gebhart/patrepeval huggingface dataset:
Flow Cytometric Analysis of Adherence of Porphyromonas gingivalis to Oral Epithelial Cells (2007)

By using fluorescence microscopy, fluorescently labeled Porphyromonas gingivalis W50 was shown to adhere to oral epithelial (KB) cells as discrete cells or small cell aggregates, whereas P. gingivalis ATCC 33277 bound as large cell aggregates. Flow cytometric analysis showed that for P. gingivalis W50 there was a logarithmic relationship between the bacterial cell ratio (BCR), that is the number of bacterial cells to KB cells, and the percentage of KB cells with W50 cells attached. This percentage of KB cells with W50 attached reached a plateau of approximately 84% cells at a BCR of 500:1. In contrast, a quadratic relationship was observed between BCR and the percentage of KB cells with P. gingivalis ATCC 33277 attached, reaching a maximum of 47% at a BCR of 100:1 but decreasing to 7% at a BCR of 1,000:1. The lower binding of ATCC 33277 at high cell concentrations was attributed to autoaggregation. P. gingivalis W50 cells treated with an inhibitor (Nalpha-p-tosyl-L-lysine chloromethyl ketone [TLCK]) of its RgpA-Kgp proteinase-adhesin complex exhibited significantly reduced binding to KB cells than to untreated cells, suggesting a role for proteinase activity in binding to KB cells. Competitive inhibition with purified proteinase-active and TLCK-inactivated RgpA-Kgp complex significantly decreased the adherence of P. gingivalis W50 cells to KB cells. Furthermore, isogenic mutants of P. gingivalis W50 lacking the kgp gene product, but not the rgpA or rgpB gene products, exhibited significantly decreased adherence to KB cells compared to the wild type.
In vivo relevance of citrullinated proteins and the challenges in their detection (2012)

Citrullination is a posttranslational modification of arginine. It plays both a physiological role, for instance during apoptosis and epigenetics, and a pathological role in cancer or diseases of the central nervous system. Most research on citrullination to date focuses on its role in auto-immune diseases such as multiple sclerosis and rheumatoid arthritis. In this context, the exact knowledge of citrullination sites in a protein can provide invaluable information about the etiological importance of these citrullinated proteins. However, few techniques exist that can accurately detect citrullination on the peptide level. This review aims to give an overview of the different methods available to date for the detection of citrullinated proteins and peptides. These include 2D-SDS-PAGE and immunodetection, as well as specific mass spectrometry (MS) approaches, both labeled and unlabeled. These MS approaches have been developed to pinpoint the exact location of citrullination on the peptide level. Improving the currently existing detection strategies while focusing on the role of citrullinated proteins will be invaluable to elucidate the importance of this posttranslational modification in vivo.
Characteristic patterns of hox gene expression in different types of human leukemia (1993)

Homeobox-containing genes are a network of genes encoding DNA-binding proteins highly conserved throughout evolution. They are involved in the control of normal development as well as in the regulation of gene expression in adult differentiating systems, including hematopoiesis. Aberrant expression of homeobox-containing genes has recently been related to leukemic phenotype. Human homeobox-containing genes of the HOX family are organized into 4 large clusters. We have analyzed the expression of HOX genes in different types of human leukemia to investigate whether the physical organization of HOX loci reflects a regulatory hierarchy involved in the differentiation of hematopoietic cells or whether HOX gene expression might contribute to the leukemic phenotype. Our results show that HOX genes are coordinately regulated in blocks in myeloid cells whereas they appear to function as isolated genes in lymphoid cells. Six contiguous genes of the HOX2 locus, highly expressed in acute non-lymphocytic leukemia, are switched off in chronic myelogenous leukemia, suggesting that down-regulation of HOX2 genes might be required for cell maturation of the myeloid lineages. In contrast, a few scattered genes are active in lymphoid populations. These observations suggest that hematopoietic cells express a repertoire of HOX genes characteristic of a particular cell lineage at a specific stage of differentiation. The characteristic patterns of HOX gene expression may reflect the potentially important role that these genes play in cell lineage determination during both normal and leukemic hematopoiesis.
Auditory Cortical Responses to Electrical Stimulation of the Inferior Colliculus: Implications for an Auditory Midbrain Implant (2006)

The success and limitations of cochlear implants (CIs) along with recent advances in deep brain stimulation and neural engineering have motivated the development of a central auditory prosthesis. In this study, we investigated the effects of electrical stimulation of the inferior colliculus central nucleus (ICC) on primary auditory cortex (A1) activity to determine the potential benefits of an auditory midbrain implant (AMI). We recorded multiunit activity in A1 of ketamine-anesthetized guinea pigs in response to single-pulse (200 micros/phase) monopolar stimulation of the ICC using multisite silicon-substrate probes. We then compared measures of threshold, dynamic range, and tonotopic spread of activation for ICC stimulation with that of published data for CI stimulation. Our results showed that compared with cochlear stimulation, ICC stimulation achieved: 1) thresholds about 8 dB lower; 2) dynamic ranges > or = 4 dB greater; and 3) more localized, frequency-specific activation, even though frequency specificity was partially lost at higher stimulus levels for low-frequency ICC regions. Our results also showed that stimulation of rostral ICC regions elicited lower thresholds but with greater activation spread along the tonotopic gradient of A1 than did stimulation of more caudal regions. These results suggest that an AMI may improve frequency and level coding with lower energy requirements compared with CIs. However, a trade-off between lower perceptual thresholds and better frequency discrimination may exist that depends on location of stimulation along the caudorostral dimension of the ICC. Overall, this study provides the foundation for future AMI research and development.
Fluorescent peptide probes for in vivo diagnostic imaging (2004)

Recently, many novel peptide-based near-infrared (NIR) fluorescent molecular probes have been developed for in vivo biomedical imaging. To report specific information of biological targets, the probes were individually designed according to the unique property or functions of their targets. These peptide-based probes can be classified into targeting, crosslinking, and enzyme-activatable probes. Several of them have been tested in various in vitro and in vivo models, and the obtained imaging information has been applied to disease detection, medical diagnosis, and drug evaluations.
Bioavailability of insulin-like growth factors (IGFs) in rats determined by the molecular distribution of human IGF-binding protein-3 (1993)

Insulin-like growth factor-binding protein-3 (IGFBP-3) forms a 140-kilodalton (kDa) complex with an acid-labile glycoprotein after complexing with IGF-I or IGF-II. To investigate the bioavailability of circulating IGFs in the rat, we determined the molecular distribution and disappearance of an iv bolus of human IGFBP-3 (130 micrograms/kg). Serum fractions were assayed after size-separation chromatography for human (h) and rat (r) IGFBP-3 with specific RIAs. Within 2 min of injection, 52.9 +/- 1.6% of the hIGFBP-3 appeared in a 140-kDa complex. This form remained in the circulation for hours, whereas hIGFBP-3 in 50- and 30-kDa forms disappeared within 30-60 min. The rapid complexing of hIGFBP-3 to the 140-kDa form did not occur in vitro. Measurement of endogenous rIGFBP-2 indicated that there was minimal exchange of hIGFBP-3 with rIGFBP-3 in the 140-kDa complex within the 60 min of the in vivo study. To determine the importance of IGF-I in regulating the molecular distribution of hIGFBP-3 in serum, the experiment was repeated in streptozotocin-diabetic rats, with total IGF-I levels 50% lower than control values. In these animals, 40.1 +/- 5.2% of the hIGFBP-3 appeared in the 140-kDa complex 2 min after injection, significantly less than that in controls (P < 0.05), and hIGFBP-3 disappeared more quickly from the circulation than in controls (P < 0.05). After coinjection of recombinant human IGF-I, the retention of hIGFBP-3 in the circulation was prolonged in both control and diabetic animals. Because IGFBP-3 must bind IGF before it can associate with the acid-labile subunit, these findings indicate a much greater availability of IGFs to the circulation than previously estimated.
Evidence for Positive and Negative Regulatory Elements in the 5′-Flanking Sequence of the Mouse Sparc (osteonectin) Gene (1989)

We have investigated the role of 5'-flanking DNA sequences in regulating the expression of the murine Sparc (osteonectin) gene in parietal endoderm cells and in F9 embryonal carcinoma cells induced to differentiate into parietal endoderm with retinoic acid and cyclic AMP. Varying lengths of flanking sequences extending up to 3.0 kilobase pairs 5' of the transcription initiation site were linked to the bacterial chloramphenicol transacetylase gene in the Bluescript M13- vector. The constructs were tested in transient assays, using a beta-galactosidase plasmid as a transfection control. Sequences between 78 and 169 base pairs upstream of the cap site are the minimum required for cell-type specific promoter activity; this region is dominated by two oligopurine/oligopyrimidine stretches or "GAGA" boxes and is highly conserved between the mouse and bovine genes. Addition of the sequence between -169 and -449, which includes part or all of a third GAGA box, results in increased parietal endoderm specific transcription, up to a maximum of 6.3-fold higher than in undifferentiated F9 cells. Further addition of sequences between -449 and -638 markedly reduces promoter activity in both cell types but parietal endoderm-specific activity is restored in constructs containing 2.2 and 3.0 kilobase pairs of flanking DNA. In addition, we have identified sequences related to the consensus sequence for steroid response elements, one of which is able to confer progesterone-enhanced transcription when tested with a heterologous promoter in steroid responsive cells. These results suggest that negative and positive elements normally interact to regulate the temporal and tissue-specific patterns of Sparc gene transcription seen in vivo.
Constitutive activation of the alpha 1B-adrenergic receptor by all amino acid substitutions at a single site. Evidence for a region which constrains receptor activation. (1992)

Mutations in an intracellular region of the alpha 1B-adrenergic receptor constitutively activate the receptor, resulting in G protein coupling in the absence of agonist, as evidenced by elevated levels of polyphosphoinositide hydrolysis. Remarkably, all 19 possible amino acid substitutions at a single site in this region (alanine 293) confer constitutive activity. This set of mutated receptors exhibits a graded range of elevated biological activities, apparently representing a spectrum of receptor conformations which mimic the "active" state of the wild type receptor. In addition to their constitutive activities, these mutated receptors all demonstrate a higher affinity for agonists, another primary characteristic of the "active" conformation of G protein-coupled receptors. The fact that all possible mutations at this particular site result in increased activity suggests that this region may function to constrain the G protein coupling of the receptor, a constraint which is normally relieved by agonist occupancy.
Supported choline chloride/urea as a heterogeneous catalyst for chemical fixation of carbon dioxide to cyclic carbonates (2006)

In this work, the catalytic efficiency of ionic liquid (IL) choline chloride/urea supported on molecular sieves for the reactions of CO2 and epoxides was studied under different conditions. It was demonstrated that this biodegradable and green catalyst is very active and selective, and choline chloride and urea showed a synergetic effect in promoting these reactions. After reaction, the solid catalyst and the products could be separated easily because the IL was insoluble in the products, and the catalyst was reusable. The origin of the high catalytic efficiency and the reaction mechanism were also discussed.
Enhanced UK Teletext Moves Towards Still Pictures (1980)

The UK teletext system has been a full public service for almost four years, and the specification of the system has remained unaltered. It is expected that by the end of 1980 there will be more than 100 000 teletext receivers in use. There is no doubt that the system rests on a firm technical foundation and the deliberate attempt made to stretch technology at the time the specification was formulated means that the system is giving the highest possible information transfer rate consistent with ruggedness and freedom from errors.
DESIGN, MANUFACTURING, AND TESTING OF A NOVEL PLASTIC BALL GRID ARRAY PACKAGE (1999)

The design, manufacturing, analysis, and measurement of a thermal and electrical enhanced cavity-down plastic ball grid array (PBGA) package are presented in this study. Because of the split via connection (SVC) design, the package consists of a very-thin single core of organic material and two-metal layers of copper and is manufactured with the conventional printed circuit board (PCB) process at very low cost. Furthermore, the heat spreader is made with bottom surface having saw-teeth to contact the ground planes disposed on the backside of the substrate. Improvements in electrical and thermal performance are achieved. Parasitic parameters of the package are extracted from time domain reflectometer (TDR) measurements. The thermal performances of the packages are studied by both 3D finite element analysis and wind-tunnel measurements. The results are compared with other well-known packages.
Toll-Like Receptor 4-Dependent Activation of Dendritic Cells by β-Defensin 2 (2002)

beta-Defensins are small antimicrobial peptides of the innate immune system produced in response to microbial infection of mucosal tissue and skin. We demonstrate that murine beta-defensin 2 (mDF2beta) acts directly on immature dendritic cells as an endogenous ligand for Toll-like receptor 4 (TLR-4), inducing up-regulation of costimulatory molecules and dendritic cell maturation. These events, in turn, trigger robust, type 1 polarized adaptive immune responses in vivo, suggesting that mDF2beta may play an important role in immunosurveillance against pathogens and, possibly, self antigens or tumor antigens.
Sphingomyelinases: enzymology and membrane activity (2002)

This paper reviews our present knowledge of sphingomyelinases as enzymes, and as enzymes acting on a membrane constituent lipid, sphingomyelin. Six types of sphingomyelinases are considered, namely acidic, secretory, Mg(2+)-dependent neutral, Mg(2+)-independent neutral, alkaline, and bacterial enzymes with both phospholipase C and sphingomyelinase activity. Sphingomyelinase assay methods and specific inhibitors are reviewed. Kinetic and mechanistic studies are summarized, a kinetic model and a general-base catalytic mechanism are proposed. Sphingomyelinase-membrane interactions are considered from the point of view of the influence of lipids on the enzyme activity. Moreover, effects of sphingomyelinase activity on membrane architecture (increased membrane permeability, membrane aggregation and fusion) are described. Finally, a number of open questions on the above topics are enunciated.
Expression, purification and characterization of recombinant human N-acetylgalactosamine-6-sulphatase (1995)

Full-length cDNA sequences encoding human N-acetylgalactosamine-6-sulphatase were stably expressed in Chinese hamster ovary cells under the transcriptional control of the human polypeptide chain elongation factor 1 alpha gene promoter. A clonal cell line overexpressing recombinant N-acetylgalactosamine-6-sulphatase to a level of approx. 3 mg/l of culture medium was isolated. The secreted precursor enzyme was purified to homogeneity by a two-column procedure with an overall yield of 53% of the activity. The physical and catalytic parameters of the recombinant enzyme were similar to those of the mature form isolated from liver. On SDS/PAGE and gel filtration, recombinant N-acetylgalactosamine-6-sulphatase had a native molecular mass of 58-60 kDa. Recombinant N-acetylgalactosamine-6-sulphatase was endocytosed by mucopolysaccharidosis IVA fibroblasts via the mannose-6-phosphate receptor-mediated pathway and was efficiently localized to lysosomes.
Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square and pentagon nanovehicles (2014)

Modulation of immune response is important in cancer immunotherapy, vaccine adjuvant development and inflammatory or immune disease therapy. Here we report the development of new immunomodulators via control of shape transition among RNA triangle, square and pentagon. Changing one RNA strand in polygons automatically induced the stretching of the interior angle from 60° to 90° or 108°, resulting in self-assembly of elegant RNA triangles, squares and pentagons. When immunological adjuvants were incorporated, their immunomodulation effect for cytokine TNF-α and IL-6 induction was greatly enhanced in vitro and in animals up to 100-fold, while RNA polygon controls induced unnoticeable effect. The RNA nanoparticles were delivered to macrophages specifically. The degree of immunostimulation greatly depended on the size, shape and number of the payload per nanoparticles. Stronger immune response was observed when the number of adjuvants per polygon was increased, demonstrating the advantage of shape transition from triangle to pentagon.
GabR, a member of a novel protein family, regulates the utilization of γ‐aminobutyrate in Bacillus subtilis (2002)

The Bacillus subtilis ycnG (gabT) and ycnH (gabD) genes were shown to encode gamma-aminobutyrate (GABA) aminotransferase and succinic semi-aldehyde dehydrogenase, respectively, and to form a GABA-inducible operon. Null mutations in gabT, gabD or the divergently transcribed ycnF (gabR) gene blocked the utilization of GABA as sole nitrogen source. GabR proved to be a transcriptional activator of the gabTD operon and a negative autoregulator. The target of GabR action was localized to an 87 bp region that includes both gabR and gabT promoters. GabR is a member of a novel but widespread family of chimeric bacterial proteins that have apparent DNA-binding and aminotransferase domains. Mutations in conserved residues of the putative aminotransferase domain abolished GabR function as a transcriptional activator, but did not affect its activity as a negative autoregulator.
Molecular Chaperone Hsp90 Is Important for Vaccinia Virus Growth in Cells (2002)

Molecular chaperones assist protein folding, and some chaperones are induced by heat, nutrient depletion, or pathogen invasion. This study investigates the role played by Hsp90 in the life cycle of vaccinia virus. The titer of vaccinia intracellular mature virions (IMV) was reduced by 2 orders of magnitude in RK13 cells treated with geldanamycin (GA), which blocks the ATPase activity of Hsp90. GA does not affect expression from the viral early promoter, but treatment with GA delays DNA replication and intermediate gene transcription and reduces expression from the viral late promoter. Vaccinia virus infection does not induce Hsp90 expression; however, intracellular distribution of Hsp90 is altered in virus-infected cells. Hsp90 is restricted to the cytoplasm of mock-infected cells; in contrast, Hsp90 is transiently associated with virosomes in virus-infected cells although it is not incorporated into IMV. In addition, Hsp90 interacts with viral core protein 4a, the mature form of the A10L gene product, in virus-infected cells. In conclusion, these results suggest that a cellular chaperone protein, Hsp90, is important for vaccinia virus growth in cultured cells and that viral core protein 4a associates with Hsp90-containing complexes in the infected cells.
Modulation of Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand-Induced Apoptosis by Chemotherapy in Thyroid Cancer Cell Lines (2003)

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) induces apoptosis in many human cancer cells but not in normal cells. Thyroid cancer cells, however, appear to be relatively resistant to TRAIL-induced apoptosis. We therefore investigated the effect of chemotherapy on TRAIL-induced apoptosis in thyroid cancer cells. We used six thyroid cancer cell lines: TPC-1, FTC-133, FTC-236, FTC-238, XTC-1, and ARO82-1. We used flow cytometry to measure apoptosis, dimethyl-thiazol-diphenyltetrazolium bromide (MTT) assay to measure antiproliferation effects and Western blot to determine the expression of Bcl family proteins. Troglitazone, paclitaxel, geldanamycin, and cycloheximide were used for pretreatment. We used the Student's t test and analysis of variance (ANOVA) for statistical analysis. All thyroid cancer cell lines, except the TPC-1 cell line, were resistant to TRAIL, and growth inhibition was less than 20% at concentration of 800 ng/mL of TRAIL. In both TPC-1 (TRAIL-sensitive) and FTC-133 (TRAIL-resistant) thyroid cancer cell lines, pretreatment with troglitazone, cycloheximide, and paclitaxel enhanced TRAIL-induced cell death significantly but pretreatment with geldanamycin did not. There were no significant changes in Bcl-2, Bcl-xl, and Bax protein expression after troglitazone treatment. In conclusion, TRAIL in combination with troglitazone, paclitaxel, and cycloheximide induces apoptosis in thyroid cancer cells at suboptimal concentrations that cannot be achieved using TRAIL alone.
Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis (2020)

World Health Organization.