gebhart/patrepeval huggingface dataset:
Phosphatidic Acid and Lysophosphatidic Acid Induce Haptotactic Migration of Human Monocytes (1995)

The present study was aimed at defining the chemotactic activity of phosphatidic acid, which is rapidly produced by phagocytes in response to chemotactic agonists. Exogenously added phosphatidic acid induced human monocyte directional migration across polycarbonate filters with an efficacy (number of cell migrated) comparable to that of "classical" chemotactic factors. In lipid specificity studies, activity of phosphatidic acid decreased with increasing acyl chain length but was restored by introducing unsaturation in the acyl chain with the most active form being the natural occurring 18:0,20:4-phosphatidic acid. Lysophosphatidic acid was also active in inducing monocyte migration. No other phospholipid and lysophospholipid tested was effective in this response. Monocyte migration was regulated by a gradient of phosphatidic acid and lysophosphatidic acid bound to the polycarbonate filter, in the absence of detectable soluble chemoattractant. Migration was also observed if phospholipids were bound to fibronectin-coated polycarbonate filters. Thus, phosphatidic acid and lysophosphatidic acid, similarly to other physiological chemoattractants (e.g. C5a and interleukin-8), induce cell migration by an haptotactic mechanism. Phosphatidic acid caused a rapid increase of filamentous actin and, at higher concentrations, induced a rise of intracellular calcium concentration. Monocyte migration to phosphatidic acid and lysophosphatidic acid, but not to diacylglycerol, was inhibited in a concentration-dependent manner by Bordetella pertussis toxin, while cholera toxin was ineffective. In the chemotactic assay, phosphatidic acid and lysophosphatidic acid induced a complete homologous desensitization and only partially cross-desensitized one with each other, or with diacyl-glycerol and monocyte chemotactic protein-1. Suramine inhibited monocyte chemotaxis with a different efficiency phosphatidic acid > lysophosphatidic acid" diacyl-glycerol On the contrary, monocyte chemotactic protein-1-induced chemotaxis was not affected by the drug. Collectively, these data show that phosphatidic acid induces haptotactic migration of monocytes that is at least in part receptor-mediated. These results support a role for phosphatidic acid and lysophosphatidic acid in the regulation of leukocyte accumulation into tissues.
Penicillin V-conjugated PEG-PAMAM star polymers (2003)

Starburst PAMAM dendrimers are potential carriers for drug delivery due to their unique structure. Drug-delivery scaffolds were designed and built up based on the polyethylene glycolpolyamidoamine (PEG-PAMAM) star polymer. Penicillin V was used as a model carboxylic group containing drug to conjugate with full- and half-generation PAMAM dendrimers. G2.5 PAMAM (with 32 carboxylic groups on the surface) dendrimers and G3.0 (with 32 primary amine groups on the surface) were typically chosen. There are two strategies given in the paper where a drug carrying a carboxylic group (e.g. penicillin V) was coupled to star polymer via amide and ester bonds, respectively. FT-IR, UV-Vis and 1H-NMR were used to characterize the intermediates and drug-star polymer conjugates. A single-strain bacterium, Staphylococcus aureus, was grown up for penicillin-conjugated PEG-PAMAM (G3.0) star polymer activity test. The result verified the bioavailability of modified penicillin after the ester bond was cleaved.
Nature of Polyphenol−Protein Interactions (1996)

Proteins and polyphenols were combined in model systems, and the resulting hazes were measured by light scattering. The amount of haze formed depends both on the concentrations of protein and polyphenol and on their ratio. A conceptual model in which a protein molecule has a fixed number of polyphenol binding sites explains the observed behavior and has implications for turbidimetric methods for estimating haze-active protein and haze-active polyphenol in beverages. The ranking of haze-forming activity of the test polypeptides was different with tannic acid than with catechin; this indicates differences in binding site availability, bridging ability, or specificity for the two polyphenols. More haze was observed when model systems were heated, suggesting that polyphenol binding sites are exposed when protein hydrogen bonds are broken. Freshly formed haze dissolved when dimethylformamide or dioxane was added; this may be useful for recovering compounds from isolated hazes for analysis. Keywords: Haze-active protein; haze-active polyphenol; beverages; model systems; gelatin; tannic acid
Isolation and Preliminary Characterization of Lytic and Lysogenic Phages with Wide Host Range within the Streptomycetes (1985)

Examination of approximately 700 soil samples yielded about 100 actinophages. Restriction analysis of phage DNA indicated that 57 are unique, and of these, 20 produce turbid plaques on one or more of the streptomycetes tested. Five phages are shown to insert into the genome of Streptomyces avermitilis. None of the phages was able to perform generalized transduction of S. avermitilis.
Human Slug Is a Repressor That Localizes to Sites of Active Transcription (2000)

Snail/Slug family proteins have been identified in diverse species of both vertebrates and invertebrates. The proteins contain four to six zinc fingers and function as DNA-binding transcriptional regulators. Various members of the family have been demonstrated to regulate cell movement, neural cell fate, left-right asymmetry, cell cycle, and apoptosis. However, the molecular mechanisms of how these regulators function and the target genes involved are largely unknown. In this report, we demonstrate that human Slug (hSlug) is a repressor and modulates both activator-dependent and basal transcription. The repression depends on the C-terminal DNA-binding zinc fingers and on a separable repression domain located in the N terminus. This domain may recruit histone deacetylases to modify the chromatin and effect repression. Protein localization study demonstrates that hSlug is present in discrete foci in the nucleus. This subnuclear pattern does not colocalize with the PML foci or the coiled bodies. Instead, the hSlug foci overlap extensively with areas of the SC-35 staining, some of which have been suggested to be sites of active splicing or transcription. These results lead us to postulate that hSlug localizes to target promoters, where activation occurs, to repress basal and activator-mediated transcription.
Band 3 is an anchor protein and a target for SHP-2 tyrosine phosphatase in human erythrocytes (2002)

Tyr phosphorylation of the multifunctional transmembrane protein band 3 has been implicated in several erythrocyte functions and disorders. We previously demonstrated that pervanadate treatment of human erythrocytes induces band-3 Tyr phosphorylation, which is catalyzed by the sequential action of tyrosine kinase Syk and tyrosine kinase(s) belonging to the Src family. In this study, we show that Tyr phosphorylation of band 3, elicited by pervanadate, N-ethylmaleimide, or diamide, greatly increases band-3 interaction with the tyrosine phosphatase SHP-2 in parallel with the translocation of SHP-2 to erythrocyte membranes. These events seem to be mediated by Src-like catalyzed phosphorylation of band 3 because both SHP-2 translocation to cellular membranes and its interaction with Tyr-phosphorylated protein are greatly counteracted by PP2, a specific inhibitor of Src kinases. Binding-competition experiments demonstrate that SHP-2 recruitment to band 3 occurs via its SH2 domain(s). In particular, our data support the view that SHP-2 docks specifically with P-Y359 of band 3. Experiments performed with intact erythrocytes in the presence of the SHP-2 inhibitor calpeptin suggest that, once recruited to Tyr-phosphorylated band 3, the tyrosine phosphatase dephosphorylates the protein. P-Y8, 21, and 904 are the residues affected by SHP-2, as judged by (32)P-peptide mapping of band 3 digested with trypsin. These results indicate that in treated erythrocytes, recruitment of cytosolic SHP-2 to band 3 is a prerequisite for the subsequent dephosphorylation of the transmembrane protein.
Lysophosphatidic acids induce proliferation of cultured vascular smooth muscle cells from rat aorta (1994)

Lysophosphatidic acids (LPA) with a C18 fatty acyl group accelerated thymidine incorporation into cultured rat aortic vascular smooth muscle cells and stimulated their cell division. LPA acted synergistically with epidermal growth factor and fibroblast growth factor but additively with platelet-derived growth factor. The stimulatory actions of LPA were suggested to be rather specific from the following findings: 1) their stimulation of DNA synthesis increased with an increase in their acyl moiety; 2) lysophosphatidylcholine, a neutral lysophospholipid, had no mitogenic action but was cytotoxic at high concentrations; and 3) LPA induced a rapid external Ca(2+)-independent increase in intracellular Ca2+ concentration ([Ca2+]i) in single fura 2-loaded cells that resembled the receptor-mediated increases in [Ca2+]i triggered by different agonists, whereas lysophosphatidylcholine provoked a slow sustained increase in [Ca2+]i in an external Ca(2+)-dependent manner. These results are discussed in relation to the possible pathophysiological role of LPA.
Integrated Cold Start of a Boost Converter at 57 mV Using Cross-Coupled Complementary Charge Pumps and Ultra-Low-Voltage Ring Oscillator (2019)

This paper demonstrates an on-chip electrical cold-start technique to achieve low-voltage and fast start up of a boost converter for autonomous thermal energy harvesting from human body heat. An improved charge transfer through high gate-boosted switches by means of cross-coupled complementary charge pumps enables voltage multiplication of the low input voltage during cold start. The start-up voltage multiplier operates with an on-chip clock generated by an ultra-low-voltage ring oscillator. The proposed cold-start scheme implemented in a general purpose 0.18μm CMOS process assists an inductive boost converter to start operation with a minimum input voltage of 57mV in 135 ms while consuming only 90 nJ of energy from the harvesting source, without using additional sources of energy or additional off-chip components.
Dynamic changes in global microRNAome and transcriptome reveal complex miRNA-mRNA regulated host response to Japanese Encephalitis Virus in microglial cells (2016)

Microglia cells in the brain play essential role during Japanese Encephalitis Virus (JEV) infection and may lead to change in microRNA (miRNA) and mRNA profile. These changes may together control disease outcome. Using Affymetrix microarray platform, we profiled cellular miRNA and mRNA expression at multiple time points during viral infection in human microglial (CHME3) cells. In silico analysis of microarray data revealed a phased pattern of miRNAs expression, associated with JEV replication and provided unique signatures of infection. Target prediction and pathway enrichment analysis identified anti correlation between differentially expressed miRNA and the gene expression at multiple time point which ultimately affected diverse signaling pathways including Notch signaling pathways in microglia. Activation of Notch pathway during JEV infection was demonstrated in vitro and in vivo. The expression of a subset of miRNAs that target multiple genes in Notch signaling pathways were suppressed and their overexpression could affect JEV induced immune response. Further analysis provided evidence for the possible presence of cellular competing endogenous RNA (ceRNA) associated with innate immune response. Collectively, our data provide a uniquely comprehensive view of the changes in the host miRNAs induced by JEV during cellular infection and identify Notch pathway in modulating microglia mediated inflammation.
An overview of logic synthesis systems (1987)

The term logic synthesis is used to describe systems that range from relatively simple mapping schemes to tools with sophisticated logic optimizations. In this tutorial, the requirements on logic synthesis systems will be discussed aand the advantages and disadvantages of different approaches to logic synthesis will be presented.
The Biology of Avian Hepatitis B Viruses (2018)

The avian hepadnaviruses so far contribute two members to the Hepadnaviridae: duck hepatitis B virus (DHBV) and heron hepatitis B virus (HHBV). Both are small, partially double-stranded enveloped DNA viruses similar in genome organization and mode of replication to the other hepadnaviruses found in man, woodchucks, and ground squirrels. DHBV can replicate in human hepatoma cell lines after transfection of cloned viral DNA. Both the decreasing susceptibility to DHBV infection and the increased pathology induced by DHBV infection with age may be linked to the maturation of the immune system. Active DHBV transcription and replication in the endodermal layer of the yolk sac tissue are identified by d 4 of incubation. The chapter describes the incidence and course of DHBV infection and its use as an experimental system, and presents in some detail hitherto unpublished DHBV DNA sequences, and provides some peculiarities of the DHBV/HHBV system.
Distinct Functions of Two RNA Ligases in Active Trypanosoma brucei RNA Editing Complexes (2002)

Trypanosome RNA editing is a unique U insertion and U deletion process that involves cycles of pre-mRNA cleavage, terminal U addition or U removal, and religation. This editing can occur at massive levels and is directed by base pairing of trans-acting guide RNAs. Both U insertion and U deletion cycles are catalyzed by a single protein complex that contains only seven major proteins, band I through band VII. However, little is known about their catalytic functions, except that band IV and band V are RNA ligases and genetic analysis indicates that the former is important in U deletion. Here we establish biochemical approaches to distinguish the individual roles of these ligases, based on their distinctive ATP and pyrophosphate utilization. These in vitro analyses revealed that both ligases serve in RNA editing. Band V is the RNA editing ligase that functions very selectively to seal in U insertion (IREL), while band IV is the RNA editing ligase needed to seal in U deletion (DREL). In combination with our earlier findings about the cleavage and the U-addition/U-removal steps of U deletion and U insertion, these results show that all three steps of these editing pathways exhibit major differences and suggest that the editing complex could have physically separate regions for U deletion and U insertion.
Human umbilical cord perivascular cells (HUCPVC) (2010)

Human bone marrow mesenchymal stem cells (hBM-MSC) have recently been employed in the clinical treatment of challenging skin defects. We have described an MSC population that can be easily harvested from human umbilical cord perivascular tissue, human umbilical cord perivascular cells (HUCPVC), which exhibit a higher proliferative rate and frequency than hBM-MSC. Our objective was to establish whether HUCPVC could promote healing of full thickness murine skin defects, and thus find utility as a cell source for dermal repair. To this end, bilateral full thickness defects were created on the dorsum of Balb/c nude mice. Fibrin was used as a delivery vehicle for 1 x 106 PKH-67 labeled HUCPVC with contralateral controls receiving fibrin only. Epifluorescent and brightfield microscopic evaluation of the wound site was carried out at 3 and 7 days while mechanical testing of wounds was carried out at 3, 7, and 10 days. Our results show that by 3 days, marked contraction of the wound was observed in the fibrin controls whilst the HUCPVC samples exhibited neither collapse nor contraction of the defect, and the dermal repair tissue was considerably thicker and more organized. By 7 days, complete re-epithelialization of the HUCPVC wounds was observed whilst in the controls re-epithelialization was limited to the wound margins. Wound strength was significantly increased in the HUCPVC treatment group by 3 and 7 days but no statistical difference was seen at 10 days. We conclude that HUCPVCs accelerate early wound healing in full thickness skin defects and thus represent a putative source of human MSCs for use in dermal tissue engineering.
Cloning and characterization of the high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae. (1986)

A gene, PDE2, has been cloned from the yeast Saccharomyces cerevisiae that, when present in high copy, reverses the phenotypic effects of RAS2Val19, a mutant form of the RAS2 gene that renders yeast cells sensitive to heat shock and starvation. It has previously been shown that the RAS proteins are potent activators of yeast adenylate cyclase. We report here that PDE2 encodes a high-affinity cAMP phosphodiesterase that shares sequence homology with animal cell phosphodiesterases. These results therefore imply that the effects of RAS2Val19 are mediated through its changes in cAMP concentration.
An efficient one-step site-directed and site-saturation mutagenesis protocol (2004)

We have developed a new primer design method based on the QuickChange site-directed mutagenesis protocol, which significantly improves the PCR amplification efficiency. This design method minimizes primer dimerization and ensures the priority of primer-template annealing over primer self-pairing during the PCR. Several different multiple mutations (up to 7 bases) were successfully performed with this partial overlapping primer design in a variety of vectors ranging from 4 to 12 kb in length. In comparison, all attempts failed when using complete-overlapping primer pairs as recommended in the standard QuickChange protocol. Our protocol was further extended to site-saturation mutagenesis by introducing randomized codons. Our data indicated no specific sequence selection during library construction, with the randomized positions resulting in average occurrence of each base in each position. This method should be useful to facilitate the preparation of high-quality site saturation libraries.
Immunological and Endocrinological Response to Growth Hormone Therapy in Short Children (1988)

We investigated the influence of human growth hormone (hGH) on mitogen-stimulated lymphoproliferation, in vitro IgM production, serum levels of immunoglobulins, somatomedin-C (Sm-C) values and serum growth-promoting activity (Thymidine Activity, TA) in 18 short children, aged between 6.6-14.5 years, undergoing a 3-month course of hGH therapy. Blood was collected the day before treatment (Group A), on the 5th day after patients were administered hGH daily (0.1 U/kg) i.m. for 4 days (Group B), after a 3-month course of hGH injected three times weekly, and finally before (Group C) and 24 h after an extra injection (Group D). In vitro IgM production from the patients' unstimulated lymphocytes decreased from 277 +/- 41 (Group A) to 168 +/- 38 (Group B), to 119 +/- 43 (Group C) and then to 119 +/- 28 ng/ml (Group D) (p less than 0.05). Using PWM-stimulated lymphocytes in vitro IgM production decreased from 2,015 +/- 464 (Group A) to 1,116 +/- 316 (Group B), then to 511 +/- 170 (Group C) and 968 +/- 295 ng/ml (Group D) (p less than 0.02). The variation of this decrease could be correlated with the variation of growth velocity during treatment (r = 0.619, p less than 0.05). In contrast, no significant changes were found following therapy either in serum levels of IgA, IgE, IgG, IgM, Sm-C and TA, or in phytohemagglutinin, concanavalin A and pokeweed mitogen-stimulated lymphoproliferation. Our data suggest that there is some relationship between growth hormone, growth and immunity.
HIV-1 Reverse Transcriptase-Pseudoknot RNA Aptamer Interaction Has a Binding Affinity in the Low Picomolar Range Coupled with High Specificity (2000)

Systematic evolution of ligands by exponential enrichment (SELEX) is a powerful method for the identification of small oligonucleotides that bind with high affinity and specificity to target proteins. Such DNAs/RNAs are a new class of potential chemotherapeutics that could block the enzymatic activity of pathologically relevant proteins. We have conducted a detailed biochemical study of the interaction of human immunodeficiency virus 1 (HIV-1) reverse transcriptase (RT) with a SELEX-derived pseudoknot RNA aptamer. Electron paramagnetic resonance spectroscopy of site-directed spin-labeled RT mutants revealed that this aptamer was selected for binding to the "closed" conformation of the enzyme. Kinetic analysis showed that the RNA inhibitor bound to HIV RT in a two-step process, with association rates similar to those described for model DNA/DNA and DNA/RNA substrates. However, the dissociation of the pseudoknot RNA from RT was dramatically slower than observed for model substrates. Equilibrium binding studies revealed an extraordinarily low K(d), of about 25 pm, for the enzyme-aptamer interaction, presumably a consequence of the slow off-rates. Additionally, this pseudoknot aptamer is highly specific for HIV-1 RT, with the closely related HIV-2 enzyme showing a binding affinity close to 4 orders of magnitude lower.
An introduction to recursive partitioning: Rationale, application, and characteristics of classification and regression trees, bagging, and random forests. (2009)

Recursive partitioning methods have become popular and widely used tools for nonparametric regression and classification in many scientific fields. Especially random forests, which can deal with large numbers of predictor variables even in the presence of complex interactions, have been applied successfully in genetics, clinical medicine, and bioinformatics within the past few years. High-dimensional problems are common not only in genetics, but also in some areas of psychological research, where only a few subjects can be measured because of time or cost constraints, yet a large amount of data is generated for each subject. Random forests have been shown to achieve a high prediction accuracy in such applications and to provide descriptive variable importance measures reflecting the impact of each variable in both main effects and interactions. The aim of this work is to introduce the principles of the standard recursive partitioning methods as well as recent methodological improvements, to illustrate their usage for low and high-dimensional data exploration, but also to point out limitations of the methods and potential pitfalls in their practical application. Application of the methods is illustrated with freely available implementations in the R system for statistical computing.
Selection of optimal DNA oligos for gene expression arrays (2001)

The program is available upon request.