gebhart/patrepeval huggingface dataset:
High-accuracy determination of Paul-trap stability parameters for electric-quadrupole-shift prediction (2022)

The motion of an ion in a radiofrequency (rf) Paul trap is described by the Mathieu equation and the associated stability parameters that are proportional to the rf and dc electric field gradients. Here, a higher-order, iterative method to accurately solve the stability parameters from measured secular frequencies is presented. It is then used to characterize an endcap trap by showing that the trap’s radial asymmetry is dominated by the dc field gradients and by measuring the relation between the applied voltages and the gradients. The results are shown to be in good agreement with an electrostatic finite-element-method simulation of the trap. Furthermore, a method to determine the direction of the radial trap axes using a “tickler” voltage is presented, and the temperature dependence of the rf voltage is discussed. As an application for optical ion clocks, the method is used to predict and minimize the electric quadrupole shift (EQS) using the applied dc voltages. Finally, a lower limit of 1070 for the cancellation factor of the Zeeman-averaging EQS cancellation method is determined in an interleaved low-/high-EQS clock measurement. This reduces the EQS uncertainty of our 88Sr+ optical clock to ≲1×10−19 in fractional frequency units.
Temporal spike pattern learning (2008)

Sachin S. Talathi,* Henry D. I. Abarbanel, and William L. Ditto J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Florida 32611, USA Marine Physical Laboratory, Scripps Institution of Oceanography, Department of Physics and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093, USA Received 16 June 2008; revised manuscript received 11 August 2008; published 23 September 2008
Eya3 partners with PP2A to induce c-Myc stabilization and tumor progression (2018)

Eya genes encode a unique family of multifunctional proteins that serve as transcriptional co-activators and as haloacid dehalogenase-family Tyr phosphatases. Intriguingly, the N-terminal domain of Eyas, which does not share sequence similarity to any known phosphatases, contains a separable Ser/Thr phosphatase activity. Here, we demonstrate that the Ser/Thr phosphatase activity of Eya is not intrinsic, but arises from its direct interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme. Importantly, Eya3 alters the regulation of c-Myc by PP2A, increasing c-Myc stability by enabling PP2A-B55α to dephosphorylate pT58, in direct contrast to the previously described PP2A-B56α-mediated dephosphorylation of pS62 and c-Myc destabilization. Furthermore, Eya3 and PP2A-B55α promote metastasis in a xenograft model of breast cancer, opposing the canonical tumor suppressive function of PP2A-B56α. Our study identifies Eya3 as a regulator of PP2A, a major cellular Ser/Thr phosphatase, and uncovers a mechanism of controlling the stability of a critical oncogene, c-Myc.
Biomachines for Medical Diagnosis (2020)

Current evolutions in medical practices induce a change of paradigm with the convergence of diagnosis and therapy, going to precision medicine and “theranostics”. One can observe the new role of biomarkers in biomedical and therapeutic applications, for instance in the development of molecular multiplex biosensors (nucleic acid, proteins, and metabolites). In addition, there is an increasing interest for point-of-care (POC) and of home monitoring/testing technologies devoted to probe patient parameters in his direct environment. The obvious constraints for such a kind of new clinical practices are simplification, drastic cost reduction while keeping high performances. Within this context, synthetic biology provides new opportunities to develop a novel generation of biological biosensors able to perform multiplexed biomarkers detection, simple computation and returning simplified relevant results. In order to design robust synthetic biological biosensor systems reliable in a clinical context and based on biochemical circuits, we developed an original methodology ensuring biochemical implementation of logical tasks within nonliving artificial cells. This methodology covers in silico design, simulation, microfluidics production and clinical validation on human samples. It ends up in very simple assay like for instance the new insulin-resistance assay, which is also quick and easy to run out of a laboratory and at low cost.
Plasma Cholesterol-Lowering Activity of Gingerol- and Shogaol-Enriched Extract Is Mediated by Increasing Sterol Excretion (2014)

The present study investigated the cholesterol-lowering activity of gingerol- and shogaol-enriched ginger extract (GSE). Thirty hamsters were divided into three groups and fed the control diet or one of the two experimental diets containing 0.5 and 1.0% GSE. Plasma total cholesterol, liver cholesterol, and aorta atherosclerotic plaque were dose-dependently decreased with increasing amounts of GSE added into diets. The fecal sterol analysis showed dietary GSE increased the excretion of both neutral and acidic sterols in a dose-dependent manner. GSE down-regulated the mRNA levels of intestinal Niemann-Pick C1-like 1 protein (NPC1L1), acyl CoA:cholesterol acyltransferase 2 (ACAT2), microsomal triacylglycerol transport protein (MTP), and ATP binding cassette transporter 5 (ABCG5), whereas it up-regulated hepatic cholesterol-7α-hydroxylase (CYP7A1). It was concluded that beneficial modification of the lipoprotein profile by dietary GSE was mediated by enhancing excretion of fecal cholesterol and bile acids via up-regulation of hepatic CYP7A1 and down-regulation of mRNA of intestinal NPC1L1, ACAT2, and MTP.
ADAM10 regulates B cell development and immunoglobulin production (138.6) (2009)

Abstract Members of the disintegrin and metalloprotease (ADAM) family can regulate lymphocyte development and function by cleaving membrane receptors. Previous studies showed that ADAM10 cleaves the B cell receptors, CD23 and Notch2, in vitro. However, in the absence of in vivo models, the physiologic impact of these events has not been examined. Thus, we generated B cell-specific ADAM10 KO and transgenic (Tg) mice to determine the role of ADAM10 in B cell development and function. Notch signaling regulates the differentiation of common lymphoid progenitors (CLPs) by promoting T cell fate. Accordingly, overexpression of ADAM10 in CLPs completely blocked B cell development. Deletion of ADAM10 from B cells in ADAM10fl/fl, CD19-cre+ mice prevented differentiation of marginal zone B cells, which is dependent on Notch2 signaling. In addition, expression of CD23 on ADAM10null B cells was dramatically elevated while levels of soluble CD23 were reduced in serum. As a result, IgE production by ADAM10fl/fl, CD19-cre+ mice was remarkably suppressed upon immunization, mimicking the response of CD23Tg mice. Finally, production of IgG1 and IgG2b was profoundly inhibited, suggesting a novel role for ADAM10 in class-switching to IgG. These results illustrate the physiologic role of ADAM10 in Notch signaling and CD23 cleavage. Moreover, they identify ADAM10 as a critical regulator of B cell development and immunoglobulin production. AHA 0815066E, NIAID R01AI18697, NIAID U19AI077435
Broad Efficacy of Cariprazine on Depressive Symptoms in Bipolar Disorder and the Clinical Implications (2020)

ClinicalTrials.gov identifiers: NCT01396447, NCT02670538, NCT02670551.
Effect of PH<sub>3</sub> on Stability of LST Ceramic Anode in Coal Syngas (2013)

Stability of La substituted SrTiO 3 anode in coal syngas fuel was investigated. La 0.25 Sr 0.75 TiO 3 and (La 0.25 Sr 0.75 ) 0.9 TiO 3 pellets were annealed in simulated coal syngas with 1 ppm PH 3 atmosphere at 900 o C for 100 hrs. Sr 3 (PO 4 ) 2 and TiO 2 were observed on the surface of each sample after the exposure test. XRD and SEM/EDS results indicate that most Sr 3 (PO 4 ) 2 was formed on the surface of stoichiometric LST. Chemical stability of LST for PH 3 was effectively improved by changing the A-site deficient composition.
Three‐dimensional cell culture models for anticancer drug screening: Worth the effort? (2017)

High attrition of new oncology drug candidates in clinical trials is partially caused by the poor predictive capacity of artificial monolayer cell culture assays early in drug discovery. Monolayer assays do not take the natural three-dimensional (3D) microenvironment of cells into account. As a result, false positive compounds often enter clinical trials, leading to high dropout rates and a waste of time and money. Over the past 2 decades, tissue engineers and cell biologists have developed a broad range of 3D in vitro culturing tools that better represent in vivo cell biology. These tools preserve the 3D architecture of cells and can be used to predict toxicity of and resistance against antitumor agents. Recent progress in tissue engineering further improves 3D models by taking into account the tumor microenvironment, which is important for metastatic progression and vascularization. However, the widespread implementation of 3D cell cultures into cell-based research programs has been limited by various factors, including their cost and reproducibility. In addition, different 3D cell culture techniques often produce spheroids of different size and shape, which can strongly influence drug efficacy and toxicity. Hence, it is imperative to morphometrically characterize multicellular spheroids to avoid generalizations among different spheroid types. Standardized 3D culturing procedures could further reduce data variability and enhance biological relevance. Here, we critically evaluate the benefits and challenges inherent to growing cells in 3D, along with an overview of the techniques used to form spheroids. This is done with a specific focus on antitumor drug screening.
Source apportionment of particle number size distribution in urban background and traffic stations in four European cities (2019)

Ultrafine particles (UFP) are suspected of having significant impacts on health. However, there have only been a limited number of studies on sources of UFP compared to larger particles. In this work, we identified and quantified the sources and processes contributing to particle number size distributions (PNSD) using Positive Matrix Factorization (PMF) at six monitoring stations (four urban background and two street canyon) from four European cities: Barcelona, Helsinki, London, and Zurich. These cities are characterised by different meteorological conditions and emissions. The common sources across all stations were Photonucleation, traffic emissions (3 sources, from fresh to aged emissions: Traffic nucleation, Fresh traffic - mode diameter between 13 and 37 nm, and Urban - mode diameter between 44 and 81 nm, mainly traffic but influenced by other sources in some cities), and Secondary particles. The Photonucleation factor was only directly identified by PMF for Barcelona, while an additional split of the Nucleation factor (into Photonucleation and Traffic nucleation) by using NO<sub>x</sub> concentrations as a proxy for traffic emissions was performed for all other stations. The sum of all traffic sources resulted in a maximum relative contributions ranging from 71 to 94% (annual average) thereby being the main contributor at all stations. In London and Zurich, the relative contribution of the sources did not vary significantly between seasons. In contrast, the high levels of solar radiation in Barcelona led to an important contribution of Photonucleation particles (ranging from 14% during the winter period to 35% during summer). Biogenic emissions were a source identified only in Helsinki (both in the urban background and street canyon stations), that contributed importantly during summer (23% in urban background). Airport emissions contributed to Nucleation particles at urban background sites, as the highest concentrations of this source took place when the wind was blowing from the airport direction in all cities.
Identifying the Mental Health Needs of Looked after Young People (2004)

Fifty looked after young people and their carers were interviewed to elicit whether, intuitively, they considered the young person to have a mental health problem and when they would seek professional help. This intuitive judgement of need was compared with responses to a mental health screen, and specific depression and conduct disorder scales. The results suggest that carers perceived 70% of young people to have significant mental health need; high levels of depression (28%) and conduct disorder (34%) were also found. Carers were four times more likely to identify mental health needs, both intuitively and on the mental health screen, than young people did themselves. Two-thirds of carers were intuitively accurate in identifying mental health need in their young people, although fewer than half of those identified as having high needs were being seen by a mental health specialist. Of concern, 23% of carers failed to identify needs, subsequently identified by the mental health screen. Perceived familial burden predicted a high mental health needs screen outcome. Given the established risks to mental health for this population of young people, the utility of a systematic mental health screen is discussed.
High precision real-time location estimates in a real-life barn environment using a commercial ultra wideband chip (2020)

Structural changes lead to an increase in the number of dairy cows and dry sows kept per group. This has consequences in how easily a farmer can supervise his herd and may be detrimental to animal welfare, specifically regarding social relations, time budget and area of residence. An automated tracking system can support the farmer in his management activities and can provide the foundation for a scientific assessment of the welfare consequences of large groups. In this study, a relatively simple and inexpensive real time location system (RTLS) was developed with the aim of achieving precise localization of several tags (animals) in real time and in a real barn environment. The RTLS was based on the ultra-wideband (UWB) technology provided by DecaWave and was adapted for a time difference of arrival (TDoA) procedure to estimate the tags’ positions. The RTLS can handle up to a hundred tags simultaneously using a Pure ALOHA random access method at 1-second intervals. The localization of the tags was estimated in 2D on a given fixed height using a constrained Gauss-Newton algorithm to increase accuracy and stability. The performance of the overall system was evaluated in two different dairy barns. To determine the precision of the system, static and dynamic positions measured at withers height of a cow (1.5 m) and closer to the ground mimicking a lying cow were compared with a reference system (theodolite). The 2D deviations between the systems were used as a measure of precision. In addition, the scalability in respect to the number of tags and the size of the observed area was examined in situations with ten tags and the situation with 100 tags was simulated with a ten-fold increase in sampling rate. According to the field test, the system as developed can be used for the individual localization of animals. At withers height, most of the measured locations deviated less than 0.5 m from the localizations as measured by the theodolite. At lower heights, and closer to the corners of the observed area, some localization estimates were somewhat larger. This was also the case close to large metal barn infrastructure. The measured collision rate of 11% for 100 tags was low. In spite of its low price, the system as a whole is therefore promising and ready for a next step, which should include the observation of large groups of real animals on working farms.
Certified reference materials for calibration of conductivity meter at the measuring of electrolytic conductivity in water: Preparation and its measurement (2019)

The electrolytic conductivity is a very important parameter in water because the amount of electrolytic conductivity can describe the quality of water. To get the accurate result of measurement, the conductivity meter must be calibrated using certified reference materials (CRM) which has traceability property to SI. Based on this, the availability of CRM for measuring electrolytic conductivity is an inevitable requirement for testing laboratories. At present in Indonesia, most CRM are obtained from foreign producers with fairly expensive import prices and limited self-life due to the shipping time. In an effort to provide standard solution reference material for conductivity meter calibration in Indonesia, a research for preparation of CRM has been carried out. The CRM, made from standard solutions of 0.1 M KCl solution, is traceable to the primary reference material CRM-1603 from Danish Fundamental Metrologi, DFM (conductivity=9.996 mS/cm with uncertainty is 0.13%) and is intended to calibrate conductivity meter in measurements of water conductivity between 1 to 20 mS/cm. The measurement of the CRM conductivity value was carried out by the secondary method, namely the Jones cell method using Cell C. The conductivity values of the secondary reference material KCl 0.1 M was 12.880 mS/cm at 25°C with uncertainty value at 0.50%. From the stability test at room temperature (20-27°C), the reference materials stored in plastic bottles were stable for 9 months, demonstrating the reference material for testing conductivity has been successfully made in Indonesia and can replace imported reference materials.
Retrieval of a chronically implanted leadless pacemaker within an isolated heart using direct visualization (2018)

Key Teaching Points•On occasion leadless pacemakers need to be retrieved despite outcomes showing reduced or minimal chronic complications. Complications might include elevated pacing thresholds, need for alternate therapy, pacemaker syndrome, or prosthetic valve endocarditis.•This case report shows the successful retrieval of a chronically implanted leadless pacemaker in a reanimated swine using direct visualization.•Images presented in this case report have notable educational value for clinicians and design engineers. •On occasion leadless pacemakers need to be retrieved despite outcomes showing reduced or minimal chronic complications. Complications might include elevated pacing thresholds, need for alternate therapy, pacemaker syndrome, or prosthetic valve endocarditis.•This case report shows the successful retrieval of a chronically implanted leadless pacemaker in a reanimated swine using direct visualization.•Images presented in this case report have notable educational value for clinicians and design engineers.
Kish Graphite Flakes as a Cathode Material for an Aluminum Chloride–Graphite Battery (2017)

Nonaqueous, ionic liquid-based aluminum chloride-graphite batteries (AlCl<sub>3</sub>-GBs) are a highly promising post-Li-ion technology for low-cost and large-scale storage of electricity because these batteries feature exclusively highly abundant chemical elements and simple fabrication methods. In this work, we demonstrate that synthetic kish graphite, which is a byproduct of steelmaking, can be used as a cathode in AlCl<sub>3</sub>-GB and exhibits high capacities of ≤142 mAh g<sup>-1</sup>. The comprehensive characterization of kish graphite flakes and other forms of graphite by X-ray diffraction, Raman spectroscopy, and Brunauer-Emmett-Teller surface area analysis provides solid evidence that the exceptional electrochemical behavior of kish graphite flakes is mainly determined by the high structural order of carbon atoms, a low level of defects, and a unique "crater morphology". In view of the nonrocking chair operation mechanism of AlCl<sub>3</sub>-GB, we have tested the achievable energy densities as a function of the composition of chloroaluminate ionic liquid (AlCl<sub>3</sub> content) and have obtained energy densities of up to 65 Wh kg<sup>-1</sup>. In addition, the kish graphite flakes can rapidly charge and discharge, offering high power densities of up to 4363 W kg<sup>-1</sup>.
Social Norms on Reddit: A Demographic Analysis (2022)

Social norms, the shared informal rules of acceptable behavior, drive and reflect the evolution of societies. As an increasingly large part of social interactions happens online, social media data offers an unprecedented opportunity to assess the perception of social norm boundaries in-the-wild. In this regard, Reddit’s r/AITA represents an invaluable source of codified social norms. This subreddit is an online forum where individuals describe how they acted in a specific situation in the past, and ask for the feedback of the community about whether their behavior was deviant or socially acceptable. Other users in the community share their views and express a judgment codified by a tag.
1516 Detection of Delamination in CFRP Laminates Using the Eddy Current Method (2008)

Carbon fiber reinforced plastic (CFRP) laminates are very sensitive to an impact which causes delaminations in the laminate. Since delamination reduces the mechanical property of the laminate, nondestructive inspection is required to maintain the structural reliability of the CFRP structure. Eddy current test (ECT) has been studied to be applied to CFRP laminate. Strong electric anisotropy, however, makes application of the method difficult. Since delamination is in-plane damage in the laminate, conventional ECT has a problem for making current-loop which should be impeded by the damage to be detected. In the present paper, rectangular twin probe for electrically anisotropic CFRP laminate is introduced to resolve the problems. The probe is made of two rectangular coils put side-by-side to induce strong uniform electric current. Delamination was made in CFRP cross-ply laminates by means of the indentation test; the applicability of the ECT with rectangular twin probe is examined experimentally.
Continuous treatment with all-trans retinoic acid causes a progressive reduction in plasma drug concentrations: implications for relapse and retinoid "resistance" in patients with acute promyelocytic leukemia [published erratum appears in Blood 1992 Aug 1;80(3):855] (1992)

Abstract Although all-trans retinoic acid (RA) induces complete remission in a high proportion of patients with acute promyelocytic leukemia (APL), all groups have described clinical relapses despite continued RA treatment. This finding suggests that resistance to the cytodifferentiating effects of the retinoid had been acquired. To investigate potential mechanisms of clinical resistance to RA, we serially evaluated the clinical pharmacology of the drug in APL patients treated with this agent. Leukemic cells from patients relapsing from RA treatment were cultured in the presence of RA and examined for evidence of morphologic maturation. We also studied messenger RNA expression of the newly described gene product of the (15;17) translocation in APL, PML/RA receptor-alpha (PML/RAR-alpha). Serial pharmacokinetic studies showed that continuous daily RA treatment was associated with a marked decrease in plasma drug concentrations at the time of relapse compared with the initial day of therapy. Doubling the RA dose in six patients failed to reinduce response at the time of relapse and also failed to significantly augment plasma RA concentrations. However, leukemic cells obtained at the time of relapse from four patients retained in vitro sensitivity to the differentiating activity of RA (10(-6) mol/L). No change was observed in the pattern of PML/RAR-alpha expression assessed by Northern blot analysis at the time of relapse compared with pretreatment in two patients who were tested. These results indicate that clinical relapse and “resistance” to continuous treatment with all- trans RA in APL is associated with progressive reduction of plasma concentrations, potentially to levels below those that sustain differentiation of leukemic cells in vivo. Long-term success of this treatment will require the development of strategies that circumvent this pharmacologic phenomenon.