gebhart/patrepeval huggingface dataset:
Cytoplasmic and nuclear accumulation of ?-catenin is rarely caused byCTNNB1 exon 3 mutations in cutaneous malignant melanoma (2001)

Beta-catenin plays an important role in the Wnt signaling pathway by activating T-cell factor (Tcf)/lymphoid enhancer factor (Lef)-regulated gene transcription. The level of beta-catenin is regulated through GSK-3beta phosphorylation of specific serine and threonine residues, all of which are encoded for in exon 3 of the beta-catenin gene (CTNNB1). Mutations altering the GSK-3beta phosphorylation sites lead to cellular accumulation of beta-catenin and constitutive transcription of Tcf/Lef target genes. Such mutations have previously been found in melanoma cell lines. In our study, primary melanomas and their corresponding metastases were screened for CTNNB1 exon 3 mutations using single-strand conformation polymorphism and nucleotide sequence analysis. One of 31 primary tumors and 1 of 37 metastases, both originating from the same patient, had a TCT to TTT mutation at codon 45, changing serine to phenylalanine. Immunohistochemical analysis revealed membranous localization of beta-catenin in a majority of the samples. The mutated primary tumor and metastasis, however, displayed widespread cytoplasmic and nuclear expression of beta-catenin. An additional 30% of the primary tumors showed focal cytoplasmic and nuclear staining. Thus, beta-catenin exon 3 mutations are rare in primary as well as metastatic melanomas and do not explain the abnormal cytoplasmic and nuclear localization of beta-catenin found in a relatively large fraction of primary melanomas.
Breath Methane Associated With Slow Colonic Transit Time in Children With Chronic Constipation (2005)

The presence of breath methane in children with chronic constipation may suggest the possibility of prolonged colonic transit time.
Clinical Application of SHR Research (1987)

The vasoconstrictor responses to electrical nerve stimulation or exogenous norepinephrine as well as endogenous norepinephrine overflow from the adrenergic nerve endings in the isolated mesenteric vasculatures were significantly increased in young SHR (7-8W) compared with their age-matched WKY. On the other hand, basal plasma norepinephrine and its responses to 20 minutes-standing were significantly increased in WHO stage I essential hypertension than those in the normotensive controls and in WHO stage II essential hypertension.Ca-induced reduction of osmotic fragility of erythrocyte, determined by Coil Planet Centrifuge System, and of erythrocyte membrane fluidity, determined by electron spin resonance method, was more prominent in essential hypertension and SHR compared with that in their normotensive controls.These results suggest that genetic abnormalities of physicochemical properties or Ca-sensitivity of the membranes could induce an exaggerated sympathetic nerve activity and vascular reactivity and contribute, at least partially, to the pathogenesis of hypertension in SHR and essential hypertension.
Preliminary Evaluation of a Scheme for Grading the Gross Morphology of the Human Intervertebral Disc (1990)

A five-category grading scheme for assessing the gross morphology of midsagittal sections of the human lumbar intervetebral disc was developed. The ability of three observers to categorize a series of 68 discs with a wide spectrum of morphologies established the comprehensiveness of the classification. Three independent observers tested the reproducibility of the procedure by assignment of grades blindly to duplicate images of 68 discs taken from 15 spines. The intraobserver agreement ranged from 87 to 91%. The interobserver agreement was 61, 64, and 88% for the three pairs, the two low values being attributable to the bias of one observer. The agreement between the assigned and average grades was 85, 92, 68, 90, and 76% for Grades I through V, respectively. Except for Grade III, the disagreements were attributable mainly to the bias of one observer. Both the increase in the grade with age and the finding that all the discs within 14 of 15 spines had a narrow range of grades demonstrated the biologic credibility of the scheme.
Multitone spread spectrum multiple access communications system in a multipath Rician fading channel (2002)

The paper proposes a new multiple access communications system based on the combination of multitone transmission and direct sequence spread spectrum (DS/SS). The performance of this system is investigated for a multipath, slowly Rician fading and frequency selective channel, and a suboptimal receiver based on matched filters. The multiple access interference is also taken into account. The system performance is investigated for selection diversity and maximal ratio combining (Rake reception).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Bioconjugation of Luminescent Silicon Quantum Dots for Selective Uptake by Cancer Cells (2011)

Conventional quantum dots have great potential in cancer-related imaging and diagnostic applications; however, these applications are limited by concerns about the inherent toxicity of their core materials (e.g., cadmium, lead). Virtually all imaging applications require conjugation of the imaging agent to a biologically active molecule to achieve selective uptake or binding. Here, we report a study of biocompatible silicon quantum dots covalently attached to biomolecules including lysine, folate, antimesothelin, and transferrin. The particles possess desirable physical properties, surface chemistry, and optical properties. Folate- and antimesothelin-conjugated silicon quantum dots show selective uptake into Panc-1 cells. This study contributes to the preclinical evaluation of silicon quantum dots and further demonstrates their potential as an imaging agent for cancer applications.
Visualization of Construction Progress Monitoring with 4D Simulation Model Overlaid on Time-Lapsed Photographs (2009)

The ability to effectively communicate progress information and represent as-built and as-planned progress discrepancies are identified as key components for successful project management that allow corrective decisions to be made in a timely manner. However, current formats of reporting (e.g., textual progress reports, progress curves, and photographs) may not properly and quickly communicate project progress. Current monitoring methods also require manual data collection and extensive data extraction from different construction documents, which distract managers from the important task of decision making. Therefore, to facilitate progress monitoring, this paper proposes visualization of performance metrics that aims to represent progress deviations through superimposition of four-dimensional (4D) as-planned model over time-lapsed photographs in single and comprehensive visual imagery. As a part of the developed system, registration of the 4D model with photographs, augmenting photographs, and occlusion removal for progress images are presented. While contextual information is preserved, the as-built photographs are enhanced and augmented with 4D as-planned model in which the performance metrics are visualized. The augmented photographs provide a consistent platform for representing as-planned, as-built, and progress discrepancies information and facilitate communication and reporting processes.
Adeno-Associated Virus-Mediated Gene Transfer to the Brain: Duration and Modulation of Expression (1999)

Adeno-associated virus (AAV) is a promising vector for central nervous system (CNS) gene transfer, but a number of issues must be addressed if AAV is to be used for widespread delivery throughout the CNS. Our aim was to test the effect of dose, route of delivery, and hydroxyurea treatment on brain expression of beta-galactosidase activity after cerebral inoculation with an rAAV-lacZ vector (rAAV-beta-gal). We also wished to test whether an immune response appeared against the vector and the transgene product. We found in BALB/c mice that beta-Gal expression increased during the first 2 months after inoculation, then decreased slightly by 4 months, and continued out to 6, 12, and 15 months in single animals. Cerebral injection produced localized beta-Gal expression that did not diffuse to other regions despite a fivefold increase in injection volume. Intraventricular injection resulted in negligible transduction. Antibodies to AAV capsid protein and beta-Gal appeared at low levels at 2 and 4 months, but correlated poorly with beta-Gal expression and did not prevent readministration of rAAV-beta-gal. Hydroxyurea treatment did not result in increased transduction in vivo. We conclude that our study confirms rAAV vectors as having considerable potential for CNS gene transfer; however, several important problems must be addressed if this vector system is to be used for long-term transduction of the entire brain. Sustained, regulatable expression will be needed if rAAV is to be used in the treatment of chronic CNS disease. The difficulty in delivering AAV to diverse regions of the brain is an important problem that must be overcome if these vectors are to be used for anything beyond localized transduction.
Oxygen-Sensing Reporter Strain of Pseudomonas fluorescens for Monitoring the Distribution of Low-Oxygen Habitats in Soil (1999)

ABSTRACT The root-colonizing bacterium Pseudomonas fluorescens CHA0 was used to construct an oxygen-responsive biosensor. An anaerobically inducible promoter of Pseudomonas aeruginosa , which depends on the FNR (fumarate and nitrate reductase regulation)-like transcriptional regulator ANR (anaerobic regulation of arginine deiminase and nitrate reductase pathways), was fused to the structural lacZ gene of Escherichia coli . By inserting the reporter fusion into the chromosomal att Tn 7 site of P. fluorescens CHA0 by using a mini-Tn 7 transposon, the reporter strain, CHA900, was obtained. Grown in glutamate-yeast extract medium in an oxystat at defined oxygen levels, the biosensor CHA900 responded to a decrease in oxygen concentration from 210 × 10 2 Pa to 2 × 10 2 Pa of O 2 by a nearly 100-fold increase in β-galactosidase activity. Half-maximal induction of the reporter occurred at about 5 × 10 2 Pa. This dose response closely resembles that found for E. coli promoters which are activated by the FNR protein. In a carbon-free buffer or in bulk soil, the biosensor CHA900 still responded to a decrease in oxygen concentration, although here induction was about 10 times lower and the low oxygen response was gradually lost within 3 days. Introduced into a barley-soil microcosm, the biosensor could report decreasing oxygen concentrations in the rhizosphere for a 6-day period. When the water content in the microcosm was raised from 60% to 85% of field capacity, expression of the reporter gene was elevated about twofold above a basal level after 2 days of incubation, suggesting that a water content of 85% caused mild anoxia. Increased compaction of the soil was shown to have a faster and more dramatic effect on the expression of the oxygen reporter than soil water content alone, indicating that factors other than the water-filled pore space influenced the oxygen status of the soil. These experiments illustrate the utility of the biosensor for detecting low oxygen concentrations in the rhizosphere and other soil habitats.
<title>Control aspects of the single-fiber scanning endoscope</title> (2001)

The Single Fiber Scanning Endoscope (SFSE) is a new class of endoscopes being developed at the University of Washington's Human Interface Technology lab which uses combinations of a resonating optical fiber and a single photodetector to produce large field of view, high-resolution images from a small flexible package. Although current prototypes show the validity of the concept, the nonlinear response of the resonant optical fiber under open loop control creates image distortion or limits the frame rate. Due to low damping and nonlinear effects in the fiber, open loop control, phase lock loops, PID control, classical and modern controllers are all unable to produce accurate, reproducible, robust high frequency 2D scans. A nonlinear control scheme, feedback linearization, is capable of accurately producing a scan and is robust to most of the unavoidable manufacturing and environmental variability in the resonant scanner. Through theoretical analysis and simulations, this paper reviews the application of the following variety of open loop and closed loop controllers to the nonlinear scanner of the SFSE: open loop control, modelless closed loop control (phase lock loop and PID control), feedforward plus feedback classical and modern state space tracking control, and nonlinear feedback linearization control.
Preoperative Circulating Tumor Cell Detection Using the Isolation by Size of Epithelial Tumor Cell Method for Patients with Lung Cancer Is a New Prognostic Biomarker (2010)

A high percentage of NSCLC patients show preoperative detection of CNHC by the ISET method. The presence and level of 50 or more CNHCs are associated with worse survival of patients with resectable NSCLC.
The fate of transplants of articular cartilage in the rabbit. (1974)

1. Articular cartilage from immature rabbits was placed in and near the rabbit knee joints for periods up to ten weeks. 2. Autografts of articular cartilage when placed free in the joint soon became adherent to its synovial lining; the cartilage with its subchondral bone remained viable. 3. Homografts remained viable in the presence of joint fluid, but when in contact with synovium antigenic cellular reaction was produced early. The presence of subchondral bone intensified this reaction and led to graft invasion and destruction. 4. Partial thickness homografts of articular cartilage were also antigenic and were absorbed. When full thickness cartilage was used, this cellular invasion was resisted by the zone of provisional calcification which appeared to function as a physical barrier against antigenic cells of the host. 5. When placed in muscle, both autogenous and homogenous grafts failed to survive through lack of nutrition, although the autogenous subchondral bone remained viable. It is inferred that subchondral circulation is not sufficient for cartilage survival and synovial fluid is essential for its proper nutrition. 6. Surviving immature articular cartilage transplants underwent ageing changes.
Agrin-induced specializations contain cytoplasmic, membrane, and extracellular matrix-associated components of the postsynaptic apparatus (1989)

The aims of the studies reported here were to determine the extent to which the specializations induced by agrin on cultured chick myotubes resemble the postsynaptic apparatus and examine how these specializations form. We found that agrin induces the formation of specializations at which at least 6 components of the postsynaptic apparatus are concentrated: one cytoplasmic component [a 43 kDa acetylcholine receptor (AChR)-associated protein], 3 membrane components [AChRs and globular forms of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE)], and 2 extracellular matrix-associated proteins (A12 asymmetric AChE and a heparan sulfate proteoglycan). The accumulation of AChE and BuChE into agrin-induced aggregates occurred in the absence of any change in the amount, rate of synthesis, accumulation, and release, or molecular forms of either enzyme. Thus, agrin affects primarily the distribution of these components of the postsynaptic apparatus and not their metabolism. Agrin-induced formation of AChR aggregates was not prevented by inhibition of protein synthesis, consistent with our previous results that agrin-induced accumulation of AChRs occurs by lateral migration. The accumulation of components of the extracellular matrix would seem less likely to occur by lateral migration and so might require release of newly synthesized proteins; indeed, formation of aggregates of heparan sulfate proteoglycan was prevented by inhibitors of protein synthesis. Thus, different components of the postsynaptic apparatus accumulate in agrin-induced specializations by different mechanisms.
Functional analysis of the individual enhancer core sequences of polyomavirus: cell-specific uncoupling of DNA replication from transcription. (1988)

Polyomavirus (Py) enhancer core elements were compared for their ability to activate Py early transcription and DNA replication in mouse 3T6 cells, lymphoid cell lines, and undifferentiated embryonal carcinoma cells. By examining the pattern of genetic change in a number of cell-specific Py variants, we identified subenhancer sequences that may be functionally important for virus replication. Four such distinct enhancer consensus sequences were synthesized and designated as the A core (homologous with adenovirus 5 E1A enhancer), B core (homologous to the simian virus 40 A enhancer core), C core (containing an inverted repeat within the Py B enhancer), and BPV core (homologous to the bovine papillomavirus enhancer). When used to replace the complete Py B enhancer, single copies of all but the BPV element were able to fully activate Py DNA replication after transfection, but this activation was usually cell type specific. In the PCC4 embryonal carcinoma cells, only the A-core sequence was able to activate transcription and DNA replication. The BPV core sequence containing the Py F441 point change was unable to activate DNA replication in the F9 embryonal carcinoma or any other cell line. No single insertion element was dominant nor did these elements display the wild-type enhancer pattern of cell-specific activation of DNA replication. In addition, differential effects were often observed on the activation of transcription versus DNA replication. In 3T6 cells, transcription could be highly activated by the A core without a corresponding activation of DNA replication. In murine T lymphoid cell lines, the B core activated DNA replication without a corresponding increase in transcription. Furthermore, both DNA replication and, to a lesser degree, transcription often showed a strong tissue-specific dependence on the polarity of the inserted core element for activation.
Self-Assembling RNA Nanorings Based on RNAI/II Inverse Kissing Complexes (2011)

RNA is an attractive biopolymer for nanodesign of self-assembling particles for nanobiotechnology and synthetic biology. Here, we experimentally characterize by biochemical and biophysical methods the formation of thermostable and ribonuclease resistant RNA nanorings previously proposed by computational design. High yields of fully programmable nanorings were produced based on several RNAI/IIi kissing complex variants selected for their ability to promote polygon self-assembly. This self-assembly strategy relying on the particular geometry of bended kissing complexes has potential for developing short interfering RNA delivery agents.
Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression (2011)

Autologous expression of recombinant human proteins in human cells for biomedical research and product development is often hampered by low expression yields limiting subsequent structural and functional analyses. Following RNA and codon optimization, 50 candidate genes representing five classes of human proteins--transcription factors, ribosomal and polymerase subunits, protein kinases, membrane proteins and immunomodulators--all showed reliable, and 86% even elevated expression. Analysis of three representative examples showed no detrimental effect on protein solubility while unaltered functionality was demonstrated for JNK1, JNK3 and CDC2 using optimized constructs. Molecular analysis of a sequence-optimized transgene revealed positive effects at transcriptional, translational, and mRNA stability levels. Since improved expression was consistent in HEK293T, CHO and insect cells, it was not restricted to distinct mammalian cell systems. Additionally, optimized genes represent powerful tools in functional genomics, as demonstrated by the successful rescue of an siRNA-mediated knockdown using a sequence-optimized counterpart. This is the first large-scale study addressing the influence of multiparameter optimization on autologous human protein expression.
Reading Turn by Turn: Hierarchical Attention Architecture for Spoken Dialogue Comprehension (2019)

Comprehending multi-turn spoken conversations is an emerging research area, presenting challenges different from reading comprehension of passages due to the interactive nature of information exchange from at least two speakers. Unlike passages, where sentences are often the default semantic modeling unit, in multi-turn conversations, a turn is a topically coherent unit embodied with immediately relevant context, making it a linguistically intuitive segment for computationally modeling verbal interactions. Therefore, in this work, we propose a hierarchical attention neural network architecture, combining turnlevel and word-level attention mechanisms, to improve spoken dialogue comprehension performance. Experiments are conducted on a multi-turn conversation dataset, where nurses inquire and discuss symptom information with patients. We empirically show that the proposed approach outperforms standard attention baselines, achieves more efficient learning outcomes, and is more robust to lengthy and out-of-distribution test samples.
Autism in Angelman syndrome: implications for autism research (2004)

Angelman syndrome (AS) is a neurodevelopmental disorder characterized by severe mental retardation, ataxia, and a happy/sociable disposition. Maternally, but not paternally, derived defects, such as duplications, within the AS critical region result in autistic symptomatology, suggesting that the UBE3A gene might be implicated in the causation of autism. This study examined the prevalence of autism in AS in 19 children representing three known molecular classes of AS. Children were studied over the course of 1 year. Forty-two percent of this population, eight of 19 children, met criteria for autism according to the Autism Diagnostic Observation Schedule (ADOS). Parents of children who were diagnosed with autism according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV criteria as well as the ADOS - Generic, Module 1 (ADOS-G) were administered the Autism Diagnostic Interview - Revised (ADI-R). Data from the ADI-R were convergent with data from the ADOS-G in all cases. Children with comorbid autism and AS scored lower on measures of language, adaptive behavior, and cognition, and demonstrated a slower rate of improvement over the course of the study. Furthermore, they demonstrated deficits in communication and socialization that mirror those observed in children with idiopathic autism. The study highlights the phenotypic overlap between autism and AS and increases the probability that dysregulation of UBE3A may play a role in the causation of autism.