gebhart/patrepeval huggingface dataset:
Optimized light–matter interaction and defect hole placement in photonic crystal cavity sensors (2012)

Photonic crystal slab cavities were investigated for increased light-matter interaction based on selective placement of sublattice hole sized defect holes inside L3 cavities. A multiple-hole defect (MHD) consisting of three defect holes placed in the regions of highest cavity mode field intensity were demonstrated through finite-difference time-domain simulations and experiments to exhibit the strongest light-matter interaction without introducing significant scattering losses. Compared to an L3 cavity without defect holes, these strategically designed three-hole MHD cavities presented higher quality factor and more than double the resonance wavelength shift upon exposure to a thin oxide and two small chemical molecules.
Abstract 13632: The Optimization of Mechanical Circulatory Support Device Combination Considering Ventricular Load in Biventricular Failure Condition: A Simulation Study (2022)

Backgrounds: Recently, the combination of Impella, a percutaneous transvalvular left ventricular assist device, and veno-arterial extracorporeal membrane oxygenation (ECMO) have improved the survival rate of cardiogenic shock by its powerful hemodynamic support effect. Meanwhile, the optimal flow control of those devices remains unclear, especially in biventricular failure (BVF). In this study, we established the mathmatical cardiovasular simulation model, and evaluated how the combination therapy impacts both right (RV) and left (LV) ventricular loading. Methods: We used SimulinkⓇ (Mathworks, Inc.) for the simulation. Both the systemic and pulmonary circulation were modeled by using 5-element resistance-capacitance net-work. Four cardiac chambers were represented by time-varying elastance with unidirectional valves (Fig. 1). In LV dysfunction (LV end-systolic elastace was set at low level: 0.4 mmHg/ml), we compared the changes of right (RAP) and left (LAP) atrial pressure, as the marker of ventricular loading, under various RV function and Impella and ECMO flows. Results: Impella slightly increased RAP and reduced LAP regardless of RV systolic function (Fig. 2). In high pulmonary vascular resistance (PVR), the increase of Impella flow augumented RAP, while Impella could not be up-titrated more than 2.8 L/min due to LV suction (Fig. 3). In BVF with high PVR, ECMO decreased RAP and increased LAP in each Impella flow (Fig. 4). Higher ECMO and Impella flows rendered LV extremely small, induced suction, and increased RV preload and RAP. Conclusion: PVR is the major determinant of stable Impella support without inducing RV loading and LV suction. In BVF with high PVR, ECMO reduced RV loading, while decreased LV filling and induced LV suction by Impella. The preemptive simulation study for an individual patient may help the optimal use of mechanical circulatory support device to maximize RV and LV unloading with improving hemodynamics.
CSIG-07. SIMULTANEOUS EXPLORATION OF A SET OF PRECLINICAL GBM-MODELS PROVIDES PREDICTIVE DATA ON CLINICALLY RELEVANT DRUGS (2016)

Glioblastoma (GBM) is characterized by genetic loss of tumor suppressors like e.g. p53, cdkn2a, PTEN, NF1 and overexpression of proto-oncogenes like e.g. PDGFRB, EGFR or EGFRvIII. Significant efforts are being made in the discovery of potential therapeutics, but without tailor-made stratification schemes and predictive markers many drug candidates fail in clinical trials. While the phytovanilloid cannabidiol (CBD) is advanced to phase II clinical trials, little is known on how it induces GBM cell-death, the exact molecular pathways it triggers, and potential biomarkers that could be used to predict therapy outcome. We engineered more than 30 different transgenic mouse glioma lines to mimic the genetic diversity of the four human GBM subtypes. Then, we investigated CBD cytotoxicity comparing our repertoire of 24 patient-derived GBMs to the transgenic mouse tumors. In both settings we show that CBD induced cytotoxicity in GBM cells with distinct genetic signatures and categorize GBMs according to genetic profiles into prospective CBD-responsive and unresponsive subsets. Furthermore, we identify the mode of CBD induced GBM death and pinpoint differentially regulated targets. With our preclinical work we contribute valuable information to stratify patients for ongoing clinical trials using CBD as a therapeutic. Overall, we show a preclinical strategy to uncover biomarkers that can gain predictive power in clinical trials.
Evaluation of an aldo-keto reductase gene signature with prognostic significance in colon cancer via activation of epithelial to mesenchymal transition and the p70S6K pathway (2020)

AKR1B1 and AKR1B10, members of the aldo-keto reductase family of enzymes that participate in the polyol pathway of aldehyde metabolism, are aberrantly expressed in colon cancer. We previously showed that high expression of AKR1B1 (AKR1B1HIGH) was associated with enhanced motility, inflammation and poor clinical outcome in colon cancer patients. Using publicly available datasets and ex vivo gene expression analysis (n = 51, Ankara cohort), we have validated our previous in silico finding that AKR1B1HIGH was associated with worse overall survival (OS) compared with patients with low expression of AKR1B1 (AKR1B1LOW) samples. A combined signature of AKR1B1HIGH and AKR1B10LOW was significantly associated with worse recurrence-free survival (RFS) in microsatellite stable (MSS) patients and in patients with distal colon tumors as well as a higher mesenchymal signature when compared with AKR1B1LOW/AKR1B10HIGH tumors. When the patients were stratified according to consensus molecular subtypes (CMS), AKR1B1HIGH/AKR1B10LOW samples were primarily classified as CMS4 with predominantly mesenchymal characteristics while AKR1B1LOW/AKR1B10HIGH samples were primarily classified as CMS3 which is associated with metabolic deregulation. Reverse Phase Protein Array carried out using protein samples from the Ankara cohort indicated that AKR1B1HIGH/AKR1B10LOW tumors showed aberrant activation of metabolic pathways. Western blot analysis of AKR1B1HIGH/AKR1B10LOW colon cancer cell lines also suggested aberrant activation of nutrient-sensing pathways. Collectively, our data suggest that the AKR1B1HIGH/AKR1B10LOW signature may be predictive of poor prognosis, aberrant activation of metabolic pathways, and can be considered as a novel biomarker for colon cancer prognostication.
Low computational complexity and minimizing training overhead for hybrid precoding in millimeter wave systems (2018)

Millimeter wave (mmWave) hybrid precoding systems are likely to have large antenna arrays to overcome the high channel path loss. In such circumstances, low cost hardware and power consumption are the main challenges. Furthermore, the hardware is tasked with computation of high dimensional optimal matrices of hybrid precoding design using Orthogonal Matching Pursuit (OMP). This paper addresses two algorithms to enhance the efficiency of the OMP reconstruction algorithm in mmWave precoding design. The spectral efficiency of the mmWave system using the proposed algorithms is compared with previous works and the optimal case (a fully digital precoder). The results show that the performance of the proposed algorithms is very close to that of the optimal design even though the complexity of the design is reduced.
Extracellular adenosine triphosphate activates phospholipase C and mobilizes intracellular calcium in primary cultures of sheep anterior pituitary cells (1989)

In primary cultures of sheep anterior pituitary cells extracellular ATP (ED50 0.4-0.8 microM) stimulated efflux of 45Ca2+ from a slow-turnover intracellular pool. ADP was also effective whereas AMP and adenosine were not. The ATP effect was not due to cell permeabilization as 100 microM ATP did not elicit efflux of 2-deoxy[3H]glucose metabolites. This 45Ca2+ mobilization may be mediated by inositol trisphosphate, since ATP (ED50 1 microM) stimulated inositol phosphate generation. These results demonstrate P2-purinoceptors in sheep anterior pituitary cells which are coupled to phospholipase C activation and intracellular Ca2+ mobilization, and raise the possibility of a regulatory role for extracellular ATP in the anterior pituitary.
Recognition and management of community-acquired acute kidney injury in low-resource settings in the ISN 0by25 trial: A multi-country feasibility study (2021)

This multicenter, non-randomized feasibility study in low-resource settings demonstrates that it is feasible to implement a comprehensive program utilizing POC testing and protocol-based management to improve the recognition and management of AKI and AKD in high-risk patients in primary care.
Numerical Simulations of Transcritical Natural Convection (2017)

In modern engineering applications, system overheating is a key issue that needs to be solved with efficient and reliable cooling technologies. Among the possible mechanisms that these are based on, natural convection cooling is one of the most frequently employed, with applications ranging from cooling of computer micro-components to large nuclear reactors. While many studies have been performed on natural convection employing supercritical or subcritical fluids, little attention has been given to fluids in their transcritical regime. The latter has the potential to yield high performances while avoiding detrimental effects of two-phase systems (e.g. cavitation). In the present study, 2D simulations of a theoretical transcritical natural convection cooling system are performed. Thermal properties changes and their influences on the overall heat transfer dynamics are investigated. To assess the performance of transcritical natural convection, heat flux and frequency content of hydrodynamic mixing are analyzed. Two fluids are employed (H20 and R134a), with four different temperature settings. Flow visualizations show circulations patterns typical of natural convection but with peculiarities due to pseudo-boiling conditions such as absence of nucleate boiling. With increasing top-down temperature difference, steady-state equilibrium heat flux is achieved sooner. Dimensional scaling techniques are used to collapse heat flux time spectra for all the temperature differences considered. This study is the first step towards high-fidelity numerical modeling and understanding of transcritical fluid behavior in natural convection systems that can be used in high-performance cooling devices.
Circuit Edit Geometric Trends (2013)

Abstract Focused ion beam (FIB) tools for backside circuit edit play a major role in the validation of integrated circuit (IC) design modifications. Process scaling is one of many significant challenges, because it reduces the accessible area to modify transistors and IC interconnects in the design. This paper examines the geometries available for FIB nanomachining, via milling/etching, and deposited metal jumpers by analyzing polygon data from computer aided design (CAD) virtual layers gathered across four process technologies, from 180nm down to 28nm. The results of this analysis demonstrate that the combination of silicon nanomachining box length and FIB via box length identifies the most challenging aspects of the FIB edit. The smallest geometries include a 300 nanometer silicon access area with a FIB milled 200 nanometer via inside it. More advanced technology nodes will require the ability to make smaller geometries without the help of integrated design features typically referred to as design for FIB/Debug.
α-Lytic Protease Precursor:  Characterization of a Structured Folding Intermediate (1999)

The bacterial alpha-lytic protease (alphaLP) is synthesized as a precursor containing a large N-terminal pro region (Pro) transiently required for correct folding of the protease [Silen, J. L., and Agard, D. A. (1989) Nature 341, 462-464]. Upon folding, the precursor is autocatalyticly cleaved to yield a tight-binding inhibitory complex of the pro region and the fully folded protease (Pro/alphaLP). An in vitro purification and refolding protocol has been developed for production of the disulfide-bonded precursor. A combination of spectroscopic approaches have been used to compare the structure and stability of the precursor with either the Pro/alphaLP complex or isolated Pro. The precursor and complex have significant similarities in secondary structure but some differences in tertiary structure, as well as a dramatic difference in stability. Correlations with isolated Pro suggest that the pro region part of the precursor is fully folded and acts to stabilize and structure the alphaLP region. Precursor folding is shown to be biphasic with the fast phase matching the rate of pro region folding. Further, the rate-limiting step in oxidative folding is formation of the disulfide bonds and autocatalytic processing occurs rapidly thereafter. These studies suggests a model in which the pro region folds first and catalyzes folding of the protease domain, forming the active site and finally causing autocatalytic cleavage of the bond separating pro region and protease. This last processing step is critical as it allows the protease N-terminus to rearrange, providing the majority of net stabilization of the product Pro/alphaLP complex.
Recombinant antineuraminidase single chain antibody: Expression, characterization, and crystallization in complex with antigen (1993)

The variable heavy (VH) and variable light (VL) genes of NC10, a monoclonal antibody with specificity toward N9 neuraminidase (NA), were cloned and sequenced. A single chain Fv (scFv) fragment of NC10, consisting of VH and VL domains joined by a peptide linker, was designed, constructed and expressed in the E. coli expression vector pPOW. The N-terminal secretion signal PelB directed the synthesized protein into the periplasm where it was associated with the insoluble membrane fraction. An octapeptide (FLAG) tail was fused to the C-terminus of the single chain Fv to aid in its detection and remained intact throughout the protein purification process. NC10 scFv was purified by solubilization of the E. coli membrane fraction with guanidinium hydrochloride followed by column chromatography. The purified NC10 scFv showed binding affinity for its antigen, NA, 2-fold lower than that of the parent Fab. The complex between NA and the scFv has been crystallized by the vapor diffusion method. The crystals are tetragonal, space group P42(1)2, with unit cell dimensions a = b = 141 A, c = 218 A.
Single Nucleotide Polymorphisms in the G-Protein Coupled Receptor Kinase 5 (GRK5) Gene are associated with Plasma LDL-Cholesterol Levels in Humans (2018)

Genetically modified mice models suggest an important role for G-protein-coupled receptor kinase 5 (GRK5) in the pathophysiology of obesity and related disorders. We investigated whether single nucleotide polymorphisms (SNPs) in the gene encoding GRK5 affect cardiometabolic traits in humans. We genotyped 3 common SNPs in intron 1 (rs1980030, rs10466210, rs9325562) and one SNP in intron 3 (rs10886471) of GRK5 in 2332 subjects at risk for type 2 diabetes. Total- and visceral fat mass were measured by magnetic resonance (MR) tomography and liver fat content by <sup>1</sup>H-MR spectroscopy. Insulin secretion and sensitivity were estimated during an OGTT and measured during the euglycemic, hyperinsulinemic clamp (n = 498). Carriers of the minor allele of rs10466210 and rs1980030 had higher total- and LDL-cholesterol levels (p = 0.0018 and p = 0.0031, respectively, for rs10466210; p = 0.0035 and p = 0.0081, respectively, for rs1980030), independently of gender, age, BMI and lipid-lowering drugs. The effects of rs10466210 withstood Bonferroni correction. Similar associations were observed with apolipoprotein B levels (p = 0.0034 and p = 0.0122, respectively). Carriers of the minor allele of rs10466210 additionally displayed a trend for higher intima-media thickness of the carotid artery (p = 0.075). GRK5 may represent a novel target for strategies aiming at lowering LDL-cholesterol levels and at modifying cardiovascular risk.
Electrooptical gaze measurement with high spatial and temporal resolution (1986)

The stringent requirements of achieving both high spatial (0.25°) and temporal (1-ms) resolution in a helmet-mounted electrooptical system permitting 2-D gaze measurements independent of head translation prohibits implementation of 2-D sensors. To meet these requirements, SRD has recently introduced a novel technique wherein two 1-D, photoelectric self-scanned arrays detect projections of the bright pupil (P) and corneal reflection (CR) images, thereby reducing the number of sampled pixels from n 2 to 2 n . To achieve subpixel resolution we have developed algorithms based on models of the P, CR, and iris signals. The pupil center is immediately provided with subpixel resolution once its elliptic model parameters are determined by a least-squares fit of the P-set of data. Alternatively it can be determined using the P-edges defined by the intersection of the P-model with the iris model. The P-model enables definition of its center and/or edges even in extreme cases where the CR obscures one of the latter. The distorted CR signal is first restored by subtraction of the P-model from the raw data. The set of 5–7 points of the restored CR signal is then used for computation of a Gaussian model to provide the center of the CR with 0.25 pixel resolution. Measurements with an artificial eye indicate resolution (and accuracy) of better than 0.25° at a rate of 1000 frames/s.
Lyapunov function-based control laws for revolute robot arms: tracking control, robustness, and adaptive control (1992)

A new class of joint level control laws for all-revolute robot arms is introduced. The analysis is similar to an energy-like Lyapunov function approach, except that the closed-loop potential function is shaped in accordance with the underlying joint space topology. This approach gives way to a much simpler analysis and leads to a new class of control designs which guarantee both global asymptotic stability and local exponential stability. When Coulomb and viscous friction and parameter uncertainty are present as model perturbations, a sliding mode-like modification of the control law results in a robustness-enhancing outer loop. Adaptive control is formulated within the same framework. A linear-in-the-parameters formulation is adopted and globally asymptotically stable adaptive control laws are derived by simply replacing unknown model parameters by their estimates.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Modular Fluted Tapered Stems for Periprosthetic Femoral Fractures (2022)

Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
A Fast Heterodyne Network Analyzer Based on Precision Linear Frequency Ramps (2001)

A system concept for a heterodyne network analyzer (NWA) is presented. In contrast to conventional frequency step-by-step signal sources, the high frequency signal sources of the fast NWA are precise and highly linear analogue frequency ramp generators. The use of fractional divider phase locked loop circuits allows to fulfill the stringent stability and linearity requirements of the analogue ramps. Not only the signal sources but also the signal processing differs from that of the conventional NWA. After filtering the raw data of the complete frequency sweep by a double Fourier transformation, the analytical signal is determined. Then conventional calibration procedures are applied in order to correct for the systematic errors of the NWA.
Synthesis and Characterization of Shape‐Memory Polyurethane–Polybenzoxazine Compounds (2012)

Abstract The study investigates the scope for significant enhancements in shape‐memory properties in blends of thermoplastic polyurethanes (PUs) and polybenzoxazine (PB). PB was expected to serve as a second fixed phase in addition to hard segment of PU. The shape‐memory compounds were prepared in three steps. First, benzoxazine monomer was dissolved in urethane prepolymer synthesized from 4,4′‐methylenebis (phenyl isocyanate) (MDI) and poly (tetramethylene) glycol (PTMG). Second, the prepolymer was chain extended with 1,4‐butanediol (BD) without curing of benzoxazine. Third, the benzoxazine was polymerized into PB by thermal curing at 180 °C for 3 h. A compound with 17 wt% PB exhibited a recovery stress (RS) of 13 MPa and strain recovery (SR) of 93% compared with RS of 6.8 MPa and SR of 72% for PU. magnified image
NEW UTILITY STRATEGIES FOR SAVING ENERGY IN THE COMMERCIAL SECTOR (1982)

The large electric and gas utilities in California have been conducting energy conservation programs for their commercial customers for several years.Although each utility tailors its conservation programs to the specific characteristics of its territory, the changes that have been introduced since the programs started reveal several important common trends.''';
Treatment of premenstrual dysphoric disorder with the GABAA receptor modulating steroid antagonist Sepranolone (UC1010)—A randomized controlled trial (2017)

This explorative study indicates promising results for UC1010 as a potential treatment for PMDD. The effect size was comparable to that of SSRIs and drospirenone containing oral contraceptives. UC1010 was well tolerated and deemed safe.
Treatment of Distal Posterior Cerebral Artery Aneurysms (2010)

Bypass techniques for the treatment of distal PCA aneurysms are associated with a higher rate of complications than once thought. In our new treatment paradigm, bypass is a last resort and reserved for patients in whom balloon-test occlusion fails, who refuse parent-vessel sacrifice, and who cannot undergo primary stenting with coiling or clip wrapping.
Supplementary Methods from Biomarker Analyses from a Placebo-Controlled Phase II Study Evaluating Erlotinib ± Onartuzumab in Advanced Non–Small Cell Lung Cancer: MET Expression Levels Are Predictive of Patient Benefit (2023)

&lt;p&gt;Additional methodology describing cell lines and tissues, as well as detailed methodology for gene expression, flow cytometry, IHC and FISH studies.&lt;/p&gt;
A transgenic Xenopus laevis reporter model to study lymphangiogenesis (2013)

The importance of the blood- and lymph vessels in the transport of essential fluids, gases, macromolecules and cells in vertebrates warrants optimal insight into the regulatory mechanisms underlying their development. Mouse and zebrafish models of lymphatic development are instrumental for gene discovery and gene characterization but are challenging for certain aspects, e.g. no direct accessibility of embryonic stages, or non-straightforward visualization of early lymphatic sprouting, respectively. We previously demonstrated that the Xenopus tadpole is a valuable model to study the processes of lymphatic development. However, a fluorescent Xenopus reporter directly visualizing the lymph vessels was lacking. Here, we created transgenic Tg(Flk1:eGFP) Xenopus laevis reporter lines expressing green fluorescent protein (GFP) in blood- and lymph vessels driven by the Flk1 (VEGFR-2) promoter. We also established a high-resolution fluorescent dye labeling technique selectively and persistently visualizing lymphatic endothelial cells, even in conditions of impaired lymph vessel formation or drainage function upon silencing of lymphangiogenic factors. Next, we applied the model to dynamically document blood and lymphatic sprouting and patterning of the initially avascular tadpole fin. Furthermore, quantifiable models of spontaneous or induced lymphatic sprouting into the tadpole fin were developed for dynamic analysis of loss-of-function and gain-of-function phenotypes using pharmacologic or genetic manipulation. Together with angiography and lymphangiography to assess functionality, Tg(Flk1:eGFP) reporter tadpoles readily allowed detailed lymphatic phenotyping of live tadpoles by fluorescence microscopy. The Tg(Flk1:eGFP) tadpoles represent a versatile model for functional lymph/angiogenomics and drug screening.