gebhart/patrepeval huggingface dataset:
Comparative localization of fibroblast growth factor receptor‐1, ‐2, and ‐3 mRNAs in the rat brain: In situ hybridization analysis (1997)

The present study provides a detailed comparative description in the adult rat brain of areas that express MRNAs coding for the fibroblast growth factor subtype receptors 1–3 (FGFR1–3). One observation in this analysis was a widespread expression in the brain of all three FGFR mRNAs, according to the following rank order: FGFR1, diencephalon < telencephalon < mesencephalon and metencephalon < myelencephalon; FGFR2 and FGFR3, telencephalon < diencephalon < mesencephalon and metencephalon < myelencephalon. Another observation was an apparent cellular specificity in their basal expression. Thus, the FGFR1 mRNA was expressed mainly in large and weakly stained cells, whereas FGFR2 transcripts were expressed primarily in small and strongly stained cells and in cells of brain regions devoid of neuronal cells, such as the white matter. FGFR3 mRNA was always detected in small and strongly stained cells with scattered distribution and was not expressed in the white matter. However, FGFR2 mRNA was weakly expressed also in large cells localized in some nuclei of the lower brainstem, in the diagonal band, and in the septum. Furthermore, in the medial habenula and in the nuclei of the pons, there exists a high density of cells expressing both FGFR1 and FGFR2 (60–100%). With neurotoxic lesions involving 6-hydroxy-dopamine microinjections in the substantia nigra, reactive glial cells in the lesioned area and surrounding the cannula tract showed an increase in the expression of both FGFR1 and FGFR2 mRNAs, whereas no increased expression was found for FGFR3 mRNA. Taken together, these findings showed that these three FGF receptors exist in all subtypes of cells of each brain region. Their apparent cellular specificity suggests that these receptor subtypes can have a differential trophic role in the brain, reflecting the various biological activities shown by the ligands of the FGF family. J. Comp. Neurol. 379:226–246, 1997. © 1997 Wiley-Liss, Inc.
Transition-Metal-Catalyzed C–N Bond Forming Reactions Using Organic Azides as the Nitrogen Source: A Journey for the Mild and Versatile C–H Amination (2015)

Owing to the prevalence of nitrogen-containing compounds in functional materials, natural products and important pharmaceutical agents, chemists have actively searched for the development of efficient and selective methodologies allowing for the facile construction of carbon-nitrogen bonds. While metal-catalyzed C-N cross-coupling reactions have been established as one of the most general protocols for C-N bond formation, these methods require starting materials equipped with functional groups such as (hetero)aryl halides or their equivalents, thus generating stoichiometric amounts of halide salts as byproducts. To address this aspect, a transition-metal-catalyzed direct C-H amination approach has emerged as a step- and atom-economical alternative to the conventional C-N cross-coupling reactions. However, despite the significant recent advances in metal-mediated direct C-H amination reactions, most available procedures need harsh conditions requiring stoichiometric external oxidants. In this context, we were curious to see whether a transition-metal-catalyzed mild C-H amination protocol could be achieved using organic azides as the amino source. We envisaged that a dual role of organic azides as an environmentally benign amino source and also as an internal oxidant via N-N2 bond cleavage would be key to develop efficient C-H amination reactions employing azides. An additional advantage of this approach was anticipated: that a sole byproduct is molecular nitrogen (N2) under the perspective catalytic conditions. This Account mainly describes our research efforts on the development of rhodium- and iridium-catalyzed direct C-H amination reactions with organic azides. Under our initially optimized Rh(III)-catalyzed amination conditions, not only sulfonyl azides but also aryl- and alkyl azides could be utilized as facile amino sources in reaction with various types of C(sp(2))-H bonds bearing such directing groups as pyridine, amide, or ketoxime. More recently, a new catalyst system using Ir(III) species was developed for the direct C-H amidation of arenes and alkenes with acyl azides under exceptionally mild conditions. As a natural extension, amidation of primary C(sp(3))-H bonds could also be realized on the basis of the superior activity of the Cp*Ir(III) catalyst. Mechanistic investigations revealed that a catalytic cycle is operated mainly in three stages: (i) chelation-assisted metallacycle formation via C-H bond cleavage; (ii) C-N bond formation through the in situ generation of a metal-nitrenoid intermediate followed by the insertion of an imido moiety to the metal carbon bond; (iii) product release via protodemetalation with the concomitant catalyst regeneration. In addition, this Account also summarizes the recent advances in the ruthenium- and cobalt-catalyzed amination reactions using organic azides, developed by our own and other groups. Comparative studies on the relative performance of those catalytic systems are briefly described.
Narrow-band interference rejection in orthogonal multi-carrier spread-spectrum communications (2002)

In order to combat strong narrow band interference, different measures called notch-filtering in the time domain (based on LMS algorithm) and in the transform domain (based on FFT) with spread-spectrum (SS) have been analyzed. Another interesting approach is based on orthogonal multi-carrier transmission called the orthogonal-frequency-division-multiple-access (OFDM) technique. This technique permits to achieve a high spectral efficiency and to combat the frequency selective fading and the interference in the channel by switching-off some sub-carriers. The aim of the article is to study the performance of the combination of a spread-spectrum system with OFDM in the presence of narrow-band interference. This combination allows one to use the spectrum in an efficient way, to exploit frequency diversity, to increase the robustness against fading and interference and to retain many advantages of a spread-spectrum system. The interference is considered as narrow-band multi-tone sine interference. A method for evaluating both interference and fading process based on frequency domain analysis is studied. The estimated interference and fading process is used for weighting each received chip before despreading. The results showed that the combination of spread-spectrum/OFDM in the presence of multi-tone narrow-band interference in a frequency/time selective fading channel is a promising approach.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Persistent Cutaneous Insulin Allergy Resulting From High-Molecular-Weight Insulin Aggregates (1990)

Cutaneous insulin allergy remains a clinical problem despite the use of highly purified human insulins. We used in vitro lymphocyte-transformation studies to examine the reactivity of various insulin formulations in diabetic patients with (n = 4) and without (n = 8) cutaneous allergies. Nonspecific response to concanavalin A demonstrated a greater than 40-fold response in both groups. Control patients did not respond to the addition of commercial insulin preparations (stimulation index [SI] less than 4), whereas allergic patients had an 11-fold response to beef (P less than 0.01), a 10-fold response to pork (P less than 0.01), and a 6-fold response to human (P less than 0.01) insulins. This response was limited to a single insulin manufacturer's preparations and was uniform in all three species tested. Efforts to identify the offending agent revealed no lymphoblast transformation when crystalline insulin was used or when commercial preparations were purified to a single peak by high-performance liquid chromatography (HPLC). Pure crystalline insulin dimers of beef, pork, and human species were tested; control subjects responded with mean SIs of 1.9, 1.9, and 1.8, respectively, whereas allergic patients showed greater reactivity to beef (SI 7.3) and pork (SI 14.8). The lymphoblast-transformation response to crystalline human dimer was dose dependent with mean SIs of 0.9 at low concentration (2.8 ng/ml) and 19.2 at a higher concentration (20.4 ng/ml). The commercial insulin preparations were run on size-exclusion HPLC to determine high-molecular-weight aggregate content. Independent of species, a single manufacturer had products demonstrating aggregate levels 3- to 6-fold higher than those found in other manufacturers' preparations.(ABSTRACT TRUNCATED AT 250 WORDS)
Induction of IFN-alpha in peripheral blood mononuclear cells by HIV-infected monocytes. Restricted antiviral activity of the HIV-induced IFN (1992)

PBMC cocultured with HIV-infected monocytes for 12 to 48 h released high levels of IFN activity. IFN titers were directly dependent upon time after virus infection and level of HIV replication in infected cells. IFN induction in PBMC was evident with HIV-infected monocytes and PBMC and with myeloid and lymphoblastoid cell lines with at least three different HIV strains. In HIV-infected cell line pairs in which virus infection occurs in both productive and restricted forms, IFN induction in PBMC occurred only with productive infection. IFN activity was acid stable and completely neutralized by antibodies against IFN-alpha. Induction of IFN required cell-cell contact between HIV-infected cells and PBMC, but was independent of MHC compatibility. With PBMC co-cultured with autologous HIV-infected monocytes, IFN induction was highly selective: IL-1 beta, IL-6, or TNF-alpha activity and mRNA were not detected. Cell surface determinants on HIV-infected monocytes that induced IFN in PBMC remained active after fixation in 4% paraformaldehyde. Both adherent and nonadherent PBMC produced IFN after coculture with HIV-infected monocytes. Ability to produce IFN by PBMC was not affected by depletion of T cell, NK cell, B cell, or monocyte subpopulations. The IFN activity produced by PBMC cocultured with HIV-infected cells was about 20-fold less active than equal quantities of rIFN-alpha 2b for inhibition of HIV replication in monocytes and at low concentrations enhanced virus growth. Clinical studies with HIV-infected patients and parallel findings in animal lentivirus disease suggest an adverse role for IFN in disease progression. Conditions for induction of IFN in the culture system described in this report may mimic those in the HIV-infected patient. Defining the molecular basis for IFN induction, the cells that produce IFN, and the altered biologic activity of this important cytokine may provide insight into the pathogenesis of HIV disease.
Scatter-Hole Cameras for X-Rays and Gamma Rays (1968)

A pinhole camera for which the entrance area, covered with a very large number of randomly dis- tributed pinholes, is 50 per cent open is shown to be a very effective way of forming images of a complex of X-ray stars. A simple statistical trick is used to reduce the multitudinous overlapping images to a single image. Less than forty detected photons are needed to form an image of a single star
FEAsy: A Sketch-Based Interface Integrating Structural Analysis in Early Design (2009)

The potential advantages of freehand sketches have been widely recognized and exploited in many fields especially in engineering design and analysis. This is mainly because the freehand sketches are an efficient and natural way for users to visually communicate ideas. However, due to a lack of fundamental techniques for understanding them, sketch-based interfaces have not yet evolved as the preferred computing platform over traditional menu-based tools. In this paper, we address the specific challenge of transforming informal and ambiguous freehand inputs to more formalized and structured representations. We present a domain-independent, multi-stroke, multi-primitive beautification method which detects and uses the spatial relationships implied in the sketches. Spatial relationships are represented as geometric constraints and satisfied by a geometric constraint solver. To demonstrate the utility of this technique and also to build a natural working environment for structural analysis in early design, we have developed FEAsy (acronym for Finite Element Analysis made easy) as shown in Fig. 1. This tool allows the users to transform, simulate and analyze their finite element models quickly and easily through freehand sketching, just as they would draw on paper. Further, we have also developed simple, domain specific rules-based algorithms for recognizing the commonly used symbols and for understanding the different contexts in finite element modeling. Finally, we illustrate the proposed approach with a few examples.
Energy Scavenging for Mobile and Wireless Electronics (2005)

Energy harvesting has grown from long-established concepts into devices for powering ubiquitously deployed sensor networks and mobile electronics. Systems can scavenge power from human activity or derive limited energy from ambient heat, light, radio, or vibrations. Ongoing power management developments enable battery-powered electronics to live longer. Such advances include dynamic optimization of voltage and clock rate, hybrid analog-digital designs, and clever wake-up procedures that keep the electronics mostly inactive. Exploiting renewable energy resources in the device's environment, however, offers a power source limited by the device's physical survival rather than an adjunct energy store. Energy harvesting's true legacy dates to the water wheel and windmill, and credible approaches that scavenge energy from waste heat or vibration have been around for many decades. Nonetheless, the field has encountered renewed interest as low-power electronics, wireless standards, and miniaturization conspire to populate the world with sensor networks and mobile devices. This article presents a whirlwind survey through energy harvesting, spanning historic and current developments.
Moesin: a member of the protein 4.1-talin-ezrin family of proteins. (1991)

Moesin (membrane-organizing extension spike protein, pronounced mó ez in) has previously been isolated from bovine uterus and characterized as a possible receptor protein for heparan sulfate. We now have cloned and sequenced its complete cDNA, which represents a single 4.2-kilobase mRNA encoding a protein of 577 amino acids. It contains no apparent signal peptide or transmembrane domain. In addition, the protein shows significant sequence identity (72%) to ezrin (cytovillin, p81), as well as similarity to protein 4.1 and talin. All of the latter proteins have been postulated to serve as structural links between the plasma membrane and the cytoskeleton. A similar role for moesin is implied by structure and domain predictions derived from the cDNA-deduced peptide sequence. Furthermore, our data indicate that moesin is identical to the 77-kDa band that copurifies with ezrin in its isolation from human placenta [Bretscher, A. (1989) J. Cell Biol. 108, 921-930].
Cholinergic modulation of microglial activation by α7 nicotinic receptors (2004)

Almost all degenerative diseases of the CNS are associated with chronic inflammation. A central step in this process is the activation of brain mononuclear phagocyte cells, called microglia. While it is recognized that healthy neurons and astrocytes regulate the magnitude of microglia-mediated innate immune responses and limit excessive CNS inflammation, the endogenous signals governing this process are not fully understood. In the peripheral nervous system, recent studies suggest that an endogenous 'cholinergic anti-inflammatory pathway' regulates systemic inflammatory responses via alpha 7 nicotinic acetylcholinergic receptors (nAChR) found on blood-borne macrophages. These data led us to investigate whether a similar cholinergic pathway exists in the brain that could regulate microglial activation. Here we report for the first time that cultured microglial cells express alpha 7 nAChR subunit as determined by RT-PCR, western blot, immunofluorescent, and immunohistochemistry analyses. Acetylcholine and nicotine pre-treatment inhibit lipopolysaccharide (LPS)-induced TNF-alpha release in murine-derived microglial cells, an effect attenuated by alpha 7 selective nicotinic antagonist, alpha-bungarotoxin. Furthermore, this inhibition appears to be mediated by a reduction in phosphorylation of p44/42 and p38 mitogen-activated protein kinase (MAPK). Though preliminary, our findings suggest the existence of a brain cholinergic pathway that regulates microglial activation through alpha 7 nicotinic receptors. Negative regulation of microglia activation may also represent additional mechanism underlying nicotine's reported neuroprotective properties.
A mechanism underlying synergy between IL-12 and IFN-gamma-inducing factor in enhanced production of IFN-gamma (1997)

IL-12 and IFN-gamma-inducing factor (IGIF) have the capacity to stimulate IFN-gamma production by T cells. Using an IL-12-responsive T cell clone, 2D6, we investigated how these two cytokines collaborate for IFN-gamma production. 2D6 obtained from cultures containing rIL-12 produced IFN-gamma in response to rIGIF. 2D6 from cultures deprived of IL-12 for 24 h produced only marginal levels of IFN-gamma production following stimulation with either rIL-12 or rIGIF alone. However, simultaneous stimulation of these 2D6 cells with both cytokines resulted in strikingly enhanced levels of IFN-gamma production. 2D6 could also be maintained in the presence of rIL-2 instead of rIL-12. 2D6 lines maintained with rIL-12 (2D6(IL-12)) or rIL-2 (2D6(IL-2)) exhibited differential IGIF responsiveness: both lines responded similarly to rIL-2 or rIL-12, whereas the 2D6(IL-12) or 2D6(IL-2) exhibited high or marginal IGIF responsiveness, respectively. The 2D6(IL-12) line expressed IGIF receptor (IGIFR), whereas the 2D6(IL-2) did not. Overnight exposure of the 2D6(IL-12) to rIL-2 reduced IGIFR expression and conversely, exposure of the 2D6(IL-2) to rIL-12 restored IGIFR expression. IGIFR expression by these 2D6 lines correlated with the capacity to produce IFN-gamma in response to rIGIF. Purified naive T cells stimulated with anti-CD3 plus anti-CD28 mAb and subsequently cultured with rIL-12 were also found to express IGIFR and induce enhanced IFN-gamma production following IGIF stimulation. These results indicate that the induction of IGIFR by IL-12 represents one of the mechanisms underlying the synergy between IL-12 and IGIF in IFN-gamma production.
Antibody-Based Detection of ERG Rearrangement-Positive Prostate Cancer (2010)

TMPRSS2-ERG gene fusions occur in 50% of prostate cancers and result in the overexpression of a chimeric fusion transcript that encodes a truncated ERG product. Previous attempts to detect truncated ERG products have been hindered by a lack of specific antibodies. Here, we characterize a rabbit anti-ERG monoclonal antibody (clone EPR 3864; Epitomics, Burlingame, CA) using immunoblot analysis on prostate cancer cell lines, synthetic TMPRSS2-ERG constructs, chromatin immunoprecipitation, and immunofluorescence. We correlated ERG protein expression with the presence of ERG gene rearrangements in prostate cancer tissues using a combined immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) analysis. We independently evaluated two patient cohorts and observed ERG expression confined to prostate cancer cells and high-grade prostatic intraepithelial neoplasia associated with ERG-positive cancer, as well as vessels and lymphocytes (where ERG has a known biologic role). Image analysis of 131 cases demonstrated nearly 100% sensitivity for detecting ERG rearrangement prostate cancer, with only 2 (1.5%) of 131 cases demonstrating strong ERG protein expression without any known ERG gene fusion. The combined pathology evaluation of 207 patient tumors for ERG protein expression had 95.7% sensitivity and 96.5% specificity for determining ERG rearrangement prostate cancer. In conclusion, this study qualifies a specific anti-ERG antibody and demonstrates exquisite association between ERG gene rearrangement and truncated ERG protein product expression. Given the ease of performing IHC versus FISH, ERG protein expression may be useful for molecularly subtyping prostate cancer based on ERG rearrangement status and suggests clinical utility in prostate needle biopsy evaluation.
A method for selection of mutations at the tdk locus in Escherichia coli (1993)

Mutants of Escherichia coli which are resistant to 5-fluorodeoxyuridine all have mutations which map at a single locus at 27.5 min on the genetic map of E. coli. Extracts prepared from each mutant were deficient in thymidine kinase activity measured in vitro. Simple selective conditions which allowed detection of one mutant in the presence of 10(7) wild-type bacteria were found. These results show that loss of thymidine kinase activity is the usual mechanism for 5-fluorodeoxyuridine resistance and that all such mutations occur at the locus previously designated tdk.
Structure from motion: a region based approach using affine transformations and moment invariants (2002)

A region-based method to solve the structure and motion problem is presented. Region matchings between images are accomplished by using affine invariants. No feature extraction or segmentation is needed in the matching process. Having recovered the region matches, a closed-form solution for the camera motion and the 3-D structures of the regions can be obtained. The advantage of this approach is that it gives complete structure and motion estimation at low computational cost.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Information exploration using The Pond (2002)

In this paper we describe The Pond, a system used to search for and visualise data elements on an engaging tabletop display. The Pond uses methods of unencumbered interaction and audio feedback to allow users to investigate data elements, and supports shoulder-to-shoulder collaboration with the physical Pond artefact mediating the collaboration between those people gathered around it. The user interface is based on an ecosystem metaphor, presenting data elements in the form of shoals of aquatic creatures inside a virtual 3D pond. The Pond is an interactive system offering an appealing and novel way to search for and interchange information. We describe the motivation and design choices behind The Pond, the system as it stands today, details of its implementation, and observations from a study of The Pond in use.
Mutations in the pre-mRNA splicing factor gene PRPC8 in autosomal dominant retinitis pigmentosa (RP13) (2001)

Retinitis pigmentosa (RP) is a genetically heterogeneous disorder characterized by progressive degeneration of the peripheral retina leading to night blindness and loss of visual fields. With an incidence of approximately 1 in 4000, RP can be inherited in X-linked, autosomal dominant or autosomal recessive modes. The RP13 locus for autosomal dominant RP (adRP) was placed on chromosome 17p13.3 by linkage mapping in a large South African adRP family. Using a positional cloning and candidate gene strategy, we have identified seven different missense mutations in the splicing factor gene PRPC8 in adRP families. Three of the mutations cosegregate within three RP13 linked families including the original large South African pedigree, and four additional mutations have been identified in other unrelated adRP families. The seven mutations are clustered within a 14 codon stretch within the last exon of this large 7 kb transcript. The altered amino acid residues at the C-terminus exhibit a high degree of conservation across species as diverse as humans, Arabidopsis and trypanosome, suggesting that some functional significance is associated with this part of the protein. These mutations in this ubiquitous and highly conserved splicing factor offer compelling evidence for a novel pathway to retinal degeneration.