gebhart/patrepeval huggingface dataset:
Systematic profiling of <i>C</i> <i>aenorhabditis elegans</i> locomotive behaviors reveals additional components in G-protein Gαq signaling (2013)

Genetic screens have been widely applied to uncover genetic mechanisms of movement disorders. However, most screens rely on human observations of qualitative differences. Here we demonstrate the application of an automatic imaging system to conduct a quantitative screen for genes regulating the locomotive behavior in Caenorhabditis elegans. Two hundred twenty-seven neuronal signaling genes with viable homozygous mutants were selected for this study. We tracked and recorded each animal for 4 min and analyzed over 4,400 animals of 239 genotypes to obtain a quantitative, 10-parameter behavioral profile for each genotype. We discovered 87 genes whose inactivation causes movement defects, including 50 genes that had never been associated with locomotive defects. Computational analysis of the high-content behavioral profiles predicted 370 genetic interactions among these genes. Network partition revealed several functional modules regulating locomotive behaviors, including sensory genes that detect environmental conditions, genes that function in multiple types of excitable cells, and genes in the signaling pathway of the G protein Gαq, a protein that is essential for animal life and behavior. We developed quantitative epistasis analysis methods to analyze the locomotive profiles and validated the prediction of the γ isoform of phospholipase C as a component in the Gαq pathway. These results provided a system-level understanding of how neuronal signaling genes coordinate locomotive behaviors. This study also demonstrated the power of quantitative approaches in genetic studies.
Quasi-equilibrium electron density along a magnetic field line (2012)

A methodology is developed to determine the density of high-energy electrons along a magnetic field line for a low-β plasma. This method avoids the expense and statistical noise of traditional particle tracking techniques commonly used for high-energy electrons in bombardment plasma generators. By preserving the magnetic mirror and assuming a mixing timescale, typically the elastic collision frequency with neutrals, a quasi-equilibrium electron distribution can be calculated. Following the transient decay, the analysis shows that both the normalized density and the reduction fraction due to collision converge to a single quasi-equilibrium solution.
Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria (2020)

Abstract Marine heterotrophic bacteria use a spectrum of nutrient uptake strategies, from that of copiotrophs—which dominate in nutrient-rich environments—to that of oligotrophs—which dominate in nutrient-poor environments. While copiotrophs possess numerous phosphotransferase systems (PTS), oligotrophs lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. Here we present a molecular-level model that explains the dichotomy between oligotrophs and copiotrophs as the consequence of trade-offs between PTS and ABC transport. When we approximate ABC transport in Michaelis–Menten form, we find, contrary to the canonical formulation, that its half-saturation concentration K M is not a constant but instead a function of binding protein abundance. Thus, oligotrophs can attain nanomolar K M values using binding proteins with micromolar dissociation constants and while closely matching transport and metabolic capacities. However, this requires large periplasms and high abundances of binding proteins, whose slow diffusion limits uptake rate. We conclude that the use of binding proteins is critical for oligotrophic survival yet severely constrains maximal growth rates, thus fundamentally shaping the divergent evolution of oligotrophs and copiotrophs.
Reversible perovskite electrocatalysts for oxygen reduction/oxygen evolution (2019)

The identification of electrocatalysts mediating both the oxygen reduction reaction (ORR) and oxygen evolution reaction (OER) are prerequisite for the development of reversible fuel cells and rechargeable metal-air batteries. The question remains as to whether a bifunctional catalyst, or a single catalyst site, will exhibit potentials converging to +1.23 V<sub>RHE</sub>. Transition metal-based perovskites provide tunable catalysts where site substitution can influence both ORR and OER, however substitution in the pseudo-binary phases results in an anti-correlation in ORR and OER activities. We reveal that La <sub><i>x</i></sub> Mn <sub><i>y</i></sub> Ni<sub>1-<i>y</i></sub> O<sub>3-<i>δ</i></sub> , compositions with lanthanum A-site sub-stoichiometry exhibit reversible activity correlating with the appearance of the Mn<sup>3+</sup>/Mn<sup>4+</sup> redox couple. The Mn<sup>3+</sup>/Mn<sup>4+</sup> couple is associated with Mn<sup>4+</sup> co-existing with Mn<sup>3+</sup> in the bulk, as La<sup>3+</sup> is substituted by Ni<sup>2+</sup> at the A-site to create a mixed valent system. We also show that a direct A-site substitution by the Ca<sup>2+</sup> cation in La <sub><i>x</i></sub> Ca<sub>1-<i>x</i></sub> Mn <sub><i>y</i></sub> O<sub>3-<i>δ</i></sub> perovskites also results in the creation of Mn<sup>4+</sup>, the appearance of the Mn<sup>3+</sup>/Mn<sup>4+</sup> redox couple, and a concomitant reversible activity. These results highlight a general strategy of optimizing oxide electrocatalysts with reversible activity.
Dynamic Humanoid Locomotion: A Scalable Formulation for HZD Gait Optimization (2018)

Hybrid zero dynamics (HZD) has emerged as a popular framework for dynamic walking but has significant implementation difficulties when applied to the high degrees of freedom humanoids. The primary impediment is the process of gait design-it is difficult for optimizers to converge on a viable set of virtual constraints defining a gait. This paper presents a methodology that allows for fast and reliable generation of dynamic robotic walking gaits through the HZD framework, even in the presence of underactuation. Specifically, we describe an optimization formulation that builds upon the novel combination of HZD and direct collocation methods. Furthermore, achieving a scalable implementation required developing a defect-variable substitution formulation to simplify expressions, which ultimately allows us to generate compact analytic Jacobians of the constraints. We experimentally validate our methodology on an underactuated humanoid, DURUS, a spring-legged machine designed to facilitate energy-economical walking. We show that the optimization approach, in concert with the HZD framework, yields dynamic and stable walking gaits in hardware with a total electrical cost of transport of 1.33.
Extraction and analysis of volatile compounds in white wines using Amberlite XAD-2 resin and capillary gas chromatography (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExtraction and analysis of volatile compounds in white wines using Amberlite XAD-2 resin and capillary gas chromatographyCharles G. Edwards and Robert B. BeelmanCite this: J. Agric. Food Chem. 1990, 38, 1, 216–220Publication Date (Print):January 1, 1990Publication History Published online1 May 2002Published inissue 1 January 1990https://pubs.acs.org/doi/10.1021/jf00091a048https://doi.org/10.1021/jf00091a048research-articleACS PublicationsRequest reuse permissionsArticle Views235Altmetric-Citations25LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Electrochemical Acetylcholine Chloride Biosensor Using an Acetylcholine Esterase Biomimic (2008)

Abstract Pure enzymes are costly and highly sensitive to change in pH, temperature, ionic strength etc. Hence biomimetic or synthetic enzymes could be useful alternatives to such natural proteins. Although the selectivity of a biomimic is somewhat less than that of enzyme, it can be used as a detector element in inexpensive but stable biosensors. An organic compound, 4-[(1E)-ethanehydrazonoyl]benzoic acid, has been designed and synthesized as biomimic for the enzyme acetylcholine esterase. An acetylcholine chloride two-electrode screen-printed sensor was first developed using the immobilized enzyme acetylcholine esterase. The performance of the mimic in the hydrolysis of acetylcholine chloride was then tested with the same transducer by immobilizing the biomimic in place of the enzyme. The response of the sensor constructed using the mimic was comparable to that of the pure acetylcholine esterase enzyme electrode.
Field Response of Alfalfa Looper and Cabbage Looper Moths (Lepidoptera: Noctuidae, Plusiinae) to Single and Binary Blends of Floral Odorants (2006)

In eld tests of oral chemicals dispensed singly, alfalfa looper moths, Autographa californica (Speyer), were captured in traps baited with phenylacetaldehyde, -myrcene, or benzyl acetate. Cabbage looper moths, Trichoplusia ni (Hu bner) were also captured in traps baited with phenylacetaldehyde, methyl salicylate, or methyl-2-methoxy benzoate. In evaluations of binary blends of those same compounds, generally more alfalfa looper moths were trapped when -myrcene was presented with phenylacetaldehyde or with benzyl acetate compared with phenylacetaldehyde alone or benzyl acetate alone. Similarly, more cabbage looper moths were trapped with -myrcene with phenylacetaldehyde compared with phenylacetaldehyde alone. These ndings provide new chemical blends for luring and trapping both sexes of alfalfa looper and cabbage looper moths and suggest differences in preferences of these two moth species for oral odorants.
Therapeutic effects of anti-CEA (CEACAM5) and anti-NCA90 (CEACAM6) antibody monovalent fragments <b><i>in vitro</i></b> and <b><i>in vivo</i></b> (2004)

2555 Background: CEA and NCA-90 are overexpressed in many cancers. We have evaluated the effect of several antibody fragments (Fabs) on in vitro tumor cell growth and in vivo survival and chemosensitivity. Methods: HT-29, LS174T, Moser (human colonic tumor lines), MCA38 and MCA38cea (murine colonic tumor lines), BT-20 (human breast tumor line) were grown in culture. MN-14 and MN-6 anti-CEA Fabs and MN-3 and MN-15 Fabs that crossreact with NCA-90 were evaluated. In vitro growth inhibition was determined with the MTT assay; in vivo therapy was done with the GW-39 human colonic intrapulmonary micrometastatic model. In one study, cells were pre-incubated with Ab Fab prior to implantation and then mice were dosed once at 24h post implantation with the Fab. In the second study, mice were treated after cell inoculation with Ab Fab alone (10 μg x 5d), CPT-11 (Camptosar) alone (160 μg x 5d) or both Ab Fab and drug. Results: None of the Fabs had a significant effect on growth of the parental MCA38 cell line, which is CEA- and NCA-90-negative. In contrast, growth of MCA38cea cells (CEA+/NCA-90-) was inhibited by 33.3% and 16.8% by MN-3 and MN-15 Fab, respectively. MN-6 and MN-14 anti-CEA Fabs caused an 8.0% and 14.0% growth inhibition (GI), respectively. MN-3 Fab was also the most effective agent tested against LS174T, Moser, and BT-20 cells, resulting in 18.2%, 26.0% and 15.0% GI, respectively. In the HT-29 line, GI was greatest for MN-6>MN-3=MN-15>MN-14 Fabs, with no effect by an irrelevant Fab. In vivo studies showed that pretreatment of GW-39 cells with MN-3 or MN-15 Fab increased survival (P<0.025 and P<0.01, respectively), while MN-14 and MN-6 did not. If cells were not pretreated with Fab, but instead were dosed after cell implantation with either 10 or 100 μg/d of the Fab, no survival advantage was observed. However, dosing with either MN-15 Fab or MN-3 Fab increased the efficacy of CPT-11 therapy in vivo (P<0.001 and P<0.05 vs. CPT-11 alone, respectively). Conclusions: Antibody Fabs targeting both CEA and NCA-90 are more effective in vitro at inducing growth inhibition and more effective in vivo at increasing the sensitivity of cells to the cytotoxic effects of CPT-11. No significant financial relationships to disclose.
Epigenetics of Estrogen Receptor Signaling: Role in Hormonal Cancer Progression and Therapy (2011)

Estrogen receptor (ERα) signaling plays a key role in hormonal cancer progression. ERα is a ligand-dependent transcription factor that modulates gene transcription via recruitment to the target gene chromatin. Emerging evidence suggests that ERα signaling has the potential to contribute to epigenetic changes. Estrogen stimulation is shown to induce several histone modifications at the ERα target gene promoters including acetylation, phosphorylation and methylation via dynamic interactions with histone modifying enzymes. Deregulation of enzymes involved in the ERα-mediated epigenetic pathway could play a vital role in ERα driven neoplastic processes. Unlike genetic alterations, epigenetic changes are reversible, and hence offer novel therapeutic opportunities to reverse ERα driven epigenetic changes. In this review, we summarize current knowledge on mechanisms by which ERα signaling potentiates epigenetic changes in cancer cells via histone modifications.
Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs (2015)

We have performed x-ray phase-contrast tomography on mouse lung tissue. Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view. Thus, macroscopic tissue samples extending over several mm can be studied in sub-cellular-level structural detail. The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel. In combination with suitable phase-retrieval algorithms, challenging radiation-sensitive and low-contrast samples can be reconstructed with minimal artefacts. The dose efficiency of the method is demonstrated by the reconstruction of living macrophages both with and without phagocytized contrast agents. We also used zoom tomography to visualize barium-labelled macrophages in the context of morphological structures in asthmatic and healthy mouse lung tissue one day after intratracheal application. The three-dimensional reconstructions showed that the macrophages predominantly localized to the alveoli, but they were also found in bronchial walls, indicating that these cells might be able to migrate from the lumen of the bronchi through the epithelium.
Complete Soft Palate Necrosis and Velopharyngeal Insufficiency Resulting From Intranasal Inhalation of Prescription Narcotics and Cocaine (2007)

Birchenough, Shawn A. MD; Borowitz, Kathleen MS, SLP-CCC; Lin, Kant Y. MD Author Information
Reflective Silicon Arrayed Waveguide Grating using One-Dimensional Photonic Crystal reflector (2019)

We report silicon arrayed waveguide grating with reflective fan-out geometry using one-dimensional photonic crystal as reflector. Wide reflection spectral range is possible with this reflector. The wavelength characteristics are obtained by fabricated device using immersion ArF lithography. We also report a device using parallel waveguide array geometry to minimize the occupational area of the device.
Advanced EWLB (Embedded Wafer Level Ball Grid Array) Solutions for Mmwave Applications (2018)

FOWLP (Fan-Out Wafer Level Packaging) has been established as one of the most versatile packaging technologies in the recent past and already accounts for a market value of over 1 billion USD due to its unique advantages. The technology combines high performance, increased functionality with a high potential for heterogeneous integration and reduces the total form factor all in a cost-effectiveness format. FOWLP volumes have largely been driven by mobile and consumer applications (RF, BB, connectivity, NFC, PMIC, audio codec, MCU etc) and are now moving to 5G communication, mmWave, automotive, MEMS/Sensor and IoT/WE applications. Advanced embedded Wafer Level Ball Grid Array (eWLB) provides a versatile platform for the semiconductor industry's technology evolution from single or multi-die 2D package designs to 2.5D interposers and 3D System-in-Package (SiP) configurations. WLP (wafer level packaging) has already been adopted in the automotive market for cabin or infotainment applications as well as 77GHz radar sensors utilizing FO-WLP.This study focuses on the development of eWLB for mmWave applications above 60GHz with CMOS IC technology. Additionally the case study of 77GHz ADAS automotive radar is discussed. Package design optimization of single-die and multi-die, electrical performance characterization and component level reliability tests are presented.
A Common Operator for FFT and Viterbi Algorithms (2010)

In the Software Radio context, the parametrization is becoming an important topic especially when it comes to multi-standard designs. This paper capitalizes on the Common Operator technique to present a new common structure for the FFT and Viterbi algorithms. A key benefit of exhibiting common operators is the regular architecture it brings when implemented in a Common Operator Bank (COB). This regularity makes the architecture open to future function mapping and adapted to accommodated silicon technology variability through dependable design. Global complexity impact is discussed in the paper.
Optoelectronic page-oriented database filter based on a single chip photonic VLSI design (2002)

A database filter suitable for accessing optical storage devices is presented. This photonic VLSI chip includes a smart pixel array that selects words matching a search criterion and control circuitry that interfaces the filter chip with an electronic host computer.
Optimal Power Flow Using Tabu Search Algorithm (2002)

This paper presents an efficient and reliable tabu search (TS)-based approach to solve the optimal power flow (OPF) problem. The proposed approach employs TS algorithm for optimal settings of the control variables of the OPF problem. Incorporation of TS as a derivative-free optimization technique in solving OPF problem significantly reduces the computational burden. One of the main advantages of TS algorithm is its robustness to its own parameter settings as well as the initial solution. In addition, TS is characterized by its ability to avoid entrapment in local optimal solution and prevent cycling by using flexible memory of search history. The proposed approach has been examined on the standard IEEE 30-bus test system with different objectives and generator cost curves. The results are promising and show the effectiveness and robustness of the proposed approach.
Coronary Endothelial Dysfunction Is Associated With an Increased Risk of Cerebrovascular Events (2003)

Presence of CED in patients without obstructive CAD is independently associated with an increased risk of cerebrovascular events. Thus, detection of this early stage of atherosclerosis may provide important information to identify patients who benefit from aggressive preventive strategies.
Improved Myocardial Function during Exercise after Successful Percutaneous Transluminal Coronary Angioplasty (1982)

Fifty-nine consecutive patients with coronary-artery disease undergoing percutaneous transluminal coronary angioplasty were evaluated with radionuclide ventriculography at rest and during exercise before angioplasty (when possible) and afterward when it was successful. Thirty-eight patients (64 per cent) had an angiographically successful procedure. Three (5 per cent) had coronary occlusion as a complication. Arterial stenosis was reduced from 74 +/- 2 per cent to 31 +/- 3 per cent (mean +/- S.E.M.). The mean ejection fraction was 55 +/- 2 per cent at rest and 51 +/- 3 per cent during exercise before the procedure. After successful angioplasty, the ejection fraction was unchanged at rest but increased to 62 +/- 2 per cent (P less than 0.001) during exercise. Regional dysfunction was present during exercise in 94 per cent of the patients before the procedure and in only 8 per cent after successful angioplasty. Of the 38 patients in whom the procedure was successful, 19 had sustained improvement for over six months, and eight for three to six months. Eleven patients had recurrence of symptoms; the second angioplasty was initially successful in nine. In 24 patients remaining asymptomatic for six months (19 after the first procedure and five after the second), the left ventricular ejection fraction during exercise remained stable or improved.
Supplementary Table S4 from ER Stress Signaling Promotes the Survival of Cancer “Persister Cells” Tolerant to EGFR Tyrosine Kinase Inhibitors (2023)

&lt;p&gt;Gene list for customized mini-screen&lt;/p&gt;
From Micro to Nano:  Analysis of Surface-Enhanced Resonance Raman Spectroscopy Active Sites via Multiscale Correlations (2005)

Effective correlation of data from a number of analytical techniques over length scales spanning several orders of magnitude is required to more fully investigate the active sites on silver nanoparticles that are responsible for surface-enhanced resonance Raman scattering (SERRS). In this paper, a method is presented that uses fluorescent beads as optical markers to allow direct correlation between a SERRS/fluorescence map and a transmission electron microscope (TEM) collage of the same area. Factors influencing the accuracy of the technique include the flatness of the substrate, the size of the fluorescent beads, and the strength of the signal from the fluorescent beads. When the effect of each of these factors on the technique is addressed, a simple and accurate correlation between the optical spectroscopy and the electron microscopy is achieved. A statistically significant number of particles can then be easily and reliably located and characterized at both optical limits, by SERRS, and with subnanometer resolution in the high-resolution TEM. Examples of HRTEM images and the locations of these particles within the SERRS map/TEM collage are presented. Our findings reveal that the relative SERRS activity of single particles is very low compared to dimers and larger aggregates of particles. The relative activity of dimers is estimated to be 12.4 times greater than single particles, and as the number of particles in the aggregate increase, the relative SERRS activity also increases. The relative SERRS activities of single particles/dimers/trimers/aggregates of 4-9 particles/aggregates of 10-20 are estimated to be 1/12.4/15.6/23.2/43.
A Target Zone Model with Expected Trend Revisions (1995)

INTEREST RATE;MONETARY POLICY