gebhart/patrepeval huggingface dataset:
Interactions between Herpes Simplex Virus Type 2 and Human Immunodeficiency Virus Type 1 Infection in African Women: Opportunities for Intervention (2000)

Sexually transmitted diseases (STDs) are cofactors for human immunodeficiency virus (HIV) transmission, but the specific role of herpes simplex virus type 2 (HSV-2) is unclear. This study aimed to examine the in vivo relationships between HSV-2 and HIV-1 in 300 women in Bangui, Central African Republic. Sera were tested for syphilis, HIV-1, HSV-2 antibody, and levels of vitamins A and E. Genital specimens were tested for other STDs. HSV-2 DNA and HIV-1 RNA were quantified in cervicovaginal lavage. The prevalences of HSV-2 antibody (91% vs. 78%, P=.02), HSV-2 shedding (43% vs. 22%, P=. 003), and levels of HSV-2 DNA (P=.01) were all significantly higher among HIV-1-seropositive than among HIV-1-seronegative women. There was a significant correlation between genital HIV-1 RNA and HSV-2 DNA levels (P=.02) among the 23 women who were shedding HSV-2 DNA. If confirmed, such associations highlight the urgent need for HSV-2 control measures in populations at high risk of both infections.
The serosal mesothelium is a major source of smooth muscle cells of the gut vasculature (2005)

Most internal organs are situated in a coelomic cavity and are covered by a mesothelium. During heart development, epicardial cells (a mesothelium) move to and over the heart, undergo epithelial-mesenchymal transition (EMT), and subsequently differentiate into endothelial and vascular smooth muscle cells. This is thought to be a unique process in blood vessel formation. Still, structural and developmental similarities between the heart and gut led us to test the hypothesis that a conserved or related mechanism may regulate blood vessel development to the gut, which, similar to the heart, is housed in a coelomic cavity. By using a combination of molecular genetics, vital dye fate mapping, organ culture and immunohistochemistry, we demonstrate that the serosal mesothelium is the major source of vasculogenic cells in developing mouse gut. Our studies show that the gut is initially devoid of a mesothelium but that serosal mesothelial cells expressing the Wilm's tumor protein (Wt1) move to and over the gut. Subsequently, a subset of these cells undergoes EMT and migrates throughout the gut. Using Wt1-Cre genetic lineage marking of serosal cells and their progeny, we demonstrate that these cells differentiate to smooth muscle of all major blood vessels in the mesenteries and gut. Our data reveal a conserved mechanism in blood vessel formation to coelomic organs, and have major implications for our understanding of vertebrate organogenesis and vascular deficiencies of the gut.
Tissue factor: identification and characterization of cell types in human placentae (1990)

This is an immunohistologic study of tissue factor (TF) in snap frozen, unfixed, human normal-term placentae. Antibodies to TF were a monoclonal to human brain TF purified on a factor VII-agarose affinity column, and a polyclonal to a synthetic polypeptide representing the carboxyl-terminal nine amino acids of human TF. The results detail the localization and distribution of TF and characterize the cells in which it is found. TF was not observed in trophoblast, trophoblastic basement membranes, or noncellular components of connective tissue. TF was identified in some but not all macrophages, most fibroblast-like cells, and occasionally in perivascular cells and endothelium. The most consistent and intense reactions were obtained with vimentin-positive fibroblast-like cells in loose connective tissue. TF usually was not identified in fetal stem vessel endothelial cells, but TF reactivity was found in some of these cells in chorionic villi with histologic evidence of chronic inflammation. Such areas are uncommonly found in normal-term placentae. The vast majority of TF-reactive cells did not react with antibody to factor VII and were not in contact with blood. The biologic purpose of producing relatively great amounts of TF in areas remote from circulating factor VII is not known.
Hedgehog Signaling Overcomes an EZH2-Dependent Epigenetic Barrier to Promote Cholangiocyte Expansion (2016)

We conclude that Shh/Gli1 signaling plays an integral role in cholangiocyte maturation in vitro by overcoming an EZH2-dependent epigenetic barrier and this mechanism also promotes biliary expansion in vivo.
A Comprehensive Model for the Cellular Uptake of Cationic Cell‐penetrating Peptides (2007)

The plasma membrane represents an impermeable barrier for most macromolecules. Still some proteins and so-called cell-penetrating peptides enter cells efficiently. It has been shown that endocytosis contributes to the import of these molecules. However, conflicting results have been obtained concerning the nature of the endocytic process. In addition, there have been new findings for an endocytosis-independent cellular entry. In this study, we provide evidence that the Antennapedia-homeodomain-derived antennapedia (Antp) peptide, nona-arginine and the HIV-1 Tat-protein-derived Tat peptide simultaneously use three endocytic pathways: macropinocytosis, clathrin-mediated endocytosis and caveolae/lipid-raft-mediated endocytosis. Antennapedia differs from Tat and R9 by the extent by which the different import mechanisms contribute to uptake. Moreover, at higher concentrations, uptake occurs by a mechanism that originates from spatially restricted sites of the plasma membrane and leads to a rapid cytoplasmic distribution of the peptides. Endocytic vesicles could not be detected, suggesting an endocytosis-independent mode of uptake. Heparinase treatment of cells negatively affects this import, as does the protein kinase C inhibitor rottlerin, expression of dominant-negative dynamin and chlorpromazine. This mechanism of uptake was observed for a panel of different cell lines. For Antp, significantly higher peptide concentrations and inhibition of endocytosis were required to induce its uptake. The relevance of these findings for import of biologically active cargos is shown.
IκB kinase regulation of the TPL‐2/ERK MAPK pathway (2012)

Nuclear factor-κB (NF-κB) and mitogen-activated protein kinase (MAPK) activation play central roles in the induction of gene expression in innate immune cells following pathogen recognition. TPL-2 (tumor progression locus 2) is the MAP 3-kinase component of an ERK-1/2 (extracellular signal-regulated kinase 1/2) MAPK pathway activated by Toll-like receptor and tumor necrosis factor receptor family stimulation. In this review, we discuss results obtained from our laboratory and others that show that TPL-2 signaling function is directly controlled by the inhibitor of NF-κB (IκB) kinase (IKK) complex. Significantly, this means that IKK controls both NF-κB and ERK activation. TPL-2 is stoichiometrically complexed with the NF-κB inhibitory protein, NF-κB1 p105, and the ubiquitin-binding protein ABIN-2, both of which are required to maintain TPL-2 protein stability. Binding to p105 also prevents TPL-2 from phosphorylating MEK (MAPK/ERK kinase), its downstream target. Agonist stimulation releases TPL-2 from p105-inhibition by IKK-mediated phosphorylation of p105, which triggers degradation of p105 by the proteasome. This facilitates TPL-2 phosphorylation of MEK, in addition to liberating p105-associated Rel subunits to translocate into the nucleus. We also examine evidence that TPL-2 is critical for the induction of inflammation and may play a role in development and/or progression of certain types of cancer. Finally, we consider the potential of TPL-2 as an anti-inflammatory drug target for treatment of certain types of inflammatory disease and cancer.
A Methodology for Evaluating Data and Output Misfits in Commercial Off-The-Shelf ERP Systems (2005)

This paper presents a methodology based on the task-technology fit theory to identify data and output misfits in the ex-ante evaluation of an off-the shelf enterprise resources planning (ERP) package. The proposed methodology consists of two stages: output misfit analysis and data misfit analysis. The purpose of the first stage is to identify corresponding field (output misfits) and data glossary for data misfit analysis. The latter stage identifies data misfits for every corresponding activity in the business process sequence. The proposed methodology provides a systematic approach to alleviate the difficulty and complexity in identifying data and output misfits. The identification results identify where the misfits are and provide a degree of mismatch, thus providing a practical basis for ERP tool selection to reduce the risk of failure in its implementation.
Leaving the neighborhood: molecular mechanisms involved during epithelial‐mesenchymal transition (2001)

Several molecular mechanisms contribute directly and mechanically to the loss of epithelial phenotype. During epithelial-mesenchymal transition (EMT), adherens junctions and desmosomes are at least partially dissociated. At the same time, a massive cytoskeleton reorganization takes place, involving the rho family and the remodeling of the actin microfilament mesh. Numerous pathways have been described in vitro that control phenotype transition in specific cell models. In vivo developmental studies suggest that transcriptional control, activated by a specific pathway involving Ras, Src and potentially the Wnt pathway, is an essential step. Recent functional and localization experiments indicate that the slug/snail family of transcription factors functions overall as an epithelial phenotype repressor and could represent a key EMT contributor.
The synthesis and properties of a series of strong but hindered organic bases (1981)

D. H. R. Barton, J. D. Elliott and S. D. Géro, J. Chem. Soc., Chem. Commun., 1981, 1136 DOI: 10.1039/C39810001136
Oligonucleotide and plasmid DNA packaging into polyoma VP1 virus‐like particles expressed in Escherichia coli (1999)

The drug delivery system described here is based on the properties of the capsoid or capsid-like structure resulting from the assembly of polyoma virus capsid protein VP1 expressed in Escherichia coli. The capsid protein VP1 was expressed as a fusion protein with a completely removable N-terminal His6 affinity tag. The pentameric morphology of the recombinant VP1 protein was confirmed by electron microscopy after affinity chromatography and factor Xa cleavage under conditions of low ionic strength. The self-assembly of VP1 capsoids can be induced from purified VP1 pentamers by increasing the ionic strength with (NH4)2SO4. These VP1 capsoid particles were packed in vitro with anti-sense oligonucleotides and plasmid DNA. The loading with DNA was pH-dependent. We observed the highest efficiency at pH 5. DNase I treatment of particles with encapsidated material showed that 37-55% of the bound oligonucleotides and fragments of 1.5-1.8 kb double-stranded DNA were protected against degradation.
Organic Light-Emitting Devices with In-Doped (4 at. %) ZnO Thin Films as the Anodic Electrode (2008)

We have investigated transparent conducting properties of using In-doped (4 at. %) zinc oxide (IZO) thin films deposited on glass substrate by pulsed DC magnetron sputtering at low processing substrate temperatures. As increase of the substrate temperature, IZO thin films with better c-axis orientations were grown in perpendicular to the substrate and work functions of IZO films slightly decrease. The optical properties showed high transmittance of higher than 85% in the UV–visible region and exhibited the absorption edge of about 350 nm. The electrical properties exhibited the low resistivity of 1.1 ×10-3 Ω cm and the high mobility of ∼7.8 cm2 V-1 s-1. The organic light emitting diodes (OLEDs) with an IZO anode achieved a maximum luminance efficiency of 2.7 cd/A and external quantum efficiency of 0.47%, which are compared to the values of a control device fabricated on commercial ITO anode. These results indicate that IZO films hold promise for anodic electrodes in the OLEDs application.
Mechanism of Vitamin B1 Destruction by a Factor in Raw Smelt (1942)

A viable yeast can protect its thiamine from destruction by a factor present in raw smelt. The antithiamine factor behaves similarly to the antibiotin factor in its inability to penetrate the living cell. The in-activation of thiamine does not appear to be due to the formation of thiamine complexes labile to hydrolysis or to the splitting of the Bi molecule but rather to an enzymatic degradation of the thiamine molecule. The destructive factor in raw smelt is labile to air drying at room temperatures, heating at 100°C and is extractable in 5% alcohol. Certain raw fish or extracts of these fish may prove valuable in the preparation of vitamin B1 free diets without the necessity of resorting to prolonged autoclaving.
The future of magnetic data storage techology (2000)

In this paper, we review the evolutionary path of magnetic data storage and examine the physical phenomena that will prevent us from continuing the use of those scaling processes which have served us in the past. It is concluded that the first problem will arise from the storage medium, whose grain size cannot be scaled much below a diameter of ten nanometers without thermal self-erasure. Other problems will involve head-to-disk spacings that approach atomic dimensions, and switching-speed limitations in the head and medium. It is likely that the rate of progress in areal density will decrease substantially as we develop drives with ten to a hundred times current areal densities. Beyond that, the future of magnetic storage technology is unclear. However, there are no alternative technologies which show promise for replacing hard disk storage in the next ten years.
THE PRESENCE OF DE NOVO DONOR SPECIFIC ANTIBODY PREDICTS POOR ALLOGRAFT SURVIVAL IN PATIENT WITH TRANSPLANT GLOMERULOPATHY (2008)

Everly, M1; Arend, L1; Govil, A1; Susskind, B1; Al-Ghawi, H1; Everly, J1; Mogilishetty, G1; Alloway, R R.1; Woodle, E S.1; Roy-Chaudhury, P1 Author Information
A Parenteral Nutrition Use Survey With Gap Analysis (2012)

The survey data are a valuable snapshot of current practices with PN. Poor compliance with some of the safe practice guidelines continues. This will help guide new safety initiatives for the PN use process.
GATA transcription factors directly regulate the Parkinson's disease-linked gene α-synuclein (2008)

Increased alpha-synuclein gene (SNCA) dosage due to locus multiplication causes autosomal dominant Parkinson's disease (PD). Variation in SNCA expression may be critical in common, genetically complex PD but the underlying regulatory mechanism is unknown. We show that SNCA and the heme metabolism genes ALAS2, FECH, and BLVRB form a block of tightly correlated gene expression in 113 samples of human blood, where SNCA naturally abounds (validated P = 1.6 x 10(-11), 1.8 x 10(-10), and 6.6 x 10(-5)). Genetic complementation analysis revealed that these four genes are co-induced by the transcription factor GATA-1. GATA-1 specifically occupies a conserved region within SNCA intron-1 and directly induces a 6.9-fold increase in alpha-synuclein. Endogenous GATA-2 is highly expressed in substantia nigra vulnerable to PD, occupies intron-1, and modulates SNCA expression in dopaminergic cells. This critical link between GATA factors and SNCA may enable therapies designed to lower alpha-synuclein production.
A growth arrest-specific (gas) gene codes for a membrane protein. (1990)

A set of growth arrest-specific (gas) genes whose expression is negatively regulated by serum has recently been identified. We report on the detailed analysis of one of these genes (gas3). The kinetics of regulation by the presence and absence of serum were investigated, and it was found that this gene is regulated at the post-transcriptional level. The encoded protein deduced from the nucleotide sequence showed some similarity to a mitochondrial oxyreductase, and in vitro translation established that the protein product is a transmembrane glycoprotein.
Single-layer, gradient refractive index antireflection films effective from 035 to 25 μ (1976)

Gradient refractive index antireflection films are produced by a chemical etch/leach process applied to glasses sensitized by a phase-separating heat treatment. The reflectance (two surfaces) is effectively reduced from ~ 8% to < 1/2% in the wavelength regime 0.35–2.5 μ. The broadband antireflection film consists of a single, porous, skeletal layer made up largely of silica. The optical properties of the film are shown to depend on the time, temperature parameters of the phase-separating heat treatment, as well as the time, temperature parameter of the film-forming etch/leach treatment. The properties of films produced under different process conditions are correlated in a fashion that suggests that progressively steeper refractive index gradients are obtained for samples phase separated and formed at higher temperatures. A number of applications for these films are suggested, including solar energy devices.
De novo design of α-helical proteins: basic research to medical applications (1996)

The two-stranded alpha-helical coiled-coil is a universal dimerization domain used by nature in a diverse group of proteins. The simplicity of the coiled-coil structure makes it an ideal model system to use in understanding the fundamentals of protein folding and stability and in testing the principles of de novo design. The issues that must be addressed in the de novo design of coiled-coils for use in research and medical applications are (i) controlling parallel versus antiparallel orientation of the polypeptide chains, (ii) controlling the number of helical strands in the assembly (iii) maximizing stability of homodimers or heterodimers in the shortest possible chain length that may require the engineering of covalent constraints, and (iv) the ability to have selective heterodimerization without homodimerization, which requires a balancing of selectivity versus affinity of the dimerization strands. Examples of our initial inroads in using this de novo design motif in various applications include: heterodimer technology for the detection and purification of recombinant peptides and proteins; a universal dimerization domain for biosensors; a two-stage targeting and delivery system; and coiled-coils as templates for combinatorial helical libraries for basic research and drug discovery and as synthetic carrier molecules. The universality of this dimerization motif in nature suggests an endless number of possibilities for its use in de novo design, limited only by the creativity of peptide-protein engineers.
Structure and Rheology Studies of Poly(oxyethylene−oxypropylene−oxyethylene) Aqueous Solution (1996)

Small-angle neutron scattering (SANS) and rheometry were used to investigate the supramolecular structure formed by a poly(oxyethylene−oxypropylene−oxyethylene) (PEO100PPO65PEO100, Pluronic F127) copolymer in aqueous solution over a temperature range of 10−75 °C and a concentration range of 10−20 wt %. At copolymer concentrations of less than 12.5% the solutions are Newtonian fluids. Gels with an ordered structure (cubic packing of spherical micelles) are observed over a well-defined temperature window when the copolymer concentrations are greater than 17 wt %. The SANS results show that the aggregation number of the micelles is independent of temperature and concentration. Low-yield stresses, very high zero shear viscosities (∼106 P), and shear thinning are the major rheological characteristics of the gels. Near, but outside, the gel phase boundary the solutions are non-Newtonian (shear thinning). However, SANS shows these solutions contain domains having the same structure as that in the gel phase. The temperature window for ordered structures and non-Newtonian behavior becomes wider with increasing copolymer concentration. The degree of overlap of the micellar shells increases with increasing copolymer concentration at a given temperature and reaches a maximum at ∼40 °C at a fixed polymer concentration. The yield stress is due to repulsive interactions of PEO chains in the overlapped micellar shell. On the basis of SANS and rheology results, the proposed mechanism of gelation is that it involves repulsive interactions among close-packed spherical micelles, rather than aggregation or transitions in micelle morphology to rods or lamellae.
Pancreatic Cancer Cell Migration and Metastasis Is Regulated by Chemokine-Biased Agonism and Bioenergetic Signaling (2015)

Patients with pancreatic ductal adenocarcinoma (PDAC) invariably succumb to metastatic disease, but the underlying mechanisms that regulate PDAC cell movement and metastasis remain little understood. In this study, we investigated the effects of the chemokine gene CXCL12, which is silenced in PDAC tumors, yet is sufficient to suppress growth and metastasis when re-expressed. Chemokines like CXCL12 regulate cell movement in a biphasic pattern, with peak migration typically in the low nanomolar concentration range. Herein, we tested the hypothesis that the biphasic cell migration pattern induced by CXCL12 reflected a biased agonist bioenergetic signaling that might be exploited to interfere with PDAC metastasis. In human and murine PDAC cell models, we observed that nonmigratory doses of CXCL12 were sufficient to decrease oxidative phosphorylation and glycolytic capacity and to increase levels of phosphorylated forms of the master metabolic kinase AMPK. Those same doses of CXCL12 locked myosin light chain into a phosphorylated state, thereby decreasing F-actin polymerization and preventing cell migration in a manner dependent upon AMPK and the calcium-dependent kinase CAMKII. Notably, at elevated concentrations of CXCL12 that were insufficient to trigger chemotaxis of PDAC cells, AMPK blockade resulted in increased cell movement. In two preclinical mouse models of PDAC, administration of CXCL12 decreased tumor dissemination, supporting our hypothesis that chemokine-biased agonist signaling may offer a useful therapeutic strategy. Our results offer a mechanistic rationale for further investigation of CXCL12 as a potential therapy to prevent or treat PDAC metastasis.
Coating of poly(dimethylsiloxane) with n-dodecyl-β-d-maltoside to minimize nonspecific protein adsorption (2005)

Poly(dimethylsiloxane)(PDMS) surface is coated with n-dodecyl-beta-D-maltoside, which reduces the nonspecifically adsorbed protein on the PDMS surface to the single molecule level.