gebhart/patrepeval huggingface dataset:
Extracellular cleaved HER2 (p95) confers partial resistance to trastuzumab but not HSP90 inhibitors in models of HER2 amplified breast cancer (2007)

10515 Background: Breast cancers containing an amplified copy of the HER2 receptor tyrosine kinase represent 20–30% of all cases and antibody directed therapy targeting the extracellular domain of HER2 with trastuzumab has proven broadly efficacious. However, resistance to trastuzumab is a common phenomenon. Recent work has identified a cleaved, 95kD version of HER2 that lacks the extracellular epitope in which the trastuzumab binding site is found. Presence of this so called “p95” has been correlated with a worse clinical prognosis. We hypothesized that p95 may enable tumor resistance to trastuzumab. Methods/Results: We established models of p95 expressing breast cancer by transfecting p95 into preexisting models of HER2 amplified breast cancer. We find that cells expressing p95 display increased resistance to the growth inhibitory effects of trastuzumab. The PI3K-AKT pathway that is downregulated by Trastuzumab is less affected in the p95 expressing cells. Furthermore, p95 demonstrates an association with HER3 that is unaffected by trastuzumab treatment. Next, we evaluated the efficacy of therapies targeted against the intracellular domain of HER2 such as the HSP90 inhibitor, 17-AAG. HER2 requires HSP90 for its conformational stability and inhibitors of HSP90 result in growth inhibition of HER2 + breast cancer. We find that p95 displays a similar requirement for HSP90 as inhibitors of HSP90 result in the degradation of p95. Moreover, cells overexpressing p95 are equally susceptible to the antitumor effects of HSP90 inhibitors as those without high levels of p95. Finally, we utilized an empirically derived, in vivo model of trastuzumab resistance that displays high level expression of p95. As with the transfected models, these tumors retain their sensitivity to HSP90 inhibitors as treatment of mice bearing tumors results in both degradation of HER2 and p95 as well as robust tumor growth inhibition. Conclusions: Given the presence of p95 in human breast tumor samples, the data suggest that p95 may play an important role in mediating clinical resistance to trastuzumab. They further suggest that such tumors may retain their sensitivity to targeted therapy against the intracellular portion of HER2 such as with lapatinib or 17-AAG. No significant financial relationships to disclose.
2305 Temperature Measurement on Air Bearing Surface of Thermal Flying-height Control Slider (2007)

To achieve ultra-low flying height, magnetic spacing variations due to manufacturing tolerances, environmental variations, and write-induced thermal protrusion need to be reduced. To solve this problem, we have developed a thermal flying-height control (TFC) slider that carries a micro-thermal actuator. Using the actuator, the magnetic spacing of these sliders can be controlled in-situ while the drive is operating. In this report, temperature rise on the air-bearing surface (ABS) of the slider induced by heat from the heater was measured by infrared rays. The temperature rise measured by infrared microscope agreed well with the temperature rise calculated by the measured resistance change of read element. It was also roughly corresponding to the simulated result. These facts showed the accuracy of the easier measurement method, that is, observing read element resistance change, and the validity of the simulation. The temperature rise in non-flying condition and that in flying condition are significantly different. Therefore, it is necessary to measure it in flying condition for exact evaluation.
Flux Noise Probed with Real Time Qubit Tomography in a Josephson Phase Qubit (2012)

We measure the dependence of qubit phase coherence and flux noise on inductor loop geometry. While wider inductor traces change neither the flux noise power spectrum nor the qubit dephasing time, increased inductance leads to a simultaneous increase in both. Using our new tomographic protocol for measuring low frequency flux noise, we make a direct comparison between the flux noise spectrum and qubit phase decay, finding agreement within 10% of theory.
Isomerizing hydroformylation of fatty acid esters: Formation of ω‐aldehydes (2005)

The isomerizing hydroformylation of fatty acid esters to oleochemicals with an additional ω-standing aldehyde group can be performed at a relatively low temperature of 115 °C and a synthesis gas pressure of 20 bar. In the case of oleic acid ester, the best yield of linear aldehyde is 26%; in the case of linoleic acid ester, it is 34%. For both fatty compounds, a strong hydrogenation side reaction is observed, which can be explained by a steering effect of the ester group. The ester function of the fatty compounds makes hydroformylation in the surrounding area of this group impossible. Reactions with the model substances ethyl crotonate and ethyl sorbate showed that hydrogenation predominates, leading to the corresponding saturated compounds.
Glycolysis on F-18 FDG PET/CT Is Superior to Amino Acid Metabolism on C-11 Methionine PET/CT in Identifying Advanced Renal Cell Carcinoma at Staging (2021)

We evaluated the value of F-18 fluorodeoxyglucose (FDG) and C-11 methionine positron emission tomography/computed tomography (PET/CT) to predict high-Fuhrman grade and advanced-stage tumours in patients with renal cell carcinoma (RCC). Forty patients with RCC underwent F-18 FDG and C-11 methionine PET/CT between September 2016 and September 2018. They were classified into limited (stages I and II, <i>n</i> = 15) or advanced stages (stages III and IV, <i>n</i> = 25) according to pathological staging. Logistic regressions were used to predict the advanced stage using various parameters, including maximum standardised uptake value (SUV<sub>max</sub>) and metabolic tumour volume (MTV). Receiver operating characteristic analyses were performed to predict high-grade tumours (Fuhrman 3 and 4). On univariate analysis, tumour size, SUV<sub>max</sub> and MTV of F-18 FDG and C-11 methionine, and Fuhrman grades were significant predictors for the advanced stage. On multivariate analysis, F-18 FDG MTV > 21.3 cm<sup>3</sup> was the most significant predictor (<i>p</i> < 0.001). The area under the curve for predicting high-grade tumours was 0.830 for F-18 FDG (<i>p</i> < 0.001) and 0.726 for C-11 methionine PET/CT (<i>p</i> = 0.014). In conclusion, glycolysis on F-18 FDG PET/CT and amino acid metabolism on C-11 methionine PET/CT were variable but increased in high-grade RCCs. Increased MTV on F-18 FDG PET/CT is a powerful predictor of advanced-stage tumours.
Restoration of Hypoxanthine Phosphoribosyl Transferase Activity in Mouse 1R Cells After Fusion with Chick-Embryo Fibroblasts (1973)

Fusion of the 1R mouse cell, which lacks activity of hypoxanthine phosphoribosyl transferase (EC 2.4.2.8), with chick-embryo fibroblasts yielded progeny cells that survived in hypoxanthine-aminopterin-thymidine selective medium. This property and the failure of the progeny to survive in 8-azaguanine indicated that hypoxanthine phosphoribosyl transferase activity was present. Electrophoretic analysis revealed that the enzyme was of mouse, not chick, origin. These observations are consistent with the operation of a regulator gene responsible for the absence of hypoxanthine phosphoribosyl-transferase activity in the 1R cell and its presence in the progeny.
A mixture of experts approach towards intelligibility classification of pathological speech (2015)

Pathological speech involves atypical speech production which may result from several factors including oral diseases, physical disabilities in the voice production system and atypical anatomy. Automatic evaluation of intelligibility in patients with pathological speech can assist accurate diagnosis of pathological conditions. Loss of intelligibility may be associated with one of the several pathological conditions, making automatic evaluation a challenging computational problem. A Mixture of Experts (MoE) models class boundaries using a weighted combination of several experts and can characterize the complex class boundaries arising due to pathological variability. We train an MoE for intelligibility evaluation using a modified Expectation Maximization (EM) algorithm based on joint simulated annealing-gradient ascent procedure. Our algorithm optimizes the expert parameters and simultaneously obtains the feature subsets for each expert. We observe that the MoE trained using the new EM algorithm not only outperforms a single classifier baseline but also the vanilla MoE. We perform further data analysis and interpret the weights assigned to each expert during inference. Also, we obtain a different feature subset per expert in the mixture. This illustrates feature use based on location of the data point in the feature space.
SUPER-DETAILED FEM SIMULATIONS FOR FULL SCALE STEEL STRUCTURE CAUSED FATAL RUPTURE AT ITS JOINT PARTS BETWEEN MEMBERS (2016)

There have been some researches on analysis using finely-meshed FE model to understand in detail the behaviors of buildings during severe earthquakes. The accuracy of such analysis is often validated by comparing the results to the corresponding full-scale shaking table test. While they are highly successful in the accuracy, no researches take account of the effect of fracture of members. In this paper, numerical analysis isconducted for asteel structure subjected to multiple series of excitations in a full-scale shaking table test considering the fracture. The structure is modeled with planar and solid finite elements and the fracture is treated by mandatory deletion of elements at time when fracture was observed in the experiment. It is shown that, by considering fracture of steel members with deletion of elements the history of input excitations and caused damages, the behaviors can be simulated by analysis with much higher accuracy.
A Hybrid State of Charge Estimation Method of a LiFePO4/Graphite Cell Using a Reduced Order Model with an Extended Kalman Filter (2019)

Estimation of state of charge (SOC) is imperative in the battery management system that ensures safe and reliable operations. Lithium iron phosphate cells are preferred for high power applications because of their electrochemical and thermal stability. On the other hand, these cells are characterized by voltage plateau and path dependence, which impede the accurate estimation of SOC. In this work, a new method is proposed to estimate the SOC using a physics-based reduced order model (ROM), where the two-phase transition of cathode is modeled and validated. In addition, an extended Kalman filter (EKF) is used to minimize the estimation errors of the SOC caused by the inaccuracy of the ROM or the initial errors. The insensitivity of voltage at the plateau is further compensated by combining Coulomb counting. This method is then validated against experimental data obtained with different C-rates at both single and multiple cycles. The effect of EKF on SOC estimation is also analyzed. The results show that the absolute SOC error is kept less than 3% for all the tested conditions.
Angular analysis of the B 0 → K *0 μ + μ − decay using 3 fb−1 of integrated luminosity (2016)

An angular analysis of the B 0 K * 0 ( K + -) + -decay is presented. The dataset corresponds to an integrated luminosity of 3.0 fb -1 of pp collision data collected at the LHCb experiment. The complete angular information from the decay is used to determine CP -averaged observables and CP asymmetries, taking account of possible contamination from decays with the K + -system in an S-wave configuration. The angular observables and their correlations are reported in bins of q 2 , the invariant mass squared of the dimuon system. The observables are determined both from an unbinned maximum likelihood fit and by using the principal moments of the angular distribution. In addition, by fitting for q 2 -dependent decay amplitudes in the region 1.1 < q 2 < 6.0 GeV 2 /c 4 , the zero-crossing points of several angular observables are computed. A global fit is performed to the complete set of CP -averaged observables obtained from the maximum likelihood fit. This fit indicates differences with predictions based on the Standard Model at the level of 3.4 standard deviations. These differences could be explained by contributions from physics beyond the Standard Model, or by an unexpectedly large hadronic effect that is not accounted for in the Standard Model predictions.
Spectroscopic Visualization of Vortex Flows Using Dye‐Containing Nanofibers (2007)

Wie herum? Ein J-aggregiertes Zinkporphyrindendrimer kann zum Nachweis der makroskopischen Chiralität eines Wirbels dienen. Das Vorzeichen des Circulardichroismus ändert sich schnell, wenn von Rühren im Uhrzeigersinn (CW) auf Rühren im Gegenuhrzeigersinn (CCW) gewechselt wird (siehe Bild). Die chiroptische Aktivität resultiert höchstwahrscheinlich aus der makroskopischen helikalen Ausrichtung von Nanofasern, die sich aus dem polymeren J-Aggregat bilden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z703083_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Clinical pharmacology and metabolism of trimetrexate. (1988)

In non-small cell lung cancer (NSCLC), if the tumor is completely resected in stage I, II, and IIIa disease, the outlook is favorable. In stage IIIa disease, preoperative chemotherapy is efficacious and also confers the potential for improved resectability rates and survival. In a study of 58 patients with locally advanced (stage IIIa) NSCLC, preoperative combination chemotherapy with mitomycin C, cisplatin, and vinca alkaloids yielded 7 complete responses and 37 partial responses. Of the 44 patients with major responses, 42 were surgically explored and 33 were completely resected. Nine patients had pathologically negative biopsy specimens. The median survival for all patients thus far is 19.5 months. These results indicate that surgery can be performed safely in patients treated preoperatively with currently available chemotherapeutic agents. Moreover, complete resections are feasible and can be accomplished in a majority of patients.
Ovine Hemisection Model of Spinal Cord Injury (2019)

We are developing ovine models of spinal cord injury to test novel neuromodulation-based methods on spasticity. The hemisection has been reported in a number of large animal studies. Our aim is to duplicate a hemisection injury in the sheep. Our effort is explored here. <i>Methods and Results</i>: Three sheep underwent hemi-sectioning of the spinal cord. Quantitative gait analysis was completed both pre- and post-injury. While measurable differences in most of the 20 gait metrics were observed, relatively few were above the predicted thresholds based on error levels expected from the data. Variations in severity of injury across the three sheep were observed. <i>Conclusions</i>: The hemisection ovine model of spinal cord injury shows promise as a large-animal platform for developing new therapies for treating spinal cord injuries. While variability in injury severity was observed across animals, as has been observed with weight drop-based SCI models, the hemi-section approach has the advantages of procedural ease and reduced technical complexity.
Effects of Cholecystokinin, Gastric Inhibitory Polypeptide, and Secretin on Insulin and Glucagon Secretion in Rats* (1982)

Pure porcine cholecystokinin-33 [the triacontatriapeptide form of cholecystokinin (CCK-33)], gastric inhibitory polypeptide (GIP), and secretin were infused in rats in doses of 1, 10 and 1000 pmol/kg . min. The peptides were administered alone or in combination with glucose (40 mg/kg . min) or arginine (50 mg/kg . min). In the basal state, CCK-33 and GIP produced significant hypoglycemia at all concentrations used, although they elevated insulin levels only at the highest dose. Secretin had no effect. CCK-33 at a dose of 1 pmol/kg . min enhanced the secretion of insulin induced by glucose or arginine. These effects were more pronounced when higher doses of CCK-33 were administered. GIP at a dose of 1 pmol/kg . min had no effect on insulin release. Higher doses of GIP significantly potentiated insulin release stimulated by glucose or arginine. Secretin (100 pmol/kg . min) had no clear-cut effect on glucose-induced insulin secretion, but it slightly enhanced arginine-induced secretion. All hormones investigated, at all doses used, significantly stimulated the arginine-induced secretion of glucagon. We conclude that CCK-33 is a potent stimulatory factor of glucose- and arginine-induced insulin secretion and should therefore be taken into consideration as an incretin candidate. In addition, CCK-33 and GIP modulate glucose homeostasis by affecting glucagon release.
Endoscopic polarization-sensitive optical coherence tomography (2006)

Development of endoscope-compatible fiber-optic probes and polarization-sensitive detection schemes have each independently expanded the utility of optical coherence tomography. Several application areas have emerged which require polarization-sensitive measurements to be combined with endoscopic imaging techniques, in order to proceed to in vivo studies. Endoscopic-OCT typically requires a section of the sample arm fiber to be scanned during image acquisition, which produces a dynamically changing polarization state of light incident on the sample. Here, we demonstrate the effects of linear-scanning, and rotary-scanning probes in the sample arm of a PS-OCT system, and demonstrate the necessary modifications to be made for successful endoscopic PS-OCT imaging.
Conservative Rationalizability and The Second-Knowledge Mechanism (2010)

In mechanism design, the traditional way of modeling the players ’ incomplete information about their opponents is “assuming a Bayesian. ” This assumption, however, is very strong and does not hold in many real applications. Accordingly, we put forward (1) a set-theoretic way to model the knowledge that a player might have about his opponents, and (2) a new class of mechanisms capable of leveraging such more conservative knowledge in a robust way. In auctions of a single good, we show that such a new mechanism can perfectly guarantee a revenue benchmark (always lying in between the second highest and the highest valuation) that no classical mechanism can even approximate in any robust way. 1 1
[[1]Benzofuro[3,2-b]pyridin-4-yl-amines - synthesis and investigation of activity against malaria]. (2004)

The ethyl 4-chlorobenzothieno[3,2-b]pyridine-3-carboxylate (2) reacted with the hydrochlorides of the mono- and bis-phenol Mannich bases 6 to yield the amodiaquine and pyronaridine analogues 9. The chloroquine analogue 10 was formed by melting 2 with the novaldiamine base (7) in phenol. The stability of the 4-aminophenols 9 was investigated by anodic oxidation using the rotating platinum electrode by means of difference pulse voltammetry. The half wave potentials were measured giving E(1/2) approximately 1.05 V. Compound 9g displayed the highest activity against the growth of the malaria parasite Plasmodium falciparum. Testing against the chloroquine sensitive 3D7 and the chloroquine resistant Dd2 strain resulted in IC50 values of 150 nM and 210 nM, respectively. Surprisingly, the 3-carbinol 4 and the 3-chloromethyl derivative 5, synthesized from the 3-carboxylic acid ester 2, reacted with the phenol Mannich base 6a and the novaldiamine base (7), respectively, to yield the 4-pyridone 8.
A new thin film phantom for performance evaluation of ultrasonic Doppler imaging systems (2002)

A novel phantom is described which incorporates a thin film of sub-resolvable scatterers and piezoelectric materials to simulate a wide variety of dynamic and static flow signals that can be precisely defined in terms of their temporal and spatial content for evaluation of ultrasonic Doppler flow measurement systems.
Control of Active Mobile Substations under system faults (2013)

While conventional mobile substations are used to bypass the whole substation in case of loss or maintenance of power transformers, Active Mobile Substations (AMS) can be used both in normal conditions as a power router and in contingencies as a recovery transformer. The AMS is a mobile substation with integrated power electronics. By controlling its throughput power, it can be connected across different transformers of the grid. This paper explores transmission-level active mobile substations that provide back-up in case of power transformer failure or forced reduced operation scenarios in addition to power flow control for seasonal renewable energy transmission. The AMS must be designed to operate satisfactorily under typical fault and unbalanced conditions. In this paper, component design considerations in development of the AMS under unbalanced operating condition will be provided, and a new control strategy is proposed to control AMS under unbalanced operating conditions when component design is not sufficient to prevent overcurrent and trips. Detailed PSCAD simulation for the proposed control scheme is performed and results are presented. Experimental results are also shown to verify the proposed control method under unbalanced operating conditions.
Randomized Phase III Trial Assessing Regional Lung Function for Thoracic Resection by Hyperpolarized 129Xenon Gas MRI (2020)

3D imaging of pulmonary function without radiation can be achieved by Hyperpolarized <sup>129</sup>Xe (HPX) inhaled in a single breath-hold 10-second MRI exam. We conducted a FDA phase III multicenter trial in patients undergoing surgical thoracic resection to establish the equivalence of HPX to evaluate regional pulmonary function with the currently approved standard, 133Xe scintigraphy (XS). Subjects being evaluated for thoracic resection were randomized to undergo either HPX followed by XS or XS followed by HPX. <sup>129</sup>Xe was hyperpolarized by the Polarean HPX system. Ventilation of the six (6) lung zones was quantified to determine the contribution of each zone to total lung function, and then these values were used to predict the % of remaining lung function if the zones were resected. The primary endpoint would be met if the 95% confidence interval (CI) of the mean intra-patient differences fell within the prospectively defined equivalence margin of ±14.7%. 32 subjects received HPX and XS, (10 females, age 62.0±9.8, O<sub>2</sub> use 2.7± 1.30 liter/min). HPX was well tolerated. Thirteen subjects (41%) underwent lung resection. The intra-patient mean difference of the remaining ventilation measured quantified by HPX vs XS was 1.4±5.93% (95% CI, -0.75-3.60%). The 95% CI for HPX fell within the pre-defined equivalence margin, demonstrating equivalence between the two imaging modalities to a significance level of p&lt;0.001. In patients undergoing thoracic resection planning, HPX demonstrated a diagnostic ability to predict post-op in vivo lung function comparable to XS. Radiation-free, high-resolution, quantitative HPX represents a notable advance from the current XS technology.