gebhart/patrepeval huggingface dataset:
In vitro selection of DNA elements highly responsive to the human T-cell lymphotropic virus type I transcriptional activator, Tax. (1994)

The human T-cell lymphotropic virus type I (HTLV-I) transactivator, Tax, the ubiquitous transcriptional factor cyclic AMP (cAMP) response element-binding protein (CREB protein), and the 21-bp repeats in the HTLV-I transcriptional enhancer form a ternary nucleoprotein complex (L. J. Zhao and C. Z. Giam, Proc. Natl. Acad. Sci. USA 89:7070-7074, 1992). Using an antibody directed against the COOH-terminal region of Tax along with purified Tax and CREB proteins, we selected DNA elements bound specifically by the Tax-CREB complex in vitro. Two distinct but related groups of sequences containing the cAMP response element (CRE) flanked by long runs of G and C residues in the 5' and 3' regions, respectively, were preferentially recognized by Tax-CREB. In contrast, CREB alone binds only to CRE motifs (GNTGACG[T/C]) without neighboring G- or C-rich sequences. The Tax-CREB-selected sequences bear a striking resemblance to the 5' or 3' two-thirds of the HTLV-I 21-bp repeats and are highly inducible by Tax. Gel electrophoretic mobility shift assays, DNA transfection, and DNase I footprinting analyses indicated that the G- and C-rich sequences flanking the CRE motif are crucial for Tax-CREB-DNA ternary complex assembly and Tax transactivation but are not in direct contact with the Tax-CREB complex. These data show that Tax recruits CREB to form a multiprotein complex that specifically recognizes the viral 21-bp repeats. The expanded DNA binding specificity of Tax-CREB and the obligatory role the ternary Tax-CREB-DNA complex plays in transactivation reveal a novel mechanism for regulating the transcriptional activity of leucine zipper proteins like CREB.
Molecular Control of Iron Transport (2007)

The iron-regulatory hormone hepcidin is a 25-amino acid peptide that is synthesized in hepatocytes. Hepcidin binds to the cellular iron export channel ferroportin and causes its internalization and degradation and thereby decreases iron efflux from iron exporting tissues into plasma. By this mechanism, hepcidin inhibits dietary iron absorption, the efflux of recycled iron from splenic and hepatic macrophages, and the release of iron from storage in hepatocytes. Hepcidin synthesis is stimulated by plasma iron and iron stores and is inhibited by erythropoietic activity, ensuring that extracellular plasma iron concentrations and iron stores remain stable and the erythropoietic demand for iron is met. During inflammation, increased hepcidin concentrations cause iron sequestration in macrophages, resulting in hypoferremia and eventually anemia of inflammation. Hepcidin deficiency plays a central role in most iron overload disorders. The role of hepcidin abnormalities in anemias that are associated with renal disease and in resistance to erythropoietic therapies remains to be elucidated.
Inflammatory Diseases of Blood Vessels (2013)

This comprehensive reference emphasizes the dynamic events that occur in the maintenance and repair of blood vessels in health and abnormalities that may result from dysregulation of inflammatory and immune responses in disease. The editors have assembled authors and topics that bring new concepts about cell and molecular biology to the clinician t
Two-dimensional image transmission through a single optical fiber by wavelength-time multiplexing (1983)

Serial transmission of image data through an optical fiber is inefficient in the utilization of the channel capacity of the fiber. Parallel image transmission techniques, on the other hand, generally limit the transmission length to a few meters. A novel approach is introduced with which 2-D image data can be transmitted efficiently at high speed over a single optical fiber using wavelength-time multiplexing. Several system configurations designed for different types of input are presented.
Normal and Cystic Fibrosis Airway Surface Liquid Homeostasis (2005)

Mammalian airways normally regulate the volume of a thin liquid layer, the periciliary liquid (PCL), to facilitate the mucus clearance component of lung defense. Studies under standard (static) culture conditions revealed that normal airway epithelia possess an adenosine-regulated pathway that blends Na+ absorption and Cl- secretion to optimize PCL volume. In cystic fibrosis (CF), the absence of CF transmembrane conductance regulator results in a failure of adenosine regulation of PCL volume, which is predicted to initiate mucus stasis and infection. However, under conditions that mimic the phasic motion of the lung in vivo, ATP release into PCL was increased, CF ion transport was rebalanced, and PCL volume was restored to levels adequate for lung defense. This ATP signaling system was vulnerable, however, to insults that trigger CF bacterial infections, such as viral (respiratory syncytial virus) infections, which up-regulated extracellular ATPase activity and abolished motion-dependent ATP regulation of CF PCL height. These studies demonstrate (i) how the normal coordination of opposing ion transport pathways to maintain PCL volume is disrupted in CF, (ii) the hitherto unknown role of phasic motion in regulating key aspects of normal and CF innate airways defense, and (iii) that maneuvers directed at increasing motion-induced nucleotide release may be therapeutic in CF patients.
Lipoprotein lipase-enhanced binding of human triglyceride-rich lipoproteins to heparan sulfate: modulation by apolipoprotein E and apolipoprotein C (1996)

The objective of this study was to investigate whether compositional variation in apolipoprotein (apo) content of triglyceride-rich lipoproteins (TRLP) modulates binding of heparan sulfate proteoglycans (HSPG). Human TRLP was enriched with apoE and apoCs and the ability to bind biotin-conjugated heparan sulfate (b-HS) was studied in the presence or absence of heat-inactivated lipoprotein lipase (LPL). TRLP, associated with LPL, showed an increased capacity to bind b-HS compared with TRLP alone. Low density lipoproteins (LDL) bound both b-HS and LPL with a higher affinity than TRLP. ApoE enrichment of TRLP resulted in an enhanced binding of b-HS. Increased binding of b-HS to TRLP by the combination of apoE enrichment and LPL addition was found to be complementary, not affecting their individual binding capacity. TRLP enrichment with apoC led to the formation of an apoC-rich, apoE-poor particle; this alteration by itself did not change the ability to bind b-HS. ApoC enrichment of TRLP resulted in a reduced capacity to bind LPL and therefore a subsequently reduced capacity to bind b-HS, compared with control TRLP associated with LPL. Competition studies revealed that b-HS binding to TRLP was fully displaceable by lactoferrin but barely by heparan sulfate, dermatan sulfate, or chondroitin-4-sulfate. Using TRLP coated to microtiter wells and associated with LPL, the b-HS displacement patterns were comparable to those obtained with coated LDL in the presence or absence of LPL. The cell-free system that was used enabled us to identify the functions of apoC and apoE in the binding of TRLP to LPL and HSPG. Both LPL and apoE increased the ability of TRLP to bind HSPG. The apoC content of TRLP regulated the docking of TRLP to LPL. ApoC enrichment reduced the affinity or capacity of TRLP to LPL binding, and this has relevance for the lipolytic cascade.
Engineering Mouse Chromosomes with Cre-loxP: Range, Efficiency, and Somatic Applications (2000)

Chromosomal rearrangements are important resources for genetic studies. Recently, a Cre-loxP-based method to introduce defined chromosomal rearrangements (deletions, duplications, and inversions) into the mouse genome (chromosome engineering) has been established. To explore the limits of this technology systematically, we have evaluated this strategy on mouse chromosome 11. Although the efficiency of Cre-loxP-mediated recombination decreases with increasing genetic distance when the two endpoints are on the same chromosome, the efficiency is not limiting even when the genetic distance is maximized. Rearrangements encompassing up to three quarters of chromosome 11 have been constructed in mouse embryonic stem (ES) cells. While larger deletions may lead to ES cell lethality, smaller deletions can be produced very efficiently both in ES cells and in vivo in a tissue- or cell-type-specific manner. We conclude that any chromosomal rearrangement can be made in ES cells with the Cre-loxP strategy provided that it does not affect cell viability. In vivo chromosome engineering can be potentially used to achieve somatic losses of heterozygosity in creating mouse models of human cancers.
The role of tyrosine kinases and their substrates in signal transmission of hematopoietic growth factors: a short review. (1995)

Both structure-function analysis of hematopoietic growth factor receptors and identification of novel signal transduction molecules have provided new insights into the processes involved in signal transmission pathways engaged by hematopoietic growth factors. These investigations have pointed to the importance of post-translational modifications of pre-existing proteins, in particular tyrosine phosphorylation, in transmitting signals and thereby linking extracellular signals to the activation of nuclear effector molecules which govern gene expression. These observations not only contribute to our understanding of the pleiotropism and redundancy ascribed to hematopoietic growth factors, but also help to trace some of the molecules conferring signal specificity. It is to be expected that this rapidly evolving research field will provide us with a significant collection of new findings in the near future and that the precise understanding of the processes involved in ligand-binding and signal transmission will also stimulate the development of novel therapeutic drugs affecting these processes. This article gives a short overview on the role of tyrosine kinases and their substrates in signal transmission processes initiated by hematopoietic growth factors.
3′-Deoxy-3′-C-trifluoromethyl Nucleosides: Synthesis and Antiviral Evaluation (1998)

Abstract 2′,3′-Dideoxy-3′-C-trifluoromethylthymidine 9a and -uridine 9b and 3′-C-trifluoromethyl-d4T 11 were prepared in a few steps from 3′-deoxy-3′-C-trifluoromethyl-D-ribose, which synthesis was recently reported. The biological assessment of these nucleoside analogues did not reveal interesting antiviral properties against HIV-1, HSV-1, CMV, Vaccine, and Cox B4.
Zymosan-induced bacterial translocation (1992)

Zymosan-induced intestinal mucosal injury and bacterial translocation do not require complement activation, or the release of macrophage or mast cell products. They appear to be mediated by xanthine oxidase-generated products and associated with disruption of the normal ileal and hepatic oxidant-antioxidant balance.
High Levels of Parasite-Specific IgG1 Correlate with the Amicrofilaremic State in Loa loa Infection (1997)

To investigate the mechanisms of protective immunity operating in Loa loa infection, 56 persons from a L. ioa-endemic village in southeast Gabon were examined over a 7-year period. The level of L. loa-specific IgG subclasses in defined parasitologic groups was compared by use of ELISA with either adult, microfilarial, or third-stage larval (L3) antigens of L. loa. With all antigen preparations, IgG1 levels were significantly higher in amicrofilaremic persons than in persons with high or low levels of microfilariae. Moreover, there was a significant negative correlation between IgG1 levels to L3 antigen and the density of microfilariae (Spearman's r(s) = -.701; P < .01). There was no correlation between density of microfilariae and levels of other IgG subclasses or of IgE. These data indicate that IgG1 may play a role in the effector mechanism(s) involved in resistance against L. loa and suggest that L3 antigens may be important in eliciting protective responses.
B cells immortalized by a mini–Epstein-Barr virus encoding a foreign antigen efficiently reactivate specific cytotoxic T cells (2002)

Lymphoblastoid cell lines (LCLs) are human B cells latently infected and immortalized by Epstein-Barr virus (EBV). Presenting viral antigens, they efficiently induce EBV-specific T-cell responses in vitro. Analogous ways to generate T-cell cultures specific for other antigens of interest are highly desirable. Previously, we constructed a mini-EBV plasmid that consists of less than half the EBV genome, is unable to cause virus production, but still immortalizes B cells in vitro. Mini-EBV-immortalized B-cell lines (mini-LCLs) are efficiently produced by infection of B cells with viruslike particles carrying only mini-EBV DNA. Mini-EBV plasmids can be engineered to express an additional gene in immortalized B cells. Here we present a mini-EBV coding for a potent CD8(+) T-cell antigen, the matrix phosphoprotein pp65 of human cytomegalovirus (CMV). By means of this pp65 mini-EBV, pp65-expressing mini-LCLs could be readily established from healthy donors in a one-step procedure. We used these pp65 mini-LCLs to reactivate and expand effector T cells from autologous peripheral blood cells in vitro. When generated from cytomegalovirus (CMV)-seropositive donors, these effector T-cell cultures displayed strong pp65-specific HLA-restricted cytotoxicity. A large fraction of CD8(+) T cells with pp65 epitope specificity was present in such cultures, as demonstrated by direct staining with HLA/peptide tetramers. We conclude that the pp65 mini-EBV is an attractive tool for CMV-specific adoptive immunotherapy. Mini-EBVs could also facilitate the generation of T cells specific for various other antigens of interest.
Directed Assembly of Block Copolymer Blends into Nonregular Device-Oriented Structures (2005)

Self-assembly is an effective strategy for the creation of periodic structures at the nanoscale. However, because microelectronic devices use free-form design principles, the insertion point of self-assembling materials into existing nanomanufacturing processes is unclear. We directed ternary blends of diblock copolymers and homopolymers that naturally form periodic arrays to assemble into nonregular device-oriented structures on chemically nanopatterned substrates. Redistribution of homopolymer facilitates the defect-free assembly in locations where the domain dimensions deviate substantially from those formed in the bulk. The ability to pattern nonregular structures using self-assembling materials creates new opportunities for nanoscale manufacturing.
Some bases of differences in vascular response to sympathetic activity. (1979)

Basic patterns of neuroeffector organization vary widely in the vasculature, in general, with vessel diameter and type, and confer distinctive properties. The smaller the vessel, the more intimate the neuroeffector relationship, the more localized the action of the released transmitter, and the more important myogenic conduction compared to transmitter diffusion for the coordination of vascular effector response. Seemingly superimposed upon these basic general patterns are other variable features, conferring upon vessels of similar size and type diversity of function. These variables include sensitivity and magnitude and possible location of alpha- and beta-receptors and their subtypes, presence and nature of intrinsic vascular tone, and the density and pattern of adrenergic innervation to mention the more important. Functional diversity in neuroeffector characteristics can, to some extent, be understood in relation to embryological development, neurotrophic influences, effector regulation of innervation, and the mural response to an increase in intravascular pressure.
Spatial heterodyne spectroscopy for atmospheric remote sensing (1999)

Spatial heterodyne spectroscopy (SHS) is a relatively new and incompletely developed method of Fourier transform spectroscopy that has advantages over conventional FTS in certain applications. In the SHS instrument, diffraction gratings replace the flat mirrors used in each arm of a conventional Michelson, and an imaging detector is used at the output to record a spatially heterodyned interferogram without any scanning elements. The mechanical simplicity of a diffraction grating is combined with the high light-gathering power of interference spectrometers. SHS systems can achieve an additional light-gathering gain of about two orders of magnitude over conventional FTS or Fabry-Perot interference spectrometers by field-widening using fixed transmitting wedges. Compared to conventional instruments, these gains translate into smaller instruments and/or higher sensitivity for a specified application. Flatness defects in the optics can largely be corrected in software, leading to relaxed tolerances which simplify extension to short wavelengths. This paper focuses on the concepts used in the design of an SHS for mesospheric OH remote sensing at 308 nm, and their validation in laboratory testing. A field-widened system has been constructed, and will soon undergo performance tests with an eye towards space application in the relative near future. Compared to a conventional grating spectrograph used previously for OH measurements, the SHS system is designed to achieve higher resolving power and several times more sensitivity in 1/10 or less of the volume, and with no moving parts.
BURN INJURY INDUCES AN INHIBITORY SIGNAL IN THE LUNG SMAD PATHWAY. (2002)

Shriners Hospitals for Children, Northern California and Dept. of Surgery, Univ. of Calif. at Davis, Sacramento, CA 95817
Parallel lossless image compression using Huffman and arithmetic coding (2003)

The authors show that high-resolution images can be encoded and decoded efficiently in parallel. They present an algorithm based on the hierarchical multi-level progressive (MLP) method, used either with Huffman coding or with a new variant of arithmetic coding called quasi-arithmetic coding. The coding step can be parallelized, even though the codes for different pixels are of different lengths; parallelization of the prediction and error modeling components is straightforward.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evolution of the EF-Hand Family of Proteins (1994)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Blocking VLA-4 Prevents Progression of Experimental Crescentic Glomerulonephritis (2003)

Leucocyte VLA-4 mediates pro-inflammatory and pro-fibrotic effects within the kidney, independent of any role in recruitment of leucocytes into the kidney. Blocking VLA-4 is a promising therapeutic approach in human glomerulonephritis.
Radiation-induced changes in the central nervous system and head and neck. (1996)

Radiation therapy of the brain, neck, and spine can be associated with radiation-induced changes that are increasingly evident radiologically. These changes affect the central nervous system (focal necrosis, diffuse white matter injury, atrophy, mineralizing microangiopathy, telangiectasia, optic neuropathy, large vessel vasculopathy), bone (fatty replacement of marrow, osteoradionecrosis, sinus inflammation), and superficial and deep soft tissues and include neoplasia. Focal necrosis, which most commonly occurs at the treatment site, is seen at computed tomography (CT) and magnetic resonance (MR) imaging as a ring-enhancing mass with edema and mass effect, findings similar to those of tumor recurrence. Diffuse white matter injury appears as hypoattenuating (at CT) or hyperintense (at MR imaging) small foci near the frontal or occipital horns or as a confluent band extending from the ventricles to the corticomedullary junction. Fatty replacement of marrow is the most common osseous complication seen on MR images. Osteoradionecrosis, which occurs most often in the mandible, appears as a focal lytic area at CT and with abnormal marrow signal and cortical destruction at MR imaging. The most common changes in the superficial soft tissues of the head and neck, edema and fibrosis, are seen radiologically as skin thickening and increased soft-tissue attenuation with stranding of subcutaneous fat. Meningioma, the most common radiation-induced CNS tumor, can be distinguished from spontaneous meningiomas on the basis of clinical characteristics (eg, presence of focal alopecia and scalp atrophy).
Dry-Contact and Noncontact Biopotential Electrodes: Methodological Review (2010)

Recent demand and interest in wireless, mobile-based healthcare has driven significant interest towards developing alternative biopotential electrodes for patient physiological monitoring. The conventional wet adhesive Ag/AgCl electrodes used almost universally in clinical applications today provide an excellent signal but are cumbersome and irritating for mobile use. While electrodes that operate without gels, adhesives and even skin contact have been known for many decades, they have yet to achieve any acceptance for medical use. In addition, detailed knowledge and comparisons between different electrodes are not well known in the literature. In this paper, we explore the use of dry/noncontact electrodes for clinical use by first explaining the electrical models for dry, insulated and noncontact electrodes and show the performance limits, along with measured data. The theory and data show that the common practice of minimizing electrode resistance may not always be necessary and actually lead to increased noise depending on coupling capacitance. Theoretical analysis is followed by an extensive review of the latest dry electrode developments in the literature. The paper concludes with highlighting some of the novel systems that dry electrode technology has enabled for cardiac and neural monitoring followed by a discussion of the current challenges and a roadmap going forward.
Origin of the first sharp diffraction peak in the structure factor of covalent glasses (1991)

A model is proposed for the ``first sharp diffraction peak'' (FSDP) in glasses. The FSDP is a chemical-order prepeak due to interstitial volume around cation-centered structural units. Calculated FSDP positions of some covalent glasses agree well with experiment, and the anomalous temperature and pressure dependences of the FSDP can be understood in terms of density effects.
Amphiphilicity determines nanostructure in protic ionic liquids (2010)

The bulk structure of the two oldest ionic liquids (ILs), ethylammonium nitrate (EAN) and ethanolammonium nitrate (EtAN), is elucidated using neutron diffraction. The spectra were modelled using empirical potential structure refinement (EPSR). The results demonstrate that EAN exhibits a long-range structure of solvophobic origin, similar to a bicontinuous microemulsion or disordered L(3)-sponge phase, but with a domain size of only 1 nm. The alcohol (-OH) moiety in EtAN interferes with solvophobic association between cation alkyl chains resulting in small clusters of ions, rather than an extended network.
Breast density segmentation using texture (2006)

This paper describes an algorithm to segment mammo- graphic images into regions corresponding to different densities. The breast parenchymal segmentation uses information extracted for statistical texture based classification which is in turn incorporated in multi-vector Markov Random Fields. Such segmentation is key to developing quantitative mammographic analysis. The algorithm's performance is evaluated quantitatively and qualitatively and the results show the feasibility of segmenting different mammographic densities.