gebhart/patrepeval huggingface dataset:
Endometrial carcinoma detected with SurePath liquid‐based cervical cytology: comparison with conventional cytology (2009)

Introduction: Conventional Pap smears (CPS) have little impact on the detection of endometrial carcinoma. Although liquid‐based cytology (LBC) is replacing CPS in the UK, experience with identification of endometrial cancers with this technique is limited. Aim: To compare the accuracy of the SurePath LBC with that of CPS for detection of endometrial cancers. Methods: Our study group comprised SurePath LBC samples reported as atypical endometrial cells and endometrial adenocarcinoma (classified respectively as borderline, code 8 and ?glandular neoplasia, code 6 for the NHS Cervical Screening Programme statistics) in 2004–2005. CPS reported as atypical endometrial cells or adenocarcinoma in 1993–1998 comprised the control group. Histological follow‐up was obtained. Results: Endometrial abnormalities were reported in 95 (0.073%) of 130 352 LBC samples, comprising 75 (0.058%) atypical endometrial cells and 20 (0.015%) endometrial adenocarcinoma reports. Of 409 495 CPS, 117 (0.029%) were diagnosed as endometrial abnormalities, comprising 59 (0.014%) atypical endometrial cells and 58 (0.014%) endometrial adenocarcinoma reports. Thus, the endometrial adenocarcinoma reporting rate was similar in both groups, but that for atypical endometrial cells was higher with LBC ( P &lt; 0.001). The positive predictive value for endometrial cancer of endometrial adenocarcinoma and atypical endometrial cell reports in the LBC group was 73.3 and 18.8%, respectively, compared with 42.3 and 6.7% in the CPS group. The endometrial adenocarcinoma patients in CPS group were older (mean age 62.5 years versus 56.5 years) and most (22/25) were symptomatic, whereas most (13/17) patients in the LBC group were asymptomatic at the time of sampling ( P &lt; 0.001). Conclusion: SurePath LBC is at least as accurate a method for detecting endometrial cancer as CPS. SurePath LBC demonstrates enhanced identification of endometrial pathology in asymptomatic women in the cervical screening programme.
Incremental learning for Adaptive Visual Place Recognition in Dynamic Indoor Environments (2006)

Vision-based place recognition is a desirable feature for an autonomous mobile system. In order to work in realistic scenarios, a visual recognition algorithm should have two key properties: robustness and adaptability. This thesis focuses on the latter, and presents a discriminative incremental learning approach to place recognition. We propose a solution based on incremental extensions of support vector machine classifier. Computational and memory efficiency are crucial for mobile robot platforms aiming to continuously work in real-world settings; thus we put the emphasis on these properties. We use a recently introduced memory-controlled incremental technique, which allows to control the memory requirements as the system updates its internal representation. At the same time, it preserves the recognition performance of the batch algorithm and runs online. In order to assess the method, we acquired a database capturing the intrinsic variability of places over time. Extensive experiments show the power and the potential of the approach.
Early Epithelial Phenotypic Changes Predict Graft Fibrosis (2008)

Chronic allograft nephropathy accounts for the loss of approximately 40% of allografts at 10 yr. Currently, no biomarker is available to detect interstitial fibrosis and tubular atrophy in the renal graft at an early stage, when intervention may be beneficial. Because tubular epithelial cells have been shown to exhibit phenotypic changes suggestive of epithelial-to-mesenchymal transition, we studied whether these changes predict the progression of fibrosis in the allograft. Eighty-three kidney transplant recipients who had undergone a protocol graft biopsy at both 3 and 12 mo after transplantation were enrolled. De novo vimentin expression and translocation of beta-catenin into the cytoplasm of tubular cells were detected on the first biopsy by immunohistochemistry. Patients with expression of these markers in >or=10% of tubules at 3 mo had a higher interstitial fibrosis score at 1 yr and a greater progression of this score between 3 and 12 mo. The intensity of these phenotypic changes positively and significantly correlated with the progression of fibrosis, and multivariate analysis showed that their presence was an independent risk factor for this progression. In addition, the presence of early phenotypic changes was associated with poorer graft function 18 mo after transplantation. In conclusion, early phenotypic changes indicative of epithelial-to-mesenchymal transition predict the progression toward interstitial fibrosis in human renal allografts.
Activation of Glutamatergic Neurotransmission by Ketamine: A Novel Step in the Pathway from NMDA Receptor Blockade to Dopaminergic and Cognitive Disruptions Associated with the Prefrontal Cortex (1997)

Subanesthetic doses of ketamine, a noncompetitive NMDA receptor antagonist, impair prefrontal cortex (PFC) function in the rat and produce symptoms in humans similar to those observed in schizophrenia and dissociative states, including impaired performance of frontal lobe-sensitive tests. Several lines of evidence suggest that ketamine may impair PFC function in part by interacting with dopamine neurotransmission in this region. This study sought to determine the mechanism by which ketamine may disrupt dopaminergic neurotransmission in, and cognitive functions associated with, the PFC. A thorough dose-response study using microdialysis in conscious rats indicated that low doses of ketamine (10, 20, and 30 mg/kg) increase glutamate outflow in the PFC, suggesting that at these doses ketamine may increase glutamatergic neurotransmission in the PFC at non-NMDA glutamate receptors. An anesthetic dose of ketamine (200 mg/kg) decreased, and an intermediate dose of 50 mg/kg did not affect, glutamate levels. Ketamine, at 30 mg/kg, also increased the release of dopamine in the PFC. This increase was blocked by intra-PFC application of the AMPA/kainate receptor antagonist, 6-cyano-7-nitroquinoxaline-2,3-dione CNQX. Furthermore, ketamine-induced activation of dopamine release and impairment of spatial delayed alternation in the rodent, a PFC-sensitive cognitive task, was ameliorated by systemic pretreatment with AMPA/kainate receptor antagonist LY293558. These findings suggest that ketamine may disrupt dopaminergic neurotransmission in the PFC as well as cognitive functions associated with this region, in part, by increasing the release of glutamate, thereby stimulating postsynaptic non-NMDA glutamate receptors.
Identification of Ubiquitin-specific Protease 9X (USP9X) as a Deubiquitinase Acting on Ubiquitin-Peroxin 5 (PEX5) Thioester Conjugate (2012)

Peroxin 5 (PEX5), the peroxisomal protein shuttling receptor, binds newly synthesized peroxisomal matrix proteins in the cytosol and promotes their translocation across the organelle membrane. During the translocation step, PEX5 itself becomes inserted into the peroxisomal docking/translocation machinery. PEX5 is then monoubiquitinated at a conserved cysteine residue and extracted back into the cytosol in an ATP-dependent manner. We have previously shown that the ubiquitin-PEX5 thioester conjugate (Ub-PEX5) released into the cytosol can be efficiently disrupted by physiological concentrations of glutathione, raising the possibility that a fraction of Ub-PEX5 is nonenzymatically deubiquitinated in vivo. However, data suggesting that Ub-PEX5 is also a target of a deubiquitinase were also obtained in that work. Here, we used an unbiased biochemical approach to identify this enzyme. Our results suggest that ubiquitin-specific protease 9X (USP9X) is by far the most active deubiquitinase acting on Ub-PEX5, both in female rat liver and HeLa cells. We also show that USP9X is an elongated monomeric protein with the capacity to hydrolyze thioester, isopeptide, and peptide bonds. The strategy described here will be useful in identifying deubiquitinases acting on other ubiquitin conjugates.
CMOS Imager with Copper Wiring and Lightpipe (2006)

A CMOS imager technology is described, which uses Cu wiring and a polymer lightpipe. The microlens height must be optimized when using the lightpipe, so that light is focused into the top of the lightpipe rather than onto the photodiode. A SiN layer is used on the sidewalls to reflect light that enters the top of the lightpipe down onto the photodiode. The SiN layer also forms a hermetic seal, which protects the Cu wiring from ambient moisture. Using this structure, high quantum efficiency can be achieved for a 2.2 mum pixel and high reliability is demonstrated
Proteinuria and hypertension. (1994)

Albuminuria is more prevalent in patients with primary hypertension than in normotensive subjects of the general population. The presence of albuminuria predicts the presence of more severe target organ damage and is related to the risk of cardiovascular events. Preliminary results show albuminuria even in some normotensive individuals with a genetic risk of hypertension and in association with insulin resistance. While albuminuria is generally more frequent in the elderly, it is also found in young patients with mild to moderate primary hypertension. It is uncertain whether in these circumstances albuminuria indicates some "renal component" in the etiology of primary hypertension. Massive albuminuria may occur in subjects with "benign" nephrosclerosis. Whether albuminuria is a predictor of hypertensive renal damage requires further study. Albuminuria is reduced by antihypertensive treatment, but diverse effects on albuminuria are seen with different antihypertensive agents.
Effect of Calcium on the Oxidative Phosphorylation Cascade in Skeletal Muscle Mitochondria (2013)

Calcium is believed to regulate mitochondrial oxidative phosphorylation, thereby contributing to the maintenance of cellular energy homeostasis. Skeletal muscle, with an energy conversion dynamic range of up to 100-fold, is an extreme case for evaluating the cellular balance of ATP production and consumption. This study examined the role of Ca(2+) in the entire oxidative phosphorylation reaction network in isolated skeletal muscle mitochondria and attempted to extrapolate these results back to the muscle, in vivo. Kinetic analysis was conducted to evaluate the dose-response effect of Ca(2+) on the maximal velocity of oxidative phosphorylation (V(maxO)) and the ADP affinity. Force-flow analysis evaluated the interplay between energetic driving forces and flux to determine the conductance, or effective activity, of individual steps within oxidative phosphorylation. Measured driving forces [extramitochondrial phosphorylation potential (ΔG(ATP)), membrane potential, and redox states of NADH and cytochromes b(H), b(L), c(1), c, and a,a(3)] were compared with flux (oxygen consumption) at 37 °C; 840 nM Ca(2+) generated an ~2-fold increase in V(maxO) with no change in ADP affinity (~43 μM). Force-flow analysis revealed that Ca(2+) activation of V(maxO) was distributed throughout the oxidative phosphorylation reaction sequence. Specifically, Ca(2+) increased the conductance of Complex IV (2.3-fold), Complexes I and III (2.2-fold), ATP production/transport (2.4-fold), and fuel transport/dehydrogenases (1.7-fold). These data support the notion that Ca(2+) activates the entire muscle oxidative phosphorylation cascade, while extrapolation of these data to the exercising muscle predicts a significant role of Ca(2+) in maintaining cellular energy homeostasis.
Immunomodulatory effect of human adipose tissue‐derived adult stem cells: comparison with bone marrow mesenchymal stem cells (2005)

Like mesenchymal stem cells from bone marrow (BM-MSCs), adipose tissue-derived adult stem cells (ADAS cells) can differentiate into several lineages and present therapeutical potential for repairing damaged tissues. The use of allogenic stem cells can enlarge their therapeutical interest, provided that the grafted cells could be tolerated. We investigate here, for the first time, the immunosuppressive properties of ADAS cells compared with the well-characterized immunosuppressive properties of BM-MSCs. ADAS cells did not provoke in vitro alloreactivity of incompatible lymphocytes and, moreover, suppressed mixed lymphocyte reaction (MLR) and lymphocyte proliferative response to mitogens. The impairment of inhibition when ADAS cells and BM-MSCs were separated from lymphocytes by a permeable membrane suggests that cell contact is required for a full inhibitory effect. Hepatocyte growth factor is secreted by both stem cells but, similar to interleukin-10 and transforming growth factor-beta (TGF-beta), the levels of which were undetectable in supernatants of MLR inhibited by ADAS cells or BM-MSCs, it did not seem implicated in the stem cell suppressive effect. These findings support that ADAS cells share immunosuppressive properties with BM-MSCs. Therefore, ADAS cell-based reconstructive therapy could employ allogenic cells and because of their immunosuppressive properties, ADAS cells could be an alternative source to BM-MSCs to treat allogenic conflicts.
GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data (2005)

The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76,000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.
Risks and Benefits of Estrogen Plus Progestin in Healthy Postmenopausal Women: Principal Results From the Women's Health Initiative Randomized Controlled Trial (2002)

Overall health risks exceeded benefits from use of combined estrogen plus progestin for an average 5.2-year follow-up among healthy postmenopausal US women. All-cause mortality was not affected during the trial. The risk-benefit profile found in this trial is not consistent with the requirements for a viable intervention for primary prevention of chronic diseases, and the results indicate that this regimen should not be initiated or continued for primary prevention of CHD.
PDF methods for combustion in high-speed turbulent flows (1995)

This report describes the research performed during the second year of this three-year project. The ultimate objective of the project is extend the applicability of probability density function (pdf) methods from incompressible to compressible turbulent reactive flows. As described in subsequent sections, progress has been made on: (1) formulation and modelling of pdf equations for compressible turbulence, in both homogeneous and inhomogeneous inert flows; and (2) implementation of the compressible model in various flow configurations, namely decaying isotropic turbulence, homogeneous shear flow and plane mixing layer.
β2-microglobulin gene duplication in cetartiodactyla remains intact only in pigs and possibly confers selective advantage to the species (2017)

Several β2-microglobulin (B2M) -bound protein complexes undertake key roles in various immune system pathways, including the neonatal Fc receptor (FcRn), cluster of differentiation 1 (CD1) protein, non-classical major histocompatibility complex (MHC), and well-known MHC class I molecules. Therefore, the duplication of B2M may lead to an increase in the biological competence of organisms to the environment. Based on the pig genome assembly SSC10.2, a segmental duplication of ~45.5 kb, encoding the entire B2M protein, was identified in pig chromosome 1. Through experimental validation, we confirmed the functional duplication of the B2M gene with a completely identical coding sequence between two copies in pigs. Considering the importance of B2M in the immune system, we performed the phylogenetic analysis of B2M duplication in ten mammalian species, confirming the presence of B2M duplication in cetartioldactyls, like cattle, sheep, goats, pigs and whales, but non-cetartiodactyl species, like mice, cats, dogs, horses, and humans. The density of long interspersed nuclear element (LINE) at the edges of duplicated blocks (39 to 66%) was found to be 2 to 3-fold higher than the average (20.12%) of the pig genome, suggesting its role in the duplication event. The B2M mRNA expression level in pigs was 12.71 and 7.57 times (2-ΔΔCt values) higher than humans and mice, respectively. However, we were unable to experimentally demonstrate the difference in the level of B2M protein because species specific anti-B2M antibodies are not available. We reported, for the first time, the functional duplication of the B2M gene in animals. The identification of partially remaining duplicated B2M sequences in the genomes of only cetartiodactyls indicates that the event was lineage specific. B2M duplication could be beneficial to the immune system of pigs by increasing the availability of MHC class I light chain protein, B2M, to complex with the proteins encoded by the relatively large number of MHC class I heavy chain genes in pigs. Further studies are necessary to address the biological meaning of increased expression of B2M.
Metal Organic Chemical Vapor Deposition of Oxide Films for Advanced Applications (2000)

Transparent and conductive films, well known for their historical roles in solar cells and displays, are receiving renewed attention due to the need for increased performance requirements and for advanced applications that are being developed. While there are many methods to deposit thin films, Metal Organic Chemical Vapor Deposition (MOCVD) is of particular importance for producing high quality films over large areas in a manufacturing mode. Important features of MOCVD include excellent conformality of deposited films, elimination of pinhole type defects, the absence of radiation process induced damage, and low particle counts. Over the past several years, we have devoted our efforts to developing and advancing the MOCVD process and systems technology, primarily using Rotating Disk Reactors (RDRs), and advancing the breadth of deposited oxide materials for several applications. The deposition technology, which will be reviewed, has been scaled from a 5 deposition diameter through to 12 diameter. We have found that MOCVD has been able to produce a wide range of oxide materials under a variety of processing conditions and that the technology is readily scalable. Systems technology, processing parameters and results for MOCVD of transparent (visible and IR) and conductive oxides will be reviewed. Advanced materials development and applications such as production of luminescent or p-type ZnO and related oxides, development of amorphous, polycrystalline and single crystal films and applicability in photovoltaics, LEDs or lasers, detectors, and others will also be addressed.
Genetic and biochemical studies of bacteriophage T4 DNA polymerase 3'-->5'-exonuclease activity. (1993)

DNA polymerase exonucleolytic proofreading is important in attaining high fidelity DNA replication. One of the most well characterized proofreading activities is the 3'-->5'-exonuclease activity of bacteriophage T4 DNA polymerase. We have used genetic analyses and protein sequence comparisons to Escherichia coli DNA polymerase I to identify amino acids in the N-terminal region of T4 DNA polymerase that are required for exonucleolytic proofreading. Mutant DNA polymerases with amino acid substitutions D112A/E114A, D219A, or D324A reduced 3'-->5'-exonuclease activity 10(2)-10(4)-fold in various in vitro assays and decreased DNA replication fidelity in vivo. DNA replication activity was also reduced for the exonuclease-deficient DNA polymerases in vitro and in vivo. Reduction in DNA replication appeared to be due primarily to the interdependence of T4 DNA polymerase replication and proofreading activities; T4 DNA polymerase requires 3'-->5'-exonuclease activity to repair primer termini that are not suitable substrates for extension. Observations reported here provide further evidence in support of the proposal that DNA polymerases have distinct 3'-->5'-exonuclease and polymerase active sites.
A MULTICENTER, PROSPECTIVE, RANDOMIZED CLINICAL TRIAL OF CONTINUOUS INFUSION I.V. RANITIDINE VS. OMEPRAZOLE SUSPENSION IN THE PROPHYLAXIS OF STRESS ULCERS (1998)

Society of Critical Care Medicine; 27th Educational and Scientific Symposium; San Antonio, Texas, USA; February 4-8, 1998: Poster Hall: Thursday, February 5, 1998 5: 45-7: 15 pm; Friday, February 6, 1998 11: 40 am-1: 00 pm; Saturday, February 7, 1998 11: 40 am-1: 00 pm: Poster Presentations: Pharmacology
Growth of Praseodymium Oxide and Praseodymium Silicate Thin Films by Liquid Injection MOCVD (2004)

Abstract Thin films of praseodymium oxide have been deposited by liquid injection MOCVD using the volatile praseodymium alkoxide, [Pr(mmp) 3 ] (mmp = 1‐methoxy‐2‐methyl‐2‐propanolate, OCMe 2 CH 2 OMe). The films were grown over a wide range of substrate temperatures (250–600 °C) and were found to consist predominantly of the Pr 6 O 11 phase. Praseodymium silicate films containing ∼ 16–22 at.‐% Si were deposited over the temperature range 350–550 °C using [Pr{N(SiMe 3 ) 2 } 3 ] in the absence of any additional Si source.
Characterization of a broad-host-range flagellum-dependent phage that mediates high-efficiency generalized transduction in, and between, Serratia and Pantoea (2009)

A phage (PhiOT8) isolated on Serratia sp. ATCC 39006 was shown to be flagellum-dependent, and to mediate generalized transduction with high efficiency (up to 10(-4) transductants per p.f.u.). PhiOT8 was shown to have a broad host range because it also infected a strain of Pantoea agglomerans isolated from the rhizosphere. Transduction of plasmid-borne antibiotic resistance between the two bacterial genera was demonstrated, consistent with purported ecological roles of phages in dissemination of genes between bacterial genera. Serratia sp. ATCC 39006 and P. agglomerans produce a number of interesting secondary metabolites that have potential applications in cancer therapy and biocontrol of fungal infections. PhiOT8 has utility as a powerful functional genomics tool in these bacteria.