gebhart/patrepeval huggingface dataset:
Argon Laser and Remineralizing Solution Treatment Effects on Root Surface Caries (2006)

Purpose: The effects of argon laser (AL) irradiation exposure and remineralizing solution (RS) treatment were evaluated alone and in combination on caries-like lesion formation in permanent tooth root surfaces in an in vitro study. Materials and Methods: Ten caries-free permanent tooth root surfaces were divided into 4 segments and each segment from each tooth was assigned to 1 of 4 treatment groups: no treatment control (n = 10), AL irradiation alone at 13.5 J/cm2 (0.270 W, 5-mm beam, 10 s, n = 10), RS treatment alone for 2 min (n = 10), and AL irradiation before RS treatment (n = 10). This allowed each tooth to serve as a matched internal control for each of the treatments. In vitro caries were created using a modified ten Cate solution. The longitudinal sections (3 per tooth segment, 30 per treatment group) were evaluated for mean lesion depth. Results: After lesion formation, mean lesion depths (± standard deviation) were 288 ± 32 μm for the no treatment controls, 198 ± 23μm for AL irradiation alone, 188 ± 19 μm for RS treatment alone, and 109 ± 14 μm for AL irradiation before RS treatment. All treatment groups had mean lesion depths that were significantly less than those for the matched no treatment control group (ANOVA, Duncan multiple range [DMR] test, p < 0.05). AL irradiation before RS treatment significantly reduced lesion depth compared with AL irradiation alone or RS treatment alone (ANOVA, DMR test, p < 0.05). Conclusion: Both AL and RS alone provided significant reductions in lesion depths for in vitro root surface caries compared with no treatment controls. However, the maximum reduction in caries-like lesion depth on permanent tooth root surfaces was achieved when the RS, containing calcium, phosphate, and fluoride in a carbopol base, was combined with AL irradiation.
Rapid High Efficiency Sensitization of CD8+ T Cells to Tumor Antigens by Dendritic Cells Leads to Enhanced Functional Avidity and Direct Tumor Recognition Through an IL-12-Dependent Mechanism (2003)

Myeloid-origin dendritic cells (DCs) can develop into IL-12-secreting DC1 or non-IL-12-secreting DC2 depending on signals received during maturation. Through rapid culture techniques that prepared either mature, CD83+ DC1 or DC2 from CD14+ monocytes in only 2 days followed by a single 6-7 day DC-T cell coculture, we sensitized normal donor CD8+ T cells to tumor Ags (HER-2/neu, MART-1, and gp100) such that peptide Ag-specific lymphocytes constituted up to 16% of the total CD8+ population. Both DC1 and DC2 could sensitize CD8+ T cells that recognized peptide-pulsed target cells. However, with DC2, a general decoupling was observed between recognition of peptide-pulsed T2 target cells and recognition of Ag-expressing tumor cells, with peptide-sensitized T cells responding to tumor only about 15% of the time. In contrast, direct recognition of tumor by T cells was dramatically increased (to 85%) when DC1 were used for sensitization. Enhanced tumor recognition was accompanied by 10- to 100-fold increases in peptide sensitivity and elevated expression of CD8beta, characteristic of high functional avidity T cells. Both of these properties were IL-12-dependent. These results demonstrate the utility of rapid DC culture methods for high efficiency in vitro T cell sensitization that achieves robust priming and expansion of Ag-specific populations in 6 days. They also demonstrate a novel function of IL-12, which is enhancement of CD8+ T cell functional avidity. A new approach to DC-based vaccines that emphasizes IL-12 secretion to enhance functional avidity and concomitant tumor recognition by CD8+ T cells is indicated.
Loss of Pin1 function in the mouse causes phenotypes resembling cyclin D1-null phenotypes (2002)

Phosphorylation of proteins on serine/threonine residues preceding proline is a key signaling mechanism. The conformation and function of a subset of these phosphorylated proteins is regulated by the prolyl isomerase Pin1 through isomerization of phosphorylated Ser/Thr-Pro bonds. Although young Pin1(-/-) mice have been previously shown to develop normally, we show here that they displayed a range of cell-proliferative abnormalities, including decreased body weight and testicular and retinal atrophies. Furthermore, in Pin1(-/-) adult females, the breast epithelial compartment failed to undergo the massive proliferative changes associated with pregnancy. Interestingly, many of these Pin1-deficient phenotypes such as retinal hypoplasia and mammary gland impairment are also the characteristic of cyclin D1-deficient mice. Cyclin D1 levels were significantly reduced in many tissues in Pin1-deficient mice, including retina and breast epithelial cells from pregnant mice. Moreover, Pin1 directly bound to cyclin D1 phosphorylated on Thr-286-Pro increased cyclin D1 in the nucleus and stabilized cyclin D1. These results indicate that Pin1 positively regulates cyclin D1 function at the transcriptional level, as demonstrated previously, and also through posttranslational stabilization, which together explain why Pin1 loss-of-function phenotypes in the mouse resemble cyclin D1-null phenotypes. Our results provide genetic evidence for an essential role of Pin1 in maintaining cell proliferation and regulating cyclin D1 function.
Advantages of multiple cell culture systems for detection of mixed-virus infections (1991)

Simultaneous infections by two or more viruses occur frequently, especially in immunosuppressed patients. In order to detect more than one viral agent in a single specimen, multiple cell systems have been employed in our laboratory. Specimens are routinely inoculated into four different cell cultures, namely: MRC-5, a human diploid lung fibroblast cell strain; A549, a human continuous cell line; primary guinea pig embryo (GPE) cell culture, and primary rhesus monkey kidney (RhMK) cell culture. For rapid detection of cytomegalovirus (CMV) antigen, MRC-5 cells grown in shell vials containing coverslips are also inoculated with the same specimens followed by centrifugation. During 1989, nine cases of multiple-virus isolations were obtained in this laboratory. In all nine patients, CMV was detected in MRC-5 cells. Five of the nine cases were co-infected with HSV-1, three were co-infected with adenovirus, and one was co-infected with both HSV-1 and adenovirus. All four adenovirus isolates were obtained in A549 cells. Of the six HSV-1 isolates, one was detected in all three cell cultures, e.g. MRC-5, A549 and GPE; one was detected in both MRC-5 and A549 cells, and four were isolated in a single-cell type only. For nine CMV-positive cases, five were obtained by both conventional and centrifugation cultures, two each were detected by centrifugation or conventional culture only. Thus for a maximum detection of viruses present in a single specimen, it is suggested that multiple-cell-culture systems, together with more than one technique, should be employed.
Chiral discrimination upon crystallisation of the diastereomeric salts of 1-arylethylamines with mandelic acid or p-methoxymandelic acid: interpretation of the resolution efficiencies on the basis of the crystal structures (1996)

The crystal structures of the diastereomeric salts of 1-arylethylamines with mandelic acid or p-methoxymandelic acid have been studied. This revealed that there was correlation between the efficiencies of the optical resolutions of the amines with the resolving reagents and the crystal structures of the salts. A characteristic hydrogen-bond layer, consisting of stable columnar structures and having a planar boundary surface, was found to be common to the less-soluble salt crystals; these crystals were considered to be stabilised from the viewpoint of both their hydrogen-bonding and van der Waals interactions. In contrast, in the corresponding more-soluble salts and in those diastereomeric salts which could not be separated by crystallisation, no such particularly stabilised crystal structure was formed; there only existed either columnar structures or planar boundary surfaces in these crystals. These results strongly suggest that for successful resolution it is necessary to realise a hydrogen-bond layer, consisting of stable columns and having planar boundary surfaces, in the crystals of one of the pair of diastereomeric salts. In order to achieve such a crystal structure, complementarily in molecular length between a target racemate and a resolving reagent must be considered the most important and fundamental factor.
Drugs of abuse and immune function (1990)

Opiates: Cell-Medicated Immunity. Ethanol and Its Effects on Mucosal Immunity. Effects of Drugs of Abuse on Granulocyte Development/Function and Myeloid Cell Differentiation. Effects of Prenatal Drugs of Abuse on Development of Lymphoid Organs. Marijuana and Immunosuppression in Man. Modulation of Murine Immune Cell Function by Marijuana Components. Nicotine and Immunology. Does Alcohol-Produced Malnutrition Lead to Immunosuppression? Immunomodulation and Tobacco. Effect of Morphine on Lymphocyte Function: Possible Mechanisms of Interaction. Ethanol and the B-Cell: Humoral Immunity. Ethanol and Overall Immunoregulation. Alcohol and the Macrophage. Opiate Binding to Cells of the Immune System. Index, c. 240 pp., 6x9, due May 1990, ISBN 0-8493-6747-6.
Pulmonary Arterial Hypertension (2006)

ost practicing cardiologists see patients with pulmo- nary hypertension (PH) on a regular basis.Although this is most commonly in the form of pulmonary venous hypertension related to elevated left heart pressures, the explosion in knowledge of and treatment for pulmonary arterial hypertension (PAH) over the past decade obligates cardiologists to be more cognizant of this disorder.In this review, we will discuss the pathobiology, classification, diagnosis, and treatment of PAH in adults.The term PAH in this context refers specifically to a pulmonary hypertensive state limited predominantly to the arterial component of the pulmonary vasculature and constitutes one of the main classifications of clinical PH diseases.
Autocrine Motility Factor Signaling Enhances Pancreatic Cancer Metastasis (2004)

The data submitted here show that AMF expression significantly contributes to the aggressive phenotype of human pancreatic cancer and thus may provide a novel prognostic and therapeutic target.
Reuse and Abuse. (2007)

As programming languages and software development paradigms have evolved, so has our conception of what is meant by the term 'software reuse'. In this paper we track these shifts in meaning up to the era of component frameworks. Our concerns, initially related to the maintenance of shared libraries, have become a study of dynamic evolution.
A 640×512 CMOS image sensor with ultrawide dynamic range floating-point pixel-level ADC (1999)

Analysis results demonstrate that multiple sampling can achieve consistently higher signal-to-noise ratio at equal or higher dynamic range than using other image sensor dynamic range enhancement schemes such as well capacity adjusting. Implementing multiple sampling, however, requires much higher readout speeds than can be achieved using typical CMOS active pixel sensor (APS). This paper demonstrates, using a 640/spl times/512 CMOS image sensor with 8-b bit-serial Nyquist rate analog-to-digital converter (ADC) per 4 pixels, that pixel-level ADC enables a highly flexible and efficient implementation of multiple sampling to enhance dynamic range. Since pixel values are available to the ADC's at all times, the number and timing of the samples as well as the number of bits obtained from each sample can be freely selected and read out at fast SRAM speeds. By sampling at exponentially increasing exposure times, pixel values with binary floating-point resolution can be obtained. The 640/spl times/512 sensor is implemented in 0.35-/spl mu/m CMOS technology and achieves 10.5/spl times/10.5 /spl mu/m pixel size at 29% fill factor. Characterization techniques and measured quantum efficiency, sensitivity, ADC transfer curve, and fixed pattern noise are presented. A scene with measured dynamic range exceeding 10000:1 is sampled nine times to obtain an image with dynamic range of 65536:1. Limits on achievable dynamic range using multiple sampling are presented.
The bronchial epithelium as a key regulator of airway inflammation and remodelling in asthma (1999)

While asthma is an inflammatory disorder of the airways involving mediator release from mast cells and eosinophils and orchestrated by T cells, inflammation alone is insufficient to explain the chronic nature of the disease and its progression. Evidence is presented that the epithelium is fundamentally disordered in chronic asthma manifest by increased fragility, and an altered phenotype to one that secretes mucus, mediators, cytokines, chemokines and growth factors. Epithelial injury is mediated by exogenous factors such as air pollutants, viruses and allergens as well as by endogenous factors including the release of proteolytic enzymes from mast cells (tryptase, chymase) and eosinophils (MMP-9). Following injury, the normal epithelium should respond with increased proliferation driven by ligands acting on epidermal growth factor (EGF) receptors or through transactivation of the receptor. The epithelial response to these stimuli in asthma appears to be impaired despite upregulation of CD44 capable of enhancing presentation of EGF ligands to epidermal growth factor receptors (EGFR). Because the epithelium is 'held' in this repair phenotype, it becomes a continuous source of proinflammatory products as well as growth factors that drive airway wall remodelling.
Information filtering and information retrieval (1992)

Information filtering is a name used to describe a variety of processes involving the delivery of information to people who need it. Although this term is appearing quite often in popular and technical articles describing applications such as electronic mail, multimedia distributed systems, and electronic office documents, the distinction between filtering and related processes such as retrieval, routing, categorization, and extraction is often not dear. It is only by making that distinction, however, that the specific research issues associated with filtering can be identified and addressed.
Molecular fluorescence, phosphorescence, and chemiluminescence spectrometry (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular fluorescence, phosphorescence, and chemiluminescence spectrometryIsiah M. Warner and Linda B. McGownCite this: Anal. Chem. 1992, 64, 12, 343–352Publication Date (Print):June 15, 1992Publication History Published online1 May 2002Published inissue 15 June 1992https://pubs.acs.org/doi/10.1021/ac00036a019https://doi.org/10.1021/ac00036a019research-articleACS PublicationsRequest reuse permissionsArticle Views324Altmetric-Citations16LEARN 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
Cell-surface levels of human carcinoembryonic antigen are inversely correlated with colonocyte differentiation in colon carcinogenesis. (1997)

Human carcinoembryonic antigen (CEA) is overexpressed in a wide variety of epithelial malignancies including colon cancer. CEA can function in vitro as a homotypic intercellular adhesion molecule and can block the terminal differentiation of rodent myoblasts, thus raising the possibility that deregulated expression of CEA might directly contribute to malignant progression. To address this question, the expression pattern and cell-surface levels of CEA were studied during malignant transformation of the colonic epithelium in sporadic and familial adenomatous polyposis-related neoplasms. The level of immunohistochemically detected CEA was higher in 30% to 62% of microadenomas and small adenomas from familial adenomatous polyposis patients compared with adjacent normal mucosa, and this proportion was positively correlated with lesion size and degree of dysplasia. Cytofluorometric analysis of highly purified single epithelial cell suspensions from freshly excised carcinomas versus adjacent normal tissue demonstrated up to a 20-fold increase of mean cell-surface CEA in a group of colon carcinomas representative of the overall majority of such tumors--from Dukes' stages A to D and ranging mainly from well to moderately differentiated, the degree of overproduction was inversely correlated with tumor differentiation and directly correlated with stage. A marked tendency toward nonpolarized versus apical cell-surface expression with progression was also noted. Nonspecific cross-reacting antigen (NCA), a CEA family member, is also a homotypic adhesion molecule and blocks terminal myogenic differentiation, whereas biliary glycoprotein is a CEA family adhesion molecule that does not. Cell-surface NCA showed even greater overexpression (up to 70-told) in dedifferentiated tumors, whereas total-cell biliary glycoprotein showed approximately 2-fold lower levels than was normal in more differentiated tumors and approximately 2-fold higher levels than in further progressed tumors. These results therefore support the suggestion that CEA and NCA can directly contribute to colon carcinogenesis by inhibiting colonocyte differentiation.
Atomic Layer Deposition of SiCxNy Using Si2Cl6 and CH3NH2 Plasma (2017)

We developed a novel process for the atomic layer deposition (ALD) of SiCxNy films using a Si2Cl6 and a CH3NH2 plasma. Under self-limiting growth conditions, this ALD process led to SiCxNy films with up to 9 atomic percent carbon with a conformality >95% in 5:1 aspect ratio nanostructures. The surface reactions during ALD, and in particular the carbon incorporation mechanism, were studied using in situ attenuated total reflection Fourier transform infrared spectroscopy. Similar to the Si2Cl6 and NH3 plasma-based process, we show that on the SiCxNy growth surface, Si2Cl6 reacts primarily with surface −NH2 species that were created after the CH3NH2 plasma cycle. During the subsequent CH3NH2 half cycle, the surface chlorine was liberated, creating −NHx (x = 1 or 2) groups, while carbon was incorporated primarily as −N═C═N– species. In situ ellipsometry showed that the growth per cycle and the refractive index were ∼1 Å and ∼1.85, respectively. Elemental depth profiling with secondary ion mass spectrometry showed that, as the plasma power was increased from 50 to 100 W, the carbon atomic fraction increased from ∼4 to ∼9%. At higher plasma powers, the CH3NH2 plasma half cycle was not self-limiting and led to continuous carbon nitride growth.
Chimeric Fatty Acyl-Acyl Carrier Protein Thioesterases Provide Mechanistic Insight into Enzyme Specificity and Expression (2018)

Medium-chain fatty acids are commodity chemicals. Increasing and modifying the activity of thioesterases (TEs) on medium-chain fatty acyl-acyl carrier protein (acyl-ACP) esters may enable a high-yield microbial production of these molecules. The plant <i>Cuphea palustris</i> harbors two distinct TEs: <i>C. palustris</i> FatB1 (<i>Cp</i>FatB1) (C<sub>8</sub> specificity, lower activity) and <i>Cp</i>FatB2 (C<sub>14</sub> specificity, higher activity) with 78% sequence identity. We combined structural features from these two enzymes to create several chimeric TEs, some of which showed nonnatural fatty acid production as measured by an enzymatic assay and gas chromatography-mass spectrometry (GC-MS). Notably, chimera 4 exhibited an increased C<sub>8</sub> fatty acid production in correlation with improved microbial expression. This chimera led us to identify <i>Cp</i>FatB2-specific amino acids between positions 219 and 272 that lead to higher protein levels. Chimera 7 produced a broad range of fatty acids and appeared to combine a fatty acid binding pocket with long-chain specificity and an ACP interaction site that may activate fatty acid extrusion. Using homology modeling and <i>in silico</i> docking with ACP, we identified a "positive patch" within amino acids 162 to 218, which may direct the ACP interaction and regulate access to short-chain fatty acids. On the basis of this modeling, we transplanted putative ACP interaction sequences from <i>Cp</i>FatB1 into <i>Cp</i>FatB2 and created a chimeric thioesterase that produced medium-chain as well as long-chain fatty acids. Thus, the engineering of chimeric enzymes and characterizing their microbial activity and chain-length specificity suggested mechanistic insights into TE functions and also generated thioesterases with potentially useful properties. These observations may inform a rational engineering of TEs to allow alkyl chain length control.<b>IMPORTANCE</b> Medium-chain fatty acids are important commodity chemicals. These molecules are used as plastic precursors and in shampoos and other detergents and could be used as biofuel precursors if production economics were favorable. Hydrocarbon-based liquid fuels must be optimized to have a desired boiling point, low freezing point, low viscosity, and other physical characteristics. Similarly, the solubility and harshness of detergents and the flexibility of plastic polymers can be modulated. The length and distribution of the carbon chains in the hydrophobic tails determine these properties. The biological synthesis of cell membranes and fatty acids produces chains of primarily 16 to 18 carbons, which give rise to current biofuels. The ultimate goal of the work presented here is to engineer metabolic pathways to produce designer molecules with the correct number of carbons in a chain, so that such molecules could be used directly as specialty commodity chemicals or as fuels after minimal processing.
Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF65 (2007)

Pre-mRNA splicing is a crucial step in gene expression, and accurate recognition of splice sites is an essential part of this process. Splice sites with weak matches to the consensus sequences are common, though it is not clear how such sites are efficiently utilized. Using an in vitro splicing-complementation approach, we identified PUF60 as a factor that promotes splicing of an intron with a weak 3' splice-site. PUF60 has homology to U2AF(65), a general splicing factor that facilitates 3' splice-site recognition at the early stages of spliceosome assembly. We demonstrate that PUF60 can functionally substitute for U2AF(65)in vitro, but splicing is strongly stimulated by the presence of both proteins. Reduction of either PUF60 or U2AF(65) in cells alters the splicing pattern of endogenous transcripts, consistent with the idea that regulation of PUF60 and U2AF(65) levels can dictate alternative splicing patterns. Our results indicate that recognition of 3' splice sites involves different U2AF-like molecules, and that modulation of these general splicing factors can have profound effects on splicing.