gebhart/patrepeval huggingface dataset:
Association of low serum levels of transforming growth factor β1 (TGF-β1) and high levels of vascular endothelial growth factor-A (VEGF-A) following neoadjuvant chemoradiotherapy with poor outcome in esophageal cancer patients receiving combined modality therapy: A preliminary analysis using proximity ligation assay. (2013)

80 Background: Currently, serum biomarkers do not influence the treatment of esophageal cancer. The purpose of this project is to investigate, using the proximity ligation assay (PLA), serum biomarkers that predict treatment response and survival outcome for patients with locally advanced esophageal cancer (LAEC) undergoing neoadjuvant concurrent chemoradiotherapy (CCRT) followed by radical esophagectomy. Methods: From 2004 to 2011, 79 patients with LAEC receiving CCRT of taxane-based chemotherapy and 40 Gy followed by curative surgery were enrolled in this study. Serum samples were collected before and within one month after CCRT. Fifteen biomarkers (Axl, BMP2/4, EGFR, FAM84B, Gas6, Her2, IGFBP3, MMP1, MMP13, OPN, PDGFR-α, Periostin, SPARC, TGF-β1, VEGF-A) were analyzed using PLA. Pathological responses were classified into complete response (CR), microscopic residual (MicroR), or macroscopic residual (MacroR). Associations between serum level of each biomarker and pathological response, disease-free survival (DFS), and overall survival (OS) were evaluated by ANOVA and Log-rank tests. Results: Of 79 patients, 30 had CR (38%), 37 had MicroR (47%) and 12 had MacroR (15%). With a median follow-up of 54.5 months, the median OS and DFS were 34 and 43 months, respectively. Among evaluated biomarkers, TGF-β1 was the most significant one associated with pathological response (p=0.009, two-way ANOVA), with higher post-CCRT TGF-β1 levels predicting better response (p=0.035, one-way ANOVA). Patients with higher post-CCRT TGF-β1 levels (≥3 rd quartile) had significantly better DFS (median not reached vs. 27 months, p=0.03). Patients with both lower levels of post-CCRT TGF-β1 and higher levels of VEGF-A had significantly worse DFS (13 months, p=0.001) and OS (18 months, p=0.035). Conclusions: Post-CCRT serum TGF-β1 and VEGF-A levels by PLA may be used to predict pathological response and survival outcome for esophageal cancer patients receiving combined modality therapy.
[Influence of insertion-deletion polymorphism of the angiotensin converting enzyme gene on left ventricular hypertrophy in patients with aortic stenosis--differences in men and women]. (2002)

1. Left ventricle hypertrophy in pts aortic stenosis is higher in men than in women. 2. In women left ventricle hypertrophy is related with ejection fraction, maximal aortic gradient, age and I/D ACE polymorphism; in men it is related to EF, MGA and I/D ACE polymorphism. 3. The influence of I/D ACE polymorphism on the left ventricle hypertrophy is divergent in women and men--in women related to the lack of DD polymorphism, in men related to the presence of DD polymorphism.
Polymerase Gamma Mutator (PolG) Mice Rely on Increased Glycolytic Flux for Energy Production (2015)

PolG mice have reduced mitochondrial oxidative capacity secondary to systemic mitochondrial dysfunction, and subsequently show exercise intolerance. While the deleterious effects on oxidative capacity in the PolG mice have been clearly documented, assessment of a compensatory increase in anaerobic capacity in PolG mice is lacking. Thus, we sought to delineate the extent of glycolysis/gluconeogensis as a means of energy production in the PolG mice. PolG and wild‐type (WT) littermates were sacrificed at 10 mths of age, and blood/tissues were harvested. Primary dermal fibroblasts were also isolated from the animals and used to measure basal/maximal glycolysis using the Glycolysis stress test (Seahorse Bioscience). PolG mice displayed higher respiratory exchange ratio (RER) values, coupled with 55% lower locomotor activity compared to littermate WT mice (P < 0.05). PolG mice displayed resting hypoglycemia (3.4 mM), concomitantly with lower glucose levels throughout the GTT test as compared to WT, ~3‐fold higher PFK content, and elevated plasma lactate levels (>10 mM)(all P < 0.05). In vitro experiments provide further proof that PolG derived dermal fibroblasts have an ~50% higher basal and maximal rate of glycolysis vs . WT control. It is likely that the higher lactate content serves as substrate for the Cori cycle to generate glucose in the liver via gluconeogenesis. Indeed the mRNA content of two important gluconeogenic liver enzymes, G6P and PEPCK, was increased by ~3‐4x fold in the POLG mice compared to WT. Lactic acidosis and hypoglycemia have been associated with poor prognosis in a variety of mitochondrial diseases, and the presence in the PolG animals is a novel finding that warrants further attention. Funded by CIHR.
Regulation of cisplatin-resistant head and neck squamous cell carcinoma by the SRC/ETS-1 signaling pathway (2019)

Our results demonstrate that the SRC/ETS-1 pathway plays a crucial role and could be a key therapeutic target in cisplatin-resistant HNSCC treatment.
Integrated-Circuit Packaging (2017)

This chapter focuses on the thermo-mechanical behavior of plastic area-array packages. The role of packaging in semiconductor electronic applications is to protect and preserve the performance of the semiconductor device from electrical, hygro-thermo-mechanical, and chemical corruption or impairment. An experimental methodology has been described integrating material characterization, experimental measurements, and modeling verification in an attempt to develop a capability to predict the thermo-mechanical behavior of the package. The concern for structural integrity due to thermal deformation of the solder balls has been recognized from the beginning of the development of flip-chip packages. The results demonstrated that the underfill properties can be modified by changing the filler content, which in turn affects the thermal deformation of the flip-chip packages. An experimental methodology has been described integrating material characterization, experimental measurements, and modeling verification in an attempt to develop a capability to predict the thermo-mechanical behavior of the package.
An insight into the role of human pancreatic lithostathine. (2003)

Human lithostathine was initially isolated from pancreatic stones in patients with alcoholic calcifying chronic pancreatitis. It is secreted into the pancreatic juice where it was believed to inhibit stone formation. The N-terminal undecapeptide was assumed to play an important role in the mechanism, by adsorption to the crystal surface. Later, the role of lithostathine in calcite formation and growth was questioned, together with the associated mechanism of action. In particular, although lithostathine adsorbs on calcite crystal, this property does not now seem to be specific. Moreover, the N-terminal undecapeptide is not likely to have, by itself, the function of the entire protein. The different aspects of this controversy are reviewed and discussed, particularly in the light of recent structural biology. Comparative biological data now available allow us to draw an interesting parallel between lithostathine and other related proteins. Finally, lithostathine might affect stone formation and may also have another function which could be investigated in the other proteins belonging to the same structural family.
Building a Repository of Background Knowledge Using Semantic Skeletons. (2006)

We build the knowledge representation machinery for answering complex questions in poorly formalized and logically complex domains. Answers are annotated with deductively linked logical expressions (semantic skeletons), which are to be matched with formal representations for questions. Technique of semantic skeletons is a further development of our semantic headerbased approach to question answering. The question-answering technique has been implemented for the financial and legal domains, which are rather sophisticated on one hand and requires fairly precise answers on the other hand.
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow/><mml:mrow><mml:mn>55</mml:mn></mml:mrow></mml:msup></mml:mrow><mml:mi>Mn</mml:mi></mml:math>NMR Investigation of Electronic Phase Separation in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi>La</mml:mi></mml:mrow><mml:mrow><mml:mn>1</mml:mn><mml:mo>−</mml:mo><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>Ca</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="italic">x</mml:mi></mml:mrow></mml:msub></mml:mrow><mml:mrow><mml:msub><mml:mrow><mml:mi>MnO</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>for<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mn>0.2</mml:mn><mml:mi>≤</mml:mi><mml:mspace/><mml:mi mathvariant="italic">x</mml:mi><mml:mspace/><mml:mi>≤</mml:mi><mml:mn>0.5</mml:mn></mml:math> (2000)

55Mn NMR line shape measurements in La1-xCaxMnO3 for 0.20< or =x< or =0.50 provide experimental evidence about the existence of two distinct regions in the T-x magnetic phase diagram, where the homogeneous ferromagnetic (FM) metallic state is separated into FM metallic and FM insulating regions. These results are in agreement with recent theoretical predictions, which reveal a novel electronic phase separation in two FM states, providing orbital ordering and Jahn-Teller phonons are taken into consideration.
SIX WEEKS OF TREADMILL TRAINING AT MILD RELATIVE EXERCISE INTENSITY ATTENUATES DISEASE PROGRESSION IN A RAT MODEL OF PULMONARY ARTERIAL HYPERTENSION (2013)

Brown, M.1; Crist, J.1; Gaidoo, R.1; Little, N.2; Fisher, A.2; Presson, R.2; Lahm, T.2; Petrache, I.2 Author Information
Domain structure of HMGB1, cysteine residues of HMGB1 and oxidation, hcDNA. (2015)

<p>(<b>A</b>) Domain structure of HMGB1 with two DNA binding domains, and polyanionic C-tail. (<b>B</b>) Schematic representation of cysteine residues of HMGB1 and formation of a disulphide bridge between Cys23 and Cys45. (<b>C</b>) Mild oxidation of HMGB1 in the presence of Cu<sup>2+</sup> results in increased mobility in PAGE due to formation of an intramolecular disulphide bond by opposing Cys23 and Cys45, in agreement with MALDI-TOF mass spectrometry. Equal amounts (4 µg) of oxidized or reduced HMGB1 samples were loaded on the SDS-15%-polyacrylamide gel. Notice that oxidization of HMGB1 compromised Coomassie blue-staining of the protein in the gel. Arrow indicates electrophoretic mobility of HMGB1 dimer (formed due to an intermolecular cross-link of two HMGB1 molecules via the disulphide bridge). (<b>D</b>) Schematic drawing of hemicatenated DNA loops (hcDNA). hcDNA was created from a sequence containing a tract of poly(CA)·poly(TG) that can form a loop maintained at its base by hemicatenane, i.e. the junction of two DNA duplexes in which one of the strands of one duplex passes between the two strands of the other duplex <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089070#pone.0089070-Gaillard2" target="_blank">[26]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089070#pone.0089070-Lyubchenko1" target="_blank">[42]</a>. The drawing was kindly provided by François Strauss (National Museum of Natural History, Paris, France).</p>
Compositional Simulation of WAG Processes for a Viscous Oil (2003)

Abstract The goal of this work is to develop a compositional model for WAG injection in a medium-viscosity oil, low-temperature reservoir like Schrader Bluff Pool in the Milne Point Unit, Alaska. Compositional simulation of WAG displacement with CO2-NGL and Prudhoe Bay gas-NGL mixtures shows that three-hydrocarbon phases form in situ because of low temperature. A four-phase relative permeability formulation has been developed by considering the mixed-wettability of the formation and the saturation paths. The simulation results are compared with the laboratory experimental results from the literature. The sensitivity of the laboratory-scale oil recovery to relative permeability, pressure and solvent composition is studied. The sensitivity of oil recovery in a 2D quarter five-spot pattern to relative permeability, WAG ratio, slug size is also studied. CO2 – NGL mixture is a very effective solvent for this reservoir. The minimum miscibility enrichment is more sensitive to pressure for Prudhoe Bay gas – NGL mixtures than in the case of CO2 – NGL mixtures. The oil production rate is sensitive to relative permeability formulation. Oil recovery is faster at lower WAG ratio and higher slug size.
Soft error reduction in combinational logic using gate resizing and flipflop selection (2006)

Soft errors in logic are emerging as a significant reliability problem for VLSI designs. This paper presents novel circuit optimization techniques to mitigate soft error rates (SER) of combinational logic circuits. First, we propose a gate sizing algorithm that trades off SER reduction and area overhead. This approach first computes bounds on the maximum achievable SER reduction by resizing a gate. This bound is then used to prune the circuit graph, arriving at a smaller set of candidate gates on which we perform incremental sensitivity computations to determine the gates that are the largest contributors to circuit SER. Second, we propose a flipflop selection method that uses slack information at each primary output node to determine the flipflop configuration that produces maximum SER savings. This approach uses an enhanced flipflop library that contains flipflops of varying temporal masking ability. Third, we propose a unified, cooptimization approach combining flipflop selection with the gate sizing algorithm. The joint optimization algorithm produces larger SER reductions while incurring smaller circuit overhead than either technique taken in isolation. Experimental results on a variety of benchmarks show SER reductions of 7.9X with gate sizing, 6.6X with flipflop assignment, and 28.2X for the combined optimization approach, with no delay penalties and area overheads within 5--6%. The runtimes for the optimization algorithms are on the order of 1--3 minutes.
Coupled thermo-mechanical-metallurgical analysis during the cooling of steel pieces (1992)

peer reviewed
Organización espontánea de puntos cuánticos de InSb crecidos por ALMBE sobre substratos de InP (1997)

El crecimiento autoorganizado de puntos cuánticos de InSb sobre substratos de InP mediante epitaxia de haces moleculares ha sido caracterizado mediante microscopía electrónica de transmisión y microscopía de fuerzas atómicas a fin de estudiar la morfología y establecer el mecanismo de relajación de las estructuras. Medidas de difracción de electrones de alta energía durante el crecimiento de las muestras indican una transición en el modo de crecimiento de bidimensional a tridimensional a partir de un espesor total equivalente depositado de 1.1 monocapas atómicas de InSb. Los puntos cuánticos tienen en general, una buena calidad cristalina así como una distribución superficial homogénea, pero una alta anisotropía en las dimensiones entre las direcciones [110] y [110]. Así mismo, se encuentra una rugosidad superficial, también afectada de un alto grado de anisotropía, siendo las crestas y los valles paralelos a la dirección de elongación de las islas. Las imágenes de microscopía electrónica revelan un facetado de las estructuras según planos (001) que las limitan por la parte superior y planos {111}, {113} y {114}, que las limitan lateralmente. Las tensiones son eficazmente relajadas por la presencia de una red de dislocaciones situada en la interficie InSb/InP.
Desarrollo y validación de un modelo de elementos finitos del segmento lumbar l4-l5-s1 para estudio biomecánico de la columna vertebral (2017)

Este libro presenta todo el proceso que llevo al desarrollo de un modelo de elementos finitos del segmento L4-L5-S1 validado experimentalmente para el estudio biomecanico de la columna lumbar humana. Con el objeto de realizar una validacion mas exacta del modelo, se realizaron experimentos In vitro a los segmentos L4-L4 y L5-S1 con el metodo de reduccion gradual, procedimiento que solo habia sido aplicado al segmento L4-L5, donde se encontraron diferencias significativas en el rango de movimiento (ROM) entre el segmento L5-S1 y el segmento L4-L5. Con los resultados experimentales, se calibro el modelo de elementos finitos agregando cada una de las estructuras del segmento paso a paso, lo cual permitio realizar una determinacion mas precisa del aporte mecanico de cada componente del segmento. Finalmente, se realizo un analisis estadistico del anillo fibroso con el objeto de estudiar la influencia en el ROM de las constantes elasticas de las fibras, del angulo de cuna y el area del anillo. Se encontro que el ROM posee una mayor sensibilidad al parametro elastico que representa la rigidez inicial de las fibras y al area del anillo fibroso
Mathematics of Information Processing (1986)

Diameters of communication networks by F. R. K. Chung The theory of data dependencies--a survey by R. Fagin and M. E. Vardi Transaction management by H. Garcia-Molina Fundamental database issues by B. E. Jacobs Data compression algorithms by V. S. Miller Application of category theory of structural sets to modelling of information bases of systems by A. A. Tuzhilin.
Target acquisition: Human observer performance studies and TARGAC model validation (Final Report) (1995)

Human target acquisition performance was studied using the thermal imagery that was collected during Battlefield Emissives Sources Trials under the European Theater Weather and Obscurants, (BEST TWO), organized by NATO AC243/Panel4/RSG.l5 in 1990. Recognition and identification probabilities were measured for a large number of stationary and moving targets at ranges between 1 and 4 km. Target detection was not investigated in a number of carefully controlled laboratory experiments. The target acquisition model (TAROAC) was validated by comparing its predictions with observed recognition ranges. For all trials used in the observer experiments, TARGAC predictions were calculated on the basis of meteorological, target, background, and time information measured in the field. The major conclusion of the observer experiments is that the human acquisition performance depends considerably on factors such as target structure, local terrain structure, and cognitive factors. In TARGAC, these factors are not modeled. For the best two situation, the model predictions were determined solely by target size and thermal imager resolution limit. A quantitative comparison between actual and predicted recognition ranges shows that TARGAC systematically underestimates human acquisition performance: on average, observed recognition ranges are a factor of 1.8 longer than the model predictions. (DTIC)
Synergistic effect of human relaxin and progesterone on human myometrial contractions (1982)

In an in vitro human myometrial strip system, both relaxin and progesterone can independently decrease the amplitude of spontaneous myometrial contractions. However, progesterone and relaxin synergize in this action. Doses of relaxin and progesterone which independently are ineffective, together inhibit myometrial contraction amplitude. Relaxin and progesterone are both products of the corpus luteum, a structure necessary for early pregnancy maintenance. The synergistic action of relaxin and progesterone in vitro suggests a similar in vivo physiologic effect in establishing uterine quiescence.
Abstract 5326: EZH2 regulation through lysine 63 linked ubiquitination in prostate cancer (2017)

Abstract Enhancer of zeste homolog 2 (EZH2) plays crucial roles on the development of cells and tissues as well as the progression of prostate cancer (PCa) and castration resistant prostate cancer (CRPC). EZH2 can upregulate and activate progenitor genes including androgen receptor (AR) and the target genes. However, the mechanisms by which EZH2 is regulated in PCa remain elusive. Literature reports that tumor necrosis factor (TNF) receptor associated factor 6 (TRAF6) is essential for both normal tissue development and regulation of oncogenic signaling pathways in cancers. In this study, we reported that EZH2 is regulated by PTEN and SKP2 network in PCa. Specifically, we showed that the aberrant upregulation of EZH2 and histone H3 lysine 27 trimethylation (H3K27me3) in both Pten null mouse embryonic fibroblasts (MEFs) in vitro and prostate tumors of Pten null mice in vivo, as compared to the controls. EZH2 levels were negatively correlated with TRAF6 in human PCa cells upon SKP2 dysregulation. Immunofluorescence (IF) staining results showed a co-localization of EZH2 and TRAF6 in nucleus of PC3 cells, and co-immunoprecipitation (co-IP) analysis further confirmed a physical binding of EZH2 and TRAF6 in PC3 cells. Ectopic expression of TRAF6 promoted the K63-linked polyubiquitination of EZH2 to decrease EZH2 and H3K27me3 levels in PCa cells. Conversely, TRAF6 knockdown resulted in a reduction of EZH2 polyubiquitination with an increase of EZH2 and H3K27me3 levels in PCa cells. Furthermore, the catalytically dead mutant TRAF6 C70A abolished the TRAF6-mediated polyubiquitination of human EZH2 in vivo in 293T cells and in vitro in the recombinant human EZH2 protein, as compared with TRAF6 WT. Together, we report for the first time a novel mechanism on EZH2 ubiquitination and an important signaling network of SKP2-TRAF6-EZH2-H3K27me3 in PCa cells. Our findings provide valuable clues on the mechanism and efficiency of targeting EZH2 in PCa and CRPC . Note: This abstract was not presented at the meeting. Citation Format: Wenfu Lu, Shenji Lu, Bo Li, Yingqiu Xie, Michael G. Izban, Billy R. Ballard, Sandeep A. Sathyanarayana, Samuel E. Adunyah, Robert J. Matusik, Zhenbang Chen. EZH2 regulation through lysine 63 linked ubiquitination in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5326. doi:10.1158/1538-7445.AM2017-5326
Tyrphostins inhibit follicle-stimulating hormone-mediated functions in cultured rat ovarian granulosa cells. (1993)

FSH induces the expression of cholesterol side-chain cleavage cytochrome P450 (P450scc) in rat ovarian granulosa cells. The present study reveals that the tyrphostin AG18, a member of novel protein tyrosine kinase inhibitors, can arrest the FSH-induced synthesis of P450scc with an apparent IC50 of 30 microM. Total inhibition of P450scc expression was achieved at 80 microM AG18. AG18-mediated inhibition of P450scc was also observed when the enzyme was induced by prostaglandin E2, forskolin, or 8-bromo-cAMP. Studies examining functional LH receptors showed that the tyrphostin inhibits the expression of FSH-induced LH receptors. The drug did not affect FSH-induced cAMP accumulation, suggesting that it may interfere with the flow of FSH signal transduction at a site distal intracellular accumulation of cAMP. Control experiments demonstrated that the inhibitory action of AG18 was reversible, did not hamper total protein synthesis in the cells, and did not change the adenine nucleotide (ATP:ADP:AMP) ratio or their levels in the treated cells. A cell-free assay of cAMP-dependent protein kinase showed that the tyrphostin AG18 does not affect this enzyme activity up to concentrations above 200 microM. These results suggest that a putative tyrosine kinase activity is involved in the gonadotropin signal transduction pathway leading to expression of functional genes in ovarian cells.