gebhart/patrepeval huggingface dataset:
The absolute number of nerve cells in substantia nigra in normal subjects and in patients with Parkinson's disease estimated with an unbiased stereological method. (1991)

Using an unbiased stereological technique, the total numbers of pigmented and non-pigmented neurons were estimated in the substantia nigra of seven patients with Parkinson's disease and seven control patients. Compared with the controls, in which the average total number of pigmented neurons was 550,000, the number of neurons was reduced by 66% in the patients. The average total number of non-pigmented neurons was 260,000 in controls and reduced by 24% in the patients. A significant correlation (r = 0.81) existed between the total numbers of pigmented and non-pigmented neurons in the controls, whereas a similar correlation (r = 0.72) in the patients fell just short of statistical significance. The stereological estimates made in this study are unbiased, in that they are independent of nerve cell size, section thickness and of dimensional changes in brain tissue induced by histological procedures. The stereological method is considerably more efficient than previous conventional methods.
Interactions, localization, and phosphorylation of the m6A generating METTL3–METTL14–WTAP complex (2018)

<i>N</i><sup>6</sup>-methyladenine (m<sup>6</sup>A) is found on many eukaryotic RNAs including mRNAs. m<sup>6</sup>A modification has been implicated in mRNA stability and turnover, localization, or translation efficiency. A heterodimeric enzyme complex composed of METTL3 and METTL14 generates m<sup>6</sup>A on mRNAs. METTL3/14 is found in the nucleus where it is localized to nuclear speckles and the splicing regulator WTAP is required for this distinct nuclear localization pattern. Although recent crystal structures revealed how the catalytic MT-A70 domains of METTL3 and METTL14 interact with each other, a more global architecture including WTAP and RNA interactions has not been reported so far. Here, we used recombinant proteins and mapped binding surfaces within the METTL3/14-WTAP complex. Furthermore, we identify nuclear localization signals and identify phosphorylation sites on the endogenous proteins. Using an in vitro methylation assay, we confirm that monomeric METTL3 is soluble and inactive while the catalytic center of METTL14 is degenerated and thus also inactive. In addition, we show that the C-terminal RGG repeats of METTL14 are required for METTL3/14 activity by contributing to RNA substrate binding. Our biochemical work identifies characteristic features of METTL3/14-WTAP and reveals novel insight into the overall architecture of this important enzyme complex.
Tranilast, a Selective Inhibitor of Collagen Synthesis in Human Skin Fibroblasts (1994)

Effects of tranilast, N-(3,4-dimethoxycinnamoyl)anthranilic acid, on collagen synthesis in cultured human skin fibroblasts were studied. Tranilast was found to inhibit collagen synthesis in a dose-dependent manner to a maximum of 55% at 300 microM during 48 h of treatment; the synthesis of type I and type III collagens was equally affected. Administered simultaneously or subsequently, tranilast reduced the stimulatory effect of transforming growth factor beta 1 (2.5 ng/ml) on collagen synthesis without affecting the accompanying stimulation of noncollagen protein synthesis. It did not affect prolyl or lysyl hydroxylase activity in vitro and in cells. The content of pro alpha 1(I) collagen mRNA was decreased 60% by tranilast. Tranilast prevented the TGF beta 1-mediated increase in pro alpha 1(I) collagen mRNA. These results indicate that tranilast specifically inhibits collagen production at a pretranslational level by interfering with TGF beta 1 effects. Tranilast also inhibited collagen synthesis in scleroderma fibroblasts to the same extent and in keloid fibroblasts to a greater extent than in normal fibroblasts, attesting to its therapeutic potential as an antifibrotic drug.
Interactive modeling from dense color and sparse depth (2004)

We are developing a system for interactive modeling of real world scenes. The acquisition device consists of a video camera enhanced with an attached laser system. As the operator sweeps the scene, the device acquires dense color and sparse depth frames that are registered and merged into a point-based model. The evolving model is rendered continually to provide immediate operator feedback. The interactive modeling pipeline runs at five frames per second. We model scenes in two modes based on their geometric complexity. Scenes that contain large smooth surfaces are modeled freehand; scenes that contain small uneven surfaces are modeled using a parallax-free camera bracket.
Multiplexed single molecule immunoassays (2013)

We have developed a method that enables the multiplexed detection of proteins based on counting single molecules. Paramagnetic beads were labeled with fluorescent dyes to create optically distinct subpopulations of beads, and antibodies to specific proteins were then immobilized to individual subpopulations. Mixtures of subpopulations of beads were then incubated with a sample, and specific proteins were captured on their specific beads; these proteins were then labeled with enzymes via immunocomplex formation. The beads were suspended in enzyme substrate, loaded into arrays of femtoliter wells--or Single Molecule Arrays (Simoa)--that were integrated into a microfluidic device (the Simoa disc). The wells were then sealed with oil, and imaged fluorescently to determine: a) the location and subpopulation identity of individual beads in the femtoliter wells, and b) the presence or absence of a single enzyme associated with each bead. The images were analyzed to determine the average enzyme per bead (AEB) for each bead subpopulation that provide a quantitative parameter for determining the concentration of each protein. We used this approach to simultaneously detect TNF-α, IL-6, IL-1α, and IL-1β in human plasma with single molecule resolution at subfemtomolar concentrations, i.e., 200- to 1000-fold more sensitive than current multiplexed immunoassays. The simultaneous, specific, and sensitive measurement of several proteins using multiplexed digital ELISA could enable more reliable diagnoses of disease.
Gene expressions of lipopolysaccharide receptors, toll-like receptors 2 and 4, are differently regulated in mouse T lymphocytes (2000)

Toll-like receptors (TLRs) are a family of mammalian proteins homologous to Drosophila Toll. Human TLR2 was shown to mediate the responsiveness to lipopolysaccharide (LPS). On the other hand, gene mutations of mouse TLR4 (mTLR4) in LPS-hyporesponsive strains have suggested that mTLR4 is essential for LPS-signaling in mice, but the role of mTLR2 has not been explored. This report describes molecular cloning of the mTLR2 cDNA. Overexpression of mTLR2 and mouse CD14 conferred LPS-inducibility of c-Jun N-terminal kinase phosphorylation and nuclear factor-kappaB activation to COS7 cells, suggesting that mTLR2 is a signaling receptor for LPS. Both mTLR2 and mTLR4 genes were expressed in T cells. Treatment with anti-CD3epsilon, PMA plus ionomycin, or interleukin-2 (IL-2)/IL-15 increased mTLR2 but not mTLR4 messenger RNA (mRNA) in some T cell lines. Specific inhibitors of mitogen-activated extracellular signal-regulated kinase and fusion protein 38 (p38) kinase inhibited mTLR2 mRNA up-regulation by PMA plus ionomycin. This suggests that extracellular signal-regulated kinase and p38 kinase pathways were involved. Additionally, LPS treatment of EL-4 cell line decreased IL-4 gene expression. Our results indicate that both mTLR2 and mTLR4 are involved in LPS signaling, but their expressions are regulated differently in T cells, and that LPS may directly affect T-cell functions by binding to TLRs. (Blood. 2000;95:1378-1385)
Mask and wafer topography effects in immersion lithography (2005)

The paper investigates the application of different modeling approaches for mask diffraction and wafer exposure analysis in the hyper imaging NA regime. Immersion lithography implies larger angles of incidence of the light which illuminates the mask. This effect limits the validity of the so called Hopkins approach for the rigorous simulation of light diffraction from the mask. It is demonstrated that strong phase shifting techniques in combination with off-axis illumination are not adequately modeled by the Hopkins approach. Moreover, the application of immersion lithography results in larger light propagation angles inside the resist/wafer stack. The application of rigorous electromagnetic field (EMF) simulation for the description of the wafer side light propagation demonstrates the limitation of the performance of single antireflective coatings (ARC). Rigorous EMF wafer simulations are also used to explore the printability of small air bubbles in the immersion liquid, which stick to the surface of the resist. Finally, a new approach (RENFT) for efficient rigorous EMF wafer simulations is proposed.
The Barbier Reaction - A One-Step Alternative for Syntheses via Organomagnesium Compounds (1977)

A survey is given of reactions of organic halides with magnesium in the presence of an added substrate in a suitable solvent. In many cases this one-step synthesis is to be preferred to the commonly used two-step procedure via Grignard compounds. The applications of metals other than magnesium for this one-step synthesis are also briefly mentioned. 1. Introduction 2. Allyl and Benzyl Halides 3. Other Organic Halides 4. Miscellaneous Syntheses 5. Applications of Other Metals 5.1. Zinc 5.2. Calcium 5.3. Lithium
Distribution and characterization of mosquitocidal toxin genes in some strains of Bacillus sphaericus (1997)

The binary toxin of Bacillus sphaericus strains forms a crystal in sporulating cells, while the mosquitocidal toxin is located in the cytoplasm of vegetative cells. The distribution of binary toxin (btx) and mosquitocidal toxin (mtx) genes in 53 strains of B. sphaericus was determined by hybridization of specific gene probes to chromosomal DNA in Southern blots. btx genes were found in all strains of serotype 5a5b examined and in some strains of serotypes 1a, 3, 6, 25, and 48, while mtx genes were detected in strains of serotypes 1a, 2a2b, 5a5b, 6, 9a9c, 25, and 48. Serotype 26a26b strains lacked both toxin genes, as did some strains of serotypes 2a2b, 3, 6, and 48. Partial DNA sequences of btx genes from five strains, together with published sequences, revealed four types of toxin among mosquitocidal B. sphaericus strains. most of the 42-kDa toxin gene of btx was identical in strains from serotypes 1a, 3, 6, and 48, and the gene is here classified as a type 1 btx gene. A serotype 3 strain isolated in Singapore possessed a unique 42-kDa toxin gene, here designated type 4; while the btx genes from strains of serotypes 5a5b and 25 are referred to as types 2 and 3, respectively.
Erratum to: ASPM-associated stem cell proliferation is involved in malignant progression of gliomas and constitutes an attractive therapeutic target (2011)

Additional file 1: Tumor spheroid characterization. Genomic stability was examined with CGHa analysis (left = DNA profile from the initial tumor; right = DNA profile from gliomasphere at passage p28). The chromosomes are indicated on the axis and copy number is on y axis. Yellow indicates the normal genomic copy number, while green indicates a loss and red indicates a gain in copy number. Although some differences are observed, the comparison of both profiles shows that overall genomic profile is quite well preserved (except for an amplicon on chromosome 8 present only in the gliomasphere).
Dynamic memory networks for visual and textual question answering (2016)

Neural network architectures with memory and attention mechanisms exhibit certain reasoning capabilities required for question answering. One such architecture, the dynamic memory network (DMN), obtained high accuracy on a variety of language tasks. However, it was not shown whether the architecture achieves strong results for question answering when supporting facts are not marked during training or whether it could be applied to other modalities such as images. Based on an analysis of the DMN, we propose several improvements to its memory and input modules. Together with these changes we introduce a novel input module for images in order to be able to answer visual questions. Our new DMN+ model improves the state of the art on both the Visual Question Answering dataset and the bAbI-10k text question-answering dataset without supporting fact supervision.
Biology And Molecular Biology Of Starch Synthesis And Its Regulation (1991)

Abstract Starch is the major reserve carbohydrate of most higher plants and is found as a water-insoluble granule which can vary in size and shape depending on its plant source and on the maturity or stage of development of the plant at the time of isolation of the starch granule. The granule usually contains two different polysaccharides, amylase and amylopectin. Usually, amylopectin constitutes about 65 to 75% of the polysaccharide component of the starch granule. Amylase is mainly found as a linear chain of a-(1-4)-linked a-O-glucopyranosyl residues of about 1000 units long. There are some molecules found in the amylase fraction that are branched to a very small extent {1-6 a-O gluco-pyranose; one per 1,000 glucosyl units). In contrast, amylopectin is more highly branched with about 4 to 5% of the glucosidic linkages being a-1-6.
Opposite Modulation of Cocaine-Seeking Behavior by D 1 - and D 2 -Like Dopamine Receptor Agonists (1996)

Activation of the mesolimbic dopamine system is known to trigger relapse in animal models of cocaine-seeking behavior. We found that this "priming" effect was selectively induced by D2-like, and not by D1-like, dopamine receptor agonists in rats. Moreover, D1-like receptor agonists prevented cocaine-seeking behavior induced by cocaine itself, whereas D2-like receptor agonists enhanced this behavior. These results demonstrate an important dissociation between D1- and D2-like receptor processes in cocaine-seeking behavior and support further evaluation of D1-like receptor agonists as a possible pharmacotherapy for cocaine addiction.
Src kinases in systemic sclerosis: Central roles in fibroblast activation and in skin fibrosis (2008)

These findings indicate that Src kinases play important roles in the activation of fibroblasts and in the development of experimental fibrosis. Thus, Src kinases might be interesting targets for novel antifibrotic therapies in SSc.
Cytotoxic T cell responses to human telomerase reverse transcriptase in patients with hepatocellular carcinoma† (2006)

Human telomerase reverse transcriptase, hTERT, has been identified as the catalytic enzyme required for telomere elongation. hTERT is expressed in most tumor cells but seldom expressed in most human adult cells. It has been reported that 80% to 90% of hepatocellular carcinomas (HCCs) express hTERT, making the enzyme a potential target in immunotherapy for HCC. In the current study, we identified hTERT-derived, HLA-A*2402-restricted cytotoxic T cell (CTL) epitopes and analyzed hTERT-specific CTL responses in patients with HCC. Peptides containing the epitopes showed high affinity to bind HLA-A*2402 in a major histocompatibility complex binding assay and were able to induce hTERT-specific CTLs in both hTERT cDNA-immunized HLA-A*2402/Kb transgenic mice and patients with HCC. The CTLs were able to kill hepatoma cell lines depending on hTERT expression levels in an HLA-A*2402-restricted manner and induced irrespective of hepatitis viral infection. The number of single hTERT epitope-specific T cells detected by ELISPOT assay was 10 to 100 specific cells per 3 x 10(5) PBMCs, and positive T cell responses were observed in 6.9% to 12.5% of HCC patients. hTERT-specific T cell responses were observed even in the patients with early stages of HCC. The frequency of hTERT/tetramer+ CD8+ T cells in the tumor tissue of patients with HCC was quite high, and they were functional. In conclusion, these results suggest that hTERT is an attractive target for T-cell-based immunotherapy for HCC, and the identified hTERT epitopes may be valuable both for immunotherapy and for analyzing host immune responses to HCC.
Efficacy of Olanzapine in Acute Bipolar Mania<subtitle>A Double-blind, Placebo-Controlled Study</subtitle> (2000)

Olanzapine demonstrated greater efficacy than placebo in the treatment of acute bipolar mania and was generally well tolerated.
Carbohydrate microarrays (2003)

Sugar chains are abundantly expressed on the outer surfaces of the vast majority of viral, bacterial, protozoan and fungal pathogens, as well as on the membranes of mammalian cells. This class of carbohydrate molecule is without peer in structural diversity and is characteristically suitable for storing and displaying biological signals for molecular and cellular recognition. Exploring the biological information contained in sugar chains is an important topic of current postgenomic research. To facilitate these investigations, we have focused on the establishment of a carbohydrate-based microarray technology. Recently, we reported that a large panel of carbohydrate-containing macromolecules, including polysaccharides, natural glycoconjugates, and the mono- and oligosaccharides coupled to carrier molecules, can be stably immobilized on a microglass slide to produce a large-scale carbohydrate microarray. In this review, we attempt to summarize our recent progress in using this technology to uncover the carbohydrate-based biological signals that are recognized by the human and animal immune systems. We also discuss the potential of various platforms of carbohydrate microarrays that were recently established and analyze the challenges to future development of carbohydrate microarray technologies and their applications.
Nerve Conduction Blockade in the Sciatic Nerve Prevents but Does Not Reverse the Activation of p38 Mitogen-activated Protein Kinase in Spinal Microglia in the Rat Spared Nerve Injury Model (2007)

After nerve injury, activity in the peripheral nerve is required for the induction but not the maintenance of p38 activation in spinal microglia.
Monoclonal antibodies specific for the phase-variant O-acetylated K1 capsule of Escherichia coli (1991)

Two monoclonal antibodies, one each of the immunoglobulin M and G2b types, were produced from mouse spleen cells. These monoclonal antibodies only reacted with approximately 50% of the Escherichia coli K1 strains and not against group B meningococci. No reaction was observed after the strains were boiled. E. coli K1 strains that reacted with the monoclonal antibodies could become nonreactive after subculture. Based on these findings, we conclude that the monoclonal antibodies react with the O-acetylated K1 capsule.
Document management in HALdoc (2002)

HALdoc is a general purpose document processing and archiving system. The documents archived in the system are not restricted only to text files. It can also archive images, sounds etc., in addition to text files. The system also includes a built-in OCR program and a scan control subsystem to get images of new documents. The general properties of the HALdoc system are introduced and how documents are managed in HALdoc is explained. The logical hierarchy used in the organization of HALdoc documents, and the client-server architecture used in accessing these documents is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mimo Antenna Selections Using Csi From Reciprocal Channel (2010)

It is well known that the channel capacity of Multiple- Input-Multiple-Output (MIMO) system increases as the number of antenna pairs between transmitter and receiver increases but it suffers from multiple expensive RF chains. To reduce the cost of RF chains, Antenna Selection (AS) method can offer a good tradeoff between expense and performance. In a transmitting AS system, Channel State Information (CSI) feedback is necessarily required to choose the best subset of antennas in which the effects of delays and errors occurred in feedback channels are the most dominant factors degrading the performance of the AS method. This paper presents the concept of AS method using CSI from channel reciprocity instead of feedback method. Reciprocity technique can easily archive CSI by utilizing a reverse channel where the forward and reverse channels are symmetrically considered in time, frequency and location. In this work, the capacity performance of MIMO system when using AS method at transmitter with reciprocity channels is investigated by own developing Testbed. The obtained results show that reciprocity technique offers capacity close to a system with a perfect CSI and gains a higher capacity than a system without AS method from 0.9 to 2.2 bps/Hz at SNR 10 dB.
Electron field emission from amorphous carbon-cesium alloys (1997)

Hard carbon films can be prepared by the condensation of energetic carbon species at and below room temperature. These hydrogen-free films are primarily tetrahedrally coordinated and contain high fractions of sp3 bonding. Field emission from these and other forms of carbon has been considered previously, but it was generally unstable or based on surface treatments that limit their operating conditions. We report electron emission from amorphous carbon-cesium (a-C:Cs) thin films at applied fields as low as 7 V/μm. This emission characteristic is relatively insensitive to surface treatment; films left under ambient laboratory environment for more than six months show these favorable characteristics with no pretreatment. We describe the fabrication process and emission properties of these films.
Abnormal development of the apical ectodermal ridge and polysyndactyly in Megf7-deficient mice (2005)

Megf7/Lrp4 is a member of the functionally diverse low-density lipoprotein receptor gene family, a class of ancient and highly conserved cell surface receptors with broad functions in cargo transport and cellular signaling. To gain insight into the as yet unknown biological role of Megf7/Lrp4, we have disrupted the gene in mice. Homozygous Megf7-deficient mice are growth-retarded, with fully penetrant polysyndactyly in their fore and hind limbs, and partially penetrant abnormalities of tooth development. The reason for this developmental abnormality is apparent as early as embryonic day 9.5 when the apical ectodermal ridge (AER), the principal site of Megf7 expression at the distal edge of the embryonic limb bud, forms abnormally in the absence of Megf7. Ectopic expression and aberrant signaling of several molecules involved in limb patterning, including Fgf8, Shh, Bmp2, Bmp4 and Wnt7a, as well as the Wnt- and Bmp-responsive transcription factors Lmx1b and Msx1, result in reduced apoptosis and symmetrical dorsal and ventral expansions of the AER. Abnormal signaling from the AER precedes ectopic chondrocyte condensation and subsequent fusion and duplication of digits in the Megf7 knockouts. Megf7 can antagonize canonical Wnt signaling in vitro. Taken together, these findings are consistent with a role of Megf7 as a modulator of cellular signaling pathways involving Wnts, Bmps, Fgfs and Shh. A similar autosomal recessive defect may also occur in man, where polysyndactyly, in combination with craniofacial abnormalities, is also part of a common genetic syndrome.