gebhart/patrepeval huggingface dataset:
Tau Filament Formation in Transgenic Mice Expressing P301L Tau (2001)

Mutations in the microtubule-associated protein tau, including P301L, are genetically coupled to hereditary frontotemporal dementia with parkinsonism linked to chromosome 17. To determine whether P301L is associated with fibril formation in mice, we expressed the longest human tau isoform, human tau40, with this mutation in transgenic mice by using the neuron-specific mouse Thy1.2 promoter. We obtained mice with high expression of human P301L tau in cortical and hippocampal neurons. Accumulated tau was hyperphosphorylated and translocated from axonal to somatodendritic compartments and was accompanied by astrocytosis and neuronal apoptosis indicated by terminal deoxynucleotidyl transferase-mediated biotinylated dUTP nick end-labeling staining. Moreover, P301L tau formed abnormal filaments. Electron microscopy of sarcosyl-insoluble protein extracts established that the filaments had a straight or twisted structure of variable length and were approximately 15 nm wide. Immunoelcecton microscopy showed that the tau filaments were phosphorylated at the TG3, AT100, AT8, and AD199 epitopes in vivo. In cortex, brain stem, and spinal cord, neurofibrillary tangles were also identified by thioflavin-S fluorescent microscopy and Gallyas silver stains. Together, our results show that expression of the P301L mutation in mice causes neuronal lesions that are similar to those seen in human tauopathies.
Modular logic built-in self-test for IP cores (2002)

The paper presents a new modular logic BIST architecture for intellectual property (IF) cores and block-oriented design methodology. The scheme involves two-step development process: design and analysis of BIST-ready IP cores and system integration. A BIST-ready core has inserted scan chains, test points, a repeater with phase shifter to perform serial to parallel conversion of test vectors, and a space-time test-response compactor. It is also simulated to determine its fault coverage and signature for a specified configuration of BIST hardware. Particulars of a method to compute the composite signature for the whole design based on signatures representing individual cores are presented altogether with a new technique to expand test vectors. At the system ASIC level, the paper demonstrates how multiple cores can be seamlessly integrated and then tested in exactly the same manner as they were analyzed by sharing the same BIST controller.
Vaccinia Virus Complement Control Protein Enhances Functional Recovery after Traumatic Brain Injury (2002)

Inflammation is a major contributor to the neuropathological consequences of traumatic brain injury (TBI). Previous studies have shown that proinflammatory complement activation fragments are present in the injured brain within the first 24 h after trauma. To investigate whether complement activation within the injured brain leads to the neuropathology and subsequent functional impairment associated with TBI, we examined what effect administration of a complement inhibitor, the vaccinia virus complement control protein (VCP), would have on spatial learning and memory in brain injured rats, as measured using the Morris Water Maze (MWM) procedure. Animals were subjected to a lateral fluid percussion brain injury of moderate severity and, 15 min later, received a 10-microL injection of either full-length VCP, a truncated version of VCP (VCPt), which lacks the complement inhibitory activity but retains the heparin binding activity of VCP, or saline directly into the cortex. Results of such intervention indicated that, at 2 weeks postinjury, both VCP and VCPt treatment attenuated impairments in spatial memory, but not neuropathological damage, as compared to the saline treated controls. These results were surprising and suggest that the neuroprotective effects following administration of VCP after acute brain injury are mediated by mechanisms other than complement inhibition. Potential mechanisms are discussed.
Inhibition of growth and metastasis of orthotopic human prostate cancer in athymic mice by combination therapy with pegylated interferon-alpha-2b and docetaxel. (2002)

We evaluated whether treatment of orthotopic human prostate cancer in nude mice with pegylated IFN-alpha-2b (PEG-IFN-alpha-2b) and docetaxel could represent a two-compartment targeting of primary tumor (tumor cells and tumor-associated endothelial cells) and inhibition of regional lymph node metastasis. The antiangiogenic properties of IFN were combined with the cytotoxic properties of docetaxel, resulting in apoptosis of both tumor cells and endothelium and hence significant inhibition of primary tumor growth. We first determined the optimal biological dose of PEG-IFN-alpha-2b (70,000 IU/week) necessary to down-regulate the expression of basic fibroblast growth factor, matrix metalloprotease-9, and matrix metalloprotease-2. The therapeutic dose of docetaxel (10 mg/kg/week) was determined by efficacy and minimal body weight loss. Therapy beginning 3 days after orthotopic implantation of PC3-MM2 prostate cancer cells reduced tumor weight by 37% in mice treated with PEG-IFN-alpha-2b, by 60% in mice treated with docetaxel, and by 83% in those given both drugs. PEG-IFN-alpha-2b also induced apoptosis of tumor-associated endothelial cells and hence a significant decrease in microvessel density. Our data indicate that the combination of PEG-IFN-alpha and docetaxel inhibits neoplastic angiogenesis by inducing a decrease in the local production of proangiogenic molecules by tumor cells, resulting in increased apoptosis of tumor-associated endothelial cells.
Megalin (gp330) possesses an antigenic epitope capable of inducing passive Heymann nephritis independent of the nephritogenic epitope in receptor-associated protein. (1995)

The Heymann nephritis antigenic complex (HNAC) consists of two glycoproteins, megalin (gp330), and the receptor-associated protein (RAP). HNAC is expressed on the surface of the glomerular epithelium where it plays a primary role in the pathogenesis of Heymann nephritis (HN). Several models were previously proposed describing how antibody binding epitopes in HNAC may contribute to the initiation and progression of HN. Although these models suggest that nephritogenic epitopes capable of initiating HN are present in both megalin and RAP, the structural relationship between these epitopes has not been established. Previously a nephritogenic epitope was identified and characterized in RAP that initiates immune complex formation in HN. In this report, the immunologic relationship between nephritogenic epitopes in megalin and RAP were examined to determine whether these epitopes are immunologically distinct or antigenically related. To this end, a polyclonal antibody to megalin was generated that does not recognize RAP by immunoblotting or immunoprecipitation and whether this antibody is capable of inducing passive HN was determined. It was found that antimegalin antibodies devoid of RAP cross-reactivity induced the formation of subepithelial immune deposits (passive HN) when injected into rats. Antibodies eluted from glomeruli of the injected rats recognized only megalin by immunoblotting a cortical extract and did not recognize a RAP fusion protein or any other renal protein. In addition, the eluted antibodies immunoprecipitated two proteolytic fragments of megalin (140 and 75 kd) identifying a pathogenic epitope within a smaller fragment of megalin.(ABSTRACT TRUNCATED AT 250 WORDS)
Staphylococcal α-Toxin:  Formation of the Heptameric Pore Is Partially Cooperative and Proceeds through Multiple Intermediate Stages (1997)

Staphylococcal alpha-toxin is a 293 residue polypeptide that assembles into pore-forming heptamers, residues 118-140, thereby inserting to form an amphipathic beta-barrel in the lipid bilayer. Fluorometric analyses were here conducted using cysteine-substitution mutants site-specifically-labeled at positions 35 or 130 with the environmentally-sensitive fluorophore acrylodan. In conjunction with functional assays, three conformational states of the heptamer were defined, which may represent transitional configurations of the toxin molecule along its way to membrane insertion and pore formation. The first was the freshly assembled, SDS-sensitive heptamer alpha7*a, where a minor alteration in the environment of H35 with no change in the environment of the membrane-inserting stem domain was observed. In transition stage alpha7*b, the stem domain moved from a hydrophilic to a more hydrophobic environment, due to protein-protein interaction. Transition to alpha7*c involved a cooperative effect, in which residue 35 was forced by a neighboring molecule into a markedly hydrophobic environment. At this stage, the heptamers acquired SDS stability. The final pore conformation alpha7 resulted when the stem domain inserted into the lipid bilayer, an event that was driven by H35 within the respective protomer. A model thus evolved in which cooperative forces first lever H35 into a position that subsequently drives the pore-forming sequence within each respective protomer into the membrane. In accord with this model, when hybrid heptamers were formed between a functionally defective H35 substitution mutant and active toxin, only the latter inserted their pore-forming domain into the membrane. In a satisfying functional correlate, pores of reduced size were then generated.
In-line holography using low-energy electrons and photons: Applications for manipulation on a nanometer scale (1995)

An in-line holography setup is used to obtain electron and photon holograms of high magnification from various samples. Electron holograms are obtained using the coherent beam of low-energy electrons that originates from the electron point-source tip. Light optical holograms are generated for comparison using a divergent laser beam. In both cases the numerical reconstruction of the holograms yields the wave front at the sample. The low-energy electron point source microscope has been modified by incorporating an additional tip for manipulating the sample under observation. With this manipulating tip, individual nanometer-sized wires have been contacted, and an electrical current has been passed through carbon fibers as well as through carbon nanotubes while the holographic electron pattern has been observed in situ.
Selective Neuronal Survival and Upregulation of PCNA in the Rat Inner Retina Following Transient Ischemia (2000)

In this study we investigated the extent and time course of neuronal cell death and the regulation of the proliferating cell nuclear antigen (PCNA) in the different retinal cell layers following ischemia-reperfusion injury. Retinal ischemia was induced by controlled elevation of the intraocular pressure for a duration of 60 min. Changes in thickness and cell numbers in the retinal cell layers were analyzed at various time points (1 h to 4 weeks) after reperfusion. In parallel, apoptotic cell death was determined by the TUNEL method and the expression of PCNA analyzed by immunocytochemistry. In addition, we tested whether PCNA is expressed in neurons by double immunocytochemistry. The reduction in thickness was found to be less pronounced in the inner nuclear layer (INL). Correspondingly, cell numbers decreased by only 33% in the inner retina, but by more than 80% in the outer nuclear layer (ONL). Alterations in glial cell numbers did not contribute significantly to postischemic changes in the INL and ONL as assessed by using immunocytochemical markers for microglial and Müller cells. The time course of cell death determined by the TUNEL technique also differed markedly in the retinal layers being rapid and transient in the inner retina but delayed and prolonged in the ONL. PCNA immunoreactivity was undetectable in the normal retina, but was specifically induced in neurons of the inner retina within 1 h after reperfusion and was sustained for at least 4 weeks. We conclude that in contrast to photoreceptors in the ONL, a significant proportion of inner retinal neurons is resistant to ischemic insult induced by transiently increased intraocular pressure and that PCNA may possibly play a role in the selective postischemic survival of these cells.
Simultaneous Respiratory Tract Colonization by Multiple Strains of NontypeableHaemophilus influenzaein Chronic Obstructive Pulmonary Disease: Implications for Antibiotic Therapy (1999)

Nontypeable Haemophilus influenzae often causes exacerbations of chronic obstructive pulmonary disease (COPD), and these exacerbations are frequently treated with oral antibiotics. The goals of this study were to determine the frequency of the simultaneous presence of multiple strains of H. influenzae in sputum and to measure the MICs of antibiotics for the isolates. In a prospective study, adults with COPD were seen monthly. Sputum cultures were obtained, and individual colonies were subjected to genomic DNA typing and MIC determinations. Multiple strains of H. influenzae were present simultaneously in the sputum of 26.3% of adults with COPD. In 64.5% of these, MICs of >/=1 antibiotic varied by >/=4-fold among the strains. Therefore, multiple strains of H. influenzae are frequently present simultaneously in the sputum of adults with COPD, and the antimicrobial susceptibility of different strains in the same sputum sometimes differs.
Structure of the human insulin-like growth factor binding protein-2 gene. (1992)

Insulin-like growth factors (IGFs) are polypeptide hormones with structural homology to proinsulin. IGFs circulate in blood bound to specific IGF binding proteins (IGFBPs). cDNA sequences of six members of a family of human and rat IGFBPs have been published. Here we present a partial characterization of the human IGFBP-2 gene. This single copy gene is located on chromosome 2 and spans a total of more than 32 kilobases (kb) of genomic sequence. It is organized in four exons with sizes of more than 568, 220, 141, and 496 nucleotides. The intron between exon one and exon two contributes 27 kb to the size of the IGFBP-2 gene. The second and the third introns comprise 1.1 kb and 1.95 kb, respectively. When the structure of the IGFBP-2 gene is compared to that of the IGFBP-1 and IGFBP-3 genes, the exon boundaries are found to be conserved in these three genes. A single transcriptional start site was localized to 113 +/- 2 nucleotides 5' of the ATG start codon of IGFBP-2 translation. Furthermore, the region between nucleotides -635 and -2 upstream of the ATG was demonstrated to exhibit promoter activity in human Jurkat K16 cells. This region is devoid of TATA or CAAT consensus sequence motifs and has a high content of dC and dG nucleotides. In this respect the putative IGFBP-2 promoter region resembles the promoters which are often associated with housekeeping genes.
A further tetranucleotide repeat polymorphism in the vWF gene (1992)

Journal Article A further tetranucleotide repeat polymorphism in the vWF gene Get access C. Kimpton, C. Kimpton * Central Research and Support Establishment, The Forensic Science ServiceAldermaston, Reading, Berks RG7 4PN, UK *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar A. Walton, A. Walton Central Research and Support Establishment, The Forensic Science ServiceAldermaston, Reading, Berks RG7 4PN, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar P. Gill P. Gill Central Research and Support Establishment, The Forensic Science ServiceAldermaston, Reading, Berks RG7 4PN, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Human Molecular Genetics, Volume 1, Issue 4, July 1992, Page 287, https://doi.org/10.1093/hmg/1.4.287 Published: 01 July 1992
A Modified Model of T-Cell Differentiation Based on mTOR Activity and Metabolism (2013)

Current models of T-helper-cell differentiation depict the generation of effector cells from a naïve T cell based on the cytokine environment upon T-cell-receptor engagement. We propose a new model of CD4(+) T-cell activation, differentiation, and function whereby the outcome of antigen recognition is dictated by mTOR activity and the subsequent up-regulation of selective metabolic function. Such a model more readily explains the generation of effector and memory cells including the concept of effector and memory Foxp3(+) regulatory cells.
Randomizing AMI configuration for proactive defense in smart grid (2013)

Smart grids are capable of bi-directional communication between smart meters and headend systems. It is a core feature of smart grid provided by the underlying Advanced Metering Infrastructure (AMI). Due to the critical nature of AMI, threats have been targeted towards it and a need of tailored defense mechanism has been highlighted in the recent studies. Since limited number of protocols and applications are supported in the AMI, it exhibits a predictable and deterministic behavior. This predictability makes it easier for an attacker to learn the network behavior and launch an evasion attack by generating similar traffic. To combat this, we present a mutable AMI configuration technique for Proactive Defense. We randomize three different configuration parameters in order to make the AMI behavior unpredictable.While providing the randomization, the approach stays deterministic for the AMI devices like smart collector in order to detect any evasion attempts. We use real-world dataset comprising of approximately 2000 meters collected at an AMI of a leading utility provider for analysis. We also use smart grid testbed to show the effectiveness of our mutation technique.
Identification of haptoglobin as an angiogenic factor in sera from patients with systemic vasculitis. (1993)

Angiogenesis is an important process in chronic inflammatory diseases. We observed that sera from patients with systemic vasculitis stimulated angiogenesis in an in vitro model using human umbilical vein endothelial cells cultured on a basement membrane (Matrigel) substrate. After 40% ammonium sulfate precipitation, angiogenic activity remained in the low molecular weight fraction and could be inactivated by heat. SDS-page of serum FPLC fractions exhibiting maximal angiogenic activity demonstrated two prominent species of 45 and 16-20 kD in patients' sera. These bands were much less apparent in sera obtained from control subjects. Amino-terminal sequencing of the 45-kD protein demonstrated that it was haptoglobin. Purified haptoglobin stimulated angiogenesis in a dose-dependent manner. The angiogenic activity of vasculitis patients' sera was partially inhibited by an antihaptoglobin antibody. Furthermore, serum haptoglobin levels in vasculitis patients correlated both with disease and angiogenic activity. Haptoglobin angiogenic activity was confirmed in two in vivo models using an implanted disc and a subcutaneous injection of basement membrane. Stimulation of angiogenesis is a newly recognized biological function of haptoglobin. The increased levels of haptoglobin found in chronic inflammatory conditions may play an important role in tissue repair. In systemic vasculitis, haptoglobin might also compensate for ischemia by promoting development of collateral vessels.
Therapeutic Efficacy of Replication-Competent Retrovirus Vector–Mediated Suicide Gene Therapy in a Multifocal Colorectal Cancer Metastasis Model (2007)

Replication-competent retrovirus (RCR) vectors are intrinsically incapable of infecting quiescent cells and have been shown to achieve highly efficient and tumor-restricted replicative spread and gene transfer in vivo after direct intratumoral injection in a variety of primary cancer models. However, i.v. delivery of RCR vectors expressing therapeutic genes has never previously been tested, particularly in an immunocompetent tumor model. Therefore, in the present study, we sought to test the therapeutic effect of an RCR vector (ACE-CD) carrying the yeast cytosine deaminase (CD) gene, which converts the nontoxic prodrug 5-fluorocytosine (5FC) into the chemotoxin 5-fluorouracil, after delivery by infusion into the locoregional circulation in a multifocal hepatic metastasis model of colon cancer. After confirmation of suicide gene cytotoxicity in vitro, multifocal hepatic tumors were established in syngeneic mice with murine CT26 colorectal cancer cells expressing firefly luciferase (CT26-Luc), and the ACE-CD vector was infused via intrasplenic injection into the portal circulation. Fourteen days after locoregional infusion, systemic administration of 5FC resulted in significant inhibition of bioluminescent signals in mice whose tumors had been infected with RCR but not in control mice. Notably, there was no detectable RCR vector spread to normal liver or bone marrow by quantitative PCR analysis. Our results thus show that locoregional delivery of a suicide gene by RCR vectors infused into the portal circulation results in progressive transduction of multiple tumor foci in the liver, without evidence of spread to adjacent normal parenchyma or extrahepatic tissues, and can achieve significant tumor growth inhibition.
Reducing respiratory motion artifacts in positron emission tomography through retrospective stacking (2006)

Respiratory motion artifacts in positron emission tomography (PET) imaging can alter lesion intensity profiles, and result in substantially reduced activity and contrast-to-noise ratios (CNRs). We propose a corrective algorithm, coined "retrospective stacking" (RS), to restore image quality without requiring additional scan time. Retrospective stacking uses b-spline deformable image registration to combine amplitude-binned PET data along the entire respiratory cycle into a single respiratory end point. We applied the method to a phantom model consisting of a small, hot vial oscillating within a warm background, as well as to 18FDG-PET images of a pancreatic and a liver patient. Comparisons were made using cross-section visualizations, activity profiles, and CNRs within the region of interest. Retrospective stacking was found to properly restore the lesion location and intensity profile in all cases. In addition, RS provided CNR improvements up to three-fold over gated images, and up to five-fold over ungated data. These phantom and patient studies demonstrate that RS can correct for lesion motion and deformation, while substantially improving tumor visibility and background noise.
Activation of the p53 pathway by small-molecule-induced MDM2 and MDMX dimerization (2012)

Activation of p53 tumor suppressor by antagonizing its negative regulator murine double minute (MDM)2 has been considered an attractive strategy for cancer therapy and several classes of p53-MDM2 binding inhibitors have been developed. However, these compounds do not inhibit the p53-MDMX interaction, and their effectiveness can be compromised in tumors overexpressing MDMX. Here, we identify small molecules that potently block p53 binding with both MDM2 and MDMX by inhibitor-driven homo- and/or heterodimerization of MDM2 and MDMX proteins. Structural studies revealed that the inhibitors bind into and occlude the p53 pockets of MDM2 and MDMX by inducing the formation of dimeric protein complexes kept together by a dimeric small-molecule core. This mode of action effectively stabilized p53 and activated p53 signaling in cancer cells, leading to cell cycle arrest and apoptosis. Dual MDM2/MDMX antagonists restored p53 apoptotic activity in the presence of high levels of MDMX and may offer a more effective therapeutic modality for MDMX-overexpressing cancers.