypermutation in vivo, deleterious mutations at the H chain may be compensated by mutations on the L chain. To our knowledge, this is the first example of mutations in IgL chains that are able to restore secretion-defective H chains to secretion competence in mammalian cells.
Evaluation of three enzymic methods as predictors of in‐vivo response to enzyme supplementation of barley‐based diets when fed to young chicks (1990)

Abstract The β‐glucan degrading ability of several commercial crude enzyme preparations was determined using three different assay procedures. The assays were based on the ability of the enzymes to reduce the viscosity of a β‐glucan solution, to produce reducing sugars from β‐glucan or to produce a blue‐coloured solution upon hydrolysis of azo‐barley‐glucan. Regression analysis showed that the relationship between the relative improvements in weight gain of chicks fed a barley‐based diet that was supplemented with different concentrations of different enzyme and in‐vitro enzyme activity when the azo‐barley‐glucan and reducing sugar assays were used was quadratic. A linear relationship was observed for the viscosity method. The R 2 values for both weight gain and feed to gain ratio were highest for the azo‐barley‐glucan method but the other methods yielded similar values under appropriate assay conditions (ie concentration of enzyme). The azo‐barley‐glucan method, nevertheless, is the assay recommended as it is by far the simplest of the three assays and it yields a low coefficient of variation.
Bias-Flip Technique for Frequency Tuning of Piezo-Electric Energy Harvesting Devices (2013)

Devices that harvest electrical energy from mechanical vibrations have the problem that the frequency of the source vibration is often not matched to the resonant frequency of the energy harvesting device. Manufacturing tolerances make it difficult to match the Energy Harvesting Device (EHD) resonant frequency to the source vibration frequency, and the source vibration frequency may vary with time. Previous work has recognized that it is possible to tune the resonant frequency of an EHD using a tunable, reactive impedance at the output of the device. The present paper develops the theory of electrical tuning, and proposes the Bias-Flip (BF) technique, to implement this tunable, reactive impedance.
Immunolocalization of Tenascin-C, α9 Integrin Subunit, and αvβ6 Integrin During Wound Healing in Human Oral Mucosa (2000)

Tenascin-C (TN-C) and its isoforms are multidomain extracellular matrix (ECM) proteins that are believed to be involved in the regulation of stromal-epithelial interactions. Some of the interactions between TN-C and cells are mediated by integrins. In this study we analyzed the expression of TN-C and its large molecular weight splice isoform (TN-C(L)) and the putative TN-C-binding alpha9 and alphavbeta6 integrins during human wound repair. In 3-day-old oral mucosal wounds, immunoreactivity for alpha9 integrin localized abundantly at the migrating basal wound epithelial cells. TN-C and TN-C(L) were localized in the matrix between and underneath alpha9-expressing epithelial cells. In parallel with gradual downregulation of alpha9 integrin immunoreactivity in 7-day and older wounds, the expression of alphavbeta6 integrin was temporarily induced. Integrin alphavbeta6 co-localized in the same area as TN-C and TN-C(L) immunoreactivity at the cell-cell contacts of the basal and suprabasal cell layers of the wound epithelium. During granulation tissue formation and reorganization from 7 to 28 days after wounding, TN-C and TN-C(L) were abundantly localized in the granulation tissue. The findings show that TN-C(L) is expressed under the migrating epithelial front and in the granulation tissue during matrix deposition in wound repair. Preferential localization of alpha9 integrin in migrating epithelial cells and of alphavbeta6 integrin in epithelium after wound closure suggests different functions for these integrins in wound repair.
Heterogeneity and hierarchy within the most primitive hematopoietic stem cell compartment (2010)

Hematopoietic stem cells (HSCs) have been extensively characterized based on functional definitions determined by experimental transplantation into lethally irradiated mice. In mice, HSCs are heterogeneous with regard to self-renewal potential, in vitro colony-forming activity, and in vivo behavior. We attempted prospective isolation of HSC subsets with distinct properties among CD34(-/low) c-Kit+Sca-1+Lin- (CD34-KSL) cells. CD34-KSL cells were divided, based on CD150 expression, into three fractions: CD150high, CD150med, and CD150neg cells. Compared with the other two fractions, CD150high cells were significantly enriched in HSCs, with great self-renewal potential. In vitro colony assays revealed that decreased expression of CD150 was associated with reduced erythroblast/megakaryocyte differentiation potential. All three fractions were regenerated only from CD150high cells in recipient mice. Using single-cell transplantation studies, we found that a fraction of CD150high cells displayed latent and barely detectable myeloid engraftment in primary-recipient mice but progressive and multilineage reconstitution in secondary-recipient mice. These findings highlight the complexity and hierarchy of reconstitution capability, even among HSCs in the most primitive compartment.
Silicon nanostructures for thermoelectric devices: A review of the current state of the art (2014)

Silicon is the most important element of modern semiconductor industry. As a thermoelectric converter material, it would be able to promote applications dramatically since device integration and scaling of the fabrication processes could be borrowed from existing technology. Though the thermoelectric performance of single crystalline silicon is only poor, silicon nanostructures have demonstrated a competitive figure of merit. To make use of these nanostructures, novel device architectures are necessary. This review provides an overview over the physical background of silicon as thermoelectric converter material as well as different nanostructures like nanowires, porous nanomeshes, and nanocrystalline bulk and their thermoelectric properties, focusing mostly on experimental data. Further, different thermoelectric converter device concepts including nanowire device concepts, pn junction thermoelectric generators and integrated spot coolers are discussed and their realization with silicon nanostructures briefly sketched. (a) Nanowires, porous nanomeshes and nanocrystalline bulk with promising thermoelectric material's figure of merit. (b) Innovative device concepts using nanowires or large area pn junctions for thermoelectric heat‐to‐electricity conversion.
Human Milk Glycomics and Gut Microbial Genomics in Infant Feces Show a Correlation between Human Milk Oligosaccharides and Gut Microbiota: A Proof-of-Concept Study (2014)

Human milk oligosaccharides (HMOs) play a key role in shaping and maintaining a healthy infant gut microbiota. This article demonstrates the potential of combining recent advances in glycomics and genomics to correlate abundances of fecal microbes and fecal HMOs. Serial fecal specimens from two healthy breast-fed infants were analyzed by bacterial DNA sequencing to characterize the microbiota and by mass spectrometry to determine abundances of specific HMOs that passed through the intestinal tract without being consumed by the luminal bacteria. In both infants, the fecal bacterial population shifted from non-HMO-consuming microbes to HMO-consuming bacteria during the first few weeks of life. An initial rise in fecal HMOs corresponded with bacterial populations composed primarily of non-HMO-consuming Enterobacteriaceae and Staphylococcaeae. This was followed by decreases in fecal HMOs as the proportion of HMO-consuming Bacteroidaceae and Bifidobacteriaceae increased. Analysis of HMO structures with isomer differentiation revealed that HMO consumption is highly structure-specific, with unique isomers being consumed and others passing through the gut unaltered. These results represent a proof-of-concept and are consistent with the highly selective, prebiotic effect of HMOs in shaping the gut microbiota in the first weeks of life. The analysis of selective fecal bacterial substrates as a measure of alterations in the gut microbiota may be a potential marker of dysbiosis.
Antimicrobial Efficacy of Two Surface Barrier Discharges with Air Plasma against In Vitro Biofilms (2013)

The treatment of infected wounds is one possible therapeutic aspect of plasma medicine. Chronic wounds are often associated with microbial biofilms which limit the efficacy of antiseptics. The present study investigates two different surface barrier discharges with air plasma to compare their efficacy against microbial biofilms with chlorhexidine digluconate solution (CHX) as representative of an important antibiofilm antiseptic. Pseudomonas aeruginosa SG81 and Staphylococcus epidermidis RP62A were cultivated on polycarbonate discs. The biofilms were treated for 30, 60, 150, 300 or 600 s with plasma or for 600 s with 0.1% CHX, respectively. After treatment, biofilms were dispensed by ultrasound and the antimicrobial effects were determined as difference in the number of the colony forming units by microbial culture. A high antimicrobial efficacy on biofilms of both plasma sources in comparison to CHX treatment was shown. The efficacy differs between the used strains and plasma sources. For illustration, the biofilms were examined under a scanning electron microscope before and after treatment. Additionally, cytotoxicity was determined by the MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay with L929 mouse fibroblast cell line. The cell toxicity of the used plasma limits its applicability on human tissue to maximally 150 s. The emitted UV irradiance was measured to estimate whether UV could limit the application on human tissue at the given parameters. It was found that the UV emission is negligibly low. In conclusion, the results support the assumption that air plasma could be an option for therapy of chronic wounds.
Metallotetrabenzoporphyrins. New phosphorescent probes for oxygen measurements (1995)

Tetrabenzoporphyrins (TBP) of Zn, Pd, Lu, Y, Sn and Pb have been synthesized and Pd, Sn and Lu complexes characterized by 1H NMR spectroscopy. Phosphorescence at room temperature in DMF solutions was measured for Pd and Lu complexes giving quantum yields of 7.9% and 3.5% and lifetimes of 250 µs and 870 µs, respectively. Pd meso-tetraphenyltetrabenzoporphyrin 1(PdPh4TBP) was synthesized, characterized by 1H NMR and showed a red shift of the Q-band to 628 nm. Electronic absorption spectra of synthesized complexes are briefly discussed with relation to their structures. Complex 1 reacted with ClSO3H and the obtained chlorosulfonato derivative 2 was converted into two water soluble chromophores: Pd meso-tetra(sulfophenyl)tetrabenzoporphyrin [PdPh4(SO3Na)4TBP]3 and the corresponding sulfonamide [PdPh4(PEG)4TBP]4 with aminopoly(ethyleneglycol)(Mav 5000). Electronic absorption and phosphorescence spectra of 1 and its derivatives were recorded and phosphorescence quantum yields and lifetimes were measured for deoxygenated solutions. The oxygen quenching constants were measured for water-soluble complexes and the effect of binding to a large protein, serum albumin, on the phosphorescence characteristics was examined.Metallotetrabenzoporphyrins were found to be useful phosphors for oxygen measurements in biological systems.
Context-aware textures (2007)

Interesting textures form on the surfaces of objects as the result of external chemical, mechanical, and biological agents. Simulating these textures is necessary to generate models for realistic image synthesis. The textures formed are progressively variant, with the variations depending on the global and local geometric context. We present a method for capturing progressively varying textures and the relevant context parameters that control them. By relating textures and context parameters, we are able to transfer the textures to novel synthetic objects. We present examples of capturing chemical effects, such as rusting; mechanical effects, such as paint cracking; and biological effects, such as the growth of mold on a surface. We demonstrate a user interface that provides a method for specifying where an object is exposed to external agents. We show the results of complex, geometry-dependent textures evolving on synthetic objects.
Complement‐induced activation of MAPKs and Akt during sepsis: role in cardiac dysfunction (2017)

Polymicrobial sepsis in mice causes myocardial dysfunction after generation of the complement anaphylatoxin, complement component 5a (C5a). C5a interacts with its receptors on cardiomyocytes (CMs), resulting in redox imbalance and cardiac dysfunction that can be functionally measured and quantitated using Doppler echocardiography. In this report we have evaluated activation of MAPKs and Akt in CMs exposed to C5a <i>in vitro</i> and after cecal ligation and puncture (CLP) <i>in vivo</i> In both cases, C5a <i>in vitro</i> caused activation (phosphorylation) of MAPKs and Akt in CMs, which required availability of both C5a receptors. Using immunofluorescence technology, activation of MAPKs and Akt occurred in left ventricular (LV) CMs, requiring both C5a receptors, C5aR1 and -2. Use of a water-soluble p38 inhibitor curtailed activation <i>in vivo</i> of MAPKs and Akt in LV CMs as well as the appearance of cytokines and histones in plasma from CLP mice. When mouse macrophages were exposed <i>in vitro</i> to LPS, activation of MAPKs and Akt also occurred. The copresence of the p38 inhibitor blocked these activation responses. Finally, the presence of the p38 inhibitor in CLP mice reduced the development of cardiac dysfunction. These data suggest that polymicrobial sepsis causes cardiac dysfunction that appears to be linked to activation of MAPKs and Akt in heart.-Fattahi, F., Kalbitz, M., Malan, E. A., Abe, E., Jajou, L., Huber-Lang, M. S., Bosmann, M., Russell, M. W., Zetoune, F. S., Ward, P. A. Complement-induced activation of MAPKs and Akt during sepsis: role in cardiac dysfunction.
Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family. (1985)

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase pairs and is split into seven exons. Its promoter contains putative TATA and CCAAT boxes and is extremely rich in G and C residues (76%). The pseudogenes share a high degree of homology with the functional gene but contain mutations that preclude the synthesis of an active triosephosphate isomerase enzyme. Sequence divergence calculations indicate that these pseudogenes arose approximately 18 million years ago. We present evidence that there is a single functional gene in the human triosephosphate isomerase gene family.
Evolution of the C-Type Lectin-Like Receptor Genes of the DECTIN-1 Cluster in the NK Gene Complex (2012)

Pattern recognition receptors are crucial in initiating and shaping innate and adaptive immune responses and often belong to families of structurally and evolutionarily related proteins. The human C-type lectin-like receptors encoded in the DECTIN-1 cluster within the NK gene complex contain prominent receptors with pattern recognition function, such as DECTIN-1 and LOX-1. All members of this cluster share significant homology and are considered to have arisen from subsequent gene duplications. Recent developments in sequencing and the availability of comprehensive sequence data comprising many species showed that the receptors of the DECTIN-1 cluster are not only homologous to each other but also highly conserved between species. Even in Caenorhabditis elegans, genes displaying homology to the mammalian C-type lectin-like receptors have been detected. In this paper, we conduct a comprehensive phylogenetic survey and give an up-to-date overview of the currently available data on the evolutionary emergence of the DECTIN-1 cluster genes.
Expression of human pim family genes is selectively up‐regulated by cytokines promoting T helper type 1, but not T helper type 2, cell differentiation (2005)

Cytokines are the most important inducers of T helper (Th) cell differentiation. Interleukin-12 (IL-12) and interferon-alpha (IFN-alpha) are responsible for human Th1-cell differentiation, while IL-4 is the critical cytokine promoting Th2-cell development. These two subsets of cells co-ordinate immunological responses to pathogens as well as autoimmune or allergic reactions. The pim family of proto-oncogenes encodes serine/threonine-specific kinases involved in cytokine-mediated signalling pathways in haematopoietic cells. Here we demonstrate that expression of pim-1 and pim-2 mRNAs is selectively up- or down-regulated in human cord-blood-derived CD4+ cells freshly induced to polarize towards Th1 or Th2 cells, respectively, whereas their expression is inhibited in both cell types by the immunosuppressive transforming growth factor beta (TGF-beta). Moreover, the Th1-specific cytokines IL-12 and IFN-alpha, but not the Th2-specific cytokine IL-4, transiently up-regulate pim-1 and pim-2 mRNA expression in human peripheral blood T cells and natural killer cells. In addition, the Pim-1 protein levels are strongly up-regulated by Th1-specific cytokines in all of these cell types. Taken together, our results suggest that pim genes and their protein products are involved in the early differentiation process of T helper cells.
Timing of Complications in Percutaneous Renal Biopsy (2004)

Percutaneous renal biopsy (PRB) is a safe and effective tool in the diagnosis and management of renal disease; however, the optimal timing of observation after biopsy is not clearly established. With the use of real-time ultrasound guidance, PRB of native kidneys was performed in 750 adult patients at an academic institution by an attending nephrologist or fellow between June 1983 and June 2002. All patients were observed for 23 to 24 h after biopsy for the presence, severity, and timing of complications. Biopsy-related complications occurred in 98 (13%) patients; minor complications occurred in 50 (6.6%) patients, and major complications occurred in 48 (6.4%) patients. One (0.1%) patient died as a result of the biopsy. Multivariate analysis using logistic regression found only serum creatinine at baseline predictive of a complication. Patients with a serum creatinine > or = 5.0 mg/dl were 2.3 times as likely to have a complication (odds ratio, 2.3; 95% confidence interval, 1.3 to 4.1; P < 0.005). Complications were identified in 38 (42%) patients by < or = 4 h, in 61 (67%) patients by < or = 8 h, in 77 (85%) patients by < or = 12 h, and in 81 (89%) patients at < or = 24 h. The PRB remains a safe procedure, but the risk of complication is higher in patients with advanced renal insufficiency. After biopsy, an observation time of up to 24 h remains optimal as an observation period of < or = 8 h risks missing > or = 33% of complications.