gebhart/patrepeval huggingface dataset:
PPARγ-Ligands Inhibit Migration Mediated by Multiple Chemoattractants in Vascular Smooth Muscle Cells (1999)

The purpose of this study was to determine the effect of the peroxisome proliferator-activated receptor gamma-(PPAR gamma) ligands troglitazone (TRO), rosiglitazone (RSG), and 15-deoxy-delta prostaglandin J2 (15d-PGJ2) on vascular smooth muscle cell (VSMC) migration directed by multiple chemoattractants. Involvement of mitogen-activated protein kinase (MAPK) in migration also was examined, because TRO was previously shown to inhibit nuclear events stimulated by this pathway during mitogenic signaling in VSMCs. Migration of rat aortic VSMCs was induced 5.4-fold by PDGF, 4.6-fold by thrombin, and 2.3-fold by insulin-like growth factor I (IGF-I; all values of p < 0.05). The PPAR gamma ligands 15d-PGJ2, RSG, or TRO all inhibited VSMC migration with the following order of potency: 15d-PGJ2 > RSG > TRO. Inhibition of MAPK signaling with PD98059 completely blocked PDGF-, thrombin-, and IGF-I-induced migration. All chemoattractants induced MAPK activation. PPAR gamma ligands did not inhibit MAPK activation, suggesting a nuclear effect of these ligands downstream of MAPK. The importance of nuclear events was confirmed because actinomycin D also blocked migration. We conclude that PPAR gamma ligands are potent inhibitors of VSMC migration pathways, dependent on MAPK and nuclear events. PPAR gamma ligands act downstream of the cytoplasmic activation of MAPK and appear to exert their effects in the nucleus. Because VSMC migration plays an important role in the formation of atherosclerotic lesions and restenosis, PPAR gamma ligands like TRO and RSG, which ameliorate insulin resistance in humans, also may protect the vasculature from diabetes-enhanced injury.
Amplifying fluorescent polymer sensors for the explosives taggant 2,3-dimethyl-2,3-dinitrobutane (DMNB) (2005)

Structural and electronic effects on the efficiency of DMNB detection with fluorescent conjugated polymers are described.
Structural Studies in Solution of the Recombinant N-Terminal Pair of Short Consensus/Complement Repeat Domains of Complement Receptor Type 2 (CR2/CD21) and Interactions with Its Ligand C3dg (2001)

Human complement receptor type 2 (CR2, CD21) is a cell surface receptor that binds three distinct ligands (complement C3d, Epstein-Barr virus gp350/220, and the low-affinity IgE receptor CD23) via the N-terminal two of fifteen or sixteen short consensus/complement repeat (SCR) domains. Here, we report biophysical studies of the CR2 SCR 1-2 domain binding to its ligand C3dg. Two recombinant forms of CR2 containing the SCR 1-2 and SCR 1-15 domains were expressed in high yield in Pichia pastoris and baculovirus, respectively. Circular dichroism spectroscopy showed that CR2 SCR 1-2 receptor possessed a beta-sheet secondary structure with a melting temperature of 59 degrees C. Using surface plasmon resonance, kinetic parameters for the binding of either CR2 SCR 1-2 or the full-length SCR 1-15 form of CR2 showed that the affinity of binding to immobilized C3d is comparable for the SCR 1-15 compared to the SCR 1-2 form of CR2. Unexpectedly, both the association and dissociation rates for the SCR 1-15 form were slower than for the SCR 1-2 form. These data show that the SCR 1-2 domains account for the primary C3dg binding site of CR2 and that the additional SCR domains of full-length CR2 influence the ability of CR2 SCR 1-2 to interact with its ligand. Studies of the pH and ionic strength dependence of the interaction between SCR 1-2 and C3d by surface plasmon resonance showed that this is influenced by charged interactions, possibly involving the sole His residue in CR2 SCR 1-2. Sedimentation equilibrium studies of CR2 SCR 1-2 gave molecular weights of 17 000, in good agreement with its sequence-derived molecular weight to show that this was monomeric. Its sedimentation coefficient was determined to be 1.36 S. The complex with C3d gave molecular weights in 50 mM and 200 mM NaCl buffer that agreed closely with its sequence-derived molecular weight of 50 600 and showed that a 1:1 complex had been formed. Molecular graphics views of homology models for the separate CR2 SCR 1 and SCR 2 domains showed that both SCR domains exhibited a distribution of charged groups throughout its surface. The single His residue is located near a long eight-residue linker between the two SCR domains and may influence the linker conformation and the association of C3d and CR2 SCR 1-2 into their complex. Sedimentation modeling showed that the arrangement of the two SCR domains in CR2 SCR 1-2 is highly extended in solution.
Specific Pathogen Free Swine (1960)

Control of diseases in domestic animals is attempted for two main reasons: 1. To reduce reservoirs of disease transmissible to man, and 2. to produce livestock more economically.
Mouse Cell Surface Antigens: Nomenclature and Immunophenotyping (1998)

This paper reviews cell surface Ags expressed on mouse hemopoietic and nonhemopoietic cells. The review will cover molecules included in the cluster of differentiation (CD) from CD1 to CD166 and lymphocyte Ag (Ly) series from Ly-1 to Ly-81 as well as some new Ags without current CD or Ly assignments. In addition to an update on mouse nomenclature, there will be a discussion of some known functions of the molecules and brief comments on the use of particular Ags for immunophenotyping of cell subsets. Several novel markers mentioned may prove useful in mouse immunology research.
Biocompatible Microfabrication of 3D Isolation Chambers for Targeted Confinement of Individual Cells and Their Progeny (2012)

We describe a technique to physically isolate single/individual cells from their surrounding environment by fabricating three-dimensional microchambers around selected cells under biocompatible conditions. Isolation of targeted cells is achieved via rapid fabrication of protein hydrogels from a biocompatible precursor solution using multiphoton lithography, an intrinsically 3D laser direct write microfabrication technique. Cells remain chemically accessible to environmental cues enabling their propagation into well-defined, high density populations. We demonstrate this methodology on gram negative (E. coli), gram positive (S. aureus), and eukaryotic (S. cerevisiae) cells. The opportunities to confine viable, single/individual-cells and small populations within user-defined microenvironments afforded by this approach should facilitate the study of cell behaviors across multiple generations.
Dosage-Related Bifidogenic Effects of Galacto- and Fructooligosaccharides in Formula-Fed Term Infants (2002)

These data indicate that supplementation of a term infant's formula with a mixture of galacto- and fructooligosaccharides has a dose-dependent stimulating effect on the growth of Bifidobacteria and Lactobacilli in the intestine and results in softer stool with increasing dosage of supplementation.
SVM-based Protein-Protein Interaction Extraction from Medline abstracts (2007)

Nowadays, protein-protein interaction (PPI) extraction has become a research focus. Many methods have been applied to this domain, such as supervised learning approaches. This paper applied support vector machine (SVM) to extract PPI, which bases on several lexical features and one syntactic feature achieved through link grammar parser. Due to syntax's complexity different sentence structure can not have the same parse tree, which leads to the data sparseness problem here. In order to solve the sparseness problem, syntactic feature is used in a simple way. This special syntactic feature helps to improve F-score nearly five percentage points in supervised learning approach.
Intravenous administration of sodium nitrite to healthy volunteers: a single ascending dose study (1998)

De mens wordt in toenemende mate, via de voeding, blootgesteld aan nitraat. De toxiciteit van nitraat is laag. In het lichaam vindt echter omzetting plaats van nitraat in nitriet in het proximale deel van de tractus digestivus. Nitriet is toxischer dan nitraat. Bij evaluatie van de gezondheidsrisico's van nitraat moet dan ook rekening worden gehouden met de omzetting in nitriet en de orale biobeschikbaarheid en toxiciteit van nitriet in het lichaam. De planning was om een orale biobeschikbaarheidsstudie van nitriet uit te voeren. Nitriet wordt in het bloed echter snel omgezet in nitraat onder de vorming van methemoglobine. Vanwege de snelle eliminatie van nitriet zijn dan ook relatief hoge nitriet doseringen nodig om de biobeschikbaarheid te bepalen. Vanwege de door nitriet geinduceerde bloeddrukverlaging en methemoglobine vorming zijn er echter grenzen aan de hoeveelheid nitriet die nog veilig kan worden toegediend tijdens een biobeschikbaarheidsstudie. De geplande biobeschikbaarheidsstudie werd daarom voorafgegaan door een pilot-studie waarin aan 3 proefpersonen opklimmende, intraveneuze doseringen van natriumnitriet gegeven werden. Het doel was om de maximale dosis te vinden die nog veilig aan proefpersonen kan worden toegediend, te weten, een dosis die ongeveer 10-15% methemoglobine induceert. Geconcludeerd kan worden dat een dosis van 0.12 mmol NaNO2 per mmol Hemoglobine (tussen 290 en 370 mg natriumnitriet), waarbij 10.8% metHb werd geinduceerd, de hoogste, nog veilige, natriumnitriet dosis is voor proefpersonen.&lt;br&gt;
A Novel GTP-binding Protein γ-Subunit, Gγ8, Is Expressed during Neurogenesis in the Olfactory and Vomeronasal Neuroepithelia (1995)

A novel heterotrimeric G-protein gamma-subunit has been cloned, and its function has been confirmed by expression and purification. This gamma-subunit is only detected in the olfactory epithelium, the vomeronasal epithelium and, to a lesser extent, the olfactory bulb. It is absent from all other tissues studied including the nasal respiratory epithelium. During development, expression of G gamma 8 in the olfactory epithelium parallels neurogenesis, peaking shortly after birth and declining in the adult. In situ hybridization studies localize expression of this novel gamma-subunit to the sensory neurons; hybridization is strongest in the region of the epithelium that contains immature neurons. Unlike proteins that are expressed only in mature olfactory neurons (e.g. olfactory marker protein or Golf alpha), expression of G gamma 8 in the olfactory epithelium is relatively unaffected by olfactory bulbectomy. In the vomeronasal epithelium expression of G gamma 8 is also highest in the developing neurons. Taken together, these findings are consistent with a very specific role for G gamma 8 in the development and turnover of olfactory and vomeronasal neurons.
Refractive index sensor with a guided-mode resonant grating filter (2001)

This paper describes a novel refractive index sensor with a guided-mode resonant grating (GMRG) filter. The GMRG filter is a narrowband wavelength reflection filter. The incident light is reflected at a resonance condition of incident angle and wavelength. When the grating filter is covered by a liquid to be tested, the resonant condition depends upon its refractive index. The refractive index of the liquid can be determined from the resonance angle for a known wavelength. Since a full-half width of incident angle for the resonance is very narrow (less than 0.1 degree(s)), a high resolution is expected. We designed the GMRG filters for the refractive index sensor. And the resonance angle of incidence was investigated experimentally for the mixture of water and ethyl alcohol.
Adeno-associated Satellite Virus Growth Supported by a Temperature-sensitive Mutant of Human Adenovirus (1970)

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.
Nucleocapsid and Matrix Protein Contributions to Selective Human Immunodeficiency Virus Type 1 Genomic RNA Packaging (1998)

The nucleocapsid protein (NC) of retroviruses plays a major role in genomic RNA packaging, and some evidence has implicated the matrix protein (MA) of certain retroviruses in viral RNA binding. To further investigate the role of NC in the selective recognition of genomic viral RNA and to address the potential contribution of MA in this process, we constructed chimeric and deletion human immunodeficiency virus type 1 (HIV-1) mutants that alter the NC or MA protein. Both HIV and mouse mammary tumor virus (MMTV) NC proteins have two zinc-binding domains and similar basic amino acid compositions but differ substantially in total length, amino acid sequence, and spacing of the zinc-binding motifs. When the entire NC coding sequence of HIV was replaced with the MMTV NC coding sequence, we found that the HIV genome was incorporated into virions at 50% of wild-type levels. Viruses produced from chimeric HIV genomes with complete NC replacements, or with the two NC zinc-binding domains replaced with MMTV sequences, preferentially incorporated HIV genomes when both HIV and MMTV genomes were simultaneously present in the cell. Viruses produced from chimeric MMTV genomes in which the MMTV NC had been replaced with HIV NC preferentially incorporated MMTV genomes when both HIV and MMTV genomes were simultaneously present in the cell. In contrast, viruses produced from chimeric HIV genomes containing the Moloney NC, which contains a single zinc-binding motif, were previously shown to preferentially incorporate Moloney genomic RNA. Taken together, these results indicate that an NC protein with two zinc-binding motifs is required for specific HIV RNA packaging and that the amino acid context of these motifs, while contributing to the process, is less crucial for specificity. The data also suggest that HIV NC may not be the exclusive determinant of RNA selectivity. Analysis of an HIV MA mutant revealed that specific RNA packaging does not require MA protein.
Development and validation of an LC-MS/MS method for the bioanalysis of psilocybin’s main metabolites, psilocin and 4-hydroxyindole-3-acetic acid, in human plasma (2020)

Psilocin is the active metabolite of psilocybin, a serotonergic psychedelic substance. It is used recreationally and investigated in substance-assisted psychotherapy. The pharmacokinetic properties of psilocin are only partially characterized. Therefore, we developed and validated a rapid LC-MS/MS method to quantify psilocin and its metabolite 4-hydroxyindole-3-acetic acid (4-HIAA) in human plasma. Plasma samples were processed by protein precipitation using methanol. The injected sample was mixed with water in front of a C<sub>18</sub> analytical column to increase retention of the analytes. Psilocin and 4-HIAA were detected by multiple reaction monitoring (MRM) in positive and negative electrospray ionisation mode, respectively. An inter-assay accuracy of 100-109% and precision of ≤8.7% was recorded over three validation runs. The recovery was near to complete (≥94.7%) and importantly, consistent over different concentration levels and plasma batches (CV%: ≤4.1%). The plasma matrix caused negligible ion suppression and endogenous interferences could be separated from the analytes. Psilocin and 4-HIAA plasma samples could be thawed and re-frozen for three cycles, kept at room temperature for 8 h or 1 month at -20 °C without showing degradation (≤10%). The linear range (R ≥ 0.998) of the method covered plasma concentrations observed in humans following a common therapeutic oral dose of 25 mg psilocybin and was therefore able to assess the pharmacokinetics of psilocin and 4-HIAA. The LC-MS/MS method was convenient and reliable for measuring psilocin and 4-HIAA in plasma and will facilitate the clinical development of psilocybin.
Image change detection algorithms: a systematic survey (2005)

Detecting regions of change in multiple images of the same scene taken at different times is of widespread interest due to a large number of applications in diverse disciplines, including remote sensing, surveillance, medical diagnosis and treatment, civil infrastructure, and underwater sensing. This paper presents a systematic survey of the common processing steps and core decision rules in modern change detection algorithms, including significance and hypothesis testing, predictive models, the shading model, and background modeling. We also discuss important preprocessing methods, approaches to enforcing the consistency of the change mask, and principles for evaluating and comparing the performance of change detection algorithms. It is hoped that our classification of algorithms into a relatively small number of categories will provide useful guidance to the algorithm designer.
αvβ Integrins Play an Essential Role in BMP-2 Induction of Osteoblast Differentiation (2005)

BMP-2 upregulates the expression of alphavbeta integrins, and these integrins, in turn, play a critical role in BMP-2 function in osteoblasts.
A phase II placebo-controlled study of tralokinumab in moderate-to-severe asthma (2012)

Pre-clinical data demonstrate a pivotal role for interleukin (IL)-13 in the development and maintenance of asthma. This study assessed the effects of tralokinumab, an investigational human IL-13-neutralising immunoglobulin G4 monoclonal antibody, in adults with moderate-to-severe uncontrolled asthma despite controller therapies. 194 subjects were randomised to receive tralokinumab (150, 300 or 600 mg) or placebo subcutaneously every 2 weeks. Primary end-point was change from baseline in mean Asthma Control Questionnaire score (ACQ-6; ACQ mean of six individual item scores) at week 13 comparing placebo and combined tralokinumab dose groups. Secondary end-points included pre-bronchodilator lung function, rescue β(2)-agonist use and safety. Numerical end-points are reported as mean±sd. At week 13, change from baseline in ACQ-6 was -0.76±1.04 for tralokinumab versus -0.61±0.90 for placebo (p=0.375). Increases from baseline in forced expiratory volume in 1 s (FEV(1)) were 0.21±0.38 L versus 0.06±0.48 L (p=0.072), with a dose-response observed across the tralokinumab doses tested. β(2)-agonist use (puffs per day) was decreased for tralokinumab -0.68±1.45 versus placebo -0.10±1.49 (p=0.020). The increase in FEV(1) following tralokinumab treatment remained evident 12 weeks after the final dose. Safety profile was acceptable with no serious adverse events related to tralokinumab. No improvement in ACQ-6 was observed, although tralokinumab treatment was associated with improved lung function.
Global and Hox-specific roles for the MLL1 methyltransferase (2005)

The mixed-lineage leukemia (MLL1/ALL-1/HRX) histone methyltransferase is involved in the epigenetic maintenance of transcriptional memory and the pathogenesis of human leukemias. To understand its role in cell type specification, we determined the human genomic binding sites of MLL1. We found that MLL1 functions as a human equivalent of yeast Set1. Like Set1, MLL1 localizes with RNA polymerase II (Pol II) to the 5' end of actively transcribed genes, where histone H3 lysine 4 trimethylation occurs. Consistent with this global role in transcription, MLL1 also localizes to microRNA (miRNA) loci that are involved in leukemia and hematopoiesis. In contrast to the 5' proximal binding behavior at most protein-coding genes, MLL1 occupies an extensive domain within a transcriptionally active region of the HoxA cluster. The ability of MLL1 to serve as a start site-specific global transcriptional regulator and to participate in larger chromatin domains at the Hox genes reveals dual roles for MLL1 in maintenance of cellular identity.
Treatment of soybean oil soapstock to reduce pollution (1972)

Abstract Often soapstock is acidulated to convert this byproduct of vegetable oil refining to a salable commodity. The acidic waste water from this treatment constitutes a significant part of the environmental pollution from refineries. A process of neutralizing and drying was investigated as a nonpolluting method for upgrading soybean oil soapstock. Neutralization with sulfuric acid was conducted in a ribbon blender. The neutral soapstock was dried to ca. 4% moisture, either batchwise in a natural circulation evaporator or continuously in a scraped film evaporator. The product is liquid while hot but solidifies to a waxy solid when cooled to room temperature. When added to a standard broiler ration, the feed efficiency and rate of gain of chickens equaled that obtained with a commercial feed fat added at the same level. The soapstock products fed, which contained 200–300 ppm xanthophyll, gave significantly better shank pigmentation than the commercial fat, which contained 3 ppm.
Ligation of Toll-Like Receptor 3 Differentially Regulates M2 and M3 Muscarinic Receptor Expression and Function in Human Airway Smooth Muscle Cells (2007)

The data indicate that poly I:C internalized by ASM cells differentially regulates M2R and M3R expression and function by interacting with TLR3 rather than with PKR, suggesting that these changes may contribute to airway hyperreactivity.
Endoglin Expression Is Regulated by Transcriptional Cooperation between the Hypoxia and Transforming Growth Factor-β Pathways (2002)

Endoglin is a transforming growth factor-beta (TGF-beta) co-receptor expressed mainly on endothelial cells and involved in cardiovascular development, angiogenesis, and vascular remodeling. This is illustrated by the fact that mutations in the endoglin gene give rise to hereditary hemorrhagic telangiectasia type 1, a dominant vascular disease with clinical manifestations that originate by a mechanism of haploinsufficiency. Thus, studies on the regulated expression of endoglin are crucial to devising therapeutic strategies for hereditary hemorrhagic telangiectasia type 1. Endoglin is highly expressed in the neovasculature associated with hypoxia such as ischemic tissues and tumors, but the molecular mechanism of this up-regulation is unknown. Here, we have investigated the possible regulation of endoglin expression by hypoxia. Surface protein, transcript, and promoter activity levels of endoglin were found to be up-regulated by hypoxia, indicating that the regulation takes place at the transcriptional level. A hypoxia-responsive element downstream of the main transcription start site of the endoglin gene was functionally characterized. Whereas hypoxia alone moderately stimulated endoglin transcription, addition of TGF-beta under hypoxic conditions resulted in transcriptional cooperation between both signaling pathways, leading to marked stimulation of endoglin expression. Because basal endoglin transcription is sustained by Sp1, and TGF-beta and hypoxia signaling pathways are mediated by Smad proteins and hypoxia-inducible factor-1 (HIF-1), respectively, the involvement of these transcription factors was analyzed. Functional and co-immunoprecipitation experiments demonstrated the existence of a multiprotein complex (Sp1.Smad3.HIF-1) on the endoglin promoter, mediating the cooperation between the hypoxia and TGF-beta pathways. Within this multiprotein complex, Smad3 appears to function not only as a coactivator factor, but also as an adaptor between HIF-1 and Sp1. We propose that basal endoglin transcription (highly dependent on Sp1) may switch from a constitutive to an inducible state through Sp1 interaction with HIF-1 and Smad transcription factors, induced by hypoxia and TGF-beta, respectively.