gebhart/patrepeval huggingface dataset:
Single-shot fringe pattern phase retrieval using improved period-guided bidimensional empirical mode decomposition and Hilbert transform (2021)

Fringe pattern analysis is the central aspect of numerous optical measurement methods, e.g., interferometry, fringe projection, digital holography, quantitative phase microscopy. Experimental fringe patterns always contain significant features originating from fluctuating environment, optical system and illumination quality, and the sample itself that severely affect analysis outcome. Before the stage of phase retrieval (information decoding) interferogram needs proper filtering, which minimizes the impact of mentioned issues. In this paper we propose fully automatic and adaptive fringe pattern pre-processing technique - improved period guided bidimensional empirical mode decomposition algorithm (iPGBEMD). It is based on our previous work about PGBEMD which eliminated the mode-mixing phenomenon and made the empirical mode decomposition fully adaptive. In present work we overcame key problems of original PGBEMD - we have considerably increased algorithm's application range and shortened computation time several-fold. We proposed three solutions to the problem of erroneous decomposition for very low fringe amplitude images, which limited original PGBEMD significantly and we have chosen the best one among them after comprehensive analysis. Several acceleration methods were also proposed and merged to ensure the best results. We combined our improved pre-processing algorithm with the Hilbert Spiral Transform to receive complete, consistent, and versatile fringe pattern analysis path. Quality and effectiveness evaluation, in comparison with selected reference methods, is provided using numerical simulations and experimental fringe data.
Electrochemical Biosensors for Environmental Monitoring (2002)

Highly sensitive electrochemical biosensors offer precision, sensitivity, rapidity, and ease of operation for on-site environmental analysis. An electrochemical biosensor is an analytical device in which a specific biological recognition element (bioreceptor) is integrated within or intimately associated with an electrode (transducer) that converts the recognition event to a measurable electrical signal for the purpose of detecting a target compound (analyte) in solution. The signal generated allows both qualitative and quantitative measurements of an analyte in real time. In most cases, a miniaturized electrochemical cell contains a low volume of analyte, which is vital when dealing with hazardous materials and makes such devices ideal for environmental monitoring. This approach not only provides the means for on-site analysis but also removes the time delay and sample alteration that can occur during transport to a centralized laboratory. We first address the basic principles of electroanalytical measurement and the merger of electrochemistry and biology into a biosensing system, and then we discuss various environmental monitoring strategies involving this technology.
Computational-sampling-moiré-based on-machine alignment for freeform optics (2023)

The manufacturing and characterization of freeform optical surfaces are influenced by their high sensitivity to misalignments. In this work, the computational sampling moiré technique combined with phase extraction is developed for the precise alignment of freeform optics during fabrication and in metrology applications. This novel, to the best of our knowledge, technique achieves near-interferometry-level precision in a simple and compact configuration. This robust technology can be applied to industrial manufacturing platforms (such as diamond turning machines, lithography, and other micro-nano-machining techniques) as well as their metrology equipment. In a demonstration of computational data processing and precision alignment using this method, iterative manufacturing of freeform optical surfaces with a final-form accuracy of about 180 nm was accomplished.
Abstract 2936: Ago2 induces Kras signaling and promotes tumor progression in mouse models of lung adenocarcinoma (2021)

Abstract Lung cancer is the deadliest malignancy in the United States. Non-small cell lung cancer (NSCLC) accounts for 85% of cases, and is frequently driven by activating mutations in the gene encoding the KRAS GTPase (e.g. KRASG12D). Our previous work demonstrated that Argonaute 2 (AGO2)—a component of the RNA induced silencing complex (RISC)—physically interacts with KRAS and stabilizes it at the protein level. In multiple cell lines, AGO2 knockdown reduces KRAS protein level and attenuates cell proliferation. We therefore hypothesized that AGO2 could promote KRASG12D-dependent NSCLC in vivo. To test the hypothesis, we evaluated the impact of Ago2 knockout in the KPC mouse model of NSCLC. In KPC mice, intratracheal delivery of adenoviral Cre drives lung-specific expression of a stop-floxed KRASG12D allele and biallelic ablation of p53. Simultaneous biallelic ablation of floxed Ago2 inhibited KPC lung nodule growth while reducing proliferative index and improving pathological grade. We next applied the KPHetC model, in which the clara cell-specific CCSP-driven Cre activates KRASG12D and ablates a single p53 allele. In these mice, Ago2 ablation also reduced tumor size and grade. In both models, Ago2 knockout inhibited ERK phosphorylation in tumor nodules, indicating impaired KRAS signaling. Furthermore, RNA-seq analysis of KPC nodules demonstrated broadly reduced expression of Kras-related genes. Taken together, our data demonstrate a novel pathogenic role for AGO2 in KRAS-dependent NSCLC. Given the prevalence of this malignancy and current difficulties in therapeutically targeting KRAS signaling, our work has future translational relevance. Citation Format: Jean C. Tien, Seema Chugh, Andrew E. Goodrum, Yunhui Cheng, Lisha Wang, Rahul Mannan, Xiaoming Wang, Vijaya L. Dommeti, Yuping Zhang, Alice Xu, Fengyu Su, Xuhong Cao, Sunita Shankar, Arul M. Chinnaiyan. Ago2 induces Kras signaling and promotes tumor progression in mouse models of lung adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2936.
Faculty Opinions recommendation of Time to first cigarette and lung cancer risk in Japan. (2014)

BACKGROUND: Cigarette smoking is the major cause of lung cancer (LC). Although the time to first cigarette (TTFC) of the day is a distinct indicator of nicotine dependence, little information is available on its possible relation to LC.PATIENTS AND METHODS: This case-control study includes a total of 1572 incident LC cases and 1572 non-cancer controls visiting for the first time the Aichi Cancer Center Hospital between 2001 and 2005. We estimated the odds ratio (OR) and 95% confidence interval (CI) for TTFC using a logistic regression model after adjustment for several potential confounders.RESULTS: TTFC was inversely associated with the risk of LC. This association was consistent across histological subtypes of LC. For all LCs considered among ever smokers and after accurate allowance for smoking quantity and duration, besides other relevant covariates, compared with TTFC >60 min, the adjusted ORs were 1.08 (95% CI, 0.73-1.61) for TTFC of 31-60 min, 1.40 (0.98-2.01) for 6-30 min and 1.86 (1.28-2.71) for within 5 min (Ptrend, < 0.001). Statistically marginally significant heterogeneity by histological subtype was observed (Pheterogeneity, 0.002).CONCLUSIONS: Nicotine dependence, as indicated by the TTFC, is associated with increased risk of LC and is therefore an independent marker of exposure to tobacco smoking. PMID: 24013511
Effect of ionizing radiation on infrared polarizers based on conductive polymer (2008)

Conductive polymers have become an extremely useful class of materials for many optical applications. We have developed an electrochemical growth method for depositing highly conductive (~100 S/cm) polypyrrole. Additionally, we have adapted advanced fabrication methods for use with the polypyrrole resulting in gratings with submicron features. This conductive polymer micro-wire grid provides an optical polarizer with unique properties. When the polymer is exposed to ionizing radiation, its conductivity is affected and the polarization properties of the device, specifically the extinction ratio, change in a corresponding manner. This change in polarization properties can be determined by optically interrogating the device, possibly from a remote location. The result is a passive radiation-sensitive sensor with very low optical visibility. The ability to interrogate the device from a safe standoff distance provides a device useful in potentially dangerous environments. Also, the passive nature of the device make it applicable in applications where external power is not available. We will review the polymer deposition, fabrication methods and device design and modeling. The characterization of the polymer's sensitivity to ionizing radiation and optical testing of infrared polarizers before and after irradiation will also be presented. These experimental results will highlight the usefulness of the conductive infrared polarizer to many security and monitoring applications.
Prostate cancer C5a receptor expression and augmentation of cancer cell proliferation, invasion, and PD‐L1 expression by C5a (2020)

C5aR expression of PC cells in patients' tissues and C5a augmentation of C5aR-dependent CRPC proliferation, invasion, and PD-L1 expression suggested participation of the C5a-C5aR system in CRPC promotion and evasion from antitumor immune responses. Targeting this signaling pathway may provide a useful therapeutic option for CRPC.
Applicability of J-Integral to Tension-Softening Materials (1997)

This brief paper addresses the application of the J-integral to fracture analysis and toughness characterization of quasi-brittle materials, with specific focus on the tension-softening behavior in the fracture process zone. Concern is often raised on the validity of the J-integral when unloading occurs in the material points along which the J-integral contour path traverses, particularly during process-zone growth. This paper clarifies that this concern is misplaced. Whereas the J-integral contour wraps around the tension-softening line springs of the bridging elements in the process zone, the material points on the J-integral contour undergoes elastic loading and unloading. Therefore application of the J-integral to quasi-brittle materials does not violate the basic tenet of the assumption of nonlinear elastic material behavior underlying the J-integral theoretical formulation.
Effect of Trimetazidine Dihydrochloride Therapy on Exercise Capacity in Patients With Nonobstructive Hypertrophic Cardiomyopathy (2019)

ClinicalTrials.gov identifier: NCT01696370.
The characterization of key physiological traits of medicinal cannabis (Cannabis sativa L.) as a tool for precision breeding (2021)

Our findings suggest that selection for taller and fast-growing genotypes is likely to lead to an increase in floral bud productivity. It was also found that the final plant height and stem diameter are determined by 5 independent factors that can be used to maximize productivity through cultivation adjustments. The proposed prediction equation can facilitate the selection of prolific genotypes without the completion of a full cultivation cycle. Future studies that will associate genome-wide variation with plants morphological traits and cannabinoid profile will enable precise and accelerated breeding through genomic selection approaches.
Timing jitter in modelocked semiconductor diode lasers (2003)

We demonstrate a simple recipe for generating ultralow timing jitter from modelocked diode lasers. The key concept relies on the fact that the residual timing jitter is influenced by the dominant corner frequency and/or super mode noise spurs. By harmonically modelocking lasers and using super mode noise suppression to select a single longitudinal mode group will provide for close-in corner frequencies without super mode noise and low integrated timing jitter.
Experimental Thermochemistry of the SiCl and SiBr Radicals; Enthalpies of Formation of Species in the Si—Cl and Si—Br Systems (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Incremental Learning for Metric-Based Meta-Learners (2020)

Majority of the modern meta-learning methods for few-shot classification tasks operate in two phases: a meta-training phase where the meta-learner learns a generic representation by solving multiple few-shot tasks sampled from a large dataset and a testing phase, where the meta-learner leverages its learnt internal representation for a specific few-shot task involving classes which were not seen during the meta-training phase. To the best of our knowledge, all such meta-learning methods use a single base dataset for meta-training to sample tasks from and do not adapt the algorithm after meta-training. This strategy may not scale to real-world use-cases where the meta-learner does not potentially have access to the full meta-training dataset from the very beginning and we need to update the meta-learner in an incremental fashion when additional training data becomes available. Through our experimental setup, we develop a notion of incremental learning during the meta-training phase of meta-learning and propose a method which can be used with multiple existing metric-based meta-learning algorithms. Experimental results on benchmark dataset show that our approach performs favorably at test time as compared to training a model with the full meta-training set and incurs negligible amount of catastrophic forgetting
Maximizing Peformance/cost Figure of Merit of Storage-type SCM based SSD by Adding Small Capacity of Memory-type SCM (2018)

Non-volatile memories called “storage class memories (SCMs)” attract attentions to realize high-performance solidstate drive (SSD). Although storage-type SCM (S-SCM) based SSD has already appeared, memory-type (M-SCM) based SSD has not been realistic yet due to the high memory cost. This paper proposes multi-SCM SSD with M-SCM as non-volatile cache of S-SCM to improve the SSD performance. In addition, the best configuration of multi-SCM SSD is discussed to balance the cost and the performance. As a result, the optimal capacity of M-SCM improves the SSD performance by up to 134% with 12% cost increase. If either M-SCM or S-SCM reaches the endurance limit, multi-SCM SSD cannot be used any longer. The optimal utilization scenario is that write erase (W/E) cycles of both M-SCM and S-SCM become their limits at the same time. To boost the SSD performance, the impact of omitting wear-leveling from both SCMs are investigated. As a result, the performance enhances by up to 28.2%. Additionally, effective wear-leveling policy is considered to balance both SSD performance and its lifetime.
Successful Treatment of PD Peritonitis Due to Morganella morganii Resistant to Third-Generation Cephalosporins – A Case Report (2017)

<i>Morganella morganii</i> is a rare cause of peritonitis in patients on peritoneal dialysis (PD). Most of the reported cases have resorted to a switch to hemodialysis. We herein report a case of peritonitis due to <i>M. morganii</i> resistant to third-generation cephalosporins, which was treated successfully with intraperitoneal (IP) tobramycin followed by oral ciprofloxacin. Early microbiologic diagnosis is essential in the treatment of peritonitis from rare microorganisms such as <i>Morganella morganii</i>, and appropriate antibiotic therapy is the key to avoiding catheter loss and subsequent switch to hemodialysis.
Hyperpolarized Water Enhances Two-Dimensional Proton NMR Correlations: A New Approach for Molecular Interactions (2019)

Protein and peptide interactions are characterized in the liquid state by multidimensional NMR spectroscopy experiments, which can take hours to record. We show that starting from hyperpolarized HDO, two-dimensional (2D) proton correlation maps of a peptide, either free in solution or interacting with liposomes, can be acquired in less than 60 s. In standard 2D NMR spectroscopy without hyperpolarization, the acquisition time required for similar spectral correlations is on the order of hours. This hyperpolarized experiment enables the identification of amino acids featuring solvent-interacting hydrogens and provides fast spectroscopic analysis of peptide conformers. Sensitivity-enhanced 2D proton correlation spectroscopy is a useful and straightforward tool for biochemistry and structural biology, as it does not recur to nitrogen-15 or carbon-13 isotope enrichment.
Methane Activation by a Mononuclear Copper Active Site in the Zeolite Mordenite: Effect of Metal Nuclearity on Reactivity (2022)

The direct conversion of methane to methanol would have a wide reaching environmental and industrial impact. Copper-containing zeolites can perform this reaction at low temperatures and pressures at a previously defined O<sub>2</sub>-activated [Cu<sub>2</sub>O]<sup>2+</sup> site. However, after autoreduction of the copper-containing zeolite mordenite and removal of the [Cu<sub>2</sub>O]<sup>2+</sup> active site, the zeolite is still methane reactive. In this study, we use diffuse reflectance UV-vis spectroscopy, magnetic circular dichroism, resonance Raman spectroscopy, electron paramagnetic resonance, and X-ray absorption spectroscopy to unambiguously define a mononuclear [CuOH]<sup>+</sup> as the CH<sub>4</sub> reactive active site of the autoreduced zeolite. The rigorous identification of a mononuclear active site allows a reactivity comparison to the previously defined [Cu<sub>2</sub>O]<sup>2+</sup> active site. We perform kinetic experiments to compare the reactivity of the [CuOH]<sup>+</sup> and [Cu<sub>2</sub>O]<sup>2+</sup> sites and find that the binuclear site is significantly more reactive. From the analysis of density functional theory calculations, we elucidate that this increased reactivity is a direct result of stabilization of the [Cu<sub>2</sub>OH]<sup>2+</sup> H-atom abstraction product by electron delocalization over the two Cu cations via the bridging ligand. This significant increase in reactivity from electron delocalization over a binuclear active site provides new insights for the design of highly reactive oxidative catalysts.
Prediction of antifolate efficacy in a rat sarcoma model (1991)

A methylcholanthrene-induced rat sarcoma propagated both in vitro and in vivo was used to examine the usefulness of a rapid biochemical in situ assay that measures thymidylate synthase (TS) activity in whole cells to predict sensitivity and resistance to the folate antagonists methotrexate (MTX), 10-ethyl-10-deazaaminopterin (10-EDAM) and trimetrexate (TMTX). There was an excellent correlation between the effects of these drugs on inhibiting TS and cytotoxicity as measured by a clonogenic assay, when the exposure time was 4 hr and those when the rat sarcoma cell line was employed (p less than 0.001). When tumor-cell suspensions were prepared from the rat sarcoma propagated in vivo, they were less sensitive to these antifolates, but the relative effectiveness of the 3 antifolates was similar: TMTX much greater than 10-EDAM greater than MTX. As expected, continuous exposure (10 to 12 days) produced cytotoxicity at a much lower dose of these drugs. When the 3 drugs were tested for anti-tumor effectiveness in rats bearing this tumor, the tumor regression measured was best with TMTX; 10-EDAM was intermediate in effectiveness as compared with MTX. These results indicate that the in situ TS assay and clonogenic assay may be used to predict anti-tumor efficacy of antifolates in vivo in this rat sarcoma.
From Hydrogen Silsesquioxane to Functionalized Silicon Nanocrystals (2016)

Silicon nanocrystals exhibit size-dependent optical and electronic properties that may be exploited for applications ranging from sensors to photovoltaics. In addition, they can be utilized in biological and environmental systems thanks to the nontoxicity of silicon. Synthesis of silicon nanocrystals has been accomplished using a variety of methods. However, creating near monodisperse systems of high purity has been a challenge. The high temperature processing of hydrogen silsesquioxane method of particle synthesis reproducibly provides pure, near monodisperse particles in scalable quantities. These particles can then be liberated using HF etching and functionalized using a variety of methods. This paper outlines our lab procedures for creating silicon nanocrystals, the various functionalization methods and the most commonly used characterization techniques.
MINIMIZING THE BONDLINE THERMAL RESISTANCE IN THERMAL INTERFACE MATERIALS WITHOUT AFFECTING RELIABILITY∗ (2006)

As electronic assemblies become more compact, with increased processing bandwidth and higher energy fluxes, thermal management is limiting several critical applications. The major technology limitation is the nonmetallic joining of devices to heat sinks using existing commercial thermal interface materials (TIMs). The present study starts a systematic study of the coupled interactions between materials formulation, manufacturing process, and thermal performance. Thermal bondlines were fabricated under controlled conditions with commercially available TIMs and a nanoparticle-modified epoxy. Force measurements during bondline fabrication provided information about the flow process. Thermal performance of the bondlines was evaluated with laser flash thermal diffusivity measurements. Relationships between flow parameters, final bondline microstructure, and bondline thermal resistance are discussed from the standpoint of reliability and performance. 1.
Nitric Oxide from IFNγ-Primed Macrophages Modulates the Antimicrobial Activity of β-Lactams against the Intracellular Pathogens Burkholderia pseudomallei and Nontyphoidal Salmonella (2014)

Our investigations show that nonlethal concentrations of nitric oxide (NO) abrogate the antibiotic activity of β-lactam antibiotics against Burkholderia pseudomallei, Escherichia coli and nontyphoidal Salmonella enterica serovar Typhimurium. NO protects B. pseudomallei already exposed to β-lactams, suggesting that this diatomic radical tolerizes bacteria against the antimicrobial activity of this important class of antibiotics. The concentrations of NO that elicit antibiotic tolerance repress consumption of oxygen (O2), while stimulating hydrogen peroxide (H2O2) synthesis. Transposon insertions in genes encoding cytochrome c oxidase-related functions and molybdenum assimilation confer B. pseudomallei a selective advantage against the antimicrobial activity of the β-lactam antibiotic imipenem. Cumulatively, these data support a model by which NO induces antibiotic tolerance through the inhibition of the electron transport chain, rather than by potentiating antioxidant defenses as previously proposed. Accordingly, pharmacological inhibition of terminal oxidases and nitrate reductases tolerizes aerobic and anaerobic bacteria to β-lactams. The degree of NO-induced β-lactam antibiotic tolerance seems to be inversely proportional to the proton motive force (PMF), and thus the dissipation of ΔH+ and ΔΨ electrochemical gradients of the PMF prevents β-lactam-mediated killing. According to this model, NO generated by IFNγ-primed macrophages protects intracellular Salmonella against imipenem. On the other hand, sublethal concentrations of imipenem potentiate the killing of B. pseudomallei by NO generated enzymatically from IFNγ-primed macrophages. Our investigations indicate that NO modulates the antimicrobial activity of β-lactam antibiotics.