gebhart/patrepeval huggingface dataset:
Analysis of intracellular osteopontin as a marker of osteoblastic cell differentiation and mesenchymal cell migration (1998)

Formation and repair of the hard and soft connective tissues of teeth and their supporting structures require stem cells to divide, differentiate and migrate to generate specific tissues in a defined temporo-spatial sequence. We have used antibodies to osteopontin (OPN) and fluorescence-activated cell sorting (FACS) to determine the relationship between OPN expression and cell differentiation in cultures of fetal rat calvarial cells. At different stages of osteogenic differentiation, OPN was expressed by 60-98% of cells. Populations of small OPN-negative cells with low cellular granularity (S cells) were isolated and shown to be enriched in stem cells, characterised by a lack of differentiation markers, high proliferative potential, capacity for self renewal and multipotentiality. Within 24 h of plating, S cells attached, spread and started expressing OPN, CD44, and collagens types I, II and III. Confocal microscopy of OPN in differentiating cells revealed two distinct phenotypes; a perinuclear distribution, characteristic of secreted OPN, and an intracellular perimembranous distribution co-localising with the CD44 receptor, characteristic of migrating cells in which OPN was increased > 10-fold as measured by immunoblotting. These studies show that OPN is expressed early in mesenchymal cell differentiation and is related to cell migration as well as osteogenesis.
Searching the expressed sequence tag (EST) databases: Panning for genes (2000)

The genomes of living organisms contain many elements, including genes coding for proteins. The portions of the genes expressed as mature mRNA, collectively known as the transcriptome, represent only a small part of the genome. The expressed sequence tag (EST) databases contain an increasingly large part of the transcriptome of many species. For this reason, these databases are probably the most abundant source of new coding sequences available today. However, the raw data deposited in the EST databases are to a large extent unorganised, unannotated, redundant and of relatively low quality. This paper reviews some of the characteristics of the EST data, and the methods that can be used to find novel protein sequences within them. It also documents a collection of databases, software and web sites that can be useful to biologists interested in mining the EST databases over the Internet, or in establishing a local environment for such analyses.
Photonic crystal waveguides and resonators (2000)

Summary form only given. Near stop-band edges, periodically microstructured media (photonic crystals) exhibit strong temporal and spatial dispersion. The challenge is to demonstrate very low out-of-plane leakage while preserving the advantages offered by photonic crystals. Among the devices being actively worked on are waveguides which are modeless within a range of frequencies, vertical emitting microcavities with very high quality factors, new kinds of efficient microlaser, and wavelength-sensitive filters for telecommunications. Simple multilayer stacks can behave like quasi-metals for incidence from low refractive index media.
Cellular processing of the neurotrophin precursors of NT3 and BDNF by the mammalian proprotein convertases (1996)

In order to define the enzymes responsible for the maturation of the precursors of brain-derived neurotrophic factor (proBDNF) and neurotrophin-3 (proNT3), we have analysed their biosynthesis and intracellular processing by the proprotein convertases furin, PC1, PC2, PACE4, PC5 and its isoform PC5/6-B. In these studies, we utilized a vaccinia virus expression system in either BSC40 or the furin activity-deficient LoVo cells. Results demonstrated that in both cells furin and, to a lesser extent, PACE4 and PC5/6-B effectively process proBDNF and proNT3. Furthermore, we have determined that human proNT3 is sulfated, suggesting that processing of proNT3 occurs following the arrival of the precursor to the Trans Golgi Network.
Differential effects of Bcl-2 on T and B cells in transgenic mice. (1992)

We have produced bcl-2 transgenic mice by using a construct which mimics the t(14;18) translocation in human follicular lymphomas. Although lymphoid tissues from all transgenic mice contained high levels of human Bcl-2 protein, transgene expression was differentially regulated within the B- and T-cell compartments of lines derived from various founder mice. We have characterized the phenotypes of two lines of bcl-2 transgenic mice (line 2 and line 6) in which bcl-2 transgene expression was restricted primarily to the T- or B-cell lineages, respectively. Analysis of line 6 lymphocytes revealed a polyclonal expansion of B cells, and these B cells exhibited prolonged survival in vitro. In line 2 mice, numbers of T cells in the peripheral lymphoid tissues were more moderately elevated despite enhanced T-cell survival in vitro. Line 2 transgenic mice also showed significantly increased proportions of thymocytes with a mature phenotype. Taken together, these findings suggest different roles for bcl-2 in the in vivo regulation of B- and T-cell development and homeostasis.
Design of Gold Nanoparticles for Magnetic Resonance Imaging (2006)

Abstract Improving the sensitivity of magnetic resonance imaging (MRI), a powerful non‐invasive medical imaging technique, requires the development of novel contrast agents with a higher efficiency than gadolinium chelates such as DTPA:Gd (DTPA: diethylenetriaminepentaacetic acid) that are currently used for clinical diagnosis. To achieve this objective, the strategy that we have explored involves the use of gold nanoparticles as carriers for gadolinium chelates. These nanoparticles are obtained by reducing a gold salt in the presence of a dithiolated derivative of DTPA. Characterization of these particles by transmission electron microscopy (TEM), X‐ray diffraction (XRD), thermogravimetric analysis (TGA), colorimetric titration, and X‐ray photoelectron spectroscopy (XPS) reveals the presence of a multilayered shell containing about 150 ligands on 2–2.5 nm sized particles. These particles exhibit a high relaxivity ( r 1 = 585 m M –1 s –1 as compared to 3.0 m M –1 s –1 for DTPA:Gd), rendering them very attractive as contrast agents for MRI.
Lysine-based peptide nucleic acids (PNAs) with strong chiral constraint: Control of helix handedness and DNA binding by chirality (2005)

Two enantiomeric chiral PNAs bearing three adjacent D- or L-lysine-based residues in the middle of the strand ("chiral box" PNAs, sequence H-GTAGA(Lys)T(Lys)C(Lys)ACT-NH2) have been used as models in order to comprehensively study the effects of the stereogenic centers on PNA conformation and on PNA binding properties to complementary PNA and DNA strands. The binding properties of the two enantiomeric PNAs and of their homologous achiral PNA have been extensively studied by UV and CD spectroscopy and by mass spectrometry, both in the antiparallel and in the parallel mode with complementary PNA and DNA strands. In the antiparallel PNA:PNA duplexes, L-Lys PNA were found to form left-handed, and D-Lys PNA right handed helices, while in parallel duplexes, the reversed helicities were observed. Correspondingly, the preferred mode of binding and the best mismatch recognition of the D-Lys containing PNA with (right handed) DNA was found to be in the antiparallel orientation, while that of L-Lys PNA was found to be in the parallel mode. A rationale which correlates the preferred handedness of the PNA-PNA duplexes to the directionality of the binding to complementary DNA duplexes has been devised according to structural data and considering the "retro-inverso" concept widely used for peptides.
Contributions of the extracellular and cytoplasmic domains of platelet-endothelial cell adhesion molecule-1 (PECAM-1/CD31) in regulating cell-cell localization (2000)

PECAM-1/CD31, a vascular cell adhesion/signaling molecule that has been implicated in a number of vascular functions (including angiogenesis and the transmigration of leukocytes through endothelium) is highly enriched at the cell-cell borders of adjacent endothelial cells. To identify the mechanisms responsible for this localization, a series of PECAM-1 mutants and chimeric PECAM-1 molecules were transfected into non-PECAM-expressing cells and the ability of the constructs to move to cell-cell borders of adjacent cells was determined using immunohistochemistry and confocal microscopy. Although neither the extracellular domain, by itself, nor the cytoplasmic domain, by itself, was sufficient to direct cell-cell localization, the combination of the extracellular and transmembrane domains with a small group of highly charged amino acids in a membrane proximal region of the cytoplasmic domain was sufficient to direct efficient localization of the molecule to cell-cell borders. Importantly, only constructs that supported PECAM-1 mediated adhesion localized to cell-cell borders. Our data are consistent with a 'diffusion trapping' model in which movement of PECAM-1 in the cell membrane occurs relatively freely until the 'stablized' extracellular domain of the molecule encounters its ligand on an adjacent cell. When this occurs, the complex is 'captured' at the cell-cell interface leading to localization at cell-cell borders.
Strategy for Systematic Assembly of Large RNA and DNA Genomes: Transmissible Gastroenteritis Virus Model (2000)

A systematic method was developed to assemble functional full-length genomes of large RNA and DNA viruses. Coronaviruses contain the largest single-stranded positive-polarity RNA genome in nature. The approximately 30-kb genome, coupled with regions of genomic instability, has hindered the development of a full-length infectious cDNA construct. We have assembled a full-length infectious construct of transmissible gastroenteritis virus (TGEV), an important pathogen in swine. Using a novel approach, six adjoining cDNA subclones that span the entire TGEV genome were isolated. Each clone was engineered with unique flanking interconnecting junctions which determine a precise systematic assembly with only the adjacent cDNA subclones, resulting in an intact TGEV cDNA construct of approximately 28.5 kb in length. Transcripts derived from the full-length TGEV construct were infectious, and progeny virions were serially passaged in permissive host cells. Viral antigen production and subgenomic mRNA synthesis were evident during infection and throughout passage. Plaque-purified virus derived from the infectious construct replicated efficiently and displayed similar plaque morphology in permissive host cells. Host range phenotypes of the molecularly cloned and wild-type viruses were similar in cells of swine and feline origin. The recombinant viruses were sequenced across the unique interconnecting junctions, conclusively demonstrating the marker mutations and restriction sites that were engineered into the component clones. Full-length infectious constructs of TGEV will permit the precise genetic modification of the coronavirus genome. The method that we have designed to generate an infectious cDNA construct of TGEV could theoretically be used to precisely reconstruct microbial or eukaryotic genomes approaching several million base pairs in length.
To code, or not to code: lossy source-channel communication revisited (2003)

What makes a source-channel communication system optimal? It is shown that in order to achieve an optimal cost-distortion tradeoff, the source and the channel have to be matched in a probabilistic sense. The match (or lack of it) involves the source distribution, the distortion measure, the channel conditional distribution, and the channel input cost function. Closed-form necessary and sufficient expressions relating the above entities are given. This generalizes both the separation-based approach as well as the two well-known examples of optimal uncoded communication. The condition of probabilistic matching is extended to certain nonergodic and multiuser scenarios. This leads to a result on optimal single-source broadcast communication.
Pathological and immunological responses associated with differential survival of Chinook salmon following Renibacterium salmoninarum challenge (2010)

Chinook salmon Oncorhynchus tshawytscha are highly susceptible to Renibacterium salmoninarum, the causative agent of bacterial kidney disease (BKD). Previously we demonstrated that introduced Chinook salmon from Lake Michigan, Wisconsin (WI), USA, have higher survival following R. salmoninarum challenge relative to the progenitor stock from Green River, Washington, USA. In the present study, we investigated the pathological and immunological responses that are associated with differential survival in the 2 Chinook salmon stocks following intra-peritoneal R. salmoninarum challenge of 2 different cohort years (2003 and 2005). Histological evaluation revealed delayed appearance of severe granulomatous lesions in the kidney and lower overall prevalence of membranous glomerulopathy in the higher surviving WI stock. The higher survival WI stock had a lower bacterial load at 28 d post-infection, as measured by reverse-transcriptase quantitative polymerase chain reaction (RT-qPCR). However, at all other time points, bacterial load levels were similar despite higher mortality in the more susceptible Green River stock, suggesting the possibility that the stocks may differ in their tolerance to infection by the bacterium. Interferon-gamma, inducible nitric oxide synthase (iNOS), Mx-1, and transferrin gene expression were up-regulated in both stocks following challenge. A trend of higher iNOS gene expression at later time points (> or = 28 d post-infection) was observed in the lower surviving Green River stock, suggesting the possibility that higher iNOS expression may contribute to greater pathology in that stock.
The fellowships of the INGs (2005)

The inhibitor of growth (ING) family of proteins is an evolutionarily conserved family, with members present from yeast to humans. The mammalian ING proteins are candidate tumor suppressor proteins and accordingly can cooperate with p53 to arrest proliferation and induce apoptosis. ING proteins are also reported to function in the promotion of cellular senescence, the regulation of DNA damage responses and the inhibition of angiogenesis. At the molecular level, ING proteins are thought to function as chromatin regulatory molecules, acting as co-factors for distinct histone and factor acetyl-transferase (H/FAT) and deacetylase (HDAC) enzyme complexes. Further, ING proteins interact with a number of additional proteins involved in the regulation of critical nuclear processes, such as gene expression and DNA replication, and also function as nuclear phosphoinositide (PtdInsP) receptors. Despite the increasing number of known molecular interacting partners for ING proteins, the specific biochemical action of mammalian ING proteins and its relationship to tumor suppression remain elusive. In this Prospect, we summarize the present understanding of the binding partners and physiologic roles of ING proteins and propose a general molecular paradigm for how ING proteins might function to prevent cancer.
A spread-spectrum based synchronization technique for digital broadcast systems (1990)

A technique that has been verified experimentally to improve the synchronization efficiency of digital communication systems over present systems without sacrificing reliability is presented. This technique is called the spread-spectrum system pilot technique (SSPT). Incorporated into this technique are elements of tone-calibrated techniques (TCT) and spread-spectrum systems. In the SSPT system, the desired pilot tone is modulated by a pseudorandom binary sequence (PRBS) generator of finite duration and then linearly added to the source (customer) data that is actually being sent. At the receiver, the same finite PRBS sequence is used to decode the received signal. The system works because it provides an accurate version of the actual data carrier to be used in demodulation of the received signal. Based on the research presented, it is expected that this type of system will lead to better performance than currently used transparent-tone-in-band and other techniques used in multipath fading environments, which are especially problematic in mobile broadcast and communication applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Influence of immunoglobulin isotype on therapeutic antibody function (2016)

Monoclonal antibody (mAb) therapeutics are revolutionizing cancer treatment; however, not all tumors respond, and agent optimization is essential to improve outcome. It has become clear over recent years that isotype choice is vital to therapeutic success with agents that work through different mechanisms, direct tumor targeting, agonistic receptor engagement, or receptor-ligand blockade, having contrasting requirements. Here we summarize how isotype dictates mAb activity and discuss ways in which this information can be used for the development of enhanced therapeutics.
Complete down‐regulation of low‐density lipoprotein receptor activity in human liver parenchymal cells by β‐very‐low‐density lipoprotein (1991)

The effect of LDL and beta-VLDL on the expression of the LDL receptor is studied in cultured human parenchymal cells. The high affinity binding of [125I]LDL to cultured human parenchymal cells was down regulated to 37.3 +/- 2.9% and 24.0 +/- 2.6% of the control value, after preincubation with LDL or beta-VLDL for 22 h, respectively. When LDL receptor synthesis was blocked at 22 h a residual receptor activity of 29% is noticed, indicating a half-life of LDL receptors in human parenchymal cells of 12 h. It is concluded that LDL receptor expression on human liver parenchymal cells is subject to complete down-regulation by beta-VLDL, which may be held responsible for the cholesterol-rich diet induced down-regulation of LDL receptors, in vivo.
Control of directionality in the site‐specific recombination system of the Streptomyces phage φC31 (2000)

The genome of the Streptomyces temperate phage phiC31 integrates into the host chromosome via a recombinase belonging to a novel group of phage integrases related to the resolvase/invertase enzymes. Previously, it was demonstrated that, in an in vitro recombination assay, phiC31 integrase catalyses integration (attP/attB recombination) but not excision (attL/attR). The mechanism responsible for this recombination site selectivity was therefore investigated. Purified integrase was shown to bind with similar apparent binding affinities to between 46 bp and 54 bp of DNA at each of the attachment sites, attP, attB, attL and attR. Assays using recombination sites of 50 bp and 51 bp for attP and attB, respectively, showed that these fragments were functional in attP/attB recombination and maintained strict site selectivity, i.e. no recombination between non-permissive sites, such as attP/attP, attB/attL, etc., was observed. Using bandshifts and supershift assays in which permissive and non-permissive combinations of att sites were used in the presence of integrase, only the attP/attB combination could generate supershifts. Recombination products were isolated from the supershifted complexes. It was concluded that these supershifted complexes contained the recombination synapse and that site specificity, and therefore directionality, is determined at the level of stable synapse formation.
Detectivity comparison between thin-film Pd/PVDF photopyroelectric interferometric and optical reflectance hydrogen sensors (1999)

A novel dual photopyroelectric interference (PPEI)/optical reflectance (OR) solid-state hydrogen sensor system has been developed and demonstrated. Based on the recently developed PPE-interference technique and the variations of optical and electronic properties of Pd metal in the presence of hydrogen, simultaneous signal responses were obtained from a polyvinylidene fluoride (PVDF) thin-film detector and an optical photodiode. The dual measurement of PPEI and OR channels provides not only a more reliable sensor system, but also a powerful tool to identify the operating mechanism(s) in the process of Pd/PVDF/hydrogen interaction. The experimental results show that the detectivity and the signal dynamic range of the PPEI method are much higher than those of the OR method due to the suppression of the large base-line signal and the signal noise. The comparison of PPEI and OR results reveals that both signals are mainly due to the same electronic mechanism.
Heterozygous PU.1 mutations are associated with acute myeloid leukemia (2002)

The transcription factor PU.1 is required for normal blood cell development. PU.1 regulates the expression of a number of crucial myeloid genes, such as the macrophage colony-stimulating factor (M-CSF) receptor, the granulocyte colony-stimulating factor (G-CSF) receptor, and the granulocyte-macrophage colony-stimulating factor (GM-CSF) receptor. Myeloid cells derived from PU.1(-/-) mice are blocked at the earliest stage of myeloid differentiation, similar to the blast cells that are the hallmark of human acute myeloid leukemia (AML). These facts led us to hypothesize that molecular abnormalities involving the PU.1 gene could contribute to the development of AML. We identified 10 mutant alleles of the PU.1 gene in 9 of 126 AML patients. The PU.1 mutations comprised 5 deletions affecting the DNA-binding domain, and 5 point mutations in 1) the DNA-binding domain (2 patients), 2) the PEST domain (2 patients), and 3) the transactivation domain (one patient). DNA binding to and transactivation of the M-CSF receptor promoter, a direct PU.1 target gene, were deficient in the 7 PU.1 mutants that affected the DNA-binding domain. In addition, these mutations decreased the ability of PU.1 to synergize with PU.1-interacting proteins such as AML1 or c-Jun in the activation of PU.1 target genes. This is the first report of mutations in the PU.1 gene in human neoplasia and suggests that disruption of PU.1 function contributes to the block in differentiation found in AML patients.
Stimulated Raman hyperspectral imaging based on spectral filtering of broadband fiber laser pulses (2012)

We demonstrate a technique of hyperspectral imaging in stimulated Raman scattering (SRS) microscopy using a tunable optical filter, whose transmission wavelength can be varied quickly by a galvanometer mirror. Experimentally, broadband Yb fiber laser pulses are synchronized with picosecond Ti:sapphire pulses, and then spectrally filtered out by the filter. After amplification by fiber amplifiers, we obtain narrowband pulses with a spectral width of <3.3 cm(-1) and a wavelength tunability of >225 cm(-1). By using these pulses, we accomplish SRS imaging of polymer beads with spectral information.