gebhart/patrepeval huggingface dataset:
Hormonal carcinogenesis (2000)

Hormone-related cancers, namely breast, endometrium, ovary, prostate, testis, thyroid and osteosarcoma, share a unique mechanism of carcinogenesis. Endogenous and exogenous hormones drive cell proliferation, and thus the opportunity for the accumulation of random genetic errors. The emergence of a malignant phenotype depends on a series of somatic mutations that occur during cell division, but the specific genes involved in progression of hormone-related cancers are currently unknown. In this review, the epidemiology of endometrial cancer and breast cancer are used to illustrate the paradigms of hormonal carcinogenesis. Then, new strategies for early detection and prevention of hormonal carcinogenesis are discussed. This includes developing polygenic models of cancer predisposition and the further development of safe and effective chemopreventives that block target sequence activity. We developed polygenic models for breast and prostate cancer after hypothesizing that functionally relevant sequence variants in genes involved in steroid hormone metabolism and transport would act together, and also interact with well-known hormonally related risk factors, to define a high-risk profile for cancer. A combination of genes each with minor variation in expressed activity could provide a degree of separation of risk that would be clinically useful as they could yield a large cumulative difference after several decades. The genes included in the breast cancer model are the 17beta-hydroxysteroid dehydrogenase 1 (HSD17B1) gene, the cytochrome P459c17alpha (CYP17) gene, the aromatase (CYP19) gene, and the estrogen receptor alpha (ER) gene. The prostate cancer model includes the androgen receptor gene (AR), steroid 5alpha-reductase type II (SRD5A2), CYP17 and the 3beta hydroxysteroid dehydrogenase (HSD3B2) gene. We present data from our multi-ethnic cohort to support these models.
Fas antigen and p55 TNF receptor signal apoptosis through distinct pathways. (1994)

The Fas Ag and the p55 TNF receptor (TNF-R1) are related molecules that can signal apoptosis. Some tumor cell lines are selectively killed by Fas activation and others by TNF-R1 activation even though both receptors are often co-expressed. TNF-R1-mediated cytotoxicity can be selectively inhibited under conditions in which Fas-mediated cell death is not affected. Activation of both receptors results in synergistic signaling of apoptosis. These results indicate that different biochemical pathways are activated by Fas and TNF-R1. Combination treatment with agonists of Fas and TNF-R1 may have therapeutic potential.
Image Denoising Methods. A New Nonlocal Principle (2010)

The search for efficient image denoising methods is still a valid challenge at the crossing of functional analysis and statistics. In spite of the sophistication of the recently proposed methods, most algorithms have not yet attained a desirable level of applicability. All show an outstanding performance when the image model corresponds to the algorithm assumptions but fail in general and create artifacts or remove fine structures in images. The main focus of this paper is, first, to define a general mathematical and experimental methodology to compare and classify classical image denoising algorithms and, second, to propose a nonlocal means (NL-means) algorithm addressing the preservation of structure in a digital image. The mathematical analysis is based on the analysis of the “method noise,” defined as the difference between a digital image and its denoised version. The NL-means algorithm is proven to be asymptotically optimal under a generic statistical image model. The denoising performance of all considered methods is compared in four ways; mathematical: asymptotic order of magnitude of the method noise under regularity assumptions; perceptual-mathematical: the algorithms artifacts and their explanation as a violation of the image model; quantitative experimental: by tables of $L^2$ distances of the denoised version to the original image. The fourth and perhaps most powerful evaluation method is, however, the visualization of the method noise on natural images. The more this method noise looks like a real white noise, the better the method.
Flavonoids stimulate Cl conductance of human airway epithelium in vitro and in vivo (1998)

The ability of the flavonoids genistein, apigenin, kaempferol, and quercetin to activate cystic fibrosis transmembrane conductance regulator-mediated Cl currents in human airway epithelium was investigated. We used the patch-clamp technique on single Calu-3 cells, transepithelial measurements in Calu-3 monolayers, and in vivo measurements of nasal potential difference. All flavonoids stimulated Cl currents in transepithelial experiments dose dependently. Half-maximal stimulatory concentrations were kaempferol (5.5 +/- 1.7 microM) </= apigenin (11.2 +/- 2.1 microM) </= genistein (13.6 +/- 3.5 microM) </= quercetin (22.1 +/- 4.5 microM). Stimulation of monolayers with forskolin significantly increased their sensitivity to flavonoids: kaempferol (2.5 +/- 0.7 microM) </= apigenin (3.4 +/- 0.9 microM) </= quercetin (4.1 +/- 0.7 microM) </= genistein (6.9 +/- 2.2 microM). Forskolin pretreatment significantly reduced the Hill coefficient (nH) for all flavonoids. Control monolayers showed nH = 2.00 +/- 0.21 (all flavonoids combined), and forskolin-stimulated monolayers showed nH = 1.07 +/- 0.07, which was not different among the flavonoids. These data imply that the activation kinetics and the binding site(s) for flavonoids were significantly altered by forskolin stimulation. In whole cell patch-clamp experiments, maximal flavonoid-stimulated currents (percentage of forskolin-stimulated currents) were apigenin (429 +/- 86%) >/= kaempferol (318 +/- 45%) >/= genistein (258 +/- 20%) = quercetin (256 +/- 26%). Stimulation of the currents was caused by an increase in channel open probability. No other Cl conductances contributed significantly to the flavonoid-activated Cl currents in Calu-3 cells. In vivo, flavonoids significantly stimulated nasal potential difference by, on average, 27.8% of isoproterenol responses.
Dual hard mask process for low-k porous organosilica dielectric in copper dual damascene interconnect fabrication (2001)

Using a low-k porous organosilisesqueoxane film, ALCAP/sup TM/-S with k=2.1, dual hard mask (DHM) process is proposed for Cu dual damascene interconnect (DDI) formation. The porous organosilica film has very high etching rate relative to those of the hard mask (HM) and/or etch-stop materials. SiO/sub 2//SiC is one of the best combinations for the DHM, in which the lower hard mask of SiC remained after metal CMP and protects the porous film from the via-etching damage in misalignnent region between the via-hole and the buried Cu-line. Applying in-situ resist-ashing with N/sub 2//H/sub 2/ gas, 0.4 /spl mu/m-pitched dual damascene structure is successfully fabricated. Increment of the dielectric constant is suppressed within 5% (k=2.2) after the Cu-interconnect fabrication, confirming that the DHM low-damage process is applicable for the Cu DDI fabrication in ultra low-k, porous organosilica systems.
Eosinophils: receptors and mediators in hypersensitivity. (1989)

The presence of receptors for IgE on eosinophils has drawn attention to their direct participation in IgE-dependent hypersensitivity reactions. Surface IgE antibodies were detected on eosinophils from parasite-infected or allergic patients. The addition of the specific antigen or anti-IgE antibodies to such purified eosinophils induced the release of eosinophil peroxidase (EPO) and major basic protein (MBP), but not of eosinophil cationic protein (ECP). In contrast, ECP was detected after the addition of anti-IgG antibodies. Moreover, PAF-acether was only produced after IgE-dependent activation of hypodense eosinophils but not after IgG triggering. These results suggest a selectivity in the mediators (pre-formed and newly formed) released in response to IgE- or IgG-dependent activation of human hypodense eosinophils. Associated with preliminary findings obtained by using electron microscopy and immunogold staining, they bring new information concerning the mechanisms of release of eosinophil mediators. Finally, they underline the essential role of eosinophils in hypersensitivity reactions.
CMP solutions for 3D-NAND staircase CMP (2015)

As NAND technology is moved from 2D to 3D, there are a few CMP steps to be newly added such as channel poly CMP and staircase (or ILD) CMP. Channel poly CMP is to polish many materials simultaneously such as SiN, oxide and poly-Si therefore it needs individual material rate tunability to meet final topography requirement. Staircase CMP process is identical to conventional ILD or IMD CMP but it needs high planarization efficiency (PE) and fast removal rate (RR) in order to meet higher step height and huge oxide removal amount. This study is to deal with slurries of 3D-NAND device integration having the rate tunability of various materials for channel poly and the high performance on PE and oxide rate for staircase CMP.
Therapeutic Targeting of Anaplastic Lymphoma Kinase in Lung Cancer: A Paradigm for Precision Cancer Medicine (2015)

The anaplastic lymphoma kinase (ALK) receptor tyrosine kinase was initially discovered as a component of the fusion protein nucleophosmin (NPM)-ALK in anaplastic large-cell lymphoma (ALCL). Genomic alterations in ALK, including rearrangements, point mutations, and genomic amplification, have now been identified in several malignancies, including lymphoma, non-small cell lung cancer (NSCLC), neuroblastoma, inflammatory myofibroblastic tumor, and others. Importantly, ALK serves as a validated therapeutic target in these diseases. Several ALK tyrosine kinase inhibitors (TKI), including crizotinib, ceritinib, and alectinib, have been developed, and some of them have already been approved for clinical use. These ALK inhibitors have all shown remarkable clinical outcomes in ALK-rearranged NSCLC. Unfortunately, as is the case for other kinase inhibitors in clinical use, sensitive tumors inevitably relapse due to acquired resistance. This review focuses on the discovery, function, and therapeutic targeting of ALK, with a particular focus on ALK-rearranged NSCLC.
Three-dimensional Fourier gravity inversion with arbitrary density contrast (1992)

Abstract The use of variable-density contrasts in gravity inversion has gained increasing importance in recent years due to the necessity of constructing more realistic models of geophysical structures such as sedimentary basins. Linear, quadratic, and exponential variations, either in the space or in the frequency domain, are the basis of several methods. See, among others, the papers by Granser (1987), Chai and Hinze (1988), Reamer and Ferguson (1989), and Rao et al. (1990). Guspi (1990) used polynomial density-depth functions for inverting gravity anomalies into 2-D polygons in the space domain.
Gröbner Bases and Numerical Analysis (1998)

By concentrating on system solving, numerical interpolation, integration, and differentiation, we show the use of Gröbner bases in numerical analysis. The ideas of the factorizing Gröbner algorithm, of system solving by solving Eigenproblems, of computing interpolation polynomials with algorithms for computing Gröbner bases, and of constructing numerical integration and differentiation formulas by Gröbner bases are presented. A short section on Gröbner bases computation using floating point arithmetics is included.
Analysis of the Mechanisms Mediating Tumor-Specific Changes in Gene Expression in Human Liver Tumors (2008)

There is widespread interest in efficient characterization of differences between tumor and normal samples. Here, we show an effective methodology for genome-scale characterization of tumors. Using matched normal and tumor samples from liver cancer patients, as well as non-cancer-related normal liver tissue, we first determined changes in gene expression as monitored on RNA expression arrays. We identified several hundred mRNAs that were consistently changed in the tumor samples. To characterize the mechanisms responsible for creation of the tumor-specific transcriptome, we performed chromatin immunoprecipitation on microarray experiments to assay binding of RNA polymerase II, H3me3K27, and H3me3K9 and DNA methylation in 25,000 promoter regions. These experiments identified changes in active and silenced regions of the genome in the tumor cells. Finally, we used a "virtual comparative genomic hybridization" method to identify copy number alterations in the tumor samples. Through comparison of RNA polymerase II binding, chromatin structure, DNA methylation, and copy number changes, we suggest that the major contributor to creation of the liver tumor transcriptome was changes in gene copy number.
Primary Structure of a Human Glandular Kallikrein Gene (1987)

To isolate a human glandular kallikrein gene, a human genomic library was screened with a probe made from a mouse kallikrein cDNA (pMK-1). Overlapping clones were obtained and nucleotide sequence determination showed that they together contained a human glandular preprokallikrein gene, hGK-1, of 5.2 kb. The gene encoded a unique preproprotein of 261 amino acids. The sequence of the mature 237-amino-acid protein had 66% homology with the sequence predicted for human kallikrein synthesized in the pancreas, kidney, and salivary gland. Moreover, it had even stronger homology (78%) with human prostate-specific antigen. The latter lacks an aspartic acid residue essential for kallikrein-specific cleavage, whereas the sequence of this new protein had all of the attributes needed to confer kallikrein-like specificity. Southern blotting indicated that the number of glandular kallikrein genes in man could be limited to three, a situation very different from mouse and rat, which each have a large multigene family. Furthermore, unlike kallikrein genes in the mouse, hGK-1 was not closely linked to other human kallikrein genes. In other respects the structure of the human kallikrein gene resembled that in mouse: coding sequences in the five exons were organized similarly, homology was higher with other members of the kallikrein gene family in the same species, and the three key amino acid residues required by serine proteases for their catalytic activity, together with the residue that confers kallikrein-specific cleavage, were conserved and located on different exons. Thus, if hGK-1 is expressed, its product represents a new, and possibly the only other enzyme with true kallikrein-like specificity in man.
Analytical model of Raman gain effects in massivewavelength division multiplexed transmission systems (1998)

An analytical model to calculate stimulated Raman scattering (SRS) effects in a wavelength division multiplexed transmission system is presented. The analytical solution is valid for any input power distribution and fully accounts for the gain saturation effects. It is found that the spectral distortion introduced by SRS is always linear on a decibel/nanometre scale and depends solely on the total input power, not on the input power distribution.
The Epidemiology of Chlamydia trachomatis within a Sexually Transmitted Diseases Core Group (1996)

Female sex workers in Nairobi were prospectively evaluated for risk factors of incident Chlamydia trachomatis infection. Independent risk factors included cervical ectopy (P=.007), gonococcal infection (P=.002), human immunodeficiency virus (HIV) seropositivity (P=.003), HIV seroconversion (P=.001), and duration of prostitution (P=.002). Eighteen different C. trachomatis outer membrane protein (omp1) genotypes were identified, with the allelic composition of the C. trachomatis population changing significantly over time (P=.005). Seventeen of 19 reinfections > or = 6 months apart were with different C. trachomatis omp1 genotypes. Women with HIV infection had an increased proportion of visits with C. trachomatis infection (P=.001) and an increased risk of reinfection (P=.008). Overall, the data demonstrate significant fluctuations in the genotype composition of the C. trachomatis population and a reduced rate of same-genotype reinfection consistent with the occurrence of strain-specific immunity.
Current treatment of oral candidiasis: A literature review (2014)

Candidiasis or oral candidosis is one of the most common human opportunistic fungal infections of the oral cavity. This pathology has a wide variety of treatment which has been studied until these days. The present study offers a literature review on the treatment of oral candidiasis, with the purpose of establish which treatment is the most suitable in each case. Searching the 24 latest articles about treatment of candidiasis it concluded that the incidence depends on the type of the candidiasis and the virulence of the infection. Although nystatin and amphotericin b were the most drugs used locally, fluconazole oral suspension is proving to be a very effective drug in the treatment of oral candidiasis. Fluconazole was found to be the drug of choice as a systemic treatment of oral candidiasis. Due to its good antifungal properties, its high acceptance of the patient and its efficacy compared with other antifungal drugs. But this drug is not always effective, so we need to evaluate and distinguish others like itraconazole or ketoconazole, in that cases when Candida strains resist to fluconazole. Key words:Candidiasis, treatment, miconazole, fluconazole, nystatin.
Topographical analysis of antigenic determinants on envelope glycoprotein V3 (E) of Japanese encephalitis virus, using monoclonal antibodies (1983)

Ten monoclonal antibodies directed against envelope glycoprotein V3 (E) of Japanese encephalitis virus were obtained. They were characterized by hemagglutination inhibition (HI), neutralization, and enzyme-linked immunosorbent assay and divided into four types: flavivirus-cross-reactive HI and non-neutralizing antibody (group 1), subgroup-specific HI and non-neutralizing antibody (group 2), low HI and neutralizing antibody (group 3), and non-HI and neutralizing antibody (groups 4 and 5, respectively). Competitive binding assays were performed to analyze the topography of antigenic determinants by enzyme-linked immunosorbent assay. The results of the competitive binding assay separated non-HI and neutralizing antibody into groups 4 and 5, respectively, and demonstrated the existence of at least five distinct antigenic determinants on V3. The site of group 1 was distinct from any other site. The sites of groups 2 and 3 seemed to be located close together. Our results suggest the following relationship between HI and neutralization: (i) The HI sites are separated from the neutralization sites, and (ii) there are two distinct HI sites, one of which is flavivirus cross-reactive, the other subgroup specific.
Effects of morphine, nalbuphine and pentazocine on gastric emptying of indigestible solids. (1998)

The effects of morphine (CAS 57-27-2), nalbuphine (CAS 20594-83-6) and pentazocine (CAS 359-83-1) on gastric emptying of indigestible solids were studied. In rats, which were fasted for 24 h, either morphine, nalbuphine, pentazocine or saline was injected intraperitoneally, and ten steel balls (1.0 mm in diameter) were inserted into the stomach. At 3 h, the number of balls which had passed into the small intestine was counted. If these drugs inhibited gastric emptying, naloxone was injected concurrently to study the mechanisms of the inhibitory effect. Morphine, nalbuphine and pentazocine significantly inhibited gastric emptying (ED50:0.041 [95% confidence interval: 0.0078-0.14] mg kg-1, 0.0012 [0.00037-0.0081] mg kg-1 and 0.81 [0.41-1.30] mg kg-1, respectively). Naloxone 0.3 mg kg-1 antagonized the inhibitory effect of both morphine 1.3 mg kg-1 (ED75) and nalbuphine 0.005 mg kg-1 (ED75). In contrast, naloxone 0.3 or 1.0 mg kg-1 did not antagonize the effect of pentazocine 1.9 mg kg-1 (ED75), but a higher dose of naloxone (3.0 mg kg-1) did so. Therefore, in the rat, morphine, nalbuphine and pentazocine inhibit gastric emptying of indigestible solids, and it is likely that morphine and nalbuphine inhibit the emptying through the same opioid receptor, whereas pentazocine does so through a different receptor interaction.
Double Dirac cones in triangular-lattice metamaterials (2012)

It is shown by tight-binding approximation and group theory that a double Dirac cone, or a pair of two identical Dirac cones, of the electromagnetic dispersion relation can be created in the Brillouin zone center by accidental degeneracy of E(1) and E(2) modes in triangular-lattice metamaterials of C(6v) symmetry. The Dirac point thus obtained is equivalent to a zero-index system, so we can expect unique optical propagation phenomena such as constant-phase waveguides and lenses of arbitrary shapes. Zitterbewegung is also expected without disturbance due to an auxiliary quadratic dispersion surface, which is present for other combinations of mode symmetries to materialize the Dirac cones. To the best of the author's knowledge, this is the first prediction of the presence of a double Dirac cone in metamaterials.
Natural History of Hepatocellular Carcinoma and Current Treatment Options (2008)

Hepatocellular carcinoma (HCC) is the most frequent primary liver cancer and the most severe complication of chronic liver disease. The annual number of new cases worldwide is approximately 550,000, representing more than 5% of human cancers and is the third leading cause of cancer-related deaths. The stages of the malignancy as well as the severity of the underlying liver disease are essential factors in planning the therapeutic approach. Curative treatment options are represented mainly by surgery (ie, resection or transplantation), but most patients are not candidates for a curative option, and only palliative treatment could be given to these patients. Among palliative treatments, only chemoembolization has been proven to be effective, but other options are currently being investigated. Major risk factors for HCC are well known and are dependent on the geographic area. In Europe, the United States, and Japan, the main risk factors are liver cirrhosis, hepatitis B and C virus, alcohol, and tobacco; in contrast, in Africa and Asia, these factors are hepatitis B and C virus, tobacco use, and aflatoxin exposure. Cirrhosis from any cause is a predisposing factor for HCC and could be considered as a premalignant condition. The present concept of carcinogenesis in HCC is a multistage process. This article describes the natural history of HCC and discusses the various treatment options available at present.