gebhart/patrepeval huggingface dataset:
Best-Matched Internal Standard Normalization in Liquid Chromatography–Mass Spectrometry Metabolomics Applied to Environmental Samples (2017)

The goal of metabolomics is to measure the entire range of small organic molecules in biological samples. In liquid chromatography-mass spectrometry-based metabolomics, formidable analytical challenges remain in removing the nonbiological factors that affect chromatographic peak areas. These factors include sample matrix-induced ion suppression, chromatographic quality, and analytical drift. The combination of these factors is referred to as obscuring variation. Some metabolomics samples can exhibit intense obscuring variation due to matrix-induced ion suppression, rendering large amounts of data unreliable and difficult to interpret. Existing normalization techniques have limited applicability to these sample types. Here we present a data normalization method to minimize the effects of obscuring variation. We normalize peak areas using a batch-specific normalization process, which matches measured metabolites with isotope-labeled internal standards that behave similarly during the analysis. This method, called best-matched internal standard (B-MIS) normalization, can be applied to targeted or untargeted metabolomics data sets and yields relative concentrations. We evaluate and demonstrate the utility of B-MIS normalization using marine environmental samples and laboratory grown cultures of phytoplankton. In untargeted analyses, B-MIS normalization allowed for inclusion of mass features in downstream analyses that would have been considered unreliable without normalization due to obscuring variation. B-MIS normalization for targeted or untargeted metabolomics is freely available at https://github.com/IngallsLabUW/B-MIS-normalization .
Quantitative phase microscopy spatial signatures of cancer cells (2017)

Abstract We present cytometric classification of live healthy and cancerous cells by using the spatial morphological and textural information found in the label‐free quantitative phase images of the cells. We compare both healthy cells to primary tumor cells and primary tumor cells to metastatic cancer cells, where tumor biopsies and normal tissues were isolated from the same individuals. To mimic analysis of liquid biopsies by flow cytometry, the cells were imaged while unattached to the substrate. We used low‐coherence off‐axis interferometric phase microscopy setup, which allows a single‐exposure acquisition mode, and thus is suitable for quantitative imaging of dynamic cells during flow. After acquisition, the optical path delay maps of the cells were extracted and then used to calculate 15 parameters derived from the cellular 3D morphology and texture. Upon analyzing tens of cells in each group, we found high statistical significance in the difference between the groups in most of the parameters calculated, with the same trends for all statistically significant parameters. Furthermore, a specially designed machine learning algorithm, implemented on the phase map extracted features, classified the correct cell type (healthy/cancer/metastatic) with 81–93% sensitivity and 81–99% specificity. The quantitative phase imaging approach for liquid biopsies presented in this paper could be the basis for advanced techniques of staging freshly isolated live cancer cells in imaging flow cytometers. © 2017 International Society for Advancement of Cytometry
Three-Dimensional Finite Element Modeling of Flip Chip Packages Under Thermal Loading (1998)

Abstract In this study, both two-dimensional and three-dimensional finite element analyses were used to study the stress distribution in and deflection of the flip chip assembly under thermal loading. It is found that the three-dimensional results compared favorably with experimental measurements, while the two-dimensional results consistently overestimate both stresses and deflection. Among the two-dimensional models, plane stress assumption seems to yield results closer to the full three-dimensional predictions. Furthermore, three-dimensional models were used to investigate the effect of printed wiring board size on the overall deflection of the flip-chip assembly. This size effect of the printed wiring board has significant implications on the design of multi-chip modules. The results indicate that a square array placement pattern is preferable to a staggered array for multiple chip modules in order to reduce mechanical interaction between chips. For square arrays, such mechanical interaction between chips can be neglected when the minimum distance between adjacent chips is more than 2 times the chip size.
Automatic composition of music by means of grammatical evolution (2002)

This work describes how grammatical evolution may be applied to the domain of automatic composition. Our goal is to test this technique as an alternate tool for automatic composition. The AP440 auxiliary processor will be used to play music, thus we shall use a grammar that generates AP440 melodies. Grammar evolution will use fitness functions defined from several well-known single melodies to automatically generate AP440 compositions that are expected to sound like those composed by human musicians.
Substrate noise-coupling characterization and efficient suppression in CMOS technology (2004)

This brief investigates the substrate noise coupling using S-parameters measurement. Radio frequency domain analysis shows that the noise isolation is strongly dependent on layout geometry, including the parameters such as p-n junction, physical separation distance, guard ring (GR), and deep n-well (DNW). We found that the noise coupling can be efficiently diminished by incorporating GR and DNW structures.
Three-Dimensionally Ordered Array of Air Bubbles in a Polymer Film (2001)

We report the formation of a three-dimensionally ordered array of air bubbles of monodisperse pore size in a polymer film through a templating mechanism based on thermocapillary convection. Dilute solutions of a simple, coil-like polymer in a volatile solvent are cast on a glass slide in the presence of moist air flowing across the surface. Evaporative cooling and the generation of an ordered array of breath figures leads to the formation of multilayers of hexagonally packed water droplets that are preserved in the final, solid polymer film as spherical air bubbles. The dimensions of these bubbles can be controlled simply by changing the velocity of the airflow across the surface. When these three-dimensionally ordered macroporous materials have pore dimensions comparable to the wavelength of visible light, they are of interest as photonic band gaps and optical stop-bands.
Markerless computer vision based localization using automatically generated topological maps (2004)

status: Published
Quantum State Engineering on an Optical Transition and Decoherence in a Paul Trap (1999)

A single ${\mathrm{Ca}}^{+}$ ion in a Paul trap has been cooled to the ground state of vibration with up to $99.9%$ probability. Starting from this Fock state $|n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}0〉$ we have demonstrated coherent quantum state manipulation on an optical transition. Up to 30 Rabi oscillations with 1.4 ms have been observed. We find a similar number of Rabi oscillations after preparation of the ion in the $|n\phantom{\rule{0ex}{0ex}}=\phantom{\rule{0ex}{0ex}}1〉$ Fock state. The coherence of optical state manipulation is limited only by laser and ambient magnetic field fluctuations. Motional heating has been measured to be as low as one vibrational quantum in 190 ms.
PaTH Forward: A Randomized, Double-Blind, Placebo-Controlled Phase 2 Trial of TransCon PTH in Adult Hypoparathyroidism (2021)

TransCon PTH enabled independence from oral active vitamin D and reduced Ca supplements (≤ 500 mg/day) for most participants, achieving normal sCa, serum phosphate, uCa, serum calcium-phosphate product, and demonstrating improved health-related quality of life. These results support TransCon PTH as a potential hormone replacement therapy for adults with hypoparathyroidism.
Remote Authentication Dial-In User Service (RADIUS) Usage for Simple Network Management Protocol (SNMP) Transport Models (2009)

This memo describes the use of a Remote Authentication Dial-In User Service (RADIUS) authentication and authorization service with Simple Network Management Protocol (SNMP) secure Transport Models to authenticate users and authorize creation of secure transport sessions. While the recommendations of this memo are generally applicable to a broad class of SNMP Transport Models, the examples focus on the Secure Shell (SSH) Transport Model.
RandNLA (2016)

Randomization offers new benefits for large-scale linear algebra computations.
Tight-binding modelling of materials (1997)

The tight-binding method of modelling materials lies between the very accurate, very expensive, ab initio methods and the fast but limited empirical methods. When compared with ab initio methods, tight-binding is typically two to three orders of magnitude faster, but suffers from a reduction in transferability due to the approximations made; when compared with empirical methods, tight-binding is two to three orders of magnitude slower, but the quantum mechanical nature of bonding is retained, ensuring that the angular nature of bonding is correctly described far from equilibrium structures. Tight-binding is therefore useful for the large number of situations in which quantum mechanical effects are significant, but the system size makes ab initio calculations impractical.
Catalytic Intermolecular Cross-Couplings of Azides and LUMO-Activated Unsaturated Acyl Azoliums (2017)

An example for the catalytic synthesis of densely functionalized 1,2,3-triazoles through a LUMO activation mode has been developed. The protocol is enabled by intermolecular cross-coupling reactions of azides with in situ-generated α,β-unsaturated acyl azoliums. High yields and broad scope as well as the investigation of reaction mechanism are reported.
Vericiguat in Patients with Heart Failure and Reduced Ejection Fraction (2020)

Among patients with high-risk heart failure, the incidence of death from cardiovascular causes or hospitalization for heart failure was lower among those who received vericiguat than among those who received placebo. (Funded by Merck Sharp & Dohme [a subsidiary of Merck] and Bayer; VICTORIA ClinicalTrials.gov number, NCT02861534.).
IMIPRAMINE FOR THERAPY RESISTANT ENURESIS: A RETROSPECTIVE EVALUATION (2004)

Imipramine is a useful treatment for enuresis when everything else has failed, especially among older children. Factors related to detrusor function provide prognostic information.
Preeclampsia (2001)

In Brief Plasma placenta growth factor levels are decreased before the clinical onset of placenta-associated pregnancy complications.
Immunomodulating actions of carotenoids: Enhancement of<i>in vivo</i>and<i>in vitro</i>antibody production to T‐dependent antigens (1994)

Previously, we demonstrated an enhancement of in vitro antibody (Ab) production in response to T-dependent antigens (TD-Ag) by astaxanthin, a carotenoid without vitamin A activity. The effects of beta-carotene, a carotenoid with vitamin A activity, and lutein, another carotenoid without vitamin A activity, on in vitro Ab production were examined with spleen cells from young and old B6 mice. In addition, the in vivo effects of lutein, astaxanthin, and beta-carotene on Ab production were studied in young and old B6 mice. Lutein, but not beta-carotene, enhanced in vitro Ab production in response to TD-Ags. The depletion of T-helper cells prevented the enhancement of Ab production by lutein and astaxanthin. In vivo Ab production in response to TD-Ag was significantly enhanced by lutein, astaxanthin, and beta-carotene. The numbers of immunoglobulin M- and G-secreting cells also increased in vivo with the administration of these carotenoids when mice were primed with TD-Ags. Antibody production in response to TD-Ags in vivo and in vitro was significantly lower in old than in young B6 mice. Astaxanthin supplements partially restored decreased in vivo Ab production in response to TD-Ags in old B6 mice. Lutein and beta-carotene also enhanced in vivo Ab production in response to TD-Ags in old B6 mice, although to a lesser extent than did astaxanthin. However, none of the carotenoids had an effect on in vivo or in vitro Ab production in response to T-independent antigen. These results indicate significant immunomodulating actions of carotenoids for humoral immune responses to TD-Ags and suggest that carotenoid supplementation may be beneficial in restoring humoral immune responses in older animals.
Understanding the switching-off mechanism in Ag+ migration based resistively switching model systems (2007)

Different coplanar Pt∕Ag structures were prepared by photolithography on SiO2 substrates, and Pt∕H2O∕Ag cells were formed by adding de-ionized H2O to the coplanar Pt∕Ag structures. The Pt∕H2O∕Ag cell is utilized here as a model system, due to the feasibility of visual inspection of the switching process. Bipolar switching was achieved for the cell. Scanning electron microscopy (SEM) investigations demonstrated that the growth and dissolution of Ag dendrites are responsible for the resistive switching. The Ag dendrite morphology is proposed to be the origin of the asymmetrical dissolution during the switching-off process, hence the bipolar nature of the switching characteristics.
Passive model-reduction of distributed networks with frequency-dependent parameters (2002)

Accurate simulation of large interconnect networks has become a necessity to address signal integrity issues in high-speed designs. Several model-reduction techniques based on Krylov-space methods have been proposed recently for fast simulation of large linear networks. However, a major limitation of these techniques is that they cannot efficiently handle distributed transmission lines with frequency-dependent parameters. In order to overcome this difficulty, a new technique is presented in this paper to handle distributed transmission lines with frequency-dependent parameters directly in a Krylov-space based algorithm.
Modulation of dopamine and noradrenaline release and of intracellular Ca<sup>2+</sup>concentration by presynaptic glutamate receptors in hippocampus (1994)

1. We studied the release of [3H]-dopamine and [3H]-noradrenaline (NA) from hippocampal synaptosomes induced by glutamate receptors and the associated Ca2+ influx through Ca2+ channels. The release of tritiated neurotransmitters was studied by use of superfusion system and the intracellular free Ca2+ concentration ([Ca2+]i) was determined by a fluorimetric assay with Indo-1 as a probe for Ca2+. 2. Presynaptic glutamate receptor activation induced Ca(2+)-dependent release of [3H]-dopamine and [3H]-NA from rat hippocampal synaptosomes. Thus, L-glutamate induced the release of both neurotransmitters in a dose-dependent manner (EC50 = 5.62 microM), and the effect of 100 microM L-glutamate was inhibited by 83.8% in the presence of 10 microM 6-cyano-7-nitroquinoxaline-2,3-dioxine (CNQX), but was not affected by 1 microM (+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]-cyclohepten-5,10-imine (MK-801). 3. Other glutamate receptor agonists also stimulated the Ca(2+)-dependent release of [3H]-dopamine and [3H]-NA as follows: N-methyl-D-aspartate (NMDA), at 200 microM, released 3.65 +/- 0.23% of the total 3H catecholamines, and this effect was inhibited by 81.2% in the presence of 1 microM MK-801; quisqualate (50 microM), S-alpha-amino-3-hydroxy-5-methyl-4-isoxazolopropionic acid (AMPA) (100 microM) or kainate (100 microM) released 1.57 +/- 0.26%, 1.93 +/- 0.17% and 2.09 +/- 0.22%, of the total 3H catecholamines, respectively. 4. The ionotropic glutamate receptor agonist, AMPA, induced an increase in the [Ca2+]i which was inhibited by 58.6% in the presence of 10 microM CNQX. In contrast, the increase in [Ca2+]i due to stimulation by glutamate was not sensitive to CNQX or MK-801.5. Nitrendipine, at I JAM, did not inhibit the neurotransmitter release induced by AMPA, but, both 0.5 micro M -conotoxin GVIA (w-CgTx) and 100 nM w-Aga IVA reduced catecholamine release to 49.03 +/- 3.79% and 46.06 +/- 10.51% of the control, respectively. In the presence of both toxins the release was reduced to 12.58 +/- 4.64% of the control.6. The results indicate that activation of presynaptic glutamate receptors of the NMDA and non-NMDA type induces the release of [3H]-dopamine and [H]-NA from rat hippocampal synaptosomes and that the release induced by AMPA involves the activation of N- and P-type Ca2" channels which allow the influx of Ca2" that triggers the 3H catecholamines release.
P38α MAPK Signaling—A Robust Therapeutic Target for Rab5-Mediated Neurodegenerative Disease (2020)

Multifactorial pathologies, involving one or more aggregated protein(s) and neuroinflammation are common in major neurodegenerative diseases, such as Alzheimer’s disease and dementia with Lewy bodies. This complexity of multiple pathogenic drivers is one potential explanation for the lack of success or, at best, the partial therapeutic effects, respectively, with approaches that have targeted one specific driver, e.g., amyloid-beta, in Alzheimer’s disease. Since the endosome-associated protein Rab5 appears to be a convergence point for many, if not all the most prominent pathogenic drivers, it has emerged as a major therapeutic target for neurodegenerative disease. Further, since the alpha isoform of p38 mitogen-activated protein kinase (p38α) is a major regulator of Rab5 activity and its effectors, a biology that is distinct from the classical nuclear targets of p38 signaling, brain-penetrant selective p38α kinase inhibitors provide the opportunity for significant therapeutic advances in neurogenerative disease through normalizing dysregulated Rab5 activity. In this review, we provide a brief summary of the role of Rab5 in the cell and its association with neurodegenerative disease pathogenesis. We then discuss the connection between Rab5 and p38α and summarize the evidence that through modulating Rab5 activity there are therapeutic opportunities in neurodegenerative diseases for p38α kinase inhibitors.
A comparison of deconvolution techniques for the ultrasonic nondestructive evaluation of materials (1992)

Several major deconvolution techniques commonly used for seismic applications are studied and adapted for ultrasonic NDE (nondestructive evaluation) applications. Comparisons of the relative merits of these techniques are presented based on a complete set of simulations on some real ultrasonic pulse echoes. Methods that rely largely on a reflection seismic model, such as one-at-a-time L(1) spike extraction and MVD (minimum variance deconvolution), are not suitable for the NDE applications discussed here because they are limited by their underlying model. L(2) and Wiener filtering, on the other hand, do not assume such a model and are, therefore, more flexible and suitable for these applications. The L(2) solutions, however, are often noisy due to numerical ill conditions. This problem is partially solved in Wiener filtering, simply by adding a constant desensitizing factor q. The computational complexities of these Wiener filtering-based techniques are relatively moderate and are, therefore, more suitable for potential real-time implementations.
Antibody specific to the alpha subunit of the guanine nucleotide-binding regulatory protein Go: developmental appearance and immunocytochemical localization in brain. (1988)

A polyclonal rabbit antibody (9120) against the alpha subunit of the "other" guanine nucleotide-binding protein Go (alpha o) was raised against a synthetic alpha o peptide fragment (Asp-Gly-Ile-Ser-Ala-Ala-Lys-Asp-Val) attached to a branched core system. Antiserum 9120, at a final dilution of 1:400, can detect alpha o in as little as 0.2 microgram of Go on immunoblots, and, at a final dilution of 1:20,000, can detect alpha o in 1 microgram of Go on immunoblots. Antiserum and affinity-purified antibody are specific to alpha o. No cross-reactivity was detected to the alpha subunits of the stimulatory or inhibitory guanine nucleotide-binding regulatory proteins or of transducin (alpha s, alpha i, or alpha T) or to the beta or gamma subunits. Immunoblots revealed a high density of alpha o in rat brain and lung membrane preparations, but other tissues (such as adipose tissue, heart, erythrocytes, and liver) have no detectable alpha o. Developmental studies showed that alpha o in rat brain was low before birth, increased after birth, and reached the full adult level at 4 weeks of age. In contrast, ADP-ribosylation of 40-kDa proteins increased for up to 1 week and then decreased. Immunocytochemistry revealed that alpha o was localized to somatic and synaptic membranes in rat brain, whereas little or no alpha o was detected in the cytoplasm of neuronal cell bodies. Our observations suggest that Go in brain might have a role in membrane signal transduction at synaptic and extrasynaptic sites.
Calcium‐dependent binding of uteroglobin (PCB‐BP/CCSP) to negatively charged phospholipid liposomes (1995)

To investigate interactions between the polychlorinated biphenyl-binding protein uteroglobin and phospholipids, we used a liposome-pelletting assay. PCB-BP/uteroglobin bound to liposomes made from negatively charged phospholipids (PtdSer and PtdIns) in the presence of 5 mM calcium. No binding to liposomes made from phospholipids without net charge (PtdChol and PtdEtn) was observed, nor could we detect binding in the absence of calcium or when magnesium was substituted for calcium. This suggests that PCB-BP/uteroglobin can bind to phospholipids in vivo and may have a role in the phospholipid homeostasis of the airway and/or secretory pathway of the Clara cell.
Guest Editorial: The New Generation and Missions - by Ruslan Zagidulin (2020)

This issue's topic of Next Generation and Missions (perhaps better termed The New Generation and Missions) might simply be reduced to issues surrounding proper integration of technologies with the theory and practice of mission. Clearly, however, such a reductionist step would be off-base. A more constructive approach involves seeing how new technologies have changed, and continue to change, the new generation's social behavior and even worldview. The new generation is not the next generation, it is the generation now. Contemporary mission is not just towards the next generation, it is mission with the new generation in every domain of life.
Meeting at the Crossroads: Women's Psychology and Girls' Development (1993)

For over a century, psychologists have described adolescence as a time of heightened psychological risk for girls. This article explores a relational impasse or crisis of connection that we have observed in girls' lives at adolescence by tracing through time the thoughts and feelings of two 12-year-old girls who were interviewed as part of a 5-year longitudinal study of girls' psychological development. Using a voice-centered relational method, we join the experiences of struggle and resistance at this developmental juncture with the problems that have been seen as central to the psychology of women.
Free carrier absorption in silicon (1978)

Free carrier absorption in heavily doped layers reduces the useful photon flux in the photoconductive region of extrinsic Si infrared detectors. A simple theory is developed which predicts the transmissivity of such layers as a function of their sheet resistance and the wavelength of the radiation. Experimental data over the 2.5-20 µm wavelength and 5-500 Ω/square sheet resistance range are given for both diffused and ion-implanted layers and also for polysilicon gases. The temperature dependence of both transmissivity and sheet resistance is investigated from 20 to 300 K.