gebhart/patrepeval huggingface dataset:
Expression of Activated Epidermal Growth Factor Receptors, Ras-Guanosine Triphosphate, and Mitogen-activated Protein Kinase in Human Glioblastoma Multiforme Specimens (1999)

We demonstrated that routine IHC techniques using commercially available antibodies are capable of identifying which GBM specimens express EGFRvIII and whether the EGFRs are activated. Such a molecular classification of GBMs might allow us to determine which patients might benefit from biologically targeted therapies. In addition, characterization of specimens with respect to their EGFRvIII status seems to be of prognostic value.
Semantic file systems (1991)

A semantic file system is an information storage system that provides flexible associative access to the system's contents by automatically extracting attributes from files with file type specific transducers . Associative access is provided by a conservative extension to existing tree-structured file system protocols, and by protocols that are designed specifically for content based access. Compatiblity with existing file system protocols is provided by introducing the concept of a virtual directory . Virtual directory names are interpreted as queries, and thus provide flexible associative access to files and directories in a manner compatible with existing software. Rapid attribute-based access to file system contents is implemented by automatic extraction and indexing of key properties of file system objects. The automatic indexing of files and directories is called "semantic" because user programmable transducers use information about the semantics of updated file system objects to extract the properties for indexing. Experimental results from a semantic file system implementation support the thesis that semantic file systems present a more effective storage abstraction than do traditional tree structured file systems for information sharing and command level programming.
Genetic Engineering of Group 2 σ Factor SigE Widely Activates Expressions of Sugar Catabolic Genes in Synechocystis Species PCC 6803 (2011)

Metabolic engineering of photosynthetic organisms is required for utilization of light energy and for reducing carbon emissions.Control of transcriptional regulators is a powerful approach for changing cellular dynamics, because a set of genes is concomitantly regulated. Here, we show that overexpression of a group 2 σ factor, SigE, enhances the expressions of sugar catabolic genes in the unicellular cyanobacterium, Synechocystis sp. PCC 6803. Transcriptome analysis revealed that genes for the oxidative pentose phosphate pathway and glycogen catabolism are induced by overproduction of SigE. Immunoblotting showed that protein levels of sugar catabolic enzymes, such as glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, glycogen phosphorylase, and isoamylase, are increased. Glycogen levels are reduced in the SigE-overexpressing strain grown under light. Metabolome analysis revealed that metabolite levels of the TCA cycle and acetyl-CoA are significantly altered by SigE overexpression. The SigE-overexpressing strain also exhibited defective growth under mixotrophic or dark conditions. Thus, SigE overexpression changes sugar catabolism at the transcript to phenotype levels, suggesting a σ factor-based engineering method for modifying carbon metabolism in photosynthetic bacteria.
X- through Q-band log-periodic antenna with monolithically integrated μ-coaxial impedance transformer/feeder (2009)

An over two octaves wideband rectangular coaxial line fed log-periodic antenna is introduced. The feed line configuration consists of a three-step quarter-wave impedance transformer designed for matching 160 Ω nominal antenna impedance to 50 Ω. The transformer (feeder) is monolithically integrated with the antenna by a sequential surface micromachining process known as PolyStrata™. Measurements and simulations have shown a VSWR &lt;2:1 from X- through Q-band.
Intramembrane Proteolysis by γ-Secretase (2008)

Gamma-secretase mediates the final proteolytic cleavage, which liberates amyloid beta-peptide (Abeta), the major component of senile plaques in the brains of Alzheimer disease patients. Therefore, gamma-secretase is a prime target for Abeta-lowering therapeutic strategies. gamma-Secretase is a protein complex composed of four different subunits, presenilin (PS), APH-1, nicastrin, and PEN-2, which are most likely present in a 1:1:1:1 stoichiometry. PS harbors the catalytically active site, which is critically required for the aspartyl protease activity of gamma-secretase. Moreover, numerous familial Alzheimer disease-associated mutations within the PSs increase the production of the aggregation-prone and neurotoxic 42-amino acid Abeta. Nicastrin may serve as a substrate receptor, although this has recently been challenged. PEN-2 is required to stabilize PS within the gamma-secretase complex. No particular function has so far been assigned to APH-1. The four components are sufficient and required for gamma-secretase activity. At least six different gamma-secretase complexes exist that are composed of different variants of PS and APH-1. All gamma-secretase complexes can exert pathological Abeta production. Assembly of the gamma-secretase complex occurs within the endoplasmic reticulum, and only fully assembled and functional gamma-secretase complexes are transported to the plasma membrane. Structural analysis by electron microscopy and chemical cross-linking reveals a water-containing cavity, which allows intramembrane proteolysis. Specific and highly sensitive gamma-secretase inhibitors have been developed; however, they interfere with the physiological function of gamma-secretase in Notch signaling and thus cause rather significant side effects in human trials. Modulators of gamma-secretase, which selectively affect the production of the pathological 42-amino acid Abeta, do not inhibit Notch signaling.
Sjögrenʼs syndrome (1995)

The literature published over the past year on Sjögren's syndrome is reviewed, including epidemiology, genetic, environmental, and clinical features. The criteria for the classification of Sjögren's syndrome remain controversial, potentially leading to confusion in clinical practice and in research publications. Dryness of the eyes and mouth can result from either interruption of the neurovascular innervation of the glands or from any infiltrative process that affects the ability of the glands to secrete. Recent studies have demonstrated that sicca symptoms also can result from autonomic neuropathy in patients with diabetes, multiple sclerosis, or systemic lupus erythematosus. It is suggested that the term Sjögren's syndrome be used to describe one subset of patients with sicca symptoms who exhibit particular major histocompatibility complex antigens, the presence of T cell lymphoid infiltrates on glandular biopsy, and specific autoantibodies in their sera. Even using these restrictive criteria for classification, no single environmental factor has been shown as necessary or sufficient for pathogenesis. Recent studies on Epstein-Barr virus have indicated a novel deleted virus in some Chinese Sjögren's syndrome patients. Other patients with sicca symptoms and autoimmune features may have infections with HIV or hepatitis C virus.
Tandem insults of prenatal ischemia plus postnatal raised intrathoracic pressure in a novel rat model of encephalopathy of prematurity (2011)

Tandem insults of IUI plus postnatal RIP recapitulate many features of the hemorrhagic forms of EP found in humans, suggesting that these insults in combination may play important roles in pathogenesis.
A Low-Power Accelerator for Deep Neural Networks with Enlarged Near-Zero Sparsity (2017)

It remains a challenge to run Deep Learning in devices with stringent power budget in the Internet-of-Things. This paper presents a low-power accelerator for processing Deep Neural Networks in the embedded devices. The power reduction is realized by avoiding multiplications of near-zero valued data. The near-zero approximation and a dedicated Near-Zero Approximation Unit (NZAU) are proposed to predict and skip the near-zero multiplications under certain thresholds. Compared with skipping zero-valued computations, our design achieves 1.92X and 1.51X further reduction of the total multiplications in LeNet-5 and Alexnet respectively, with negligible lose of accuracy. In the proposed accelerator, 256 multipliers are grouped into 16 independent Processing Lanes (PL) to support up to 16 neuron activations simultaneously. With the help of data pre-processing and buffering in each PL, multipliers can be clock-gated in most of the time even the data is excessively streaming in. Designed and simulated in UMC 65 nm process, the accelerator operating at 500 MHz is $&gt;$ 4X faster than the mobile GPU Tegra K1 in processing the fully-connected layer FC8 of Alexnet, while consuming 717X less energy.
A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors (1991)

Journal Article A simple and efficient method for direct cloning of PCR products using ddT-tailed vectors Get access T.A. Holton, T.A. Holton * Calgene Pacific Pty. Ltd16 Gipps St., Collingwood, Victoria 3066, Australia * To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar M.W. Graham M.W. Graham Calgene Pacific Pty. Ltd16 Gipps St., Collingwood, Victoria 3066, Australia Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 5, 11 March 1991, Page 1156, https://doi.org/10.1093/nar/19.5.1156 Published: 11 March 1991 Article history Accepted: 07 December 1990 Published: 11 March 1991
A logic design structure for LSI testability (1977)

The ability to put hundreds of logic gates on a single chip of silicon offers great potential for reducing power, increasing speed, and reducing cost. Unfortunately, several problems must be solved in order to exploit these advantages of large-scale integration, LSI. This paper will describe a logic design method that will greatly simplify problems in testing, diagnostics, and field service for LSI. The design method is based on two concepts that are nearly independent but combine efficiently and effectively. The first is to design sequential logic structures so that correct operation is not dependent on signal rise and fall time or on circuit or wire delay. The second is to design all the internal storage elements (other than memory arrays) so that they can also be operated as shift registers to facilitate testing and diagnostics. Sequential logic, which is difficult to test, can then be transformed to combinational logic, which is less difficult. The transformation is performed during test generation. Advantages and cost impact will also be discussed qualitatively.
Fluorescence Resonance Energy Transfer Analysis of Cytochromes P450 2C2 and 2E1 Molecular Interactions in Living Cells (2003)

The molecular organization of microsomal cytochromes P450 (P450s) and formation of complexes with P450 reductase have been studied previously with isolated proteins and in reconstituted systems. Although these studies demonstrated that some P450s oligomerize in vitro, neither oligomerization nor interactions of P450 with P450 reductase have been studied in living cells. Here we have used fluorescence resonance energy transfer (FRET) to study P450 oligomerization and binding to P450 reductase in live transfected cells. Cytochrome P450 2C2, but not P450 2E1, forms homo-oligomeric structures, and this self-association is mediated by the signal-anchor sequence. Because P450 2C2, in contrast to P450 2E1, is directly retained in the endoplasmic reticulum (ER), these results could suggest that oligomerization may prevent transport from the ER. However, P450 2C1 signal-anchor sequence chimera defective in ER retention also formed oligomers, and chimera containing the cytoplasmic domain of P450 2C2, which is directly retained in the ER, did not exhibit self-oligomerization, which indicates that oligomerization is not correlated with direct retention. By using FRET, we have also detected binding of P450 2C2 and P450 2E1 to P450 reductase. In contrast to self-oligomerization, the catalytic domain can mediate an interaction of P450 2C2 with P450 reductase. These results suggest that microsomal P450s may differ in their quaternary structure but that these differences do not detectably affect interaction with the reductase or transport from the ER.
Pineal Function in Mammals and Birds is Altered by Earth-Strength Magnetic Fields (1992)

The discovery of the magnetic sensitivity of the mammalian pineal gland (electrophysiology: Semm et al., 1980; biochemistry: Welker et al., 1983) initiated for the first time the possibility of measuring influences of the magnetic environment in the central nervous system. We found this remarkable property of the pineal gland during a research program dealing with electrophysiological characteristics of mammalian pinealocytes. However, we were mainly interested in the physiological basis of the magnetic compass in migrating and homing animals. After it became clear that the pineal is not directly involved in magnetic compass orientation (Maffei et al., 1983; Semm et al., 1987), we used the magnetic sensitivity of the gland as a tool for finding other nerve cells that might be involved in magnetic orientation (Beason and Semm, 1987; Semm et al., 1984; Semm and Demaine, 1986).
Current Density Imaging and Electrically Induced Skin Burns Under Surface Electrodes (2005)

The origin of electrical burns under gel-type surface electrodes is a controversial topic that is not well understood. To investigate the phenomenon, we have developed an excised porcine skin-gel model, and used low-frequency current density imaging (LFCDI) to determine the current density (CD) distribution through the skin before and after burns were induced by application of electrical current (200 Hz, 70% duty cycle, 20-35 mA monophasic square waveform applied to the electrodes for 30-135 min). The regions of increased CD correlate well with the gross morphological changes (burns) observed. The measurement is sensitive enough to show regions of high current densities in the pre-burn skin, that correlate with areas were burn welts were produced, thus predicting areas where burns are likely to occur. Statistics performed on 28 skin patches revealed a charge dependency of the burn areas and a relatively uniform distribution. The results do not support a thermal origin of the burns but rather electro-chemical mechanisms. We found a statistically significant difference between burn area coverage during anodic and cathodic experiments.
Increased Expression of the Na+/I− Symporter in Cultured Human Thyroid Cells Exposed to Thyrotropin and in Graves’ Thyroid Tissue* (1997)

The Na+/I- symporter (NIS) is important in hormone synthesis in the thyroid gland. NIS activity, as reflected by I- uptake, was increased by TSH (1 mU/mL) or forskolin (10 mumol/L) in primary cultured human thyroid cells. Northern blot analysis revealed that incubation of these cells with TSH or forskolin for 24 h increased the abundance of NIS messenger ribonucleic acid (mRNA) 2.3- and 2.5-fold, respectively. Immunoblot analysis revealed 2.7- and 2.4-fold increases, respectively, in the amount of NIS protein after 48 h, suggesting that elevated levels of intracellular cAMP induced the expression of NIS in human thyrocytes. We then studied the levels of NIS mRNA and protein in Graves' thyroid tissue and found that the amount of NIS mRNA in thyroid tissue from individuals with Graves' disease (n = 5) was 3.8 times that in normal thyroid tissue (n = 5). The abundance of NIS mRNA was significantly correlated with that of thyroid peroxidase or thyroglobulin mRNAs, but not with that of TSH receptor mRNA, in the Graves' and normal thyroid tissue specimens. The amount of NIS protein was also increased 3.1-fold in Graves' thyroid tissue compared with that in normal thyroid tissue. The increased expression of NIS may thus contribute to the development of Graves' disease.
Tumor necrosis factor-alpha inhibits collagen alpha1(I) gene expression and wound healing in a murine model of cachexia. (1996)

The mechanisms responsible for impaired wound healing in patients with cachexia-associated infection, inflammation, and cancer are unknown. As tumor necrosis factor (TNF)-alpha is elevated in these diseases, and TNF-alpha inhibits collagen alpha1(I) gene expression in cultured fibroblasts, we analyzed whether chronically elevated serum TNF-alpha affects collagen metabolism in vivo by inoculating nude mice with Chinese hamster ovary cells secreting TNF-alpha (TNF-alpha mice) or control Chinese hamster ovary cells (control mice). Before the onset of weight loss, TNF-alpha mice had a selective decrease in collagen synthesis and collagen alpha1(I) mRNA in the skin. In addition, TNF-alpha mice displayed impaired healing of incisional and excisional skin wounds, compared with control animals, before the onset of cachexia. The expression of transforming growth factor-beta1, a potent fibrogenic factor, was inhibited by TNF-alpha in the skin. In studies with transgenic mice expressing the human growth hormone under the direction of 5' regulatory regions of the human collagen alpha1(I) gene, TNF-alpha treatment inhibited the expression of the collagen alpha1(I) human growth hormone transgene containing -2.3 kb of the 5' region, whereas transgene expression directed by -0.44 kb of the 5' region was not affected. These experiments suggest that TNF-alpha may play an important role in the impaired wound healing of chronic diseases that are characterized by a high production of this cytokine and provide insights for potential therapeutic approaches.
Association of Elevated Stearate with Agronomic and Seed Traits of Soybean (1997)

Soybean [ Glycine max (L.) Merr.] genotypes with elevated stearate content in the seed oil may be useful for food and industrial applications. The objective of this study was to determine the association of elevated stearate with agronomic and seed traits of soybean. Two high‐yielding cultivars with normal stearate content of ≈ 40 g kg −1 were crossed to lines with the genotype fasa fasa that had an elevated stearate content of &gt;200 g kg −1 . From each of the two populations, 75 F 3 ‐ or F 5 ‐derived lines that ranged in stearate content from ≈ 40 to 230 g kg −1 were selected for replicated testing at two locations in Iowa during 1993 and 1994. There were significant differences between the means of the elevated and normal stearate lines for seed yield, maturity, lodging, plant height, and content of protein, oil, palmitate, oleate, linoleate, and linolenate. The coefficients obtained from the linear regression of mean seed yield of the lines on their mean stearate content were negative and significant. Although the fasa allele generally had a negative influence on seed yield across a range of elevated stearate contents, there were lines with elevated stearate contents that were not significantly different in seed yield than the highest yielding line in the population. The results indicated that it may be possible to develop cultivars with the fasa fasa genotype that have acceptable seed yield and moderately elevated stearate content.
Deficit of resolution receptor magnifies inflammatory leukocyte directed cardiorenal and endothelial dysfunction with signs of cardiomyopathy of obesity (2020)

Chronic unresolved inflammation is the primary determinant of cardiovascular disease. Precise mechanisms that define the genesis of unresolved inflammation in heart failure with preserved ejection fraction (HFpEF) are of interest due to the obesity epidemic. To examine the obesity phenotype and its direct/indirect consequences, multiple approaches were employed using the lipoxin receptor (abbreviated as ALX) dysfunction mouse model. Indirect calorimetry analyses revealed that the deletion of ALX dysregulated energy metabolism driving toward age-related obesity. Heart function data suggest that obesity-prone ALX deficient mice had impaired myocardium strain. Comprehensive measurement of chemokines, extracellular matrix, and arrhythmogenic arrays confirmed the dysregulation of multiple ion channels gene expression with amplified inflammatory chemokines and cytokines response at the age of 4 months compared with WT counterparts. Quantitative analyses of leukocytes demonstrated an increase of proinflammatory Ly6C<sup>hi</sup> CCR2<sup>+</sup> macrophages in the spleen and heart at a steady-state resulting in an inflamed splenocardiac axis. Signs of subtle inflammation were marked with cardiorenal, endothelial defects with decreased CD31 and eNOS and an increased iNOS and COX2 expression. Thus, ALX receptor deficiency serves as an experimental model that defines multiple cellular and molecular mechanisms in HFpEF that could be a target for the development of HFpEF therapy in cardiovascular medicine.
Lipid-Based Nanoformulation of Irinotecan: Dual Mechanism of Action Allows for Combination Chemo/Angiogenic Therapy (2011)

A number of studies have outlined the antiangiogenic effects of cytotoxic agents when administered frequently at low doses. These studies suggest that the effect of the cytotoxic agent is on the vasculature within the tumor and it is assumed that there is little or negligible cytotoxicity. Liposomal drug delivery systems have the ability to provide a dual mechanism of activity where tumor accumulation can deliver high local concentrations of the drug at the site of action with concomitant slow release of the drug from carriers in the blood compartment that results in antivascular effects, similar to that achieved when dosing frequently at low levels. Although this dual mechanism of activity may be linked to other lipid nanoparticle formulations of anticancer drugs, this article summarizes the evidence supporting direct (cytotoxic) and indirect (antivascular) actions of a liposomal formulation of irinotecan.
Characterization of protein-protein interactions for optimizing formulation and physical stability of high protein concentration solutions (2007)

Body weight is a predictor of clopidogrel response. However, no prospective studies have compared pharmacodynamic (PD) and pharmacokinetic (PK) data based on body weight. We compared PD and PK effects of clopidogrel 75 mg in low body weight (LBW, <60 kg) and higher body weight (HBW, ≥60 kg) patients with stable coronary artery disease. LBW (n = 34, 56.4 ± 3.7 kg) and HBW (n = 38, 84.7 ± 14.9 kg) aspirin-treated patients received clopidogrel 75 mg for 10-14 days. The area under the concentration-time curve of active metabolite (Clop-AM) calculated through the last quantifiable concentration up to 4 h postdose, AUC(0-tlast), was calculated by noncompartmental methods. Light transmission aggregometry (LTA) (maximum platelet aggregation and inhibition of platelet aggregation to 20 μM adenosine diphosphate (ADP), and residual platelet aggregation to 5 μM ADP), VerifyNow(®) P2Y12 reaction units (PRU), and vasodilator-associated stimulated phosphoprotein phosphorylation platelet reactivity index (VASP-PRI) were performed. Mean AUC(0-tlast) was lower in HBW than LBW patients: 12.8 versus 17.9 ng h/mL. HBW patients had higher platelet reactivity as measured by LTA (all p ≤ 0.01), PRU (207 ± 68 vs. 152 ± 57, p < 0.001), and VASP-PRI (56 ± 18 vs. 39 ± 17, p < 0.001). More HBW patients exhibited high on-treatment platelet reactivity (HPR) using PRU (35 vs. 9%) and VASP-PRI (65 vs. 27%). Body weight correlated with PRU and VASP-PRI (both p < 0.001), and inversely with log transformed AUC(0-tlast) (p < 0.001). In conclusion, HBW patients had lower levels of Clop-AM, and higher platelet reactivity and rates of HPR than LBW subjects, contributing to their suboptimal response to clopidogrel.