gebhart/patrepeval huggingface dataset:
Interaction of two translational components, lysyl‐tRNA synthetase and p40/37LRP, in plasma membrane promotes laminin‐dependent cell migration (2012)

Although human lysyl-tRNA synthetase (KRS), an enzyme for protein synthesis, is often highly expressed in various cancer cells, its pathophysiological implications have not been understood. Here we found that KRS induces cancer cell migration through interaction with the 67-kDa laminin receptor (67LR) that is converted from ribosomal subunit p40. On laminin signal, KRS was phosphorylated at the T52 residue by p38MAPK and dissociated from the cytosolic multi-tRNA synthetase complex for membrane translocation. The importance of T52 phosphorylation for membrane translocation of KRS was confirmed by site-directed mutagenesis. In the membrane, turnover of 67LR was controlled by Nedd4-mediated ubiquitination, and KRS inhibited ubiquitin-dependent degradation of 67LR, thereby enhancing laminin-induced cell migration. This work thus unveiled a unique function of KRS in the control of cell migration and its pathological implication in metastasis.
Aminopyridazines as Acetylcholinesterase Inhibitors (1999)

Following the discovery of the weak, competitive and reversible acetylcholinesterase (AChE)-inhibiting activity of minaprine (3c) (IC50 = 85 microM on homogenized rat striatum AChE), a series of 3-amino-6-phenylpyridazines was synthesized and tested for inhibition of AChE. A classical structure-activity relationship exploration suggested that, in comparison to minaprine, the critical elements for high AChE inhibition are as follows: (i) presence of a central pyridazine ring, (ii) necessity of a lipophilic cationic head, (iii) change from a 2- to a 4-5-carbon units distance between the pyridazine ring and the cationic head. Among all the derivatives investigated, 3-[2-(1-benzylpiperidin-4-yl)ethylamino]-6-phenylpyridazine (3y), which shows an IC50 of 0.12 microM on purified AChE (electric eel), was found to be one of the most potent anti-AChE inhibitors, representing a 5000-fold increase in potency compared to minaprine.1
<title>Developing a predictive model of human skin coloring</title> (1996)

A model of color formation within human skin has been developed to aid the characterization of pigmented skin lesions from their digitized color images. The model is based on the Kublenka-Munk theory of scattering and absorption within inhomogeneous materials and the physics pertaining to their color properties. By considering the skin to be a layered construction of such materials, the stratum corneum, epidermis, papillary dermis and reticular dermis, and by exploiting the physics related to the optical interface between these layers, the model generates all possible colors occurring within normal human skin. In particular, the model predicts that all skin colors have to lie on a simple curved surface patch within a three- dimensional color space bounded by two physiologically meaningful axes, one corresponding to the amount of melanin within the epidermis and the other to the amount of blood within the dermis. These predictions were verified by comparing the CIE LMS coordinates of a representative, cross-racial sample of fifty skin images with the LMS coordinates predicted by the model. The results show that, within the predicted error bounds, the coordinates for normal skin colors do indeed lie on the curved surface generated by the model. Several possible applications of this representation are outlined, including images representing the melanin and blood components separately, as well as the possibility of measuring the Breslow thickness of melanocytic invasion within malignant melanoma.
Normal human neutrophils are a source of a specific interleukin 1 inhibitor. (1986)

In the course of our study on neutrophil production of an interleukin 1 (IL-1)-like factor, we found that the addition of polymorphonuclear neutrophils (PMN) to monocytes cultured in the presence of zymosan resulted in decreased IL 1 activity of the resultant supernatant, suggesting that PMN may contain an inhibitor of IL 1. The objective of this investigation was to study this IL 1 inhibitor which normal human PMN contain. The inhibitor is constitutively present in the PMN because 0 hr PMN lysates and unstimulated PMN supernatants also show inhibitory activity. The PMN inhibitor inhibits IL 1 (crude and partially purified) in a dose-response manner and does not affect basal [3H]thymidine incorporation in the presence or absence of PHA-P. The PMN inhibitor does not have any effect on interleukin 2 (IL 2)-induced proliferation of the IL 2-dependent CTLL cells. The inhibitor can be generated in the absence of serum and is not produced as a result of proteolytic activity from PMN enzymes. The inhibitor is heat-labile and is most stable at neutral pH. Gel filtration studies on Sephadex G-200 indicate that the inhibitor is heterogeneous in size. Two inhibitory peaks, at 45,000 to 70,000 m.w. and at greater than 160,000 m.w., were observed. When zymosan-stimulated PMN supernatant was chromatographed, there was separation of inhibitory factor from a 17,000 m.w. proliferating factor. Presence of this PMN inhibitor may be important in negative regulation of IL 1.
Transcript profiling of human platelets using microarray and serial analysis of gene expression (2003)

Human platelets are anucleate blood cells that retain cytoplasmic mRNA and maintain functionally intact protein translational capabilities. We have adapted complementary techniques of microarray and serial analysis of gene expression (SAGE) for genetic profiling of highly purified human blood platelets. Microarray analysis using the Affymetrix HG-U95Av2 approximately 12 600-probe set maximally identified the expression of 2147 (range, 13%-17%) platelet-expressed transcripts, with approximately 22% collectively involved in metabolism and receptor/signaling, and an overrepresentation of genes with unassigned function (32%). In contrast, a modified SAGE protocol using the Type IIS restriction enzyme MmeI (generating 21-base pair [bp] or 22-bp tags) demonstrated that 89% of tags represented mitochondrial (mt) transcripts (enriched in 16S and 12S ribosomal RNAs), presumably related to persistent mt-transcription in the absence of nuclear-derived transcripts. The frequency of non-mt SAGE tags paralleled average difference values (relative expression) for the most "abundant" transcripts as determined by microarray analysis, establishing the concordance of both techniques for platelet profiling. Quantitative reverse transcription-polymerase chain reaction (PCR) confirmed the highest frequency of mt-derived transcripts, along with the mRNAs for neurogranin (NGN, a protein kinase C substrate) and the complement lysis inhibitor clusterin among the top 5 most abundant transcripts. For confirmatory characterization, immunoblots and flow cytometric analyses were performed, establishing abundant cell-surface expression of clusterin and intracellular expression of NGN. These observations demonstrate a strong correlation between high transcript abundance and protein expression, and they establish the validity of transcript analysis as a tool for identifying novel platelet proteins that may regulate normal and pathologic platelet (and/or megakaryocyte) functions.
A relaxation method for understanding spontaneous speech utterances (1992)

This paper describes an extension to the MIT ATIS (Air Travel Information Service) system, which allows it to answer a question when a full linguistic analysis fails. This "robust" parsing capability was achieved through minor extensions of pre-existing components already in place for the full linguistic analysis component. Robust parsing is applied only after a full analysis has failed, and it involves the two stages of 1) parsing a set of phrases and clauses, and 2) gluing them together to obtain a single semantic frame encoding the full meaning of the sentence. We have assessed the degree of success of the robust parsing mechanism through a breakdown of the performance of robustly parsed vs. fully parsed sentences on the October '91 "dry-run" test set. It was clear that the robust parser allowed us to answer many more questions correctly, as over a third of the sentences were not covered by the grammar. We also report here on the performance of the system on the February '92 test sentences, and discuss some issues with regard to the evaluation methodology.
Punicic acid modulates mucosal immune responses and prevents gut inflammation through PPAR γ and δ‐dependent mechanisms (2010)

Punicic acid (PUA) is a conjugated linolenic acid isomer that has shown promise in suppressing gut inflammation. The goal of this study is to elucidate the mechanisms by which PUA modulates mucosal immunity and prevents or ameliorates gut inflammation. The expression of peroxisome proliferator‐activated receptor (PPAR) α, γ and δ and their responsive genes was examined in the colonic mucosa of two mouse models of experimental inflammatory bowel disease (IBD). Immune cell‐specific PPAR γ null, PPAR δ null and wild‐type (WT) mice were administered control or PUA‐supplemented diets and challenged with 2.5% DSS. The phenotype of immune cell subsets was examined in the mucosal and peripheral immune system. The prophylactic efficacy of PUA was also examined in an IL‐10−/− model of IBD. PUA intake upregulated colonic PPAR δ, keratinocyte growth factor and the orphan nuclear receptor RORγt expression and suppressed colonic and M1 macrophage‐derived TNF‐α. In the mesenteric lymph nodes (i.e., mucosal inductive sites), PUA increased the levels of IL‐17 and IFN‐γ in CD8 + T cells. Clinically, PUA ameliorated DSS colitis in WT mice and spontaneous pan‐enteritis in IL‐10−/− mice. The loss of PPAR γ or δ impaired the preventive effects of PUA in IBD. Our studies provide molecular evidence in vivo suggesting that PUA modulates mucosal immune responses and ameliorates gut inflammation through PPAR γ and δ‐dependent mechanisms
Intrathecal Ziconotide for Complex Regional Pain Syndrome: Seven Case Reports (2009)

Ziconotide is a nonopioid analgesic currently indicated as monotherapy, but frequently used in combination with opioids, for the management of severe chronic pain in patients for whom intrathecal (IT) therapy is warranted and who are intolerant of, or whose pain is, refractory to other treatments. There is a paucity of information regarding ziconotide use in patients with complex regional pain syndrome (CRPS). Seven cases in which IT ziconotide was used in patients with CRPS were analyzed. All patients (4 male, 3 female; age range, 14 to 52 years) had experienced inadequate pain relief with multiple conventional and interventional treatments. Three patients received ziconotide monotherapy exclusively; 4 patients received ziconotide monotherapy initially, then combination IT therapy. The mean ziconotide dose was 5.2 mcg/d (range, 0.5 to 13 mcg/d) at initiation and 24.7 mcg/d (range, 0.06 to 146 mcg/d) at the last available assessment. The mean duration of ziconotide therapy was 3.1 years (range, 26 days to 8 years). At ziconotide initiation, the mean visual analog scale (VAS) score was 89.3 mm (range, 75 to 100 mm); VAS scores decreased by a mean of 47.5% (range, 5% to 100%) at last assessment. Of the 5 patients who experienced substantial improvement in pain, edema, skin abnormalities, and/or mobility with ziconotide therapy, 2 have discontinued ziconotide and are pain free. Another patient experienced marked reversal of both edema and advanced skin trophic changes. Adverse events included urinary retention, depression, anxiety, and hallucinations. Adverse events generally resolved spontaneously, with treatment, or with ziconotide discontinuation/dose reduction. Although further studies are required, ziconotide holds promise as an effective treatment for CRPS.
Hepatic gene transfer in animals using retroviruses containing the promoter from the gene for phosphoenolpyruvate carboxykinase. (1990)

Two methods are described for directing the expression of genes to the livers of animals using retroviral vectors containing the predominantly liver-specific promoter from the gene for phosphoenolpyruvate carboxykinase (PEPCK)-linked to the structural gene for either amino 3'-glycosyl phosphotransferase (neo) or bovine growth hormone (bGH). Replication-incompetent retrovirus was used to infect the livers of fetal rats by intraperitoneal injection of animals in utero or to infect adult rats by direct injection into the portal vein after partial hepatectomy. The proviruses were integrated into the hepatic DNA, and the chimeric genes were expressed from the PEPCK promoter for as long as 8 months after infection. The expression of the PEPCK-bGH gene was regulated by diet and hormones in a manner similar to the regulation of the endogenous PEPCK gene in the liver. The potential of this method for targeting genes to the liver is discussed.
Role for Periodontitis in the Progression of Lipid Deposition in an Animal Model (2003)

Epidemiologic studies have implicated periodontitis as a risk factor for the development of cardiovascular disease. However, no prospective studies investigating this potential relationship have been carried out. Age- and sex-matched New Zealand White rabbits were maintained on a diet consisting of 0.5% fat for 13 weeks to induce the accumulation of lipid deposits in the aorta as a model for atherogenesis. One-half of the animals received silk ligatures around their mandibular premolars followed by an application of a periodontal pathogen, Porphyromonas gingivalis, to induce periodontitis. Animals were sacrificed after 14 weeks. Periodontal disease severity was quantified radiographically, histologically, and by direct visualization of bone loss on defleshed skulls. Lipid deposition was evaluated by computer-assisted morphometry in the aortas en face after lipid deposits were stained with Sudan IV. Animals with experimentally induced periodontitis had more extensive accumulations of lipids in the aorta than did nonperiodontitis animals (P < 0.05), and there was a positive correlation between the severity of periodontal disease and the extent of lipid deposition (r(2) = 0.9501). The results provide direct evidence that periodontitis may be a risk factor and may contribute to the pathogenesis of atherosclerosis. The data support the concept that infections at remote locations can modulate atherosclerotic events distantly.
Electrochemical and optical processing of microstructures by scanning probe microscopy (SPM) (2002)

Two micro processing techniques based on scanning probe microscopy (SPM) are described. One is electrochemical etching and deposition using a scanning tunneling microscope (STM). STM is very useful tool of nm-scaled observation, and it can be also used as precise positioner in micro processing. In micro electrochemical processing system, a potentiostat for processing is externally attached to STM system, a STM probe was set very closely to a metal substrate in electrolyte solution, and voltage was applied between the substrate and the probe. Then electrochemical reaction occurs in restricted area of the substrate. Therefore, micrometer-size structures are produced by faradic current. A line pattern, which is 200-300 nm in width and 100 nm in depth, was electrochemically etched. When polarity of applied voltage was inverted, a bump pattern, 300 nm in diameter, 200 nm in height, was electrochemically deposited. Another processing method is using a scanning near-field optic/atomic force microscope (SNOAM). The SNOAM provides simultaneous topographic and optical images with high resolution beyond the diffraction limit, better than 100 nm. The optical processing is demonstrated in the photoresist film by the SNOAM. We obtained pit and line patterns down to 100 nm in diameter and width, respectively.
Muscle regeneration in amphibians and mammals: Passing the torch (2003)

Skeletal muscle in both amphibians and mammals possesses a high regenerative capacity. In amphibians, a muscle can regenerate in two distinct ways: as a tissue component of an entire regenerating limb (epimorphic regeneration) or as an isolated entity (tissue regeneration). In the absence of epimorphic regenerative ability, mammals can regenerate muscles only by the tissue mode. This review focuses principally on the regeneration of entire muscles and covers what is known and what remains to be elucidated about fundamental mechanisms underlying muscle regeneration at this level.
Gaussian Belief Propagation: Theory and Application (2008)

The canonical problem of solving a system of linear equations arises in numerous contexts in information theory, communication theory, and related fields. In this contribution, we develop a solution based upon Gaussian belief propagation (GaBP) that does not involve direct matrix inversion. The iterative nature of our approach allows for a distributed message-passing implementation of the solution algorithm. In the first part of this thesis, we address the properties of the GaBP solver. We characterize the rate of convergence, enhance its message-passing efficiency by introducing a broadcast version, discuss its relation to classical solution methods including numerical examples. We present a new method for forcing the GaBP algorithm to converge to the correct solution for arbitrary column dependent matrices. 
In the second part we give five applications to illustrate the applicability of the GaBP algorithm to very large computer networks: Peer-to-Peer rating, linear detection, distributed computation of support vector regression, efficient computation of Kalman filter and distributed linear programming. Using extensive simulations on up to 1,024 CPUs in parallel using IBM Bluegene supercomputer we demonstrate the attractiveness and applicability of the GaBP algorithm, using real network topologies with up to millions of nodes and hundreds of millions of communication links. We further relate to several other algorithms and explore their connection to the GaBP algorithm.
Fabrication of high-mobility Ge p -channelMOSFETs on Si substrates (1999)

The first fabrication of Ge p-channel MOSFETs (p-MOSFETs) on Si substrates is reported. A CMOS compatible process based on relaxed Ge layers grown on Si(111) substrates by surfactant-mediated epitaxy (SME) was used. The non-optimised low temperature process yielded normally-off Ge p-MOSFETs with record channel drift mobilities of 430 cm2/Vs.
IL‐12‐Deficient Mice Are Defective but Not Devoid of Type 1 Cytokine Responses (1996)

Interleukin-12 (IL-12) has been described as a pivotal molecule in the immune response based in part on its ability to influence the differentiation of T helper (Th) cells into a type 1 (Th1) phenotype. This event is crucial in that appropriate differentiation of naive T cells can determine susceptibility or resistance to given pathogens by influencing the balance between cellular and humoral immunity. In order to further delineate the role of IL-12 in the immune response, we generated mice deficient for this cytokine. IL-12 knockout mice were viable, fully fertile, and displayed no obvious developmental abnormalities. Upon immunological analysis, these mice demonstrated an impaired ability to effect a Th1 response as well as an impaired ability to produce interferon-gamma in response to endotoxin in vivo. These data establish an essential role for IL-12 in the generation of optimal Th1 responses in vivo, but weak responses can occur independently of IL-12.
The efficacy of a malarial antibody enzyme immunoassay for establishing the reinstatement status of blood donors potentially exposed to malaria (2005)

The study findings support the efficacy and safety of a targeted screening strategy combining antibody screening with a 6-month cellular component restriction period for donors with a declared malarial risk.
Benzophenone-Type Photoactivatable Derivatives of α-Neurotoxins and α-Conotoxins in Studies onTorpedoNicotinic Acetylcholine Receptor (1999)

AbstractBy chemical modification of different lysine residues, benzoylbenzoyl (BzBz) groups were introduced into neurotoxin II Naja naja oxiana (NT-II), a short-chain snake venom α-neurotoxin, while p-benzoylphenylalanyl (Bpa) residue was incorporated in the course of peptide synthesis at position 11 of α-conotoxin G1, a neurotoxic peptide from marine snails. Although the crosslinking yields for iodinated BzBz derivatives of NT-II and for Bpa analogue of G1 to the membrane-bound Torpedo californica nicotinic acetylcholine receptor (AChR) are relatively low, the subunit labeling patterns confirm the earlier conclusions, derived from arylazide or diazirine photolabels, that α-neurotoxins and α-conotoxins bind at the subunit interfaces. Detecting the labeled α-subunit with iodinated Bpa analogue of G1 provided a direct proof for the contact between this subunit and α-conotoxin molecule.
On Real-Time AER 2-D Convolutions Hardware for Neuromorphic Spike-Based Cortical Processing (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> In this paper, a chip that performs real-time image convolutions with programmable kernels of arbitrary shape is presented. The chip is a first experimental prototype of reduced size to validate the implemented circuits and system level techniques. The convolution processing is based on the address–event-representation (AER) technique, which is a spike-based biologically inspired image and video representation technique that favors communication bandwidth for pixels with more information. As a first test prototype, a pixel array of 16<formula formulatype="inline"> <tex Notation="TeX">$\,\times\,$</tex></formula>16 has been implemented with programmable kernel size of up to 16<formula formulatype="inline"><tex Notation="TeX">$\, \times\,$</tex></formula>16. The chip has been fabricated in a standard 0.35-<formula formulatype="inline"><tex Notation="TeX">${\mu }$</tex></formula>m complimentary metal–oxide–semiconductor (CMOS) process. The technique also allows to process larger size images by assembling 2-D arrays of such chips. Pixel operation exploits low-power mixed analog–digital circuit techniques. Because of the low currents involved (down to <emphasis emphasistype="bold"><emphasis emphasistype="italic">nanoamperes</emphasis></emphasis> or even <emphasis emphasistype="bold"><emphasis emphasistype="italic">picoamperes</emphasis></emphasis>), an important amount of pixel area is devoted to mismatch calibration. The rest of the chip uses digital circuit techniques, both synchronous and asynchronous. The fabricated chip has been thoroughly tested, both at the pixel level and at the system level. Specific computer interfaces have been developed for generating AER streams from conventional computers and feeding them as inputs to the convolution chip, and for grabbing AER streams coming out of the convolution chip and storing and analyzing them on computers. Extensive experimental results are provided. At the end of this paper, we pro</para>
Some Thermodynamics of Photochemical Systems (1967)

A limit on the thermodynamic potential difference between the ground and excited states of any photochemical system is established by evaluating the potential difference at which the rate of photon absorption and emission are equal; the relationship between absorption and emission is given by a Planck-law relation, provided that there is thermal equilibrium between the sublevels of each electronic band. The actual potential developed may be evaluated if the quantum yield of luminescence is known. The maximum amount of power storage obtainable is evaluated by lowering the potential difference until the product of the potential difference and the fraction of the quanta retained is maximized. The history and applications of the Planck-law relation between absorption and emission spectra are discussed briefly, and applications of the potential difference calculation are mentioned.