gebhart/patrepeval huggingface dataset:
Papillomaviruses Causing Cancer: Evasion From Host-Cell Control in Early Events in Carcinogenesis (2000)

During the past 20 years, several types of human papillomaviruses (HPVs) have been identified that cause specific types of cancers. The etiology of cancer of the cervix has been linked to several types of HPV, with a high preponderance of HPV16. The role of these virus infections has been established 1) by the regular presence of HPV DNA in the respective tumor biopsy specimens, 2) by the demonstration of viral oncogene expression (E6 and E7) in tumor material, 3) by the identification of transforming properties of these genes, 4) by the requirement for E6 and E7 expression for maintaining the malignant phenotype of cervical carcinoma cell lines, 5) by the interaction of viral oncoproteins with growth-regulating host-cell proteins, and 6) by epidemiologic studies pointing to these HPV infections as the major risk factor for cervical cancer development. In addition to cancer of the cervix, a major proportion of anal, perianal, vulvar, and penile cancers appears to be linked to the same HPV infections. In addition, close to 20% of oropharyngeal cancers contain DNA from the same types of HPV. Recent evidence also points to a possible role of other HPV infections in squamous cell carcinomas of the skin. This review covers recent developments in understanding molecular mechanisms of HPV carcinogenesis, mainly discussing functions of viral oncoproteins and the regulation of viral oncogenes by host-cell factors. Modifications in host-cell genes, most likely engaged in the control of HPV gene expression in proliferating cells, emerge as important events in HPV-mediated carcinogenesis.
Fractionation of lignocellulosics by steam-aqueous pretreatments (1987)

Abstract Physical processing or pretreatment of lignocellulosics concerns the ultrastructural modification of materials such as wood, straw and bagasse. The substrates produced can be subsequently converted by chemicals. The various pretreatment options will be discussed in the light of the ultrastructural, polymeric and chemical modifications that are obtained. The processes can be classified as follows: (i) steam; (ii) aqueous; and (iii) organosolvolysis treatments. All of these have their antecedents in the thermomechanical processes developed by the pulp and paper or fibreboard industries. Sequential application of thermomechanical technology leads to fractionation of the substrate into the major polymeric fractions: cellulose, hemicellulose and lignin in varying degrees of modification. A number of pretreatment concepts are now at a commercial scale and are being applied to produce foodstuffs from lignocellulosics for use by ruminant animals. The same techniques are being piloted in the energy and chemicals from lignocellulosics field.
Dispersive magnetometry with a quantum limited SQUID parametric amplifier (2011)

There is currently fundamental and technological interest in measuring and manipulating nanoscale magnets, particularly in the quantum coherent regime. To observe the dynamics of such systems one requires a magnetometer with not only exceptional sensitivity but also high gain, wide bandwidth, and low backaction. We demonstrate a dispersive magnetometer consisting of a two-junction superconducting quantum interference device (SQUID) in parallel with an integrated, lumped-element capacitor. Input flux signals are encoded as a phase modulation of the microwave drive tone applied to the magnetometer, resulting in a single quadrature voltage signal. For strong drive power, the nonlinearity of the resonator results in quantum limited, phase sensitive parametric amplification of this signal, which improves flux sensitivity at the expense of bandwidth. Depending on the drive parameters, the device performance ranges from an effective flux noise of 0.29 $\ensuremath{\mu}{\ensuremath{\Phi}}_{0}$Hz${}^{\ensuremath{-}1/2}$ and 20 MHz of signal bandwidth to a noise of 0.14 $\ensuremath{\mu}{\ensuremath{\Phi}}_{0}$Hz${}^{\ensuremath{-}1/2}$ and a bandwidth of 0.6 MHz. These results are in excellent agreement with our theoretical model.
T cells with regulatory activity in hepatitis C virus infection: what we know and what we don’t (2008)

The mechanism behind the apparent lack of effective antiviral immune response in patients with chronic hepatitis C virus (HCV) infection is poorly understood. Although multiple levels of abnormalities have been identified in innate and adaptive immunity, it remains unclear if any of the subpopulations of T cells with regulatory capacity (Tregs) contribute to the induction and maintenance of HCV persistence. In this review, we summarize the current knowledge about Tregs as they relate to HCV infection.
Polymorphism of genes in the lipid metabolism pathway and the risk of biliary tract cancers: a population-based study in Shanghai, China (2005)

2557 Cancers of the biliary tract, encompassing the gallbladder, extrahepatic bile duct, and ampulla of Vater, are rare, but often fatal. Their etiology remains poorly understood, with gallstones being one of the few known risk factors. Since cholesterol supersaturation of the bile is an essential component of gallstone formation, variants of genes encoding cholesterol transport and metabolism may affect the function of lipoproteins, thereby increasing the risk of gallstones and biliary tract cancers. In a population-based case-control study conducted in Shanghai, China, we examined the role of genetic susceptibility related to lipid metabolism in biliary tract stone and cancer etiology. The study included 406 incident biliary tract cancer cases (235 gallbladder, 125 extrahepatic bile duct, 46 ampulla of Vater), 880 biliary tract stone cases (663 gallbladder, 217 bile duct), and 779 healthy controls randomly selected from the general population and frequency matched to cancer cases on age and sex. Genomic DNA extracted from buffy coat was used to genotype the following 14 single nucleotide polymorphisms (SNPs) of five genes using Taqman assays: arachidonate 5-lipoxygenase (ALOX5 IVS3+99), apolipoprotein B (ApoB T98I, P2739L, IVS23-79, IVS6+360), apolipoprotein E (ApoE IVS1+69), low-density lipoprotein receptor (LDLR 3’UTR, IVS9-30, R471, R744, IVS17-53, IVS17-42, 441), and lipoprotein lipase (LPL IVS5+948). The success rate of genotyping was > 98%, and the concordance of genotyping in duplicate samples was > 99%. All genotype frequencies were in Hardy-Weinberg equilibrium among population controls. Variants in two of the five genes were associated with biliary tract stones or cancers. Relative to individuals with the CC genotype of the ApoE IVS1+69 polymorphism those with the G allele (GC+GG genotypes) had a 2-fold (95% CI 1.3-3.1) and 2.5-fold (95% CI 1.2-5.1) risk of bile duct and ampulla of Vater cancers, respectively. These risks were more pronounced among men and among individuals without diabetes or with a lower body mass index (BMI ≤ 23 kg/m2). Among men, but not women, the ApoE IVS1+69 G variant was also associated with a significant excess risk of gallstones and gallbladder cancer. There was a suggestive association between LDLR IVS9-30 and bile duct cancer. Men who carried both high-risk alleles for ApoE IVS1+69 and LDLR IVS9-30 had a 5-fold risk of bile duct cancer (OR=5.34, 95% CI 2.1-13.8). These results suggest that the etiology of biliary tract stones and cancers involves a complex interplay of the ApoE gene, which encodes the ApoE protein that is essential for lipoprotein binding and cholesterol homeostasis, with other risk factors. Further studies are needed to confirm these results and clarify the underlying mechanisms.
The bacterial signal indole increases epithelial-cell tight-junction resistance and attenuates indicators of inflammation (2009)

Interkingdom signaling is established in the gastrointestinal tract in that human hormones trigger responses in bacteria; here, we show that the corollary is true, that a specific bacterial signal, indole, is recognized as a beneficial signal in intestinal epithelial cells. Our prior work has shown that indole, secreted by commensal Escherichia coli and detected in human feces, reduces pathogenic E. coli chemotaxis, motility, and attachment to epithelial cells. However, the effect of indole on intestinal epithelial cells is not known. Because intestinal epithelial cells are likely to be exposed continuously to indole, we hypothesized that indole may be beneficial for these cells, and investigated changes in gene expression with the human enterocyte cell line HCT-8 upon exposure to indole. Exposure to physiologically relevant amounts of indole increased expression of genes involved in strengthening the mucosal barrier and mucin production, which were consistent with an increase in the transepithelial resistance of HCT-8 cells. Indole also decreased TNF-alpha-mediated activation of NF-kappaB, expression of the proinflammatory chemokine IL-8, and the attachment of pathogenic E. coli to HCT-8 cells, as well as increased expression of the antiinflammatory cytokine IL-10. The changes in transepithelial resistance and NF-kappaB activation were specific to indole: other indole-like molecules did not elicit a similar response. Our results are similar to those observed with probiotic strains and suggest that indole could be important in the intestinal epithelial cells response to gastrointestinal tract pathogens.
Translocation of Analogues of the Antimicrobial Peptides Magainin and Buforin across Human Cell Membranes (2003)

Cationic antimicrobial peptides play important roles in innate immunity. Compared with extensive studies on peptide-bacteria interactions, little is known about peptide-human cell interactions. Using human cervical carcinoma HeLa and fibroblastic TM12 cells, we investigated the cellular uptake of fluorescent analogues of the two representative antimicrobial peptides magainin 2 and buforin 2 in comparison with the representative Arg-rich cell-penetrating Tat-(47-57) peptide (YGRKKRRQRRR). The dose, time, temperature, and energy dependence of translocation suggested that the three peptides cross cell membranes through different mechanisms. The magainin peptide was internalized within a time scale of tens of minutes. The cooperative concentration dependence of uptake suggested that the peptide forms a pore as an intermediate similar to the observations in model membranes. Furthermore, the translocation was coupled with cytotoxicity, which was larger for tumor HeLa cells. In contrast, the buforin peptide translocated within 10 min by a temperature-independent, less concentration-dependent passive mechanism without showing any significant cytotoxicity at the highest concentration investigated (100 microm). The uptake of the Tat peptide was proportional to the peptide concentration, and the concentration dependence was lost upon ATP depletion. The peptide exhibited a moderate cytotoxicity at higher concentrations. The time course did not show saturation even after 120 min. The buforin peptide, covalently attached to the 28-kDa green fluorescent protein, also entered cells, suggesting a potency of the peptide as a vector for macromolecular delivery into cells. However, the mechanism appeared to be different from that of the parent peptide.
Application of methylotrophic yeast Pichia pastoris in the field of food industry - A review (2009)

Since ancient times, the utilization of yeasts by the man has a great impact on the socio-economic development. After the advent of the technology of recombinant DNA, great advances have occurred due to the acquisition of strains of mutant yeasts in the field of applied research, and Saccharomyces cerevisiae has soon been outstanding as an interesting candidate for the expression of heterologous proteins of biotechnological interest. As the time goes by other alternative systems of expression have been shown because they have advantages over Saccharomyces cerevisiae. Among those new systems, Pichia pastoris is outstanding as methylotrophic yeast capable of growing in a culture medium containing methanol as the only source of carbon and energy. The induction of production of glycerol-3-phosphate dehydrogenase (GPD, NAD(+): oxido-redutase EC 1.1. 1.8) by Pichia pastoris was accomplished in the medium containing methanol. One of the most important key parameters in Pichia pastoris expression system is the methanol concentration. Bibliographic reviews on the Pichia pastoris production system have shown that the best culture conditions vary according to the strain used and/or kind of heterologous protein desired to be expressed. Therefore, we have sought to develop a system, involving expression of glycerol-3-phosphate dehydrogenase in the yeast Pichia pastoris, for generating sufficient quantities of the enzyme in order to asses its potential value for use in various food bioanalytical determination. Dehydrogenases have been widely used in the enzymatic assays of diverse composites of industrial interest, being enclosed among them glycerol and a number of important bioanalytical applications.
The distribution and migration of White-necked petrel, Pterodroma externa cervicalis, in the west area of North Pacific Ocean and the Japanese waters (1981)

The observations of occurrence of Pterodroma externa cervicalis were carried out in the west area of North Pacific Ocean during the several cruises by R. V. Hakuho Maru as follows: KH 74-2 (30 April to 26 June, 1974), KH 74-4 (6 November to 7 December, 1974), KH 75-3 (14 May to 2 June, 1975), KH 80-2 (25 April to 18 June, 1980), KH 80-3 (14 July to 6 September, 1980), and KH 80-4 (24 September to 13 October, 1980).1) P. externa cervicalis did not appear in the area of 30°N and northward in May and June, but this bird was found in the same area late in July. In August, the flocks of P, externa cervicalis (individual number of 2 to 15) associated with several species of tropical and subtropical sea birds, wedge-tailed shearwater Puffinus pacificus, sooty tern Sterna fuscata, white noddy Anous albus and common noddy Anous stolidus, occurred frequently in the east of Mariana Islands and they attacked the fish schools on water surface. And the flyings of solitary or two individuals of this bird scattered widely in the west area of North Pacific Ocean between 25°N and 35°N from September through November.2) P. externa cervicalis occurred in the area where the water temperature of sea surface ranged from 20.7°C to 31.4°C, and especially this bird distributed abundantly in the area between 27°C and 30°C.3) From those observations, it is concluded that some considerable number of P. externa cervicalis migrated regularly to the west area of North Pacific Ocean during the period from July through November.
Electrospun Zwitterionic Poly(Sulfobetaine Methacrylate) for Nonadherent, Superabsorbent, and Antimicrobial Wound Dressing Applications (2012)

Zwitterionic poly(sulfobetaine methacrylate) (PSBMA) has been well studied for its superhydrophilic and ultralow biofouling properties, making it a promising material for superabsorbent and nonadherent wound dressings. Electrospinning provides multiple desirable features for wound dressings, including high absorptivity due to high surface-area-to-volume ratio, high gas permeation, and conformability to contour of the wound bed. The goal of this work is to develop a fibrous membrane of PSBMA via electrospinning and evaluate its properties related to wound dressing applications. Being superhydrophilic, PSBMA fibers fabricated by a conventional electrospinning method would readily dissolve in water, whereas if cross-linker is added, the formation of hydrogel would prevent electrospinning. A three-step polymerization-electrospinning-photo-cross-linking process was developed in this work to fabricate the cross-linked electrospun PSBMA fibrous membrane. Such electrospun membrane was stable in water and exhibited high water absorption of 353% (w/w), whereas the PSBMA hydrogel only absorbed 81% water. The electrospun membrane showed strong resistance to protein adsorption and cell attachment. Bacterial adhesion studies using Gram negative P. aeruginosa and Gram positive S. epidermidis showed that the PSBMA electrospun membrane was also highly resistant to bacterial adhesion. The Ag(+)-impregnated electrospun PSBMA membrane was shown microbicidal, against both S. epidermidis and P. aeruginosa. Such electrospun PSBMA membrane is ideal for a novel type of nonadherent, superabsorbent, and antimicrobial wound dressing. The superior water absorption aids in fluid removal from highly exudating wounds while keeping the wound hydrated to support healing. Because of the resistance to protein, cell, and bacterial adhesion, the dressing removal will neither cause patients' pain nor disturb the newly formed tissues. The dressing also prevents the attachment of environmental bacteria and offers broad-spectrum antimicrobial activity. It is the first work to develop the water-stable electrospun PSBMA membrane, which has great potential for wound dressing and other applications.
Identification of urocortin III, an additional member of the corticotropin-releasing factor (CRF) family with high affinity for the CRF2 receptor (2001)

The corticotropin-releasing factor (CRF) family of neuropeptides includes the mammalian peptides CRF, urocortin, and urocortin II, as well as piscine urotensin I and frog sauvagine. The mammalian peptides signal through two G protein-coupled receptor types to modulate endocrine, autonomic, and behavioral responses to stress, as well as a range of peripheral (cardiovascular, gastrointestinal, and immune) activities. The three previously known ligands are differentially distributed anatomically and have distinct specificities for the two major receptor types. Here we describe the characterization of an additional CRF-related peptide, urocortin III, in the human and mouse. In searching the public human genome databases we found a partial expressed sequence tagged (EST) clone with significant sequence identity to mammalian and fish urocortin-related peptides. By using primers based on the human EST sequence, a full-length human clone was isolated from genomic DNA that encodes a protein that includes a predicted putative 38-aa peptide structurally related to other known family members. With a human probe, we then cloned the mouse ortholog from a genomic library. Human and mouse urocortin III share 90% identity in the 38-aa putative mature peptide. In the peptide coding region, both human and mouse urocortin III are 76% identical to pufferfish urocortin-related peptide and more distantly related to urocortin II, CRF, and urocortin from other mammalian species. Mouse urocortin III mRNA expression is found in areas of the brain including the hypothalamus, amygdala, and brainstem, but is not evident in the cerebellum, pituitary, or cerebral cortex; it is also expressed peripherally in small intestine and skin. Urocortin III is selective for type 2 CRF receptors and thus represents another potential endogenous ligand for these receptors.
Phase Change Microvalve for Integrated Devices (2004)

An active microvalve that uses a meltable piston in place of a conventional solid material to obstruct fluid flow in a microfluidic channel has been developed. This phase change valve is simple to operate and requires no additional fabrication steps. The valve is inherently latched, reusable, and leak-proof (to at least 250 psi) and can be electronically addressed using resistive heaters. The valve has been characterized for a range of operational parameters that will serve as a design guide. For the designs tested, piston displacements of 5 mm or more in 1 s have been achieved. Valves 1.4 mm in length in a 50 microm x 200 microm channel have been integrated on a biochemical reaction device, and successful DNA amplification using PCR has been achieved. The phase change valve can be easily implemented in an array format that can be used to realize complex microfluidic circuits.
CDMA-based RFID Systems in Dense Scenarios: Concepts and Challenges (2008)

Radiofrequency identification (RFID) applications with large tag populations often require the fast identification of the tags present. Conventional RFID systems using framed ALOHA based medium access control algorithms waste bandwidth during the singulation process when tag replies collide on the shared wireless channel. In this paper, we investigate how code division multiplexing techniques can be used to decode tag replies in such collisions. Our analysis focusses on the choice of code set and detector for use in a spread spectrum RFID system. The paper also presents a method to estimate the number of tags in the range of such a spread spectrum RFID system.
The diverse signaling network of EGFR, HER2, HER3 and HER4 tyrosine kinase receptors and the consequences for therapeutic approaches. (2005)

The HER family of receptor tyrosine kinase couples binding of extracellular growth factor ligands to intracellular signal transduction pathways, contributing in this fashion to the ability of the cell to respond correctly to its environment. The HER family and its ligands are critically involved in the carcinogenesis of the mammary gland. Abnormal function of the members of HER family resulting in receptor hyper-activation (due to gene amplification, protein overexpression or abnormal transcriptional regulation) has been linked with breast cancer prognosis. It is also extensively studied as the predictive factor and target for therapy. There are clinical indications supporting the concept that none of the receptors: EGFR, HER2, HER3 and HER4 can be considered as the stand-alone receptor in breast cancer development and clinical course of the disease. There is a growing body of evidence that cooperation between them contributes to more aggressive tumor phenotype and influences the response to therapy. This underlines the importance of quantification of all HER family members and indicates the urgent need for implementation of methods that can efficiently and reliably examine four HER receptors as a whole panel in breast cancer patients.
Acceleration sensing glove (ASG) (2003)

A glove with 2-axis accelerometers on the finger tips and back of the hand has been built using commercial-off-the-shelf components. Taking advantage of gravity induced acceleration offsets, we have been able to identify pseudo static gestures. We have also developed software that allows the glove to be used as a mouse pointing device for a Windows 95 or NT machine.
Enzymatic peptidyl .alpha.-amidation proceeds through formation of an .alpha.-hydroxyglycine intermediate (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymatic peptidyl .alpha.-amidation proceeds through formation of an .alpha.-hydroxyglycine intermediateStanley D. Young and Paul P. TamburiniCite this: J. Am. Chem. Soc. 1989, 111, 5, 1933–1934Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/ja00187a088https://doi.org/10.1021/ja00187a088research-articleACS PublicationsRequest reuse permissionsArticle Views313Altmetric-Citations87LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts