gebhart/patrepeval huggingface dataset:
Antitumorigenic effect of a mammalian lignan precursor from flaxseed (1996)

Secoisolariciresinol diglycoside (SD), a mammalian lignan precursor found in high-fiber foods, was isolated from flaxseed and tested for effects on mammary tumorigenesis in rats fed a high-fat (20%) diet. Ingestion of purified SD at 1.5 mg/day for 20 weeks starting 1 week after treatment with the carcinogen dimethylbenzanthracene resulted in a 37% reduction (p < 0.05) in the number of tumors per tumor-bearing rat and a 46% reduction (p < 0.05) in the number of tumors per tumor-bearing rat and a 46% reduction (p < 0.05) in the number of tumors per number of rats in each group. Urinary mammalian lignan excretion significantly increased (p < 0.0001) with SD treatment, indicating the conversion of SD to mammalian lignans. No enlargement or gross abnormalities of the major organs were observed in the SD-treated rats. This study showed, for the first time, that SD has an antitumor effect when provided at the early promotion stage of tumorigenesis and may contribute to the health benefits of high-fiber foods.
Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA (2012)

Plasma of cancer patients contains cell-free tumor DNA that carries information on tumor mutations and tumor burden. Individual mutations have been probed using allele-specific assays, but sequencing of entire genes to detect cancer mutations in circulating DNA has not been demonstrated. We developed a method for tagged-amplicon deep sequencing (TAm-Seq) and screened 5995 genomic bases for low-frequency mutations. Using this method, we identified cancer mutations present in circulating DNA at allele frequencies as low as 2%, with sensitivity and specificity of >97%. We identified mutations throughout the tumor suppressor gene TP53 in circulating DNA from 46 plasma samples of advanced ovarian cancer patients. We demonstrated use of TAm-Seq to noninvasively identify the origin of metastatic relapse in a patient with multiple primary tumors. In another case, we identified in plasma an EGFR mutation not found in an initial ovarian biopsy. We further used TAm-Seq to monitor tumor dynamics, and tracked 10 concomitant mutations in plasma of a metastatic breast cancer patient over 16 months. This low-cost, high-throughput method could facilitate analysis of circulating DNA as a noninvasive "liquid biopsy" for personalized cancer genomics.
Prostate-specific antigen: its clinical use and application in screening for prostate cancer (1995)

Prostate cancer in most European countries is the second most frequent cancer in males and the second most frequent cause of cancer death. Prostate specific antigen (PSA) is an important tumour marker, which relates to many aspects of this disease. It has been shown that PSA is helpful in the early diagnosis of prostate cancer and in this respect is superior to other available tests like rectal examination and transrectal ultrasonography. PSA is also helpful in staging of locally confined disease. It can be used to identify or exclude local extension of disease, if combined with T category and grade of differentiation determined on biopsy. The same parameters also give an indication of the presence of lymph node metastases, which may prevent unnecessary and invasive staging procedures in certain groups of patients with favourable prognostic factors and a low PSA value. PSA is less suitable as a marker for metastatic disease. Progression of untreated prostate cancer in various stages can be monitored by PSA. The true value of the marker in this respect is still underexplored. It may be possible that PSA will be shown to differentiate effectively between aggressive and non-progressive disease. In this respect, it could become an essential tool to identify those patients that may not require treatment at all. PSA is also a useful marker for therapy response. An elevation of PSA after radical prostatectomy indicates local or metastatic progression, which will occur within 1-2 years. PSA is an androgen dependent enzyme and decreases under endocrine treatment. It is unexplained why in spite of its endocrine dependent character, PSA rises with endocrine independent progression of prostate cancer.
Role for the Adenosine Triphosphate-Dependent Proteolytic Pathway in Reticulocyte Maturation (1982)

As reticulocytes mature into erythrocytes, organelles and many enzymes are lost. Protein degradation during reticulocyte maturation was measured by monitoring the release of tyrosine from cell proteins. Proteolysis in rabbit red blood cells was directly proportional to the number of reticulocytes and was low in erythrocytes. This process was inhibited by blockers of cellular adenosine triphosphate production and by agents, such as o-phenanthroline, N-ethylmaleimide, and hemin, which inhibit the soluble adenosine triphosphate-dependent proteolytic system. The breakdown of endogenous proteins in reticulocyte extracts was also inhibited by these agents and required adenosine triphosphate. Inhibitors of lysosomal function, however, did not affect proteolysis. Thus, the proteolytic system that degrades abnormal proteins also catalyzes the elimination of proteins during red cell development.
An efficient location and routing scheme for mobile computing environments (1995)

One of the most important issues affecting host mobility is the location and routing scheme that allows hosts to move seamlessly from one site to another. This paper presents a method that exploits the locality properties of a host's pattern of movement and access history. Two concepts, "local region" and "patron service" are introduced based on the locality features. For each mobile host, the local region is a set of designated subnetworks within which a mobile host often moves, and the patrons are the hosts from which the majority of traffic for the mobile host originated. These are used to confine the effects of a host moving, so location updates are sent only to its local area, and to those source hosts which are most likely to call again. Our scheme has the advantages of limiting location updates, and providing optimal routing, while increasing network and host scalability.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
<title>Physical presence: palettes in virtual spaces</title> (1999)

We have built a hand-held palette for touch-based interaction in virtual reality. this palette incorporates a high-resolution digitizing touch screen for input. It is see-through, and therefore does not occlude objects displayed behind it. These properties make it suitable for direct manipulation techniques in a range of virtual reality display systems. We implemented several interaction techniques based on this palette for an interactive scientific visualization task. These techniques, the tool's design, and its limitations are discussed in this paper.
Measuring earthquakes from optical satellite images (2000)

Système pour l'Observation de la Terre images are used to map ground displacements induced by earthquakes. Deformations (offsets) induced by stereoscopic effect and roll, pitch, and yaw of satellite and detector artifacts are estimated and compensated. Images are then resampled in a cartographic projection with a low-bias interpolator. A subpixel correlator in the Fourier domain provides two-dimensional offset maps with independent measurements approximately every 160 m. Biases on offsets are compensated from calibration. High-frequency noise (0.125 m(-1)) is approximately 0.01 pixels. Low-frequency noise (lower than 0.001 m(-1)) exceeds 0.2 pixels and is partially compensated from modeling. Applied to the Landers earthquake, measurements show the fault with an accuracy of a few tens of meters and yields displacement on the fault with an accuracy of better than 20 cm. Comparison with a model derived from geodetic data shows that offsets bring new insights into the faulting process.
Noise-Driven Anisotropic Diffusion Filtering of MRI (2009)

A new filtering method to remove Rician noise from magnetic resonance images is presented. This filter relies on a robust estimation of the standard deviation of the noise and combines local linear minimum mean square error filters and partial differential equations for MRI, as the speckle reducing anisotropic diffusion did for ultrasound images. The parameters of the filter are automatically chosen from the estimated noise. This property improves the convergence rate of the diffusion while preserving contours, leading to more robust and intuitive filtering. The partial derivative equation of the filter is extended to a new matrix diffusion filter which allows a coherent diffusion based on the local structure of the image and on the corresponding oriented local standard deviations. This new filter combines volumetric, planar, and linear components of the local image structure. The numerical scheme is explained and visual and quantitative results on simulated and real data sets are presented. In the experiments, the new filter leads to the best results.
ER–resident chaperone interactions with recombinant antibodies in transgenic plants (2002)

In this study, we demonstrate that the folding and assembly of IgG in transgenic tobacco plants is orchestrated by BiP (binding protein), an endoplasmic reticulum resident chaperone. Expression of BiP and calreticulin was examined in transgenic tobacco plants that express immunoglobulin chains, either singly or in combination to form IgG antibody. BiP mRNA expression was lowest in wild-type nontransformed plants and those that expressed immunoglobulin light chain alone. Higher mRNA levels were detected in plants expressing fully assembled immunoglobulin (light and heavy chains), and the most abundant levels of RNA transcript were found in those plants that expressed immunoglobulin heavy chain alone. Estimation of total BiP demonstrated a similar pattern, with the highest levels detected in plants expressing immunoglobulin heavy chain alone. Immunoprecipitation studies demonstrated that BiP was associated with immunoglobulin chains extracted from protoplast lysates, but not from secreted fluids. Again, most BiP was coprecipitated from plants expressing heavy chain only and those that produced full length IgG. The binding of BiP to Ig heavy chains was ATP-sensitive. Co-expression of heavy and light chain resulted in IgG assembly and displacement of BiP from the heavy chain as the amount of light chain increased. Although calreticulin mRNA and total protein levels varied in a similar manner to those of BiP in the transgenic plants, there was no evidence for association between calreticulin and Ig chains, by coimmunoprecipitation. The results indicate that BiP, but not calreticulin, takes part in immunoglobulin folding and assembly in transgenic plants.
High expression of Toll-like receptor 4/myeloid differentiation factor 88 signals correlates with poor prognosis in colorectal cancer (2010)

Our findings suggest that high expression of TLR4 and MyD88 is associated with liver metastasis and is an independent predictor of poor prognosis in patients with CRC.
A case for parallelism in data warehousing and OLAP (2002)

In recent years the database community has experienced a tremendous increase in the availability of new technologies to support efficient storage and retrieval of large volumes of data, namely data warehousing and On-Line Analytical Processing (OLAP) products. Efficient query processing is critical in such an environment, yet achieving quick response times with OLAP queries is still largely an open issue. We propose a solution approach to this problem by applying parallel processing techniques to a warehouse environment. We suggest an efficient partitioning strategy based on the relational representation of a data warehouse (i.e., star schema). Furthermore, we incorporate a particular indexing strategy, DataIndexes, to further improve query processing times and parallel resource utilization, and propose a preliminary parallel star-join strategy.
Inhibition of Multiple Myeloma Cell Adhesion to Fibronectin by Ephrin Ligation. (2004)

Abstract Multiple myeloma (MM) cell adhesion to fibronectin (FN), mediated via VLA-4 and VLA-5, has been shown to induce resistance to several chemotherapeutic drugs. Disruption of MM cell adhesion to FN and other marrow microenvironment elements might therefore enhance the effects of therapy. We now present the first evidence that Eph-ephrin signaling may be exploited to inhibit MM cell binding to fibronectin. Ephs are transmembrane tyrosine kinases and ephrins are their cell-surface ligands. There are two classes of Ephs and ephrins, A and B. Both Ephs and ephrins can transduce repulsive signals that cause interacting cells to lose contact with each other and with extracellular matrix. We are not aware of any previous systematic study of Eph and ephrin expression or function in MM cells. We have found MM cell lines H929, U266, and RPMI 8226 express members of the A classes of both Ephs and ephrins, but not the B classes. First, we demonstrated ligation with commercially available anti-ephrin A3 antibody was followed by ephrin capping and shedding from the cell surface. We next explored whether ephrin ligation affects MM cell adhesiveness in culture. Whereas H929, U266, and RPMI 8226 cells adhered rapidly to fibronectin-coated plastic surfaces, all three cell lines failed completely to adhere to a mixed coating of FN and rabbit anti-ephrin A3 antibody for a period of 2 hrs. This effect was not seen with FN + normal rabbit Ig. This suggests binding of ephrin A3 (or another cross-reacting A-class ephrin) by solid-state antibody triggers intracellular signals that interfere with initial steps of integrin-mediated adhesion. After 2 hr, spontaneous partial recovery of adhesion occurred, reaching a plateau of approximately 30% of control values by 24 hr. We postulate this recovery occurs via clipping of the extracellular ephrin domain by transmembrane metalloproteases, since recovery of FN adhesion was partially prevented by the metalloprotease inhibitor GM6001 (25 uM). Also consistent with this theory, we found in a separate experiment that GM6001 reduced the shedding of cross-linked A-class ephrins from MM cell lines. In summary, we have demonstrated that manipulation of EPH-ephrin signaling can impair MM-cell adhesion to FN, and that this effect is enhanced by simultaneous inhibition of metalloprotease activity. We are currently studying the effect of A-class ephrin ligation on adhesion-mediated drug resistance in MM cell lines. We also intend to evaluate EPH-ephrin expression in marrow specimens from patients with MM.
Regression of collagen‐induced arthritis with taxol, a microtubule stabilizer (1994)

Taxol completely prevented the induction of CIA and caused significant regression of existing arthritis.
Rabta: A Case Study in International Action (1994)

The allegations concerning the development of a Libyan facility at Rabta for the production of chemical warfare agents, and for the filling of chemical munitions, have already been examined in detail by several authors.1 There is no need to repeat their work, but the Rabta allegations and the response which they generated remain highly instructive; they shed light upon critical questions involved in any study of chemical weapons proliferation, including the difficulties of using intelligence information, the task of co-ordinating action, both nationally and internationally, the relative merits of quiet diplomacy and public disclosure, the achievements of multilateral export controls after several years of endeavour by the Australia Group, and the process of developing a clandestine programme. The controversy exposed the differing priorities of allied governments, aroused tensions between them, and provoked mutual recriminations. In brief, it revealed the many and varied problems involved in trying to curb the spread of chemical weaponry.
A survey on ontology mapping (2006)

Ontology is increasingly seen as a key factor for enabling interoperability across heterogeneous systems and semantic web applications. Ontology mapping is required for combining distributed and heterogeneous ontologies. Developing such ontology mapping has been a core issue of recent ontology research. This paper presents ontology mapping categories, describes the characteristics of each category, compares these characteristics, and surveys tools, systems, and related work based on each category of ontology mapping. We believe this paper provides readers with a comprehensive understanding of ontology mapping and points to various research topics about the specific roles of ontology mapping.
A transgenic mouse model of metastatic prostate cancer originating from neuroendocrine cells (1998)

A transgenic mouse model of metastatic prostate cancer has been developed that is 100% penetrant in multiple pedigrees. Nucleotides -6500 to +34 of the mouse cryptdin-2 gene were used to direct expression of simian virus 40 T antigen to a subset of neuroendocrine cells in all lobes of the FVB/N mouse prostate. Transgene expression is initiated between 7 and 8 weeks of age and leads to development of prostatic intraepithelial neoplasia within a week. Prostatic intraepithelial neoplasia progresses rapidly to local invasion. Metastases to lymph nodes, liver, lung, and bone are common by 6 months. Tumorigenesis is not dependent on androgens. This model indicates that the neuroendocrine cell lineage of the prostate is exquisitely sensitive to transformation and provides insights about the significance of neuroendocrine differentiation in human prostate cancer.
Depletion of mitochondrial DNA in fibroblast cultures from patients with POLG1 mutations is a consequence of catalytic mutations (2008)

We investigated clinical and cellular phenotypes of 24 children with mutations in the catalytic (alpha) subunit of the mitochondrial DNA (mtDNA) gamma polymerase (POLG1). Twenty-one had Alpers syndrome, the commonest severe POLG1 autosomal recessive phenotype, comprising hepatoencephalopathy and often mtDNA depletion. The cellular mtDNA content reflected the genotype more closely than did clinical features. Patients with tissue depletion of mtDNA all had at least one allele with either a missense mutation in a catalytic domain or a nonsense mutation. Four out of 12 patients exhibited a progressive, mosaic pattern of mtDNA depletion in cultured fibroblasts. All these patients had mutations in a catalytic domain in both POLG1 alleles, in either the polymerase or exonuclease domain or both. The tissue mtDNA content of patients who had two linker mutations was normal, and their phenotypes the mildest. Epilepsy and/or movement disorder were major features in all 21. Previous studies have implicated replication stalling as a mechanism for mtDNA depletion. The mosaic cellular depletion that we have demonstrated in cell cultures may be a manifestation of severe replication stalling. One patient with a severe cellular and clinical phenotype was a compound heterozygote with POLG1 mutations in the polymerase and exonuclease domain intrans. This suggests that POLG1 requires both polymerase and 3'-5' exonuclease activity in the same molecule. This is consistent with current functional models for eukaryotic DNA polymerases, which alternate between polymerizing and editing modes, as determined by competition between these two active sites for the 3' end of the DNA.
Multifactorial Analysis of Epidural Spinal Cord Stimulation (1991)

In order to provide a data bank to allow a more precise and effective implementation of spinal cord stimulation, a computerized analysis of 1,375 combinations obtained from electrode arrays located in the thoracic and cervical epidural area was performed. 67 electrode arrays implanted in 34 subjects were subjected to analysis. During the stimulation trial, all the available combinations were systematically tested and the results entered into a computerized database. The study was not meant to analyze the clinical results or the indications of epidural spinal cord stimulation. Parameters studied include position of each electrical contact as related to midline, vertebral level of each contact, distribution of stimulation-induced paresthesiae, and electrical parameters (voltage, rate, pulse width, perception threshold, discomfort threshold, usage range). Analysis of the data allow the surgeon (1) to define the characteristics of the stimulation-induced paresthesiae; (2) to define the spectrum of the electrical parameters used to stimulate the spinal cord; (3) to define the population of implanted electrode arrays/contacts; (4) to study objectively how the position of the electrodes within the spinal canal, their vertebral level and the interelectrode distance affect the electrical parameters and the stimulation-induced responses. The multifactorial systematic analysis of such a large number of combinations provides the basis for further developments in the area of electrical stimulation of the nervous system.
Quantitative Abnormalities of Fetal DNA in Maternal Serum in Preeclampsia (1999)

These observations suggest that preeclampsia is associated with disturbances in the liberation and/or clearance mechanisms of circulating DNA. These results also raise the possibility that measurement of circulating DNA may prove useful as a marker for the diagnosis and/or monitoring of preeclampsia.
Model Based Air Fuel Ratio Control for Reducing Exhaust Gas Emissions (1995)

&lt;div class="htmlview paragraph"&gt;In order to satisfy future demands of low exhaust emission vehicles (LEV), a new fuel injection control system has been developed for SI engines with three-way catalytic converters. An universal exhaust gas oxygen sensor (UEGO) is mounted on the exhaust manifold upstream of the catalytic converter to rapidly feedback the UEGO output signal and a heated exhaust gas oxygen sensor (HEGO) is mounted on the outlet of the converter to achieve an exact air fuel ratio control at stoichiometry. The control law is derived from mathematical models of dynamic air flow, fuel flow and exhaust oxygen sensors (HEGO and UEGO). Experimental results on FTP (Federal Test Procedure) exhaust emissions show a dramatic reduction of HC, CO and NOx emissions and a possibility of practical low emission vehicles at low cost.&lt;/div&gt;