gebhart/patrepeval huggingface dataset:
Aging reduces adaptive capacity and stress protein expression in the liver after heat stress (2000)

A decline in an organism's ability to cope with stress through acute response protein expression may contribute to stress intolerance with aging. We investigated the influence of aging on stress tolerance and the capacity to synthesize the 70-kDa heat shock protein (HSP70) in young and old rats exposed to an environmental heating protocol. Livers were assessed for injury and HSP70 expression after heat stress by use of immunohistochemical and immunoblotting techniques. The inducible HSP70 response in the cytoplasm and nucleus was markedly reduced with age at several time points over a 48-h recovery period, although senescent rats were able to strongly express HSP70 early in recovery. Older animals had extensive zone-specific liver injury, which corresponded to the diminished HSP70 response observed in these regions, and a significant reduction in thermotolerance compared with their young counterparts. These data highlight the regional nature of stress-induced injury and HSP70 expression in the liver and the impact of aging on these responses. Furthermore, the results suggest a functional link between the age-related decrements in the expression of inducible HSP70 and the pathophysiological responses to heat stress.
Double-strand break repair by homologous recombination in primary mouse somatic cells requires BRCA1 but not the ATM kinase (2013)

Homology-directed repair (HDR) is a critical pathway for the repair of DNA double-strand breaks (DSBs) in mammalian cells. Efficient HDR is thought to be crucial for maintenance of genomic integrity during organismal development and tumor suppression. However, most mammalian HDR studies have focused on transformed and immortalized cell lines. We report here the generation of a Direct Repeat (DR)-GFP reporter-based mouse model to study HDR in primary cell types derived from diverse lineages. Embryonic and adult fibroblasts from these mice as well as cells derived from mammary epithelium, ovary, and neonatal brain were observed to undergo HDR at I-SceI endonuclease-induced DSBs at similar frequencies. When the DR-GFP reporter was crossed into mice carrying a hypomorphic mutation in the breast cancer susceptibility gene Brca1 , a significant reduction in HDR was detected, showing that BRCA1 is critical for HDR in somatic cell types. Consistent with an HDR defect, Brca1 mutant mice are highly sensitive to the cross-linking agent mitomycin C. By contrast, loss of the DSB signaling ataxia telangiectasia-mutated (ATM) kinase did not significantly alter HDR levels, indicating that ATM is dispensable for HDR. Notably, chemical inhibition of ATM interfered with HDR. The DR-GFP mouse provides a powerful tool for dissecting the genetic requirements of HDR in a diverse array of somatic cell types in a normal, nontransformed cellular milieu.
Orphan Nuclear Receptor NOR-1 Enhances 3′,5′-Cyclic Adenosine 5′-Monophosphate-Dependent Uncoupling Protein-1 Gene Transcription (2008)

Prolonged cold exposure induces nonshivering thermogenesis primarily through beta-adrenergic- and cAMP-mediated regulation of uncoupling protein-1 (UCP1) in brown adipose tissue. Molecular mechanisms involved in this induction of Ucp1 gene transcription consists of an intricate interplay between many nuclear receptors in coordination with coactivators/corepressors. Recently, it has been shown that members of the nuclear receptor-4A (NR4A) family of orphan nuclear receptors (Nur77, Nurr1, and NOR-1) are highly responsive to cAMP-second messenger pathways. Here we have identified a new regulatory motif in the Ucp1 promoter that binds NR4As to stimulate Ucp1 gene transcription. Upon cold exposure of mice, or beta-agonist treatment of mouse and human adipocytes, the expression of NR4A nuclear receptors is rapidly induced, with NOR-1 being the most robust, and this precedes increases in Ucp1 expression. A dominant-negative mutant Nur-77 receptor that prevents the transcriptional activity of NR4A receptors blocked beta-adrenergic receptor-stimulated Ucp1 gene transcription. By gel shift and chromatin immunoprecipitation assays, we defined the sequence (-5.64 kb) in the Ucp1 promoter to which NOR-1 binds. In transient reporter assays, this element significantly augments the activity of a 3.7-kb Ucp1 promoter. These results extend our understanding of the combinatorial complexity in the signaling pathways that control this tissue-specific gene.
Well-known serial buses for distributed control of backup power plants. RS-485 versus controller area network (CAN) solutions (2003)

Networking is increasingly becoming a feature of industrial products such as those for medical devices, vending machines, machine tool, and, the example analyzed here, modular power plants. As many such systems depend on cheap microcontrollers, a common approach to networking has been based on the combination of the available standard serial communication controller (UART) normally included in such devices and RS-485 drivers. However UART-based network protocols do have some potential disadvantages. Controller area network (CAN) offers an attractive alternative due to the availability and low cost of CAN based devices. This paper compares these two approaches in the design of a serial bus, devoted to internal interconnection in a commercial range of modular power backup systems, and describes the migration process from the first to the second solution.
Harmine and Imipramine Promote Antioxidant Activities in Prefrontal Cortex and Hippocampus (2010)

A growing body of evidence has suggested that reactive oxygen species (ROS) may play an important role in the physiopathology of depression. Evidence has pointed to the β-carboline harmine as a potential therapeutic target for the treatment of depression. The present study we evaluated the effects of acute and chronic administration of harmine (5, 10 and 15 mg/kg) and imipramine (10, 20 and 30 mg/kg) or saline in lipid and protein oxidation levels and superoxide dismutase (SOD) and catalase (CAT) activities in rat prefrontal cortex and hippocampus. Acute and chronic treatments with imipramine and harmine reduced lipid and protein oxidation, compared to control group in prefrontal cortex and hippocampus. The SOD and CAT activities increased with acute and chronic treatments with imipramine and harmine, compared to control group in prefrontal cortex and hippocampus. In conclusion, our results indicate positive effects of imipramine antidepressant and β-carboline harmine of oxidative stress parameters, increasing SOD and CAT activities and decreasing lipid and protein oxidation.
Electromechanical coupling to Lamb and shear-horizontal modes in piezoelectric plates (1989)

Recent theoretical studies and experiments have been shown that interdigital transducers can couple strongly to plate modes in piezoelectric materials and in piezoelectric-on-nonpiezoelectric composite membranes. The calculated velocity dispersion and electromechanical coupling factors for plate modes in representative piezoelectric materials are described. The frequency dependence of velocity and electromechanical coupling factors are given, under different metallization conditions, for generalized stiffened-Lamb, pure stiffened-Lamb, and stiffened-shear (shear-horizontal) modes, for various plate orientations in lithium niobate, lithium tantalate, quartz, bismuth germanium oxide, and zinc oxide. For lithium niobate, electromechanical-coupling values as high as 15% are found under narrowband bandpass conditions, and 5% under wideband low-pass conditions. For lithium tantalate, bismuth germanium oxide, coupling values of 0.5, 2, and 4% are obtained. For quartz with its weaker piezoelectricity, the coupling is still made smaller.
Tissue Engineering of Smooth Muscle under a Mechanically Dynamic Condition (2003)

In order for engineered tissues to find clinical utility, the engineered tissues must function appropriately. However, smooth muscle (SM) tissues engineered in vitro with a conventional tissue engineering technique may not exhibit contractile functions, because smooth muscle cells (SMCs) cultured in vitro typically revert from a contractile, differentiated phenotype to a synthetic, nondifferentiated phenotype and lose their ability to contract. SMCs in vivo typically reside in mechanically dynamic environments. We hypothesized that cyclic mechanical stretch induces the features of SMCs in in vitro engineered tissues to be similar to those of SMCs in native tissues. To test the hypothesis, aortic SMCs were seeded onto elastic, three-dimensional scaffolds and cultured in vitro under a cyclic mechanical stretching condition for 4 weeks. A significant cell alignment in a direction parallel to the cyclic stretching direction was found in the SM tissues exposed to cyclic stretching. The cellular alignment and alignment direction were consistent with those of native vascular SM tissues, in which SMCs in vivo align in the radial direction (parallel to stretching direction). In control tissues (SM tissues engineered without stretching), cells randomly aligned. The expression of SM alpha-actin and SM myosin heavy chain, phenotypic markers of SMCs in a contractile state, was upregulated in the stretched tissues by 2.5- and 2.0-fold, respectively, compared to SMCs in the control tissues. The cellular features of alignment and contractile phenotype of SMCs in the SM tissues engineered under a mechanically dynamic environment could allow the engineered SM tissues to exhibit contractile functions.
Angiopoietin-1 Is an Antipermeability and Anti-Inflammatory Agent In Vitro and Targets Cell Junctions (2000)

Inflammation is a basic pathological mechanism that underlies many diseases. An important component of the inflammatory response is the passage of plasma components and leukocytes from the blood vessel into the tissues. The endothelial monolayer lining blood vessels reacts to stimuli such as thrombin or vascular endothelial growth factor by changes in cell-cell junctions, an increase in permeability, and the leakage of plasma components into tissues. Other stimuli, such as tumor necrosis factor-alpha (TNF-alpha), are responsible for stimulating the transmigration of leukocytes. Here we show that angiopoietin-1, a cytokine essential in fetal angiogenesis, not only supports the localization of proteins such as platelet endothelial cell adhesion molecule-1 (PECAM-1) into junctions between endothelial cells and decreases the phosphorylation of PECAM-1 and vascular endothelial cadherin, but it also strengthens these junctions, as evidenced by a decrease in basal permeability and inhibition of permeability responses to thrombin and vascular endothelial growth factor. Furthermore, angiopoietin-1 inhibits TNF-alpha-stimulated leukocyte transmigration. Angiopoietin-1 may thus have a major role in maintaining the integrity of endothelial monolayers.
Inhibition of melanocortin-4 receptor dimerization by substitutions in intracellular loop 2 (2013)

Obesity is one of the most challenging global health problems. One key player in energy homeostasis is the melanocortin-4 receptor (MC4R), which is a family A G-protein-coupled receptor (GPCR). It has recently been shown that MC4R has the capacity to form homo- or heterodimers. Dimerization of GPCRs is of great importance for signaling regulation, with major pharmacological implications. Unfortunately, not enough is yet known about the detailed structural properties of MC4R dimers or the functional consequences of receptor dimerization. Our goal, therefore, was to explore specific properties related to MC4R dimerization. First, we aimed to induce the dissociation of dimers to monomers and to compare the functional parameters of wild-type and MC4R variants. To inhibit homodimerization, we designed MC4R chimeras with the cannabinoid-1 receptor, a receptor that does not interact with MC4R. Indeed, we identified several substitutions in the intracellular loop 2 (ICL2) and adjacent regions of transmembrane helix 3 (TMH3) and TMH4 that lead to partial dimer dissociation. Interestingly, the capacity for signaling activity was generally increased in these MC4R variants, although receptor expression remained unchanged. This increase in activity for dissociated receptors might indicate a link between receptor dimerization and signaling capacity. Moreover, dimer dissociation was also observed in a naturally occurring activating MC4R mutation in ICL2. Taken together, this study provides new information on the structural prerequisites for MC4R dimerization and identifies an approach to induce the dissociation of MC4R dimers. This might be useful for further investigation of pharmacological properties.
EFFECT OF CILASTATIN ON CYCLOSPORINE-INDUCED ACUTE NEPHROTOXICITY IN KIDNEY TRANSPLANT RECIPIENTS (1997)

Our findings support the hypothesis that cilastatin administration can reduce CsA-induced acute nephrotoxicity after kidney transplantation.
Potential Mechanisms of Photodynamic Inactivation of Virus by Methylene Blue I. RNA–Protein Crosslinks and Other Oxidative Lesions in Qβ Bacteriophage (1998)

A spectrum of oxidative lesions was observed in a bacteriophage-based model system that is very sensitive to the photodynamic activity of selected dyes. When suspensions of the intact bacteriophage Q beta were exposed to methylene blue plus light (MB + L), inactivating events, or "hits" occurred that were oxygen-dependent and that were associated with the formation of several specific lesions: (1) carbonyl moieties on proteins, (2) 8-oxo-7,8-dihydroguanine (8-oxoGua), and (3) single-strand breaks (ssb) in the RNA genome and (4) RNA-protein crosslinks. Formation of carbonyl groups associated with protein in the Q beta phage preparation correlated positively with photoinactivation of the phage with increasing doses of either of the sensitizers MB or rose bengal. Strand breaks in the Q beta genomic RNA were observable at high MB concentrations but appeared not to be significant at the lower concentrations of MB, as full-length Q beta RNA was observable well beyond the 99% inactivation point in MB dosage. It was shown that the number of 8-oxoGua lesions were unlikely to be sufficient to account for the number of lethal events. Following exposure to MB + L, crosslink formation between Q beta RNA and protein was observed by virtue of the location of RNA at the interface of phenol-aqueous extractions of phage suspensions. A significant increase over background of RNA-protein complexes (including full-length Q beta RNA) was observed at the lowest concentration of MB tested (0.5 microM), which corresponded roughly to an average of 2 lethal hits per phage or approximately 13% survival compared to the zero MB control (100% survival). Due to its close correlation with Q beta inactivation and its expected lethality, RNA-protein crosslink formation may be important as an inactivating lesion in bacteriophage Q beta following MB + L exposure.
Membrane Topology and Function of Dengue Virus NS2A Protein (2013)

Flavivirus nonstructural protein 2A (NS2A) is a component of the viral replication complex that functions in virion assembly and antagonizes the host immune response. Although flavivirus NS2A is known to associate with the endoplasmic reticulum (ER) membrane, the detailed topology of this protein has not been determined. Here we report the first topology model of flavivirus NS2A on the ER membrane. Using dengue virus (DENV) NS2A as a model, we show that (i) the N-terminal 68 amino acids are located in the ER lumen, with one segment (amino acids 30 to 52) that interacts with ER membrane without traversing the lipid bilayer; (ii) amino acids 69 to 209 form five transmembrane segments, each of which integrally spans the ER membrane; and (iii) the C-terminal tail (amino acids 210 to 218) is located in the cytosol. Nuclear magnetic resonance (NMR) structural analysis showed that the first membrane-spanning segment (amino acids 69 to 93) consists of two helices separated by a "helix breaker." The helix breaker is formed by amino acid P85 and one positively charged residue, R84. Functional analysis using replicon and genome-length RNAs of DENV-2 indicates that P85 is not important for viral replication. However, when R84 was replaced with E, the mutation attenuated both viral RNA synthesis and virus production. Remarkably, an R84A mutation did not affect viral RNA synthesis but blocked intracellular formation of infectious virions. Collectively, the mutagenesis results demonstrate that NS2A functions in both DENV RNA synthesis and virion assembly/maturation. The topology model of DENV NS2A provides a good starting point for studying how flavivirus NS2A modulates viral replication and evasion of host immune response.
Laser-Induced Alteration of Collagen Substructure Allows Microsurgical Tissue Welding (1986)

Tissue welding is a potentially important biomedical application of laser technology. The structural alterations basic to this phenomenon were studied in experimental repair of lesions of the rat carotid artery and sciatic nerve. A modified neodymiumdoped yttrium-aluminum-garnet laser operating at a wavelength of 1.319 micrometers was used in conjunction with conventional suture techniques. Histological and fine-structural analysis revealed a homogenizing change in collagen with interdigitation of altered individual fibrils that appeared to be the structural basis of the welding effect.
Solutions for Better Production in Tight Gas Reservoirs Through Hydraulic Fracturing (2009)

Abstract The challenge to make best producers for the least investment in tight gas reservoirs has always been with the oil and gas industry since production in many tight gas reservoirs is oftentimes marginal, at best. This paper presents solutions for better production in tight gas reservoirs through hydraulic fracturing. Properly engineered hydraulic fracture treatments are enablers to achieve overall economies of scale with development of tight gas reservoirs. These treatments are conducted to bypass completion damage and stimulate production from low permeability reservoirs. They are designed using simulators with a range of capabilities in an effort to maximize the economic benefit of the treatment, effective fracture length, and number of zones producing, fracture conductivity, acceleration of recovery, addition of reserves, and minimize job failures and treatment costs. To accomplish these goals, substantial amount of information is required to describe reservoir flow capacity and provide the data needed to predict treatment pressure response as well as fracture geometry and conductivity. These data will determine the optimum size of the treatment, the maximum proppant concentration that can be pumped, and the expected production response to the stimulation. When sufficient input data are available to characterize the reservoir, the fracture geometry can be accurately modeled with a capable simulator, the treatment goals listed above can be realized and an optimum design can be reached. The design process, including selection of proppants and fluids, pumping schedule, injected proppant concentrations, total job size, pump rate, and other parameters requires an idea of the desired outcome of the job: required fracture length, possible pack concentration and clean-up time. Critical measurements from testing of actual cores has allowed to sift through the chaff to find those "gems" in hydraulic fracturing that materially improve the completion efficiency in tight gas reservoirs.
D‐TMPP: A novel androgen‐regulated gene preferentially expressed in prostate and prostate cancer that is the first characterized member of an eukaryotic gene family (2005)

We describe the novel prostate-restricted molecule D-TMPP widely expressed in prostate cancer tissues.
Activation of phosphoipase D by platelet-derived growth factor (PDGF) in rat C6 glioma cells: Possible role in mitogenic signal transduction (1992)

The effects of platelet-derived growth factor (PDGF) on phospholipase D (PLD) activity and deoxyribonucleic acid (DNA) synthesis in rat C6 glioma cells have been investigated. Pretreatment of serum-starved C6 cells with PDGF results in enhanced choline production and the phosphatidylethanol (PEt) formation in the presence of ethanol, indicating the activation of PLD acting on phosphatidylcholine (PC). The dose-response curve for choline generation and DNA synthesis were comparable. In addition, the effects of PDGF on both PEt formation and [3H]thymidine incorporation into acid-precipitable material was blocked by the potent protein kinase C (PKC) inhibitor 1-(5-isoquinolinesulphonyl)-2-methylpiperazine (H-7) but not by N-(2-guanidinoethyl)-5-isoquinolinesulphonamide (HA1004), a relatively weak inhibitor of PKC, suggesting that PDGF plays an important role as a positive regulator of glioma cell growth via a PLD-mediated mitogenic signal transduction cascades, which depends largely on the activation of PKC.
GlyR α3: An Essential Target for Spinal PGE 2 -Mediated Inflammatory Pain Sensitization (2004)

Prostaglandin E2 (PGE2) is a crucial mediator of inflammatory pain sensitization. Here, we demonstrate that inhibition of a specific glycine receptor subtype (GlyR alpha3) by PGE2-induced receptor phosphorylation underlies central inflammatory pain sensitization. We show that GlyR alpha3 is distinctly expressed in superficial layers of the spinal cord dorsal horn. Mice deficient in GlyR alpha3 not only lack the inhibition of glycinergic neurotransmission by PGE2 seen in wild-type mice but also show a reduction in pain sensitization induced by spinal PGE2 injection or peripheral inflammation. Thus, GlyR alpha3 may provide a previously unrecognized molecular target in pain therapy.
A 4-Mbit DRAM with trench-transistor cell (1986)

An experimental 5-V-only 1M-word/spl times/4-bit dynamic RAM with page and SCD modes has been built in a relatively conservative 1-/spl mu/m CMOS technology with double-level metal and deep trenches. It uses a cross-point one-transistor trench-transistor cell that measures only 9 /spl mu/m/SUP 2/. A double-ended adaptive folded bit-line architecture used on this DRAM provides the breakthrough needed to take full density advantage of this cross-point cell. The 30-fF storage capacitance of this cell is expected to provide high alpha immunity since the charge is stored in polysilicon and is oxide isolated from the substrate. A 150-ns now-address-stable access time and 40-ns column-address-strobe access time have been observed.
<title>Affine models for motion and shape recovery</title> (1992)

This paper presents an affine model for 3-D motion and shape recovery using two perspective views and their relative 2-D displacement field. The 2-D displacement vectors are estimated as parameters of a 2-D affine model that generalizes standard block matching by allowing affine shape deformations of image blocks and affine intensity transformations. The matching block size is effectively found via morphological size histograms. The parameters of the 3-D affine model are estimated using a least-squares algorithm that requires solving a system of linear equations with rank three. Some stabilization of the recovered motion parameters under noise is achieved through a simple form of MAP estimation. A multi-scale searching in the parameter space is also used to improve accuracy without high computational cost. Experiments on applying these affine models to various real world image sequences demonstrate that they can estimate dense displacement fields and recover motion parameters and object shape with relatively small errors.
Use of molecular imaging to quantify response to IKK‐2 inhibitor treatment in murine arthritis (2006)

Our data demonstrate that IKK-2 inhibition in the murine model of antibody-induced arthritis suppresses both inflammation and joint destruction. In addition, this study highlights how gene expression profiling can facilitate the identification of surrogate biomarkers of disease activity and treatment response in an experimental model of arthritis.