gebhart/patrepeval huggingface dataset:
Optical properties of deep lamellar Gratings: A coupled Bloch-mode insight (2006)

A coupled-Bloch-mode model for explaining various optical properties of strongly modulated subwavelength lamellar gratings is proposed. The model evidences the key role played by propagative Bloch modes, which bounce inside the grating and couple at the grating interfaces. Many optical properties of these gratings, such as their broadband reflectance, their polarization effect, and the presence of sharp anomalies, are understood as resulting from vertical resonances of the coupled-resonator modes. The approach provides a new insight on the physical mechanisms or optical behaviors observed, which is different from the classical study of the poles and zeros of the scattering operator.
Circulating oncoproteins HER2/neu, EGFR and CAIX (MN) as novel cancer biomarkers (2007)

Pharmaceutical companies have developed targeted therapies such as trastuzumab and lapatinib for human epidermal growth factor receptor (HER)2/neu-positive tumors, while others have developed antiepidermal growth factor receptor (EGFR) therapies, such as tarceva and erbitux for EGFR-positive tumors. A drug called rencarex is targeted to an oncoprotein designated carbonic anhydrase IX (CAIX), which is being evaluated in renal cell carcinoma patients. Based on these targeted therapeutic approaches, this review describes clinical research studies performed with enzyme-linked immunosorbent assays specific for the circulating oncoproteins, HER2/neu, EGFR and CAIX. These circulating biomarkers have the potential to be used in conjunction with the specific targeted therapies for patient selection, monitoring and management. With the variety of new therapeutic options, the major challenge ahead will be to select the appropriate therapy or combinations of therapies for each patient. Specific biomarker tests, either alone or in panels, will be needed at the appropriate time in the course of disease to ensure that patients receive the right drug at the right time. These tests will also be valuable in monitoring the efficacy of the targeted therapies. A circulating biomarker such as serum HER2/neu may be able to specifically identify patients with progressing HER2/neu-positive disease and provide the information needed by physicians to choose from the variety of HER2/neu-targeted therapies that will soon be available to cancer patients.
Mutations in RLBP1 associated with fundus albipunctatus in consanguineous Pakistani families (2011)

These results strongly suggest that mutations in RLBP1 are responsible for fundus albipunctatus in the affected individuals of these consanguineous Pakistani families.
A Chimeric Receptor with NKG2D Specificity Enhances Natural Killer Cell Activation and Killing of Tumor Cells (2013)

Natural killer (NK) cells rely on surface receptors to distinguish healthy cells from cancer cells. We designed a receptor termed NKG2D-DAP10-CD3ζ that is composed of the NK cell activating molecule NKG2D plus 2 key signaling molecules, DAP10 and CD3ζ, and evaluated its capacity to promote cancer cell killing. Retroviral transduction of NKG2D-DAP10-CD3ζ markedly increased NKG2D surface expression in NK cells, which became consistently more cytotoxic than mock-transduced cells against leukemia and solid tumor cell lines. In contrast, there was no increase in cytotoxicity against nontransformed blood and mesenchymal cells. NKG2D blockade abrogated gains in cytotoxicity to cancer cells. Receptor stimulation triggered signal transduction, secretion of IFN-γ, GM-CSF, IL-13, MIP-1α, MIP-1β, CCL5, and TNF-α, and massive release of cytotoxic granules, which persisted after 48 hours of continuous stimulation. NKG2D-DAP10-CD3ζ-expressing NK cells had considerable antitumor activity in a mouse model of osteosarcoma, whereas activated NK cells were ineffective. Thus, the cytotoxic potential of NK cells against a wide spectrum of tumor subtypes could be markedly enhanced by expression of NKG2D-DAP10-CD3ζ receptors. The development of an electroporation method that permits rapid expression of the receptor in a large number of human NK cells facilitates clinical translation of this NK-based strategy for a generalized cellular therapy that may be useful to treat a wide range of cancers.
Lung Cancer—Where Are We Today?: Current Advances in Staging and Nonsurgical Treatment (2002)

Lung cancer remains the commonest cause of cancer death in both men and women in the developed world, although mortality rates for men are dropping. Spiral computed tomography (CT) of the chest in middle-aged, smoking subjects may identify two to four times more lung cancers than a chest X-ray, with more than 70% of tumors being Stage I. The incidence of benign nodules is high, making interpretation difficult. Randomized controlled trials are required to determine whether spiral CT detects lung cancer early enough to improve mortality. Preoperative staging has relied on CT scans, but positron emission tomography scanning has greater sensitivity, specificity, and accuracy than CT and is recommended as the final confirmatory investigation when the CT shows resectable disease. In locally advanced non-small cell lung cancer, there is a small advantage for the addition of chemotherapy to radiotherapy, but no advantage for postoperative radiotherapy. Chemotherapy gives no benefit when given as neoadjuvant or adjuvant treatment around surgery. In advanced disease, newer cytotoxic agents confer a small survival advantage over older combinations, but the advantage in median survival over best supportive care remains a few months with modest improvements in quality of life. Survival with small cell lung cancer has shown little increase over the last 15 years despite multiple attempts to manipulate the timing, dose intensity of chemotherapy, and the potential of radiotherapy. Novel therapies are urgently needed for all cell types of lung cancer.
Recombinant Listeria monocytogenes vaccination eliminates papillomavirus-induced tumors and prevents papilloma formation from viral DNA (1997)

Listeria monocytogenes is a gram-positive, facultative intracellular bacterium that enters the cytoplasm of infected cells and spreads directly into neighboring cells without encountering the extracellular environment. Cytoplasmic L. monocytogenes efficiently presents secreted proteins to the major histocompatibility complex class I pathway which can stimulate protective T-cell-mediated immune responses. We have used a cottontail rabbit papillomavirus (CRPV) rabbit model to test the ability of recombinant L. monocytogenes strains secreting the viral E1 protein (E1-rLm) to protect outbred rabbits against CRPV- and CRPV DNA-induced tumors. CRPV infection of outbred rabbits serves as a model for oncogenic papillomaviruses since CRPV-induced papillomas progress with high frequency to malignant carcinoma. Rabbits were vaccinated with wild-type L. monocytogenes or E1-rLm and then challenged with CRPV or viral DNA. In contrast to 0% papilloma regression in control animals, 77% of E1-rLm-vaccinated rabbits generated protective immunity that controlled and induced complete regression of tumors induced by CRPV. Latent viral DNA was not detected at 71% of the papilloma regression sites examined 4.5 months postregression. E1-rLm responder rabbits were completely resistant to papilloma formation from viral DNA. In contrast to controls, peripheral blood mononuclear cells from E1-rLm responder rabbits were able to proliferate in response to in vitro E1 stimulation. These results indicate that E1-rLm immunization generated a systemic anti-CRPV E1 cell-mediated immune response which protected outbred rabbits from tumors induced by CRPV or CRPV DNA challenge.
An analysis of data corruption in the storage stack (2008)

An important threat to reliable storage of data is silent data corruption. In order to develop suitable protection mechanisms against data corruption, it is essential to understand its characteristics. In this article, we present the first large-scale study of data corruption. We analyze corruption instances recorded in production storage systems containing a total of 1.53 million disk drives, over a period of 41 months. We study three classes of corruption: checksum mismatches, identity discrepancies, and parity inconsistencies. We focus on checksum mismatches since they occur the most. We find more than 400,000 instances of checksum mismatches over the 41-month period. We find many interesting trends among these instances, including: (i) nearline disks (and their adapters) develop checksum mismatches an order of magnitude more often than enterprise-class disk drives, (ii) checksum mismatches within the same disk are not independent events and they show high spatial and temporal locality, and (iii) checksum mismatches across different disks in the same storage system are not independent. We use our observations to derive lessons for corruption-proof system design.
Activation of Protein Kinase A During Human Sperm Capacitation and Acrosome Reaction (2002)

Spermatozoa undergo a variety of changes during their life that are prerequisites to their maturation and ability to fertilize eggs. Mammalian sperm capacitation and acrosome reaction are regulated by signal transduction systems involving cyclic adenosine monophosphate (cAMP) as a second messenger. This second messenger acts through the activation of protein kinase A (PKA) and indirectly regulates protein tyrosine phosphorylation. cAMP levels are controlled by a balance of phosphodiesterases (PDEs) and adenylyl cyclase (AC) enzymatic activities, which are responsible for its degradation and production, respectively. The aim of this study was to evaluate the possible relationship between the intracellular levels of cAMP and PDE and PKA activities during human sperm capacitation induced by fetal cord serum ultrafiltrate (FCSu) and acrosome reaction induced by calcium ionophore A23187. We report that PKA activity was higher in capacitating than in noncapacitating spermatozoa and that intracellular levels of cAMP decreased but that PDE activity remained constant during capacitation. The acrosome reaction induced by A23187 was associated with increases in cAMP and PKA activity but not in PDE activity. These results strongly suggest that net cAMP concentration is under the control of AC, since PDE activity is constant during sperm capacitation and the acrosome reaction. Moreover, the results suggest that low levels of cAMP are sufficient for capacitation and PKA activation and/or that the cAMP concentration measured in whole spermatozoa does not reflect the effective intracellular cAMP levels present in specific compartments of these cells.
Guidebook to Molecular Chaperones and Protein-Folding Catalysts (1997)

Abstract The precise shape of a protein is a crucial factor in its function. How do proteins become folded into the right conformation? Molecular chaperones and protein folding catalysts bind to developing polypeptides in the cytoplasm and ensure correct folding and transport. This Guidebook catalogues the latest information on nearly 200 of these molecules, including the important class of heat shock proteins; each entry is written by leading researchers in the field.
Smallpox and pan -Orthopox Virus Detection by Real-Time 3′-Minor Groove Binder TaqMan Assays on the Roche LightCycler and the Cepheid Smart Cycler Platforms (2004)

We designed, optimized, and extensively tested several sensitive and specific real-time PCR assays for rapid detection of both smallpox and pan-orthopox virus DNAs. The assays are based on TaqMan 3'-minor groove binder chemistry and were performed on both the rapid-cycling Roche LightCycler and the Cepheid Smart Cycler platforms. The hemagglutinin (HA) J7R, B9R, and B10R genes were used as targets for the variola virus-specific assays, and the HA and DNA polymerase-E9L genes were used as targets for the pan-orthopox virus assays. The five orthopox virus assays were tested against a panel of orthopox virus DNAs (both genomic and cloned) at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID). The results indicated that each assay was capable of detecting both the appropriate cloned gene and genomic DNA. The assays showed no cross-reactivity to the 78 DNAs in the USAMRIID bacterial cross-reactivity panel. The limit of detection (LOD) of each assay was determined to be between 12 and 25 copies of target DNA. The assays were also run against a blind panel of DNAs at the Centers for Disease Control and Prevention (CDC) on both the LightCycler and the Smart Cycler. The panel consisted of eight different variola virus isolates, five non-variola virus orthopox virus isolates, two varicella-zoster virus isolates, and one herpes simplex virus isolate. Each sample was tested in triplicate at 2.5 ng, 25 pg, 250 fg, and 2.5 fg, which represent 1.24 x 10(7), 1.24 x 10(5), 1.24 x 10(3), and 1.24 x 10(1) genome equivalents, respectively. The results indicated that each of the five assays was 100% specific (no false positives) when tested against both the USAMRIID panels and the CDC blind panel. With the CDC blind panel, the LightCycler was capable of detecting 96.2% of the orthopox virus DNAs and 93.8% of the variola virus DNAs. The Smart Cycler was capable of detecting 92.3% of the orthopox virus DNAs and between 75 and 93.8% of the variola virus DNAs. However, all five assays had nearly 100% sensitivity on both machines with samples above the LOD (>12 gene copies). These real-time PCR assays represent a battery of tests to screen for and confirm the presence of variola virus DNA. The early detection of a smallpox outbreak is crucial whether the incident is an act of bioterrorism or an accidental occurrence.
Crystal Structures Of The Helix-Loop-Helix Calcium-Binding Proteins (1989)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Phenotype correction in retinal pigment epithelium in murine mucopolysaccharidosis VII by adenovirus-mediated gene transfer. (1995)

We have studied the use of adenovirus-mediated gene transfer to reverse the pathologic changes of lysosomal storage disease caused by beta-glucuronidase deficiency in the eyes of mice with mucopolysaccharidosis VII. A recombinant adenovirus carrying the human beta-glucuronidase cDNA coding region under the control of a non-tissue-specific promoter was injected intravitreally or subretinally into the eyes of mice with mucopolysaccharidosis VII. At 1-3 weeks after injection, the treated and control eyes were examined histochemically for beta-glucuronidase expression and histologically for phenotypic correction of the lysosomal storage defect. Enzymatic expression was detected 1-3 weeks after injection. Storage vacuoles in the retinal pigment epithelium (RPE) were still present 1 week after gene transfer but were reduced to undetectable levels by 3 weeks in both intravitreally and subretinally injected eyes. There was minimal evidence of ocular pathology associated with the viral injection. These data indicate that adenovirus-mediated gene transfer to the eye may provide for adjunctive therapy for lysosomal storage diseases affecting the RPE in conjunction with enzyme replacement and/or gene therapies for correction of systemic disease manifestations. The data also support the view that recombinant adenovirus may be useful as a gene therapy vector for retinal degenerations that result from a primary genetic defect in the RPE cells.
Nanotailoring of polyurethane adhesive by polyhedral oligomeric silsesquioxane (POSS) (2006)

Abstract The development and commercialization of nanoparticles such as nanoclays (NCs), carbon nanotubes (CNTs) and polyhedral oligomeric silsesquioxanes (POSS) offers new possibilities to tailor adhesives at the nanoscale. Four types of POSS, with reactive mono-functional groups of isocyanatopropyl, glycidoxypropyl, aminoethyl and non-reactive octaphenyl, were incorporated in concentrations of 1, 3 and 5 wt% into a polyurethane (PU)-based adhesive. Thermo-mechanical bulk properties were studied using dynamic mechanical analysis (DMA). Adhesive properties were characterized in shear and peel modes. Atomic force microscopy (AFM) was used to study the nanoscale morphology. DMA measurements indicated that the neat PU possessed a glass transition temperature (T g) of ≈ 30°C. The T g of PU/POSS-glycidoxypropyl nanocomposite adhesive increased gradually with POSS concentration to 50°C for 5 wt%. PU/POSS-octaphenyl nanocomposite adhesive exhibited an increased T g by 10°C for 5 wt%. The incorporation of POSS-isocyanatopropyl in the PU had no effect on the T g. With respect to shear properties of POSS-octaphenyl-, POSS-isocyanatopropyl- and POSS-glycidoxypropyl-based PU nanocomposite adhesives, shear strength improved by 230, 178 and 137%, respectively, compared to neat PU. POSS-aminoethyl exhibited lower shear and peel strengths, while POSS-isocyanatopropyl provided the best balance of both higher shear and peel strengths compared to neat PU. It was concluded that the grafted functional group on the POSS and its reactivity with the PU network components were the decisive factors with respect to the thermo-mechanical, morphological and adhesive properties of the resulting nanocomposite adhesives. Consequently, the POSS/polyurethane based nanocomposite adhesives could be tailored for a large range of applications. Keywords: NANOTAILORINGPOLYHEDRAL OLIGOMERIC SILSESQUIOXANE (POSS)DYNAMIC MECHANICAL ANALYSISATOMIC FORCE MICROSCOPY
Dropout-GAN: Learning from a Dynamic Ensemble of Discriminators (2018)

We propose to incorporate adversarial dropout in generative multi-adversarial networks, by omitting or dropping out, the feedback of each discriminator in the framework with some probability at the end of each batch. Our approach forces the single generator not to constrain its output to satisfy a single discriminator, but, instead, to satisfy a dynamic ensemble of discriminators. We show that this leads to a more generalized generator, promoting variety in the generated samples and avoiding the common mode collapse problem commonly experienced with generative adversarial networks (GANs). We further provide evidence that the proposed framework, named Dropout-GAN, promotes sample diversity both within and across epochs, eliminating mode collapse and stabilizing training.
Cardiac glycosides stimulate Ca2+ increases and apoptosis in androgen-independent, metastatic human prostate adenocarcinoma cells. (2000)

Cardiac glycosides are used clinically to increase contractile force in patients with cardiac disorders. Their mechanism of action is well established and involves inhibition of the plasma membrane Na+/K+-ATPase, leading to alterations in intracellular K+ and Ca(2+) levels. Here, we report that the cardiac glycosides oleandrin, ouabain, and digoxin induce apoptosis in androgen-independent human prostate cancer cell lines in vitro. Cell death was associated with early release of cytochrome c from mitochondria, followed by proteolytic processing of caspases 8 and 3. Oleandrin also promoted caspase activation, detected by cleavage poly(ADP-ribose) polymerase and hydrolysis of a peptide substrate (DEVD-pNA). Comparison of the rates of apoptosis in poorly metastatic PC3 M-Pro4 and highly metastatic PC3 M-LN4 subclones demonstrated that cell death was delayed in the latter because of a delay in mitochondrial cytochrome c release. Single-cell imaging of intracellular Ca(2+) fluxes demonstrated that the proapoptotic effects of the cardiac glycosides were linked to their abilities to induce sustained Ca(2+) increases in the cells. Our results define a novel activity for cardiac glycosides that could prove relevant to the treatment of metastatic prostate cancer.
The Involvement of TNF-α-Related Apoptosis-Inducing Ligand in the Enhanced Cytotoxicity of IFN-β-Stimulated Human Dendritic Cells to Tumor Cells (2001)

TNF-alpha-related apoptosis-inducing ligand (TRAIL) is characterized by its preferential induction of apoptosis of tumor cells but not normal cells. Dendritic cells (DCs), besides their role as APCs, now have been demonstrated to exert cytotoxicity or cytostasis on some tumor cells. Here, we report that both human CD34(+) stem cell-derived DCs (CD34DCs) and human CD14(+) monocyte-derived DCs (MoDCs) express TRAIL and exhibit cytotoxicity to some types of tumor cells partially through TRAIL. Moderate expression of TRAIL appeared on CD34DCs from the 8th day of culture and was also seen on freshly isolated monocytes. The level of TRAIL expression remained constant until DC maturation. TRAIL expression on immature CD34DCs or MoDCs was greatly up-regulated after IFN-beta stimulation. Moreover, IFN-beta could strikingly enhance the ability of CD34DCs or MoDCs to kill TRAIL-sensitive tumor cells, but LPS did not have such an effect. The up-regulation of TRAIL on IFN-beta-stimulated DCs partially contributed to the increased cytotoxicity of DCS: Pretreatment of TRAIL-sensitive tumor cells with caspase-3 inhibitor could significantly increase their resistance to the cytotoxicity of IFN-beta-stimulated DCS: In contrast, NF-kappaB inhibitor could significantly increase the sensitivity of tumor cells to the killing by nonstimulated or LPS-stimulated DCS: Our studies demonstrate that IFN-beta-stimulated DCs are functionally cytotoxic. Thus, an innate mechanism of DC-mediated antitumor immunity might exist in vivo in which DCs act as effectors to directly kill tumor cells partially via TRAIL. Subsequently, DCs act as APCs involved in the uptake, processing, and presentation of apoptotic tumor Ags to cross-prime CD8(+) CTL cells.
The Protein Phosphatase Activity of PTEN Regulates Src Family Kinases and Controls Glioma Migration (2008)

Phosphatase and tensin homologue deleted on chromosome 10 (PTEN) is mutated or lost in 60% to 70% of advanced gliomas and is associated with malignant phenotypic changes such as migration, which contribute to the morbidity and mortality of this disease. Most of the tumor suppressor function of PTEN has been attributed to its ability to dephosphorylate the second messenger, phosphatidylinositol 3,4,5-triphosphate, resulting in the biological control of the phosphatidylinositol 3-kinase (PI3K)/AKT pathway. Despite recent work suggesting that the protein phosphatase activity of PTEN controls glioma cell migration, the mechanisms by which this occurs are unclear. Herein, we show using glioma cell lines (U87MG and U373MG) stably transfected with wild-type PTEN or catalytically altered mutants of PTEN that PTEN controls integrin-directed migration in a lipid phosphatase, PI3K/AKT-independent manner. Confirming this observation, we show that the stable overexpression of COOH-terminal Src kinase, the physiologic negative regulator of SRC family kinases (SFK), or treatment with the SFK inhibitor PP1 abrogates glioma migration. The results provide direct evidence that the downstream effect of the protein phosphatase activity of PTEN is to suppress SFK and FYN, and to regulate RAC-GTPase activity after alpha(v) integrin stimulation. Furthermore, studying vitronectin-directed migration using (a) Fyn small interfering RNA and (b) astrocytes from Fyn heterozygous (+/-) mice, Pten heterozygous (+/-) mice, Pten and Fyn double heterozygous (+/-) mice, or Fyn knockout (-/-) mice confirmed a role of FYN in alpha(v) integrin-mediated haptotaxis in glial cells. Our combined results provide direct biochemical and genetic evidence that PTEN's protein phosphatase activity controls FYN kinase function in glioma cells and regulates migration in a PI3K/AKT-independent manner.