gebhart/patrepeval huggingface dataset:
A Versatile Tumor Gene Deletion System Reveals a Crucial Role for FGFR1 in Breast Cancer Metastasis (2017)

RCAS avian viruses have been used to deliver oncogene expression and induce tumors in transgenic mice expressing the virus receptor TVA. Here we report the generation and characterization of a novel RCAS-Cre-IRES-PyMT (RCI-PyMT) virus designed to specifically knockout genes of interest in tumors generated in appropriate mutant mouse hosts. FGF receptor 1 (FGFR1) is a gene that is amplified in human breast cancer, but there have been no definitive studies on its function in mammary tumorigenesis, progression, and metastasis in vivo in spontaneous tumors in mice. We used the retroviral tumor knockout, or TuKO, strategy to delete fgfr1 in PyMT-induced mammary tumors in K19-tva/fgfr1<sup>loxP/loxP</sup> mice. The similarly injected control K19-tva mice developed mammary tumors exhibiting high metastasis to lung, making this an ideal model for breast cancer metastasis. The fgfr1 TuKO tumors showed significantly decreased primary tumor growth and, most importantly, greatly reduced metastasis to lung. In contrast to previous reports, FGFR1 action in this spontaneous mammary tumor model does not significantly induce epithelial-to-mesenchymal transition. Loss of FGFR1 does generate a gene signature that is reverse correlated with FGFR1 gene amplification and/or upregulation in human breast cancer. Our results suggest that FGFR1 signaling is a key pathway driving breast cancer lung metastasis and that targeting FGFR1 in breast cancer is an exciting approach to inhibit metastasis.
Performance Analysis of Fixed Gain Relay Systems With a Single Interferer in Nakagami- $m$ Fading Channels (2012)

We investigate the outage probability and average bit error rate (BER) of a dual-hop fixed gain relaying system in the presence of interference and noise at the relay and destination. Our analysis assumes Nakagami-m fading for the source-relay, relay-destination, and interfering channels. We present new closed-form/series expressions for the outage probability, as well as the average BER. It is concluded that the presence of interference results in a floor point in both outage and BER performance. This floor point holds for signal-to-noise ratio (SNR) values higher than a certain threshold such that the larger the difference between the received powers of the useful and interfering signals, the higher the SNR value at which this floor point commences. Moreover, it is shown that the performance is practically not affected by the Nakagami-m shape parameter of the fading at the interfering link.
Growing Through Innovation (2007)

OVERVIEW:Innovation has always been a marriage of what's needed with what's possible. Originally, “what's possible” was about technology, but at Procter & Gamble today it's about creating and delivering a superior experience for the consumer. And that comes from truly understanding consumer needs. This requires a new kind of R&D leader, someone who combines imagination and worldwide knowledge with action, and, in addition, is an inspirational individual who exhibits curiosity and courage, practices collaboration, asks the right questions, and is able to “communicate the dream.”KEY CONCEPTS:: innovationconnect and developProcter & GambleR&D leadership
Passivation of GaSb using molecular beam epitaxy Y2O3 to achieve low interfacial trap density and high-performance self-aligned inversion-channel p-metal-oxide-semiconductor field-effect-transistors (2014)

Molecular beam epitaxy deposited rare-earth oxide of Y2O3 has effectively passivated GaSb, leading to low interfacial trap densities of (1–4) × 1012 cm−2 eV−1 across the energy bandgap of GaSb. A high saturation drain current density of 130 μA/μm, a peak transconductance of 90 μS/μm, a low subthreshold slope of 147 mV/decade, and a peak field-effect hole mobility of 200 cm2/V-s were obtained in 1 μm-gate-length self-aligned inversion-channel GaSb p-Metal-Oxide-Semiconductor Field-Effect-Transistors (MOSFETs). In this work, high-κ/GaSb interfacial properties were better in samples with a high substrate temperature of 200 °C than in those with high κ's deposited at room temperature, in terms of the interfacial electrical properties, particularly, the reduction of interfacial trap densities near the conduction band and the MOSFET device performance.
CSF1R-Inhibition and Reduction of Macrophages Delays Multiple Myeloma Growth in a Non-T-Cell-Dependent Manner (2014)

Abstract Macrophages are important tumor-promoting cells, and can constitute up to half of the tumor mass, orchestrating remodeling, inducing angiogenesis and suppressing the immune system to terminate local inflammatory responses. Colony stimulating factor (CSF-1), also known as macrophage colony-stimulating factor (M-CSF), is the most important cytokine involved in survival, proliferation and differentiation of tissue macrophages and their precursors. Previous experiments from our group has shown that amount of CSF-1 in the tumor bed correlates with successful rejection of cancer cells in a TCR-transgenic model where CD4+ T cells recognize a tumor specific antigen produced by multiple myeloma cells. We therefore tested if reduced signaling via CSF-1R, and thereby a decrease in tumor infiltrating macrophages, would results in decreased growth of multiple myeloma cells. . PLX3397, a tyrosine kinase inhibitor with specificity for CSF1R and KIT, has been demonstrated to delay tumor growth in a CD8+ T-cell-dependent manner after chemotherapeutic treatment in a murine model of mammary carcinogenesis. Here, we show that MOPC315 multiple myeloma cells implanted subcutaneously in matrigel plugs in SCID mice become infiltrated with M2 phenotype macrophages that enhances their growth. When given chow containing PLX3397, recruitment of macrophages is strikingly reduced, with significant delay in tumor growth. Importantly, this delay in tumor development is not T cell dependent, since the anti-tumor effect is seen in T cell deficient SCID-mice as well as in BALB/c mice. Importantly, treatment with PLX3397 does not abrogate efficient tumor killing, and does not affect survival, when tested in a TCR-transgenic model where CD4+ T cells via induction of M1 macrophages reject multiple myeloma. In conclusion, PLX3397 delays tumor growth by reducing amounts of tumor infiltrating M2 macrophages, while rendering effective tumor killing by M1 macrophages uninhibited. Thus, drugs that inhibit signaling of CSF-1 could be of value in treatment of multiple myeloma. Disclosures No relevant conflicts of interest to declare.
Isolation and Insolubilisation of Human F VIII by Affinity Chromatography (1978)

A simple procedure has been developed for the isolation of coagulation factor VIII (F VIII) from plasma in a form which induces a monospecific antibody in rabbits. Amino acid precipitation from plasma was followed by gel filtration on Sepharose 4B and further purification was achieved by affinity chromatography on heparin-Sepharose. The material so isolated was identified by immunoelectrophoresis and lacked coagulant activity. The antiserum produced in rabbits inhibited F VIII coagulant activity and von Willebrand factor activity as measured by ristocetin platelet agglutination. The isolated IgG fraction insolubilised with CNBr-Sepharose 4B retained the ability to complex with F VIII. This complex possessed F VIII coagulant activity which could be removed in 0.6 M NaCl and dissociated in 8 M urea.
Reduced Intensity Compared to High Dose Conditioning for Allotransplantation in Acute Myeloid Leukemia and Myelodysplastic Syndrome: A Comparative Clinical Analysis. (2004)

We evaluated the comparative safety and efficacy of stem cell transplantation using reduced intensity (RI) vs myeloablative (MA) conditioning for patients with acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) who underwent allogeneic hematopoietic stem cell transplantation (HSCT). Thirty two patients [18 males, median age 54 (range 19–69)] underwent a RI HSCT from January 2000- September 2003, and these were compared to 187 patients [93 males, median age 39 (range 18.4–60.3)] who received MA transplants between January 1990 – September 2003. Disease status in the 2 groups was similar, (AML in CR1: RI 38% vs MA 38%; CR2: 22% vs 15%; AML relapse: 13% vs 20% and MDS 28% vs 27%). Patients were eligible for RI if age &gt;55 with HLA matched sibling donor (Sib) or &gt;45 with unrelated bone marrow (BM) or umbilical cord blood (UCB) donor; extensive previous therapy including previous transplant or major co-morbidity. RI donors were Sib (n=17, 53%), unrelated UCB (n=14, 44%), or unrelated BM (n=1). MA donors were Sib (n=176, 94%) and UCB (n=11, 6 %), p&lt;0.01. RI conditioning included an alkylator (busulfan (Bu) or cyclophosphamide (Cy), a nucleoside analogue (fludarabine or cladribine) and 200 cGy total body irradiation (TBI), while MA conditioning was Cy/TBI (1320 cGy) (n=177) or Bu/Cy (n=10). Median follow up is 1.7 years in RI recipients and 4.2 years in MA. Neutrophil engraftment was more rapid in the RI group (median =11.5 days vs 21 days) with 3% and 6% graft failure respectively in the RI and MA groups. The cumulative incidence of Grade III–IV acute graft versus host disease (GVHD) was 22%±14% in RI vs 12±4% after MA HSCT. The cumulative incidence of relapse or disease progression at 1 year was 31% after RI vs 22% after MA HSCT (p=0.06). Disease free survival (DFS) at 1 year was 31± 16% in RI and 37%± 7% in the MA group (p=0.14). Multivariate regression analysis showed that neither conditioning intensity (NST RR=1.4, p=0.14) nor donor choice (UCB RR 0.9, p=0.63) significantly altered DFS. More failures (relapse or death) followed transplant for AML in relapse (RR=1.5, p=0.05), recipient seropositive for CMV (RR1.4, p=0.03) and development of Grade III/IV GVHD (RR 1.9, p&lt;0.01), with MDS having an outcome similar to AML in remission (RR 1.2,p=0.28). These data suggest that allografts for AML or MDS using RI conditioning, even for older patients or using unrelated UCB can yield satisfactory outcomes and extended DFS. Advances in GVHD management and new approaches for patients in relapse are needed to improve these outcomes.
Gold-cyanide biosorption withL-cysteine (2000)

L-Cysteine increased gold-cyanide biosorption by protonated Bacillus subtilis, Penicillium chrysogenum and Sargassum fluitans biomass. At pH 2, the maximum Au uptakes were 20.5 µmol g−1, 14.2 µmol g−1 and 4.7 µmol g−1 of Au, respectively, approximately 148–250% of the biosorption performance in the absence of cysteine. Au biosorption mainly involved anionic AuCN2− species adsorbed by ionizable functional groups on cysteine-loaded biomass carrying a positive charge when protonated [(biomass–cysteine–H+)–(AuCN2−)]. Deposited gold could be eluted from Au-loaded biomass at pH 3–5. The elution efficiencies were higher than 92% at pH 5.0 with the Solid-to-Liquid ratio, S/L, = 4. Increasing solution ionic strength (NaNO)3 decreased Au uptake. FTIR analyses indicated that the main functional groups involved in gold biosorption in the presence of L-cysteine are probably N-, S- and O-containing groups. The present results confirm that certain waste microbial biomaterials are capable of effectively removing and concentrating gold from solutions containing residual cyanide if applied under appropriate conditions. © 2000 Society of Chemical Industry
How to Improve the Performance Prediction of a Pump as Turbine by Considering the Slip Phenomenon (2018)

Nowadays Pumps working as Turbines (PaT) are devices widely used to perform energy recovery in hydraulic grids, thus improving their overall efficiency, and to build small hydropower plants. In this work, a centrifugal pump has been numerically investigated in turbine operating mode by means of the open-source CFD code OpenFOAM with emphasis on the flow field at the runner outlet. Due to the reduced number of blades in a PaT, the mean outlet relative velocity angle differs from the blade angle. In order to account for this phenomenon, the slip factor is introduced. The slip factor is investigated and its application to a 1D model is shown in order to highlight the improvement in predicting the characteristic curve of a centrifugal pump used in reverse mode as a turbine (PaT) especially at its part-load.
Thermal trimming and tuning of hydrogenated amorphous silicon nanophotonic devices (2010)

Deposited silicon and, in particular, hydrogenated amorphous silicon forms an attractive alternative platform for realizing compact photonic integrated circuits. In this paper we report on trimming (toward lower wavelengths) and tuning (toward higher wavelengths) of photonic devices through a suitable thermal treatment. The former is achieved by a material density change, the latter through the thermo-optic effect. By using Fourier transform infrared spectroscopy, a change in the hydrogen content is identified as the source of the density change. A total wavelength tuning range of 24.6 nm is achievable, which can be used for compensating fabrication imperfections.
CathROB: A Highly Compact and Versatile Remote Catheter Navigation System (2017)

Several remote catheter navigation systems have been developed and are now commercially available. However, these systems typically require specialized catheters or equipment, as well as time-consuming operations for the system set-up. In this paper, we present CathROB, a highly compact and versatile robotic system for remote navigation of standard tip-steerable electrophysiology (EP) catheters. Key features of CathROB include an extremely compact design that minimizes encumbrance and time for system set-up in a standard cath lab, a force-sensing mechanism, an intuitive command interface, and functions for automatic catheter navigation and repositioning. We report in vitro and in vivo animal evaluation of CathROB. In vitro results showed good accuracy in remote catheter navigation and automatic repositioning (1.5 ± 0.6 mm for the left-side targets, 1.7 ± 0.4 mm for the right-side targets). Adequate tissue contact was achieved with remote navigation in vivo. There were no adverse events, including absence of cardiac perforation or cardiac damage, indicative of the safety profile of CathROB. Although further preclinical and clinical studies are required, the presented CathROB system seems to be a promising solution for an affordable and easy-to-use remote catheter navigation.
High Temperature Corrosion of Titanium Under Conditions Relevant to Pressure Leaching: Mass Loss and Electrochemistry (2014)

The corrosion behavior of titanium was studied using mass loss and electrochemical measurements in sulfuric acid with Cl−, Cu2+, and Fe3+ additions up to 175°C. The corrosion rate of titanium in 30 g L−1 H2SO4 + 12 g L−1 Cl− solution at 150°C measured by mass loss was higher than 62 mm y−1. The corrosion rates of titanium under simulated pressure-leaching conditions determined by both mass loss and polarization resistance measurements were consistent, and also suggest that Cu2+ and Fe3+ ions are excellent corrosion inhibitors for titanium. Results from mass loss and electrochemical measurements all confirmed that the corrosion rate of titanium decreased remarkably with the addition of 1 g L−1 Fe3+ to the leaching solution at 150°C, and that the presence of Fe3+ is the most important factor for the growth of titanium oxide films under pressure-leaching conditions. In addition, iso-corrosion diagrams, with 0.1, 0.5, and 1 mm y−1 lines for titanium in H2SO4 solutions from room temperature to 175°C, were constructed from mass loss data.
Synthesis of 2,5-Disubstituted Furans via Palladium-Catalyzed Annulation of Alkyl 3-Oxo-6-heptynoates (1997)

The reaction of the readily available alkyl 3-oxo-6-heptynoates with aryl halides in the presence of K2CO3 and catalytic amounts of Pd(PPh3)4 at 100 °C provides a valuable new route to 2,5-disubstituted furans 3. Most probably, the furan ring is generated through an annulation reaction promoted by σ-arylpalladium complexes generated in situ and involving the nucleophilic attack of the ketonic oxygen across the carbon−carbon triple bond coordinated to palladium, followed by the base-catalyzed isomerization of the resultant stereoisomeric 2,5-dialkylidenetetrahydrofuran intermediates 4 and 5. The reaction is highly chemoselective. No evidence was obtained of carboannulation products. The reaction temperature has proven to be crucial for the success of the methodology. The K2CO3:alkyne ratio also affects the reaction outcome. The highest yields of furan derivatives have been obtained with aryl halides containing electron-withdrawing substituents, very likely because the higher acidity of the methylene protons of 4 and 5 favors the isomerization step. Extension of the methodology to methyl 3-oxo-7-substituted-6-heptynoates leads to the formation of 2,5-disubstituted furans containing a branched side chain. The presence of an alkyl substituent on the C-2 of the staring alkyne, however, seems to prevent the isomerization step. Treatment of ethyl 2-methyl-3-oxo-6-heptynoate under our standard conditions produced in fact the 2,5-dialkylidene derivative 5p in 42% yield, and no evidence of the corresponding furan derivative was attained.
Dynamics of railway vehicle systems (1984)

This book covers the development of mathematical models and their applications to dynamic analyses and the design of railway vehicles. It should help to put in perspective the role of analytical models in various railway vehicle design activities.
Reproducibility of superhydrophobic and oleophobic polymeric micro surface topographies (2020)

Abstract Micro-structured surfaces can provide useful material properties, such as repellency to water, oil, or alcohols. Multiple polymers were investigated based on micro molding replication fidelity of repellent structures using both advancing and receding contact angle measurements. Five different polymers (Loctite 3525, ST-1060, TC-854, TC-8740, and Teflon AF) were chosen based on a range of durometers, for each of which, a recommended curing process was presented. These polymers were micro-structured via a one-step replica molding to create mushroom shaped fibers with overhanging caps. Teflon AF, a low surface energy polymer, produced innovative superhydrophobic as well as oleophobic Micro Surface Topographies (MSTs). Advancing contact angles (CAs) of these microstructures were 166 ± 4.2, 151 ± 2.9, and 119 ± 2.2 when in contact with a water, ethylene, and olive oil droplet respectively. The highest reproducibility was achieved by using a curing procedure of 100 °C for 2 h. However, even in these conditions, 35% of MSTs were not fully reproduced. ST-1060 was considered a good alternative to Teflon AF since, even after five uses of the same casting mold, the advancing CAs decreased less than 2% when in contact with any liquid tested. Polymeric MSTs resistance to an external force was also examined using a gyratory shaker suggesting that softer materials, such as ST-1060, were required to survive exposure to environmental conditions.
976. The reaction between ethane and oxygen at 600–630° (1963)

R. J. Sampson, J. Chem. Soc., 1963, 5095 DOI: 10.1039/JR9630005095
Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation (2022)

Understanding the relationship between protein structure and experimental data is crucial for utilizing experiments to solve biochemical problems and optimizing the use of sparse experimental data for structural interpretation. Tandem mass spectrometry (MS/MS) can be used with a variety of methods to collect structural data for proteins. One example is surface-induced dissociation (SID), which is used to break apart protein complexes (via a surface collision) into intact subcomplexes and can be performed at multiple laboratory frame SID collision energies. These energy-resolved MS/MS experiments have shown that the profile of the breakages depends on the acceleration energy of the collision. It is possible to extract an appearance energy (AE) from energy-resolved mass spectrometry (ERMS) data, which shows the relative intensity of each type of subcomplex as a function of SID acceleration energy. We previously determined that these AE values for specific interfaces correlated with structural features related to interface strength. In this study, we further examined the structural relationships by developing a method to predict the full ERMS plot from the structure, rather than extracting a single value. First, we noted that for proteins with multiple interface types, we could reproduce the correct shapes of breakdown curves, further confirming previous structural hypotheses. Next, we demonstrated that interface size and energy density (measured using Rosetta) correlated with data derived from the ERMS plot (<i>R</i><sup>2</sup> = 0.71). Furthermore, based on this trend, we used native crystal structures to predict ERMS. The majority of predictions resulted in good agreement, and the average root-mean-square error was 0.20 for the 20 complexes in our data set. We also show that if additional information on cleavage as a function of collision energy could be obtained, the accuracy of predictions improved further. Finally, we demonstrated that ERMS prediction results were better for the native than for inaccurate models in 17/20 cases. An application to run this simulation has been developed in Rosetta, which is freely available for use.
Imaging vertical interfaces using acoustic time reversal (2019)

We have developed a novel approach to image vertical structures using multiply scattered waves. This method requires only a smooth seismic velocity model and data recorded at the surface. Previous methods to image near-vertical interfaces or faults using migration methods all require prior information about small-scale details in the seismic velocity model to infer the locations of multiple-scattering wave interactions. We used waves that had their last scattering interaction with near-vertical interfaces, while their other scattering points might be anywhere in the earth, including at the free surface. Our algorithm then images the final scattering point using a time-reversed mirror-style imaging condition, so we refer to the method as time-reversed mirror imaging. Artifacts in the images produced have clear causes and can be filtered out by stacking over shots and including contributions from multiples. Our numerical examples demonstrate the successful application of the method for staircase structures and a section of the Marmousi model. They also reveal a new way to diagnose errors in the smooth or reference velocity model used. In addition, our method can be used to image point scatterers in active seismic surveys or for event location in passive surveys.
Pyruvate Suppresses Hippocampal MMP‐2 Activity Following Cardiac Arrest‐Resuscitation (2015)

Cardiac arrest (CA) imposes ischemia-reperfusion on the brain and activates matrix metalloproteinases (MMPs) which degrade the extracellular matrix and, thus, disrupt the blood-brain barrier (BBB). Pyruvate, a metabolic fuel and antioxidant, suppressed MMP activities in myocardium and brain in mammalian models of cardiopulmonary bypass and stroke. Hypothesis By lowering MMP activities, iv pyruvate during resuscitation preserves BBB and fosters post-CA neurocognitive recovery in swine. Methods: Yorkshire swine (25-35 kg; n = 28) were subjected to pacing-induced CA, precordial compressions (100/min) at 6-10 min CA, and transthoracic countershocks to restore sinus rhythm. NaCl or Na-pyruvate was infused iv (0.1 mmol/kg/min) during compressions and the first 60 min recovery. MMP activities in brain biopsies were measured by gelatin zymography. Results: At 4h recovery, Na-pyruvate lowered hippocampal MMP-2 activity by 70% (P= 0.006); MMP-9 was unchanged. At 3 days, MMP-2 and -9 activities, neurological deficit scores and behavior were similar among the non-CA sham, NaCl and pyruvate groups. Conclusions MMP-2 may contribute to initial brain injury after CA and its activity is blunted by pyruvate. NINDS support: R01 NS076975