gebhart/patrepeval huggingface dataset:
Id2 and Id3 Inhibit Development of Cd34+ Stem Cells into Predendritic Cell (Pre-Dc)2 but Not into Pre-Dc1 (2000)

We found previously that Id3, which inhibits transcriptional activities of many basic helix-loop-helix transcription factors, blocked T and B cell development but stimulated natural killer (NK) cell development. Here we report that ectopic expression of Id3 and another Id protein, Id2, strongly inhibited the development of primitive CD34(+)CD38(-) progenitor cells into CD123(high) dendritic cell (DC)2 precursors. In contrast, development of CD34(+)CD38(-) cells into CD4(+)CD14(+) DC1 precursors and mature DC1 was not affected by ectopic Id2 or Id3 expression. These observations support the notion of a common origin of DC2 precursors, T and B cells. As Id proteins did not block development of NK cells, a model presents itself in which these proteins drive common lymphoid precursors to develop into NK cells by inhibiting their options to develop into T cells, B cells, and pre-DC2.
Control of multiple bandgap shifts in InGaAs-AlInGaAs multiple-quantum-well material using different thicknesses of PECVD SiO2 protection layers (2000)

A useful development of the sputtered SiO/sub 2/ intermixing technique is reported, which uses a single stage of sputtered SiO/sub 2/ deposition and annealing to achieve precise tuning of the bandgap energy in the InGaAs-AlInGaAs material system. The blue shift of photoluminescence spectra can be varied in the range of 0-160 nm. Bandgap-tuned lasers were integrated on a single chip using this technique to assess the post-processed material characteristics and demonstrate its application in optoelectronic integration.
MRI abnormalities of the brain in one‐year‐old children with sickle cell anemia (2008)

Silent brain infarcts occur in a small but significant number of infants with SCA as early as a year of age. This finding indicates a need for thorough evaluation of the CNS very early in life in children with SCA in order to develop timely intervention strategies.
Carbon Flux Distributions at the Pyruvate Branch Point in Corynebacterium glutamicum during Lysine Overproduction (1994)

Abstract In order to achieve the theoretical maximum yield of lysine from glucose (75% molar), flux partitioning at principal branch points (glucose 6‐phosphate, phosphoenolpyruvate, and pyruvate) in the primary metabolic network of Corynebacterium glutamicum must be significantly altered from that observed during balanced growth, so that lysine precursors are synthesized in optimal stoichiometric ratios. In this article, we employ flux analysis, which provides a snapshot of metabolic flux distributions from extracellular measurements, in conjunction with two metabolic perturbations of the pyruvate dehydrogenase complex (PDC) to examine the possibility that flux partitioning at the pyruvate (Pyr) branch point ( i. e. , pyruvate availability) limits lysine yield. The two perturbation experiments involved (1) isolation and flux analysis of a PDC‐attenuated mutant of C. glutamicum and (2) flux analysis following the addition of fluoropyruvate (FP) to a standard fermentation during the initial period of lysine overproduction. No significant alteration in flux partition was observed at any of the three principal nodes in the PDC‐attenuated strain. However, the PDC mutation did cause a 70% uniform decrease in carbon flow throughout the network, which indicates that the lysine yield is not limited solely by a weakly rigid Pyr branch point. The addition of FP did not affect the lysine synthesis rate, but did temporarily redirect carbon flow away from the TCA cycle toward pyruvate excretion, which further confirms that the lysine yield is not pyruvate‐limited and that the Pyr branch point is not weakly rigid.
Negative Regulation of Monocyte Adhesion to Arterial Elastic Laminae by Signal Regulatory Protein α and Src Homology 2 Domain-containing Protein-Tyrosine Phosphatase-1 (2005)

Elastic laminae are extracellular matrix constituents that not only contribute to the stability and elasticity of arteries but also play a role in regulating arterial morphogenesis and pathogenesis. We demonstrate here that an important function of arterial elastic laminae is to prevent monocyte adhesion, which is mediated by the inhibitory receptor signal regulatory protein (SIRP) alpha and Src homology 2 domain-containing protein-tyrosine phosphatase (SHP)-1. In a matrix-based arterial reconstruction model in vivo, elastic laminae were resistant to leukocyte adhesion and transmigration compared with the collagen-dominant arterial adventitia. The density of leukocytes within the elastic lamina-dominant media was about 58-70-fold lower than that within the adventitia from 1 to 30 days. An in vitro assay confirmed the inhibitory effect of elastic laminae on monocyte adhesion. The exposure of monocytes to elastic laminae induced activation of SIRP alpha, which in turn activated SHP-1. Elastic lamina degradation peptides extracted from arterial specimens could also activate SIRP alpha and SHP-1. The knockdown of SIRP alpha and SHP-1 by specific small interfering RNA diminished the inhibitory effect of elastic laminae, resulting in a significant increase in monocyte adhesion. These observations suggest that SIRP alpha and SHP-1 potentially mediate the inhibitory effect of elastic laminae on monocyte adhesion.
Characterization of the A subunit mutants of Stx1 and Stx2 in Saccharomyces cerevisiae (2009)

Shiga toxins are a family of related toxins with two major groups, Stx1 and Stx2. The most common sources for Shiga toxin are the bacteria Shigella dysenteriae and the Shigatoxigenic group of Escherichia coli (STEC), which includes serotype O157:H7. Shiga-like toxin 1 and 2 (Stx1 and Stx2) are produced by some E. coli strains. Stx produced by S. dysenteriae differs from Stx1 by one amino acid. Stx1 and Stx2 have only 56% sequence homology.E. coli O157:H7 has been the major cause of food-borne illnesses. Symptoms include abdominal cramping, bloody diarrhea, vomiting and a low-grade fever. Serious complications can lead to Hemolytic Uremic Syndrome (HUS).Stx1 and Stx2 are categorized as and AB5 toxin. The A complex is responsible for toxicity and has enzymatic activity inside the host cell. The B subunits bind to a receptor on the surface of the host cell. Shiga toxin acts as an N-glycosidase. It cleaves a specific adenine residue in the conserved α- sarcin ricin loop in the 28S subunit of the eukaryotic rRNA. This interferes with the translocation step in protein synthesis and leads to inhibition of translation and cell death.When Stx1A and Stx2A cDNA was cloned downstream of the GAL1 promoter and transformed into Saccharomyces cerevisiae, cells growth was greatly reduced when expression of the toxin was induced. To identify residues critical for cytotoxicity or Stx1A and Stx2A random and site-directed mutations were made. The ability of the mutant proteins to depurinate ribosomes in vivo in yeast was determined by dual primer extension analysis. The amount of translation was measured by incorporation of [35S]-methionine in the cell.The results of these assays show mutations in N75, Y77, E167, R170, and R176 are critical for toxicity in both toxins. Also C-terminal deletions after L240 in Stx1A and I238 in Stx2A abolished toxicity. Several of these mutants, even though they are non-toxic still have the ability to depurinate ribosomes. This indicates cytotoxicity and depurination may not be directly related. This provides evidence that cytotoxicity is not necessarily a direct result of depurination, and other potential mechanisms may contribute in Stx1A and Stx2A cytotoxicity in yeast.
Screening of large protein libraries by the “cell immobilized on adsorbed bead” approach (2004)

Screening of mutant libraries for in vitro enzyme evolution is carried out primarily by physical separation of the cells, followed by growth of individual clones and screening of biocatalytic activity on the basis of color or fluorescence signal development. Currently, most frequently employed methods are labor-intensive or require robotic equipment, resulting in screening limited to a relatively small fraction of the potential inherent in a given library. In this study we present a design, development, and feasibility demonstration of a new screening approach, providing convenient handling of large libraries consisting of 106 to 107 clones and screening based on a simultaneous enzymatic assay with commercially available substrates. This new screening method is based on the "cell immobilized on adsorbed bead" approach: the cell population to be screened is mixed with an excess of medium pre-equilibrated polyacrylamide beads, chemically derivatized to affect quantitative cell immobilization by adsorption. The resulting bead population, comprising of single cell on a bead or blank beads, is then immobilized on a solid glass support. After removal of the freely flowing liquid, the cells immobilized on the adsorbed beads are allowed to grow into microcolonies, utilizing the medium retained within the supporting hydrogel matrix. These colonies are subsequently equilibrated with chromogenic or fluorogenic substrate and screening is affected under a stereomicroscope, resulting in readily retrieved of the most active colonies. This technique may be particularly useful when the screened mutants are expressed and displayed on the cell surface, providing an active and homogeneous "naturally immobilized" enzyme population with minimal substrate diffusion limitations.
Optical characterization of Pseudomonas fluorescens on meat surfaces using time-resolved fluorescence (2006)

A scanning optical system for the detection of bacteria on meat surfaces based on fluorescence lifetime and intensity measurements is described. The system detects autofluorescent light emitted by naturally occurring fluorophores in bacteria. The technique only requires minimal sample preparation and handling, thus the chemical properties of the specimen are preserved. This work presents the preliminary results obtained from a time-resolved fluorescence imaging system for the characterization of a nonpathogenic gram-negative bacteria, Pseudomonas fluorescens. Initial results indicate that the combination of fluorescence lifetime and intensity measurements provides a means for characterizing biological media and for detecting microorganisms on surfaces.
Endemic Venezuelan Equine Encephalitis in Northern Peru (2004)

Since Venezuelan equine encephalitis virus (VEEV) was isolated in Peru in 1942, >70 isolates have been obtained from mosquitoes, humans, and sylvatic mammals primarily in the Amazon region. To investigate genetic relationships among the Peru VEEV isolates and between the Peru isolates and other VEEV strains, a fragment of the PE2 gene was amplified and analyzed by single-stranded conformation polymorphism. Representatives of seven genotypes underwent sequencing and phylogenetic analysis. The results identified four VEE complex lineages that cocirculate in the Amazon region: subtypes ID (Panama and Colombia/Venezuela genotypes), IIIC, and a new, proposed subtype IIID, which was isolated from a febrile human, mosquitoes, and spiny rats. Both ID lineages and the IIID subtype are associated with febrile human illness. Most of the subtype ID isolates belonged to the Panama genotype, but the Colombia/Venezuela genotype, which is phylogenetically related to epizootic strains, also continues to circulate in the Amazon basin.
Involvement of CXCR4 and IL-2 in the homing and retention of human NK and NK T cells to the bone marrow and spleen of NOD/SCID mice (2003)

Human natural killer (NK) and NK T cells play an important role in allogeneic bone marrow (BM) transplantation and graft-versus-leukemia (GVL) effect. The mechanisms by which these cells home to the BM and spleen are not well understood. Here we show that treatment of these cells with pertussis toxin and neutralizing antibodies to the chemokine receptor CXCR4 inhibited homing of the cells to the BM, but not the spleen, of NOD/SCID mice. The retention of NK and NK T cells within the spleen and BM was dependent on Galphai signaling and CXCR4 function. The chemokine receptors CXCR4 and CXCR3 are expressed predominantly on the cell surface of NK T cells. Following activation with interleukin-2 (IL-2), the levels of CXCR4 on NK and NK T cells decreased significantly. Treatment of cells with IL-2 inhibited their migration in response to CXCL12 and their homing and retention in the BM and spleen of NOD/SCID mice. In contrast to CXCR4, the expression levels of the chemokine receptor CXCR3 and the migration of cells in response to CXCL9 and CXCL10 increased after IL-2 treatment. Thus, down-regulation of CXCR4 and up-regulation of CXCR3 may direct the trafficking of cells to the site of inflammation, rather than to hematopoietic organs, and therefore may limit their alloreactive potential.
Optimization of Pulley-Type Ring Resonators (2015)

We show the theoretical and experimental results of the pulley-type microring in which we propose to enlarge the propagation constant difference between the bus waveguide and the ring waveguide to enhance the Q-factor. The waveguide offset to tune the light coupling between the bus waveguide and the cavity can also improve the performance of the device. The experimental result shows that the Q-factor can be over 170,000 by tuning the bus waveguide width.
Correlation of presenting symptoms and patient characteristics with endometrial cancer prognosis in Japanese women (2005)

Lower abdominal pain was found to be an independent prognostic factor in endometrial cancer among Japanese women.
Preparation and characterization of polypyrrole/magnetite nanocomposites synthesized by in situ chemical oxidative polymerization Part B Polymer physics (2008)

This work describes the preparation and characterization of polypyrrole (PPy)/iron oxide nanocomposites fabricated from monodispersed iron oxide nanoparticles in the crystalline form of magnetite (Fe₃O₄) and PPy by in situ chemical oxidative polymerization. Two spherical nanoparticles of magnetite, such as 4 and 8 nm, served as cores were first dispersed in an aqueous solution with anionic surfactant sodium bis(2-ethylhexyl) sulfosuccinate to form micelle/magnetite spherical templates that avoid the aggregation of magnetite nanoparticles during the further preparation of nanocomposites. The PPy/magnetite nanocomposites were then synthesized on the surface of the spherical templates. Structural and morphological analysis showed that the fabricated PPy/magnetite nanocomposites are core (magnetite)-shell (PPy) structures. Morphology of the PPy/magnetite nanocomposites containing monodispersed 4-nm magnetite nanoparticles shows a remarkable change from spherical to tube-like structures as the content of nanoparticles increases from 12 to 24 wt %. Conductivities of these PPy/magnetite nanocomposites show significant enhancements when compared with those of PPy without magnetite nanoparticles, in particular the conductivities of 36 wt % PPy/magnetite nanocomposites with 4-nm magnetite nanoparticles are about six times in magnitude higher than those of PPy without magnetite nanocomposites. These results suggest that the tube-like structures of 36 wt % PPy/magnetite nanocomposites may be served as conducting network to enhance the conductivity of nanocomposites. The magnetic properties of 24 and 36 wt % PPy/magnetitenanocomposites show ferromagnetic behavior and supermagnetism, respectively.
Water repellency induced by pulmonary surfactants. (1982)

1. Pure cotton fabric was partially carboxylated to produce a tough, porous, hydrophilic sub-phase to stimulate the epithelial membrane of the alveolar wall from a permeability standpoint. 2. Two of the predominant pulmonary surfactants, dipalmitoyl lecithin (DPL) and dipalmitoyl phosphatidylethanolamine (DPPE), were found to inhibit wetting of this synthetic membrane and of human cutaneous epithelium as manifest by a large contact angle. 3. When treated with DPL at physiological concentrations, the porous synthetic membrane was found to support a head of saline well in excess of systolic pulmonary artery pressure with no penetration and could do so for periods well in excess of 1 hr; untreated control samples allowed almost immediate fluid filtration. 4. Filtration could be initiated in the DPL-treated membranes by wetting the reverse side, confirming that the threshold pressure for fluid penetration was afforded by capillarity and, hence, by water repellency induced by the surfactant. 5. Water repellency induced by the amphoteric surfactants occurring naturally in the lung is discussed as a possible factor contributing to the pressure threshold to be exceeded for alveolar oedema to form. 6. Evidence is reviewed and several advantages discussed for the implied concept of an essentially dry lining to the alveolus with a discontinuous liquid layer largely confined to convex corners which could slowly resolve any oedema by surface forces.
The Miniature Pig as an Animal Model in Biomedical Research (2005)

Crucial prerequisites for the development of safe preclinical protocols in biomedical research are suitable animal models that would allow for human-related validation of valuable research information gathered from experimentation with lower mammals. In this sense, the miniature pig, sharing many physiological similarities with humans, offers several breeding and handling advantages (when compared to non-human primates), making it an optimal species for preclinical experimentation. The present review offers several examples taken from current research in the hope of convincing the reader that the porcine animal model has gained massively in importance in biomedical research during the last few years. The adduced examples are taken from the following fields of investigation: (a) the physiology of reproduction, where pig oocytes are being used to study chromosomal abnormalities (aneuploidy) in the adult human oocyte; (b) the generation of suitable organs for xenotransplantation using transgene expression in pig tissues; (c) the skin physiology and the treatment of skin defects using cell therapy-based approaches that take advantage of similarities between pig and human epidermis; and (d) neurotransplantation using porcine neural stem cells grafted into inbred miniature pigs as an alternative model to non-human primates xenografted with human cells.
Gene therapy for Parkinson's disease: recent achievements and remaining challenges. (2001)

Gene therapy is the use of nucleic acids as drugs. Thus, ways had to be developed to deliver this new generation of drugs to target tissues. Various viral and non-viral vectors have been engineered to carry potentially therapeutic nucleic acids into diseased organs or target cells. The brain offers a particular challenge for gene delivery to its constituent cells: it is encased by the skull, separated from the general circulation by the blood brain barrier, and made up of mostly non-dividing cells. The skull limits direct injection of vectors into the brain, the blood brain barrier inhibits the easy entry of vectors injected into the bloodstream, and post mitotic target cells restrict what type of vector can be used to deliver genes to the brain. We will discuss the main challenges faced by gene delivery to the brain, i.e. immune responses to the delivery vectors and therapeutic transgenes and length of duration of the therapy specifically as applied to Parkinson's disease. We will also discuss therapeutic strategies, which could be implemented to treat Parkinson's disease, and the models in which they have been tested.
Transgenic induction of mitochondrial rearrangements for cytoplasmic male sterility in crop plants (2007)

Stability of the mitochondrial genome is controlled by nuclear loci. In plants, nuclear genes suppress mitochondrial DNA rearrangements during development. One nuclear gene involved in this process is Msh1. Msh1 appears to be involved in the suppression of illegitimate recombination in plant mitochondria. To test the hypothesis that Msh1 disruption leads to the type of mitochondrial DNA rearrangements associated with naturally occurring cytoplasmic male sterility in plants, a transgenic approach for RNAi was used to modulate expression of Msh1 in tobacco and tomato. In both species, these experiments resulted in reproducible mitochondrial DNA rearrangements and a condition of male (pollen) sterility. The male sterility was, in each case, heritable, associated with normal female fertility, and apparently maternal in its inheritance. Segregation of the transgene did not reverse the male sterile phenotype, producing stable, nontransgenic male sterility. The reproducible transgenic induction of mitochondrial rearrangements in plants is unprecedented, providing a means to develop novel cytoplasmic male sterile lines for release as non-GMO or transgenic materials.
Interaction of the 70,000-mol-wt amino-terminal fragment of fibronectin with the matrix-assembly receptor of fibroblasts. (1985)

Plasma fibronectin binds saturably and reversibly to substrate-attached fibroblasts and is subsequently incorporated into the extracellular matrix (McKeown-Longo, P.J., and D. F. Mosher, 1983, J. Cell Biol., 97:466-472). We examined whether fragments of fibronectin are processed in a similar way. The amino-terminal 70,000-mol-wt catheptic D fragment of fibronectin bound reversibly to cell surfaces with the same affinity as intact fibronectin but did not become incorporated into extracellular matrix. The 70,000-mol-wt fragment blocked binding of intact fibronectin to cell surfaces and incorporation of intact fibronectin into extracellular matrix. Binding of the 70,000-mol-wt fragment to cells was partially abolished by cleavage into 27,000-mol-wt heparin-binding and 40,000-mol-wt gelatin-binding fragments and more completely abolished by reduction and alkylation of disulfide bonds. Binding of the 70,000-mol-wt fragment to cells was not blocked by gelatin or heparin. When coated onto plastic, the 70,000-mol-wt fragment did not mediate attachment and spreading of suspended fibroblasts. Conversely, fibronectin fragments that had attachment and spreading activity did not block binding of exogenous fibronectin to substrate-attached cells. These results indicate that there is a cell binding site in the 70,000-mol-wt fragment that is distinct from the previously described cell attachment site and is required for assembly of exogenous fibronectin into extracellular matrix.
Optical Co-registration of MRI and On-scalp MEG (2019)

To estimate the neural generators of magnetoencephalographic (MEG) signals, MEG data have to be co-registered with an anatomical image, typically an MR image. Optically-pumped magnetometers (OPMs) enable the construction of on-scalp MEG systems providing higher sensitivity and spatial resolution than conventional SQUID-based MEG systems. We present a co-registration method that can be applied to on-scalp MEG systems, regardless of the number of sensors. We apply a structured-light scanner to create a surface mesh of the subject's head and the sensor array, which we fit to the MR image. We quantified the reproducibility of the mesh and localised current dipoles with a phantom. Additionally, we measured somatosensory evoked fields (SEFs) to median nerve stimulation and compared the dipole positions between on-scalp and SQUID-based systems. The scanner reproduced the head surface with <1 mm error. Phantom dipoles were localised with 2.1 mm mean error. SEF dipoles corresponding to the P35m response for OPMs were well localised to the somatosensory cortex, while SQUID dipoles for two subjects were erroneously localised to the motor cortex. The developed co-registration method is inexpensive, fast and can easily be applied to on-scalp MEG. It is more convenient than traditional co-registration methods while also being more accurate.