gebhart/patrepeval huggingface dataset:
Epidermal Growth Factor and Ionizing Radiation Up-regulate the DNA Repair Genes<i>XRCC1</i>and<i>ERCC1</i>in DU145 and LNCaP Prostate Carcinoma through MAPK Signaling (2003)

This work examined the importance of radiation-induced and ligand-induced EGFR-ERK signaling for the regulation of DNA repair proteins XRCC1 and ERCC1 in prostate carcinoma cells, DU145 (TP53(mut)), displaying EGFR-TGFA-dependent autocrine growth and high MAPK (ERK1/2) activity, and LNCaP (TP53(wt)) cells expressing low constitutive levels of ERK1/2 activity. Using quantitative RT-PCR and Western analyses, we determined that ionizing radiation activated the DNA repair genes XRCC1 and ERCC1 in an ERK1/2-dependent fashion for each cell line. After irradiation, a rapid increase followed by a decrease in ERK1/2 activity preceded the increase in XRCC1/ERCC1 expression in DU145 cells, while only the rapid decrease in ERK1/2 preceded the increase in XRCC1/ERCC1 expression in LNCaP cells. Administration of EGF, however, markedly increased the up-regulation of phospho-ERK, ERCC1 and XRCC1 in both cell lines. Although the EGFR inhibitor tyrphostin (AG-1478) and the MEK inhibitor PD90859 both attenuated EGF-induced levels of the ERCC1 and XRCC1 protein, PD98059 blocked the induction of ERCC1 and XRCC1 by radiation more effectively in both cell lines. Inhibition of ERK at a level that reduced the up-regulation of DNA repair led to the persistence of apurinic/apyrimidinic (AP) sites of DNA damage and increased cell killing. Taken together, these data imply a complex control of DNA repair activation that may be more generally dependent on MAPK (ERK1/2) signaling than was previously noted. These data provide novel insights into the capacity of the EGFR-ERK signaling to modulate DNA repair in cancer cells and into the functional significance of this signaling.
Regulation of human neutrophil‐mediated cartilage proteoglycan degradation by phosphatidylinositol‐3‐kinase (2001)

The ability of neutrophils to degrade cartilage proteoglycan suggests that the neutrophils that accumulate in the joints of rheumatoid arthritis patients are mediators of tissue damage. The regulatory mechanisms which are relevant to the proteoglycan-degrading activity of neutrophils are poorly understood. Since phosphatidylinositol 3-kinase (PI3-K), protein kinase C (PKC), the extracellular signal-regulated protein kinase (ERK)1/ERK2 and cyclic adenosine monophosphate (cAMP) have been reported to regulate neutrophil respiratory burst and/or degranulation, a role for these signalling molecules in regulating proteoglycan degradation was investigated. Preincubation of human neutrophils with GF109203X (an inhibitor of PKC), PD98059 (an inhibitor of MEK, the upstream regulator of ERK1/ERK2) or with forskolin or dibutyryl cAMP, failed to suppress proteoglycan degradation of opsonized bovine cartilage. In contrast, preincubation of neutrophils with wortmannin or LY294002, specific inhibitors of PI3-K, inhibited proteoglycan degradation. Incubation of neutrophils with cartilage resulted in the activation of PI3-K in neutrophils, consistent with a role for PI3-K in proteoglycan degradation. Activation of PI3-K and proteoglycan degradation was enhanced by tumour necrosis factor-alpha. Degradation caused by neutrophils from the synovial fluid of rheumatoid arthritis patients was also inhibited by wortmannin. These data demonstrate that the proteoglycan degradative activity of neutrophils required PI3-K but not PKC or the ERK1/ERK2/ERK5 cascades and was insensitive to increases in intracellular cAMP concentrations.
Exercise training increases size of hippocampus and improves memory (2011)

The hippocampus shrinks in late adulthood, leading to impaired memory and increased risk for dementia. Hippocampal and medial temporal lobe volumes are larger in higher-fit adults, and physical activity training increases hippocampal perfusion, but the extent to which aerobic exercise training can modify hippocampal volume in late adulthood remains unknown. Here we show, in a randomized controlled trial with 120 older adults, that aerobic exercise training increases the size of the anterior hippocampus, leading to improvements in spatial memory. Exercise training increased hippocampal volume by 2%, effectively reversing age-related loss in volume by 1 to 2 y. We also demonstrate that increased hippocampal volume is associated with greater serum levels of BDNF, a mediator of neurogenesis in the dentate gyrus. Hippocampal volume declined in the control group, but higher preintervention fitness partially attenuated the decline, suggesting that fitness protects against volume loss. Caudate nucleus and thalamus volumes were unaffected by the intervention. These theoretically important findings indicate that aerobic exercise training is effective at reversing hippocampal volume loss in late adulthood, which is accompanied by improved memory function.
Affinity Chromatography and Binding Studies on Immobilized Adenosine 5′‐Monophosphate and Adenosine 2′,5′‐Bisphosphateof Nicotinamide Nucleotide Transhydrogenasefrom <i>Pseudomonas aeruginosa</i> (1976)

Nicotinamide nucleotide transhydrogenase from Pseudomonas aeruginosa was purified to apparent homogeneity with an improved method employing affinity chromatography on N 6 ‐(6‐aminoyl)‐adenosine‐2′,5′‐bisphosphate‐Sepharose 4B. Polyacrylamide gel electrophoresis of the purified transhydrogenase carried out in the presence of sodium dodecyl sulphate, indicated a minimal molecular weight of 55000 ± 2000. The kinetic and regulatory properties of the purified transhydrogenase resembled those of the crude enzyme, i.e., NADPH, adenosine 2′‐monophosphate and Ca 2+ were activators whereas NADP + was inhibitory. Nicotinamide nucleotide‐specific release of binding of the transhydrogenase to N 6 ‐(6‐aminohexyl)‐adenosine‐2′,5′‐bisphosphate‐Sepharose and N 6 ‐(6‐aminohexyl)‐adenosine‐5′‐monophospliate‐Sepharose suggests the presence of at least two separate binding sites for nicotinamide nucleotides, one that is specific for NADP(H) and one that binds both NAD(H) and NADP(H). Binding of transhydrogenase to N 6 ‐(6‐aminohexyl)‐adenosine‐2′,5′‐bisphosphate‐Sepharose and activation of the enzyme by adenosine‐2′,5′‐bisphosphate showed a marked pH dependence. In contrast, inhibition of the Ca 2+ ‐activated enzyme by adenosine 2′,5′‐bisphosphate was virtually constant at various pH values. This discrepancy was interpreted to indicate the existence of separate nucleotide‐binding effector and active sites.
Pathways for aberrant angiogenesis in pancreatic cancer. (2003)

Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease. Although the specific mechanisms that dictate its biological aggressiveness are not clearly established, it is characterized by a variety of molecular alterations as well as by the overexpression of mitogenic and angiogenic growth factors and their receptors. PDACs also express high levels of vascular endothelial growth factor (VEGF). Recent studies indicate that suppression of VEGF expression attenuates pancreatic cancer cell tumorigenicity in a nude mouse model, and that VEGF can exert direct mitogenic effects on some pancreatic cancer cells. These findings suggest that cancer cell derived VEGF promotes pancreatic cancer growth in vivo via a paracrine angiogenic pathway and an autocrine mitogenic pathway, and provide novel opportunities for therapeutic intervention in this deadly disease.
The CAAX peptidomimetic compound B581 specifically blocks farnesylated, but not geranylgeranylated or myristylated, oncogenic ras signaling and transformation. (1994)

Recently developed CAAX peptidomimetic compounds have been shown to be potent and specific inhibitors of farnesyl protein transferase activity and to block the growth of Ras-transformed cells. However, whether this growth inhibitory action is specifically a consequence of blocking oncogenic Ras signaling has not been determined. To address this question, we have utilized mutants of the normally farnesylated oncogenic Ras protein (Ras-F) that are modified by alternative lipids, a geranylgeranyl isoprenoid (Ras-GG) or the fatty acid myristate (Myr-Ras), to determine the specificity of the CAAX peptidomimetic compound, B581. Like Ras-F, both Ras-GG and Myr-Ras are membrane-associated and transforming. Unexpectedly, NIH 3T3 cells transformed by each of the three Ras mutants underwent morphological alteration to a less transformed, but not normal, morphology. However, B581 inhibited the ability of only Ras-F-transformed cells, but not Ras-GG- or Myr-Ras- (or Raf-) transformed cells, to grow in soft agar. Furthermore, although all three lipid-modified versions of Ras stimulated mitogen-activated protein kinase activation, and both Jun and Elk-1 transcriptional activity, B581 inhibited only farnesylated Ras activation of these three downstream components of Ras signaling. Therefore, B581 prevents the growth of Ras-transformed cells by specifically antagonizing Ras-mediated signaling.
Techniques in fractal geometry (1997)

Mathematical Background. Review of Fractal Geometry. Some Techniques for Studying Dimension. Cookie-cutters and Bounded Distortion. The Thermodynamic Formalism. The Ergodic Theorem and Fractals. The Renewal Theorem and Fractals. Martingales and Fractals. Tangent Measures. Dimensions of Measures. Some Multifractal Analysis. Fractals and Differential Equations. References. Index.
Vitamin D Inhibits Adipokine Production and Inflammatory Signaling Through the Vitamin D Receptor in Human Adipocytes (2021)

Vitamin D acts through VDR to inhibit inflammatory pathways and adipokine expression in human adipocytes. Increasing vitamin D status may ameliorate obesity-associated metabolic complications by decreasing adipose tissue inflammation.
Complete attenuation of genetically engineered <i>Plasmodium falciparum</i> sporozoites in human subjects (2017)

Immunization of humans with whole sporozoites confers complete, sterilizing immunity against malaria infection. However, achieving consistent safety while maintaining immunogenicity of whole parasite vaccines remains a formidable challenge. We generated a genetically attenuated Plasmodium falciparum (Pf) malaria parasite by deleting three genes expressed in the pre-erythrocytic stage (Pf p52<sup>-</sup>/p36<sup>-</sup>/sap1<sup>-</sup>). We then tested the safety and immunogenicity of the genetically engineered (Pf GAP3KO) sporozoites in human volunteers. Pf GAP3KO sporozoites were delivered to 10 volunteers using infected mosquito bites with a single exposure consisting of 150 to 200 bites per subject. All subjects remained blood stage-negative and developed inhibitory antibodies to sporozoites. GAP3KO rodent malaria parasites engendered complete, protracted immunity against infectious sporozoite challenge in mice. The results warrant further clinical testing of Pf GAP3KO and its potential development into a vaccine strain.
Plasmons in the Metallic Nanoparticle−Film System as a Tunable Impurity Problem (2005)

We show that the plasmon resonances of a metallic nanoparticle interacting with the surface plasmons of a metallic film is an electromagnetic analogue of the spinless Anderson-Fano model. This is the same model used to describe the interaction of a localized electronic state with a continuous band of electronic states. The three characteristic regimes of this model are realized here, where the energy of the nanoparticle plasmon resonance lies above, within, or below the energy band of surface plasmon states. These three interaction regimes are controlled by film thickness. The latter regime is experimentally observed and identified.
Image Cytometric Measurement of Nuclear Proliferation Markers (MIB-1, PCNA) in Astrocytomas:<i>Prognostic Significance</i> (1998)

Proliferative activity in astrocytomas, measured by image cytometry, was related to prognosis. Fifty-eight astrocytic neoplasms (grade 1 or 2, 11; grade 3, 31; glioblastoma multiforme, 16) were immunostained for Ki-67 (MIB-1; 1:50) and proliferating cell nuclear antigen (PCNA; prediluted). Proliferative activity (nuclear immunostain) was measured as the percentage positive nuclear area by image cytometry. With a median of 12.0% and 24.0% for MIB-1 and PCNA, respectively, for all astrocytomas, the mean percentage positive nuclear area for MIB-1 and PCNA was, respectively, 3.06% and 13.11% in low-grade (1 or 2) astrocytomas, 14.34% and 29.68% in high-grade (3) astrocytomas, and 18.77% and 44.11% in glioblastoma multiforme (grade 4). One-way analysis of variance showed a significant correlation between the histologic grade and MIB-1 and between the histologic grade and PCNA. The Cox Proportional Hazards Regression Model showed a statistically significant correlation between survival and MIB-1 and between survival and PCNA. Increasing proliferation correlated with shortened survival. Proliferation in astrocytomas, measured as MIB-1 and PCNA by image cytometry, correlates significantly with histologic grade and patient survival, providing useful additional information for determining the diagnosis and prognosis.
Characterizing and removing strong TMS-induced artifacts from EEG (2010)

Transkraniaalisen magneettistimulaation (TMS) ja elektroenkefalografian (EEG) avulla voidaan stimuloida aivokuorta ei-invasiivisesti ja samalla tarkkailla aiheutetun aivoaktivaation leviämistä. TMS-stimulaatio kuitenkin aiheuttaa EEG-signaaliin artefaktoja, jotka voivat kestää jopa kymmeniä millisekunteja ja kokonaan peittää tutkittavan aivoaktiivisuuden. Lihasten aktivoituminen aiheuttaa artefaktoja erityisesti lateraalisilla aivoalueilla, mm. stimuloitaessa aivojen pääasiallisia kielialueita. \n\nTämän työn on tarkoitus oli määrittää, mistä artefaktat johtuvat, ja kuinka niitä voitaisiin pienentää mittauksen aikana ja sen jälkeisessä data-analyysissä. Artefaktojen todettiin olevan suurimmillaan stimuloitaessa anteriorisia ja lateraalisia aivoalueita. Näillä alueilla artefaktojen poistoa vaikeuttavat niiden voimakkuus ja pitkä kesto. \n\nArtefaktojen poistoon analyysivaiheessa kokeiltiin kahta menetelmää. Riippumattomien komponenttien analyysi (independent component analysis, ICA) ja monilähdemalliin perustuva korjaus pystyivät poistamaan osan häiriöpiikeistä, mutta vaikuttivat myös aivoperäiseen signaaliin artefaktan aikana ja jälkeen.
WAIO: Improving Virtual Machine Live Storage Migration for the Cloud by Workload-Aware IO Outsourcing (2015)

Virtual Machine (VM) live storage migration is widely performed in the current cloud data centers, for the purposes of load balance, hardware maintenance and system upgrade. Nevertheless, conventional migration approaches, such as Dirty Block Tracking (DBT), do not address the problem of IO interference between VM IO requests and Migration IO requests during the migration period, which degrades both the VM IO performance and the migration performance. In this paper, we propose a Workload-Aware IO Outsourcing scheme, short for WAIO, to improve the VM live storage migration efficiency. WAIO effectively outsources the VM's working set to a surrogate device during the migration and creates separate IO path for servicing the VM IO requests. By outsourcing VM IO requests from the original storage to the surrogate device, the VM live storage migration process can be performed on the original storage, no longer interfered, while the outsourced VM IO requests are serviced separately and thus much more quickly. Our lightweight prototype implementation of WAIO and extensive trace-driven experiments demonstrate that, compared with the existing migration approach DBT, WAIO significantly improves the VM's IO performance during the migration process. Moreover, WAIO allows the hypervisor to migrate a VM at a higher migration speed, without sacrificing the VM's IO performance.
Social cues in animated conversational agents (2005)

In human-computer interaction people often interpret the interaction with the computer as interactions with humans. The social agency theory suggests that social cues like the face and voice of the agent motivate this interpretation. In two off-line experiments in which comprehension scores and liking ratings were collected, we found that participants preferred natural agents with natural voices, as predicted by the social-cue hypothesis. Although female agents with male voices formed an exception, this was explained by a stereotype effect. These findings support the social-cue hypothesis and the social agency theory that human characteristics are applied in the perception of computational animated conversational agents. Copyright © 2005 John Wiley & Sons, Ltd.
Unique phenotype of hepatocellular cancers with exon‐3 mutations in beta‐catenin gene† (2008)

Thus, HCCs that harbor missense mutations in exon-3 of CTNNB1 exhibit, histologically, a more aggressive phenotype. Also, CTNNB1 mutations might lead to HCC in the absence of cirrhosis. Finally, FL-HCC cases display a unique up-regulation of tyrosine-phosphorylated-beta-catenin, suggesting robust receptor tyrosine kinase signaling in this tumor type.
La ciencia cognitiva de la emoción y la aproximación psicoterapeutica EMDR en el tratamiento de la depresión. Una breve revisión teórica (2006)

A negative surgical margin is mandatory for the effective local control of PT recurrence, and a minimal margin clearance may be sufficient. For distant metastases, the inherent characteristics of PTs are important, thus it may be prudent to evaluate additional histologic features, including necrosis, for patients' prognostication.
C5b-9 Terminal Complex Protects Oligodendrocytes from Apoptotic Cell Death by Inhibiting Caspase-8 Processing and Up-Regulating FLIP (2006)

Activation of the terminal complement cascade involving C5 to C9 proteins has a beneficial role for oligodendrocytes (OLG) in experimental allergic encephalomyelitis, an animal model of multiple sclerosis, by protecting them from apoptotic cell death. We have previously shown that sublytic C5b-9 complexes, through posttranslational regulation of Bad, inhibit the mitochondrial pathway of apoptosis induced by serum deprivation. In the present study, we examined the possible involvement of the caspase-8 and Fas pathway in OLG apoptosis and the role of C5b-9 in this process. In a serum-free defined medium, OLG undergo apoptosis and differentiation concomitantly. Under this condition, we found that caspase-8 processing was increased in association with Bid cleavage and markedly reduced expression of cellular FLIP long isoform protein. The caspase-8 inhibitor Z-IETD-FMK inhibited cell death associated with differentiation in a dose-dependent manner. Exposure to C5b-9 induced an inhibition of caspase-8 activation, Bid cleavage, and a significant increase in expression of cellular FLIP long isoform. These C5b-9 effects were reversed by PI3K inhibitor LY294002. C5b-9 also down-regulated the expression of FasL and the Fas-induced apoptosis. These data suggest that C5b-9 through PI3K signaling can rescue OLG from Fas-mediated apoptosis by regulating caspase-8 processing.
Authoring sensor-based interactions by demonstration with direct manipulation and pattern recognition (2007)

Sensors are becoming increasingly important in interaction design. Authoring a sensor-based interaction comprises three steps: choosing and connecting the appropriate hardware, creating application logic, and specifying the relationship between sensor values and application logic. Recent research has successfully addressed the first two issues. However, linking sensor input data to application logic remains an exercise in patience and trial-and-error testing for most designers. This paper introduces techniques for authoring sensor-based interactions by demonstration. A combination of direct manipulation and pattern recognition techniques enables designers to control how demonstrated examples are generalized to interaction rules. This approach emphasizes design exploration by enabling very rapid iterative demonstrate-edit-review cycles. This paper describes the manifestation of these techniques in a design tool, Exemplar, and presents evaluations through a first-use lab study and a theoretical analysis using the Cognitive Dimensions of Notation framework.
Colloidal particle-size determination by gel filtration. (1979)

The particle sizes of technetium-99m sulfur colloid and technetium-99m antimony sulfide colloid are determined by gel filtration. These results are compared with those obtained by electron microscopy and by ultrafiltration. It is shown that gel filtration is suitable for particle-size determination below 100 nm, whereas above this size ultrafiltration provides the most convenient method.
Quick positional health assessment for industrial robot prognostics and health management (PHM) (2017)

Robot calibration and performance will degrade if proper maintenance isn't performed. There have been challenges for manufacturers to optimize the maintenance strategy and minimize unexpected shutdowns. Prognostics and health management (PHM) can be applied to industrial robots through the development of performance metrics, test methods, reference datasets, and supporting tools. A subset of this research involves developing a quick health assessment methodology emphasizing the identification of the positional health (position and orientation accuracy) changes. This methodology enables manufacturers to quickly assess the static/dynamic position and orientation accuracies of their robot systems. In this paper, the National Institute of Standards and Technology's (NIST) effort to develop the measurement science to support this development is presented, including the modeling and algorithm development for the test method, the advanced sensor development to measure 7-D information (time, X, Y, Z, roll, pitch, and yaw), algorithms to analyze the data, and a use case to present the results.
Kamikaze Truckers in Postwar Japan (2019)

Many Japanese workers in lower-paying positions were drawn to the growing trucking sector in the 1950s and 1960s, characterized by contingency and the thrill of risk and reward, in contrast to the stasis of lifetime employment guarantees emerging in other sectors of the economy. The gamified reward structure in trucking, however, led to a spike in traffic accidents and a backlash against “kamikaze trucks.” Only after regulations and enforcement limited the most dangerous kinds of incentives did meaningful forms of play emerge at work from the bottom up, rather than the stultified forms imposed by businesses from the top down.
Discovering Feedback and Coupled Feedback Loops in KEGG Pathways through Cross-Map Identification (2013)

Each gene regulatory network (GRN) involves a set of DNA components and indirectly interacts each other to control gene expression rates. Especially, some sub-networks appear in a GRN holding feedback loop or coupled feedback loop mechanisms, which possess specific relationships and aim to maintain certain functional conditions. Many cases have been reported and experimentally verified the existence of feedback and coupled feedback loops in transcription regulatory networks. However, most feedback loops were not shown directly from the pathways reported by KEGG database. In this study, we integrated all possible cross-regulatory pathways within KEGG maps through examining the feedback relationship among all genes. A total of 427 biological pathway maps were verified individually and an on-line web based system was designed for identifying a specified gene for its possible feedback relationship. In addition, paralogous gene information was also considered for discovering potential coupled feedback loop relationships. There are 50 newly identified feedback loops and 124 coupled feedback loops were found in this study, of which 48 (96%) feedback loops were constructed from different KEGG maps. The built cross-linked pathways could facilitate biologists in understanding how the unveiled dynamic patterns of gene regulation maintain the balance of a specific biological function.