gebhart/patrepeval huggingface dataset:
Yellow Brain Culinary-Medicinal Mushroom, Tremella mesenterica Ritz.:Fr. (Higher Basidiomycetes), is Subjectively but not Objectively Effective for Eradication of Helicobacter pylori: A Prospective Controlled Trial (2012)

Inhibitory effects of the higher Basidiomycetes mushrooms, including species of genus Tremella, on the growth of Helicobacter pyroli (Hp) have been described. This study aimed to test T. mesenterica (Tm) efficacy in vivo on eradication of Hp. This IRB-approved study included 52 consenting patients diagnosed with Hp infections. The patients were selected for 10-day treatments with one of the three arms of the protocol, namely, (i) Tm 2 g, (ii) Tm given with omeprazole 20 mg, or (iii) omeprazole 20 mg, clarithromycin 500 mg, and amoxicillin 1000 mg (all regimens given twice daily). The Tm submerged cultivated mycelium in the form of tablets (1 g) was supplied free of charge to patients. Three weeks after completing the therapy, breath testing was assessed for Hp eradication. The patients who took the standard triple therapy had a 70% (n = 14) eradication rate of Hp. Of the patients taking Tm, with and without omeprazole, only one had a breath test indicative of eradication of Hp, p < 0.000. Tm-treated patients had fewer adverse events and equivalent symptomatic relief. Limitations of this study include the brief duration of Tm therapy. Longer treatment might achieve better results, but was judged to be not warranted, so as to not excessively further delay accepted therapy. Ten-day Tm was not found to be effective in vivo in eradicating Hp, whether if given with or without omeprazole. Significant symptomatic relief found among Tm-treated patients suggests that further study of Tm is well justified.
Discovery of a Small Molecule Activator of the Hypoxia Inducible Factor Pathway (2013)

Hypoxia and ischemia are related to numerous public health problems affecting most major organ systems. Examples include the cardiovascular, pulmonary, renal, neurologic, and musculoskeletal systems. Furthermore, angiogenesis is required for tissue repair and regeneration. In cases of ischemia, whether due to injury or disease, enhancing blood supply is a common goal. The most significant pathway for cellular response to hypoxia is the hypoxia inducible factor (HIF) pathway. HIFs are transcription factors responsible for the activation of genes which encode proteins that mediate adaptive responses to reduced oxygen availability. The molecular probe (ML228) described in this report demonstrated activity in a cell-based HIF-mediated gene reporter assay with an EC50 around 1 μM. This probe did not inhibit the proteasome, activated HIF stabilization and nuclear translocation, and induced expression of a HIF specific downstream gene (VEGF). It had no apparent toxicity below 30 μM and appeared to be an iron chelator.
Phase I Trial of a PSA based vaccine and ipilimumab in patients (pts) with metastatic castrate resistant prostate cancer (CRPC) (2007)

A142 Background: Therapeutic options for CRPC pts are limited, but a promising therapeutic modality is the combination of vaccines in concert with immunomodulating adjuvants. The vaccine utilized in this study (designated PSA-TRICOM) is comprised of poxviral vectors which encode a modified agonist epitope of PSA and 3 costimulatory molecules, ICAM, LFA-3 and B7.1. A phase II trial evaluating recombinant vaccinia (rV) and fowlpox (rF) PSA-TRICOM previously demonstrated PSA declines and an objective response (OR) with a significant (p grade 2 toxicities attributed to vaccine. irAE attributed to ipilimumab included colitis (n=6), panhypophysitis (n=3), rash (n=1) and neutropenia (n=1). The median number of cycles with ipilimumab was 3, (range 1-6) with 5 pts receiving only 2 cycles and 3 pts receiving only 1 cycle with ipilimumab due to irAE. Only one pt has received 6 does of ipilimumab.  The six patients with prior chemotherapy (all treated at the 1 and 3 mg/kg doses) had no evidence of clinical benefit (no decrease in PSA or objective response) with a median time to progression (TTP) of 3.2 months (mean 2.8; range 1.6-3.7).  Of the 9 pts treated on the 3 and 5 mg/kg dose who had no prior chemotherapy, the median TTP was 5 months (mean 5.4; range 2.9-9.3) with 2 patients still on trial at 5 and 8 months. 5 of these 9 patients had declines in PSA by at least 50% from peak PSA during study. This may be clinically significant as 4 of these pts had radiographically and clinically stable disease for at least 6 months (TTP 6, 7, 8+ and 9.3 months). There was one unconfirmed PR (out of 10 evaluable pts) by RECIST and another patient with a sustained decrease in PSA >95% who remains on study at 8 months.  3 pts have been enrolled in the 10mg/kg cohort. One patient had a solitary new lesion at L2 on bone scan with stable soft tissue disease and PSA and was taken off study and the other 2 patients remain with stable disease on study at 2.5 and 4 months.  Conclusions:  This combination has activity in pts with chemotherapy naive metastatic CRPC and is associated with manageable side effects. From data thus far, it is unclear if safety events or responses seen are related to the dose of anti-CTLA4. Further expansion of the 3 mg/kg and 5 mg/kg cohorts for additional toxicity and efficacy data are planned.
High-Speed Phase-Correlated Signal Generation by Phase-Reconstruction of OTDM Signals through Differential Cross-Phase Modulation in an SOA-MZI (2007)

We propose a method to generate high-speed coherent phase-modulated signals using DXPM in an SOA-MZI. Results include generation of 80-Gb/s RZ-DPSK, CSRZ, GAP-CSRZ, PAP-CSRZ, and AMI modulation formats. The technique also enables output pulse-width control.
Tetrathiafulvalenes as building-blocks in supramolecular chemistry (1994)

T. Jørgensen, T. K. Hansen and J. Becher, Chem. Soc. Rev., 1994, 23, 41 DOI: 10.1039/CS9942300041
Effect of ginseng extract on the TGF-β1 signaling pathway in CCl4-induced liver fibrosis in rats (2017)

ginseng extract had an anti-fibrosis effect via the regulation of the TGF-β1/Smad signaling pathway in the CCl<sub>4</sub>-induced liver fibrosis model. The major target was the inhibition of the expression of TGF-β1, Smad2, and Smad3.
Intracellular signaling by a mutant human insulin receptor lacking the carboxyl-terminal tyrosine autophosphorylation sites. (1992)

We have recently characterized a mutant insulin receptor (Y/F2) in which the two tyrosines in the carboxyl terminus (Tyr1316, Tyr1322) were mutated to phenylalanine. Compared with wild type receptors, the Y/F2 receptor exhibited markedly enhanced sensitivity to insulin-stimulated DNA synthesis with normal insulin-stimulated glucose uptake (Takata, Y., Webster, N. J. G., and Olefsky, J. M. (1991) J. Biol. Chem. 266, 9135-9139). In this paper, we present further evidence for the divergence of the metabolic and mitogenic signaling pathways utilized by the insulin receptor. The mutant receptor showed normal sensitivity and responsiveness for insulin-stimulated glucose incorporation into glycogen. The insulin sensitivity for phosphorylation of two substrates (pp180 and pp220) was the same in both Y/F2 cells and HIRc cells. Phosphotyrosine content, however, was greater in Y/F2 cells than in HIRc cells, especially in the basal state. Insulin stimulated S6 kinase activity 2-6-fold, with an ED50 of -10 nM in Rat 1 cells and 0.5 nM in HIRc cells. The sensitivity to insulin was enhanced in Y/F2 cells with an ED50 of 0.1 nM. These effects were insulin-specific, since insulin-like growth factor (IGF)-I-stimulated mitogenesis was normal. In summary: 1) Y/F2 receptors exhibit normal metabolic and enhanced mitogenic signaling; 2) the enhanced mitogenic signaling is specific for the insulin receptor in the Y/F2 cells, since IGF-I-stimulated mitogenesis is normal; 3) Y/F2 cells display increased endogenous substrate phosphorylation and augmented insulin-stimulated S6 kinase activity placing these responses among insulin's mitogenic effects; and 4) these results are consistent with the concept that the COOH-terminal tyrosine residues of the insulin receptor are normally inhibitory to mitogenic signaling.
Structure–Activity Relationship of N,N′-Disubstituted Pyrimidinetriones as CaV1.3 Calcium Channel-Selective Antagonists for Parkinson’s Disease (2013)

CaV1.3 L-type calcium channels (LTCCs) have been a potential target for Parkinson's disease since calcium ion influx through the channel was implicated in the generation of mitochondrial oxidative stress, causing cell death in the dopaminergic neurons. Selective inhibition of CaV1.3 over other LTCC isoforms, especially CaV1.2, is critical to minimize potential side effects. We recently identified pyrimidinetriones (PYTs) as a CaV1.3-selective scaffold; here we report the structure-activity relationship of PYTs with both CaV1.3 and CaV1.2 LTCCs. By variation of the substituents on the cyclopentyl and arylalkyl groups of PYT, SAR studies allowed characterization of the CaV1.3 and CaV1.2 LTCCs binding sites. The SAR also identified four important moieties that either retain selectivity or enhance binding affinity. Our study represents a significant enhancement of the SAR of PYTs at CaV1.3 and CaV1.2 LTCCs and highlights several advances in the lead optimization and diversification of this family of compounds for drug development.
Mechanical simulation of stress engineering solutions in highly strained p-type FDSOI MOSFETs for 14-nm node and beyond (2015)

Stress engineering is a powerful tool to enhance nanoscale device performances. In this study we developed a methodology of 14nm strained pMOS FDSOI device mechanical simulation in order to carefully evaluate different stress effects on device performances. Mechanical simulation results are presented for different process solutions, such as Gate-First (GF) and Gate-Last (GL) processes but also for variation of germanium contents in source/drain and channel regions.
The Free Fatty Acid Receptor G Protein-coupled Receptor 40 (GPR40) Protects from Bone Loss through Inhibition of Osteoclast Differentiation* (2013)

The mechanisms linking fat intake to bone loss remain unclear. By demonstrating the expression of the free fatty acid receptor G-coupled protein receptor 40 (GPR40) in bone cells, we hypothesized that this receptor may play a role in mediating the effects of fatty acids on bone remodeling. Using micro-CT analysis, we showed that GPR40(-/-) mice exhibit osteoporotic features suggesting a positive role of GPR40 on bone density. In primary cultures of bone marrow, we showed that GW9508, a GRP40 agonist, abolished bone-resorbing cell differentiation. This alteration of the receptor activator of NF-κB ligand (RANKL)-induced osteoclast differentiation occurred via the inhibition of the nuclear factor κB (NF-κB) signaling pathway as demonstrated by decrease in gene reporter activity, inhibitor of κB kinase (IKKα/β) activation, inhibitor of κB (IkBα) phosphorylation, and nuclear factor of activated T cells 1 (NFATc1) expression. The GPR40-dependent effect of GW9508 was confirmed using shRNA interference in osteoclast precursors and GPR40(-/-) primary cell cultures. In addition, in vivo administration of GW9508 counteracted ovariectomy-induced bone loss in wild-type but not GPR40(-/-) mice, enlightening the obligatory role of the GPR40 receptor. Then, in a context of growing prevalence of metabolic and age-related bone disorders, our results demonstrate for the first time in translational approaches that GPR40 is a relevant target for the design of new nutritional and therapeutic strategies to counter bone complications.
Experimental Investigations, Modeling, and Analyses of High-Temperature Devices for Space Applications. Part 1 (1999)

Abstract : The Institute of Space and Nuclear Power Studies at the University of New Mexico has developed a computer simulation of cylindrical geometry alkali metal thermal-to-electric converter cells using a standard Fortran 77 computer code. The objective and use of this code was to compare the experimental measurements with computer simulations, upgrade the model as appropriate, and conduct investigations of various methods to improve the design and performance of the devices for improved efficiency, durability, and longer operational life-time. The Institute of Space and Nuclear Power Studies participated in vacuum testing of PX series alkali metal thermal-to-electric converter cells and developed the alkali metal thermal-to-electric converter Performance Evaluation and Analysis Model. This computer model consisted of a sodium pressure loss model, a cell electrochemical and electric model, and a radiation/conduction heat transfer model. The code closely predicted the operation and performance of a wide variety of PX series cells which led to suggestions for improvements to both lifetime and performance. The code provides valuable insight into the operation of the cell, predicts parameters of components within the cell, and is a useful tool for predicting both the transient and steady state performance of systems of cells.
Application of a Microfabricated Microwave Resonator in a Co-Pd–Based Magnetic Hydrogen-Gas Sensor (2022)

We investigate the ferromagnetic resonance (FMR) response of microfabricated microwave resonators loaded with small ${\mathrm{Co}}_{16}{\mathrm{Pd}}_{84}$ alloy rectangles. A major increase in the FMR signal-to-noise ratio is achieved by employing the microwave-resonator structure. A FMR peak shift similar to that of ${\mathrm{Co}}_{16}{\mathrm{Pd}}_{84}$ continuous films is measured in the presence of hydrogen gas in the sample environment. We show that the very high sensitivity of the FMR signal of the ${\mathrm{Co}}_{16}{\mathrm{Pd}}_{84}$ alloy rectangle to hydrogen exposure can be used to measure relatively small hydrogen-concentration steps near 100% ${\mathrm{H}}_{2}$. Additionally, we also demonstrate that this structure can measure hydrogen over a concentration range from 3% to 100% ${\mathrm{H}}_{2}$ in ${\mathrm{N}}_{2}$. In time-dependent FMR measurements, we discover a temperature dependence of the FMR signal, which we relate to intrinsic temperature-dependent changes in saturation magnetization and the magnetic anisotropy of the $\mathrm{Co}$-$\mathrm{Pd}$ alloy.
Recent Developments in Quantum‐Circuit Refrigeration (2022)

Abstract The recent progress in direct active cooling of the quantum‐electric degrees of freedom in engineered circuits, or quantum‐circuit refrigeration is reviewed. In 2017, the discovery of a quantum‐circuit refrigerator (QCR) based on photon‐assisted tunneling of quasiparticles through normal‐metal–insulator–superconductor junctions inspired a series of experimental studies demonstrating the following main properties: i) the direct‐current (dc) bias voltage of the junction can change the QCR‐induced damping rate of a superconducting microwave resonator by orders of magnitude and give rise to nontrivial Lamb shifts, ii) the damping rate can be controlled in nanosecond time scales, and ii) the dc bias can be replaced by a microwave excitation, the amplitude of which controls the induced damping rate. Theoretically, it is predicted that state‐of‐the‐art superconducting resonators and qubits can be reset with an infidelity lower than 10 −4 in tens of nanoseconds using experimentally feasible parameters. A QCR‐equipped resonator has also been demonstrated as an incoherent photon source with an output temperature above 1 K yet operating at millikelvin. This source has been used to calibrate cryogenic amplification chains. In the future, the QCR may be experimentally used to quickly reset superconducting qubits, and hence assist in the great challenge of building a practical quantum computer.
Compressing μJ-level pulses from 250  fs to sub-10  fs at 38-MHz repetition rate using two gas-filled hollow-core photonic crystal fiber stages (2015)

Compression of 250-fs, 1-μJ pulses from a KLM Yb:YAG thin-disk oscillator down to 9.1 fs is demonstrated. A kagomé-PCF with a 36-μm core-diameter is used with a pressure gradient from 0 to 40 bar of krypton. Compression to 22 fs is achieved by 1200 fs<sup>2</sup> group-delay-dispersion provided by chirped mirrors. By coupling the output into a second kagomé-PCF with a pressure gradient from 0 to 25 bar of argon, octave spanning spectral broadening via the soliton-effect is observed at 18-W average output power. Self-compression to 9.1 fs is measured, with compressibility to 5 fs predicted. Also observed is strong emission in the visible via dispersive wave generation, amounting to 4% of the total output power.
Welcome from the Program Co-chairs (2009)

It is our great pleasure to welcome you to the 1st
Soft-Tissue Fluid Determination by Dichromatic Absorptiometry (1977)

Dichromatic absorptiometry (DA) in a noninvasive method for individually determining the amount of lipid, bone mineral, and protein and water present in a mixture by differential attenuation of radiation beams emitted from a dual photon source. The physics involved permit these components to be determined extremely accurately and precisely. The present study investigated the ability of DA limb scans to measure changes in total body water produced in dogs and in patients. Dichromatic absorptiometry was determined to be a valid method of measuring changes in total body water content as reflected by limb fluid content changes. Precision was limited by the accuracy in positioning the limb for repeated scanning. Dichromatic absorptiometry has the potential of becoming a clinically useful instrument for measuring fluid content changes in limbs produced either by changes in total body water content or by conditions causing limb edema.
Influence of breathing state on the accuracy of automated patient positioning in thoracic CT using a 3D camera for body contour detection (2021)

Abstract Objective To assess the influence of breathing state on the accuracy of a 3D camera for body contour detection and patient positioning in thoracic CT. Materials and methods Patients who underwent CT of the thorax with both an inspiratory and expiratory scan were prospectively included for analysis of differences in the ideal table height at different breathing states. For a subgroup, an ideal table height suggestion based on 3D camera images at both breathing states was available to assess their influence on patient positioning accuracy. Ideal patient positioning was defined as the table height at which the scanner isocenter coincides with the patient’s isocenter. Results The mean (SD) difference of the ideal table height between the inspiratory and the expiratory breathing state among the 64 included patients was 10.6 mm (4.5) ( p &lt; 0.05). The mean (SD) positioning accuracy, i.e., absolute deviation from the ideal table height, within the subgroup ( n = 43) was 4.6 mm (7.0) for inspiratory scans and 7.1 mm (7.7) for expiratory scans ( p &lt; 0.05) when using corresponding 3D camera images. The mean (SD) accuracy was 14.7 mm (7.4) ( p &lt; 0.05) when using inspiratory camera images on expiratory scans; vice versa, the accuracy was 3.1 mm (9.5) ( p &lt; 0.05). Conclusion A 3D camera allows for accurate and precise patient positioning if the camera image and the subsequent CT scan are acquired in the same breathing state. It is recommended to perform an expiratory planning image when acquiring a thoracic CT scan in both the inspiratory and expiratory breathing state. Key Points • A 3D camera for body contour detection allows for accurate and precise patient positioning if the camera image and the subsequent CT scan are acquired in the same breathing state . • It is recommended to perform an expiratory planning image when acquiring a thoracic CT scan in both the inspiratory and expiratory breathing state .
Three Views of a Train Wreck (2016)

Despite and arguably because of the enormous public health benefits arising from the introduction of new medicines, the industry is in the midst of crisis. We detail in this chapter the decline in research and development efficiency, which has been termed “Eroom's Law,” a playful inversion of the bettern known Moore's Law of Computing. An explanation of declining efficiency follows as is a brief summary of some remedies taken by many biopharmaceutical entities, including the abandonment of therapeutics targeting particularly difficult indications such as Alzheimer's disease and antibiotics. We also convey how the industry has developed into a sort of food chain, with smaller companies and government grants supporting the earliest stages of research, which are then acquired by medium-sized companies, which in turn are consolidated into large companies. This food chain is fundamentally in doubt based on shrinking Federal spending on research combined with a decline in venture capital support for early-stage start-ups.
A framework for subsurface monitoring by integrating reservoir simulation with time-lapse seismic surveys (2023)

Reservoir simulations for subsurface processes play an important role in successful deployment of geoscience applications such as geothermal energy extraction and geo-storage of fluids. These simulators provide time-laps dynamics of the coupled poro-mechanical processes within the reservoir and its over-, under-, and side-burden environments. For more reliable operations, it is crucial to connect these reservoir simulation results with the seismic surveys (i.e., observation data). However, despite being crucial, such integration is challenging due to the fact that the reservoir dynamics alters the seismic parameters. In this work, a coupled reservoir simulation and time-lapse seismic methodology is developed for multiphase flow operations in subsurface reservoirs. To this end, a poromechanical simulator is designed for multiphase flow and connected to a forward seismic modeller. This simulator is then used to assess a novel methodology of seismic monitoring by isolating the reservoir signal from the entire reflection response. This methodology is shown to be able to track the development of the fluid front over time, even in the presence of a highly reflective overburden with strong time-lapse variations. These results suggest that the proposed methodology can contribute to a better understanding of fluid flow in the subsurface. Ultimately, this will lead to improved monitoring of reservoirs for underground energy storage or production.
Route Distribution Incentives (2009)

We present an incentive model for route distribution in the context of path vector routing protocols and we focus on the Border Gateway Protocol (BGP). BGP is the de-facto protocol for interdomain routing on the Internet. We model BGP route distribution and computation using a game in which a BGP speaker advertises its prefix to its direct neighbors promising them a reward for further distributing the route deeper into the network, the neighbors do the same thing with their neighbors, and so on. The result of this cascaded route distribution is an advertised prefix and hence reachability of the BGP speaker. We first study the convergence of BGP protocol dynamics to a unique outcome tree in the defined game. We then proceed to study the existence of equilibria in the full information game considering competition dynamics. We focus our work on the simplest two classes of graphs: 1) the line (and the tree) graphs which involve no competition, and 2) the ring graph which involves competition.
Evaluation of the Isotropic Coverage of an Antenna in a Multipath Environment (2006)

Handheld devices as well as various network sensors are expected to keep a constant wireless connectivity whatever their orientation relative to the environment or the access point. In order to assess antenna performances in this context, we propose a novel method for the computation of the antenna coverage over all 3D orientations. Coverage is computed from the antenna far field sampled in every direction. Environment effects are taken into account through the implementation of a statistical multipath channel model. Coverage curves of five well-known antennas are presented for three different environments: free space, indoor line of sight (LOS) and indoor non line of sight (NLOS)