gebhart/patrepeval huggingface dataset:
Rigorous 3-dimensional spectral data activity relationship approach modeling strategy for ToxCast estrogen receptor data classification, validation, and feature extraction (2016)

The estrogenic potential (expressed as a score composite of 18 high throughput screening bioassays) of 1528 compounds from the ToxCast database was modeled by a 3-dimensional spectral data activity relationship approach (3D-SDAR). Due to a lack of <sup>17</sup> O nuclear magnetic resonance (NMR) simulation software, the most informative carbon-carbon 3D-SDAR fingerprints were augmented with indicator variables representing oxygen atoms from carbonyl and carboxamide, ester, sulfonyl, nitro, aliphatic hydroxyl, and phenolic hydroxyl groups. To evaluate the true predictive performance of the authors' model the United States Environmental Protection Agency provided them with a blind test set consisting of 2008 compounds. Of these, 543 had available literature data-their binding affinity served to estimate the external classification accuracy of the developed model: predictive accuracy of 0.62, sensitivity of 0.71, and specificity of 0.53 were obtained. Compared with alternative modeling techniques, the authors' model displayed very little reduction in performance between the modeling and the prediction set. A 3D-SDAR mapping technique allowed identification of structural features essential for estrogenicity: 1) the presence of a phenolic OH group or cyclohexenone, 2) a second aromatic or phenolic ring at a distance of 6 Å to 8 Å from the oxygen of the first phenol ring, 3) the presence of a methyl group approximately 6 Å away from the centroid of a phenol ring, and 4) a carbonyl group in close proximity (∼4 Å measured to the centroid) to 1 of the phenol rings. Environ Toxicol Chem 2017;36:823-830. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Zoledronate Attenuates Accumulation of DNA Damage in Mesenchymal Stem Cells and Protects Their Function (2015)

Mesenchymal stem cells (MSCs) undergo a decline in function following ex vivo expansion and exposure to irradiation. This has been associated with accumulation of DNA damage and has important implications for tissue engineering approaches or in patients receiving radiotherapy. Therefore, interventions, which limit accumulation of DNA damage in MSC, are of clinical significance. We were intrigued by findings showing that zoledronate (ZOL), an anti-resorptive nitrogen containing bisphosphonate, significantly extended survival in patients affected by osteoporosis. The effect was too large to be simply due to the prevention of fractures. Moreover, in combination with statins, it extended the lifespan in a mouse model of Hutchinson Gilford Progeria Syndrome. Therefore, we asked whether ZOL was able to extend the lifespan of human MSC and whether this was due to reduced accumulation of DNA damage, one of the important mechanisms of aging. Here, we show that this was the case both following expansion and irradiation, preserving their ability to proliferate and differentiate in vitro. In addition, administration of ZOL before irradiation protected the survival of mesenchymal progenitors in mice. Through mechanistic studies, we were able to show that inhibition of mTOR signaling, a pathway involved in longevity and cancer, was responsible for these effects. Our data open up new opportunities to protect MSC from the side effects of radiotherapy in cancer patients and during ex vivo expansion for regenerative medicine approaches. Given that ZOL is already in clinical use with a good safety profile, these opportunities can be readily translated for patient benefit.
69.1: Image Quality Assessment of Ultra‐High Resolution Mobile Display Utilizing New RGBW Method (2013)

Abstract In this paper, newly‐developed 5.0‐inch full‐HD (1080 × RGBW × 1920) and 7.0‐inch WQXGA (2560 × RGBW × 1600) prototype LCDs utilizing a new RGBW method are described in detail. The assessment of the image quality of the new RGBW technology is described, such as color image reproducibility, white color tracking in the low power mode and tone curve correction in the outdoor bright mode.
Recovery of the neonatal heart after normothermic ischemia. Effect of oxygen and catalase. (1991)

The objective of this study was to determine the effect of oxygen and the oxygen radical-scavenging enzyme catalase on the neonatal rabbit heart exposed to global ischemia. The experiments were performed with an isolated neonatal (7 to 10 days of age) working heart model in which normothermic (37 degrees C) ischemia was produced for 60 minutes. Left ventricular developed pressure, ratio of change of ventricular pressure to change in time, and aortic flow were measured before ischemia and 30 minutes after reperfusing the hearts with physiologic saline solution. In the control group (ischemia only), developed pressure and ratio of change of ventricular pressure to change in time recovered to 27% +/- 3% (mean +/- standard error of the mean) and 24% +/- 7% of baseline; the hearts were incapable of ejecting (aortic flow = 0). Treatment of hearts before and after ischemia with catalase (150 units/ml of perfusate) was studied in a second group (control plus catalase), but functional recovery (developed pressure = 32% +/- 1%; ratio of change of ventricular pressure to change in time = 24% +/- 2%, and aortic flow = 0) was not significantly different from the control group. The effect of washout midway through the ischemic period with a low oxygen (oxygen concentration less than 35 mm Hg) solution was measured in a third group (hypoxic physiologic saline solution). Functional recovery (developed pressure = 13% +/- 3%; ratio of change of ventricular su pressure to change in time = 13% + 2%; aortic flow = 0) was not significantly different from the control and control plus catalase groups. In marked contrast were the effects of washout with an oxygenated (oxygen concentration greater than 500 mm Hg) solution (oxygenated physiologic saline solution) in which functional recovery (developed pressure = 78% +/- 3%; ratio of change of ventricular pressure to change in time = 80% +/- 3%; aortic flow = 39% +/- 9%) was significantly better than in the control, control plus catalase, and hypoxic physiologic saline solution groups. Use of modified St. Thomas' Hospital cardioplegic solution (cardioplegic solution group) during the ischemic period also resulted in substantial functional recovery (developed pressure = 80% +/- 3%; ratio of change of ventricular pressure to change in time = 78% +/- 5%; aortic flow = 64% +/- 7%) that did not differ significantly from that in the oxygenated physiologic saline solution group.(ABSTRACT TRUNCATED AT 400 WORDS)
Laser Polarimetric Imaging of Surface Defects of Semiconductor Wafers, Microelectronics, and Spacecraft Structures (2006)

The purpose of this paper is to present novel optical imaging techniques, based on all active optical polarimetric principles, for efficient detection, inspection, and monitoring of semiconductor components, microelectronic components, and spacecraft structures. The experimental results of this paper indicate that the polarimetric imaging techniques are highly efficient in detecting defects on the semiconductor structures when compared to nonpolarimetric techniques
Requirements for IPv6 Prefix Delegation (2004)

s network (or "site").
Exchange transfusion with synthetic oxygen‐carrying plasma protein “albumin‐heme” into an acute anemia rat model after seventy‐percent hemodilution (2004)

Recombinant human serum albumin (rHSA) incorporating the synthetic heme "albumin-heme" is an oxygen-carrying plasma protein that has the potential to be a red blood cell substitute. The physiological responses to a 30% exchange transfusion with two types of albumin-heme (rHSA-FecycP, rHSA-FepivP) solutions after 70% isovolemic hemodilution with 5 g/dL rHSA were investigated using anesthetized rats. The circulation parameters, blood parameters, renal cortical oxygen pressure (pO2), and muscle tissue pO2 were carefully monitored for 60 min after the injection. The declined mean arterial pressure and the mixed venous partial pO2 significantly recovered to 70.8 and 91.9% of the basal values by intravenous infusion of albumin-hemes, respectively. The lowered renal cortical pO2 also increased, indicating oxygen transport by this synthetic hemoprotein. The administration of albumin-heme into the acute anemia rat model after hemorrhage improved the circulatory volume and resuscitated the shock state. Both rHSA-FecycP and rHSA-FepivP transported oxygen through the body.
Quantitative High-Field NMR- and Mass Spectrometry-Based Fatty Acid Sequencing Reveals Internal Structure in Ru-Catalyzed Deuteration of Docosahexaenoic Acid (2022)

Ru-based catalysis results in highly unsaturated fatty acid (HUFA) ethyl esters (EE) deuterated to various extents. The products carry <sup>2</sup>H (D) mainly at their <i>bis</i>-allylic positions, where they are resistant to autoxidation compared to natural HUFA and are promising as neurological and retinal drugs. We characterized the extent of deuteration at each allylic position of docosa-4,7,10,13,16,19-hexaenoic acid deuterated to completion at <i>bis</i>-allylic and allylic positions (D-DHA) by two-dimensional (2D) and high-field (600 and 950 MHz) NMR. In separate experiments, the kinetics of docosahexaenoic acid (DHA) EE deuteration was evaluated using Paternò-Büchi (PB) reaction tandem mass spectrometry (MS/MS) analysis, enabling deuteration to be quantitatively characterized for isotopologues (D0-D14 DHA) at each internal allylic position. NMR analysis shows that the net deuteration of the isotopologue mixture is about 94% at the <i>bis</i>-allylic positions, and less than 1% remained as the protiated -CH<sub>2</sub>-. MS analysis shows that deuteration kinetics follow an increasing curve at <i>bis</i>-allylic positions with higher rate for internal <i>bis</i>-allylic positions. Percent D of <i>bis</i>-allylic positions increases linearly from D1 to D9 in which all internal <i>bis</i>-allylic positions (C9, C12, C15) deuterate uniformly and more rapidly than external <i>bis</i>-allylic positions (C6, C18). The <i>mono</i>-allylic positions near the methyl end (C21) show a steep increase of D only after the D10 isotopologue has been deuterated to >90%, while the <i>mono</i>-allylic position near the carboxyl position, C3, deuterates last and least. These data establish detailed methods for the characterization of Ru-catalyzed deuteration of HUFA as well as the phenomenological reaction kinetics as net product is formed.
Consequences of Chirality in Directing the Pathway of Cholesteric Helix Inversion of π‐Conjugated Polymers by Light (2020)

Control over main-chain motion of chiral π-conjugated polymers can lead to unexpected new functionalities. Here, it is shown that by combining photoswitchable azobenzene units in conjugation with chiral fluorene comonomers and appropriate plasticizers, the polymer organization and chiroptical properties of these alternating copolymers steered by light and its state of polarization can be dynamically controlled. The configuration of the stereogenic centers in the side chains of the fluorene units determines the handedness of the cholesteric organization in thermally annealed films, indicating cooperative behavior. The polymer alignment and helicity of the supramolecular arrangement can be switched by irradiating with linearly and circularly polarized light, respectively. Intriguingly, when switching the handedness of thermally induced cholesteric organizations by illuminating with circularly polarized light that is opposite to the handedness of the cholesteric phases, a nematic-like intermediate state is observed during helix interconversion. By the sequence of irradiation with left and right circularly polarized light followed by thermal annealing, an asymmetric motion, reminiscent of that seen in molecular motors is observed. These findings suggest that functional conjugated polymers can exhibit emergent properties at mesoscopic scale.
Oligosphaera ethanolica gen. nov., sp. nov., an anaerobic, carbohydrate-fermenting bacterium isolated from methanogenic sludge, and description of Oligosphaeria classis nov. in the phylum Lentisphaerae (2012)

A mesophilic, obligately anaerobic, carbohydrate-fermenting bacterium, designated 8KG-4(T), was isolated from an upflow anaerobic sludge blanket reactor treating high-strength organic wastewater from salted vegetable production processes. Cells of strain 8KG-4(T) were non-motile, spherical and 0.7-1.5 µm in diameter (mean, 1.0 µm). Spore formation was not observed under any culture conditions tested. The strain grew optimally at 37 °C (range for growth 25-40 °C) and pH 7.0 (range, pH 6.5-7.5), and could grow fermentatively on glucose, ribose, xylose, galactose and sucrose. The main end products of glucose fermentation were acetate, ethanol and hydrogen. Organic acids, alcohols and amino acids were not utilized for growth. Yeast extract was not required for growth. Nitrate, sulfate, thiosulfate, elemental sulfur, sulfite and Fe(III) nitrilotriacetate were not used as terminal electron acceptors. The G+C content of the genomic DNA was 61.1 mol%. 16S rRNA gene sequence analysis revealed that the isolate represented a previously uncultured lineage at the subphylum level within the phylum Lentisphaerae known as 'WWE2 subgroup I'. The major cellular fatty acids were anteiso-C(15 : 0), iso-C(16 : 0), C(16 : 0) and anteiso-C(17 : 0). Respiratory quinones were not detected. The most abundant polar lipid of strain 8KG-4(T) was phosphatidylethanolamine. A novel genus and species, Oligosphaera ethanolica gen. nov., sp. nov., is proposed to accommodate strain 8KG-4(T) ( = JCM 17152(T) = DSM 24202(T) = CGMCC 1.5160(T)). In addition, we formally propose Oligosphaeria classis nov. and the subordinate taxa Oligosphaerales order nov. and Oligosphaeraceae fam. nov.
Transition Edge Sensors and Kinetic Inductance Detectors in Astronomical Instruments (2018)

Superconducting detector arrays have become the standard technology for the current generation of millimeter-wave and submm-wave astronomical instruments on individual (single dish) telescopes. Superconducting heterodyne arrays are used for spectroscopic surveys and direct detector arrays are used for photometric imaging and low resolution spectroscopy. Most of these direct detector arrays consist of bolometers with superconducting thermometers called Transition Edge Sensors (TES) and are read out with multiplexed superconducting quantum interference device (SQUID) current amplifiers. Another superconducting detector technology called Kinetic Inductance Detectors (KIDs) is starting to be used in new astronomical instruments as well. This review describes the properties of these two types of detectors and the prospects for future development of both types of technologies toward larger pixel counts and more capable instruments.
Cross Domain Regularization for Neural Ranking Models using Adversarial Learning (2018)

Unlike traditional learning to rank models that depend on hand-crafted features, neural representation learning models learn higher level features for the ranking task by training on large datasets. Their ability to learn new features directly from the data, however, may come at a price. Without any special supervision, these models learn relationships that may hold only in the domain from which the training data is sampled, and generalize poorly to domains not observed during training. We study the effectiveness of adversarial learning as a cross domain regularizer in the context of the ranking task. We use an adversarial discriminator and train our neural ranking model on a small set of domains. The discriminator provides a negative feedback signal to discourage the model from learning domain specific representations. Our experiments show consistently better performance on held out domains in the presence of the adversarial discriminator---sometimes up to 30% on [email protected]$.
Mixed signal DFT/BIST automation using behavioral modeling (2002)

One of the hurdles in mixed signal built in self test is automation. This paper presents a robust mixed signal design for test and built in self test library based approach for BIST circuit creation, insertion, verification and test pattern generation that fits into the existing design flow.
Breed-specific differences in the immune response to lipopolysaccharide in ewes (2018)

Innate immune response to a lipopolysaccharide (LPS) challenge varies among sheep breeds. How different breeds respond to bacterial infections impacts management practices of sheep producers. Hence, clinical response, acute-phase response, and gene expression of pro- and anti-inflammatory markers in peripheral white blood cells (WBCs) were examined after an LPS challenge in Dorset and Suffolk ewes. Ewes received either PBS or 2.5 µg/kg LPS (i.v.) 4 to 5 d after onset of synchronized estrus. Blood was collected via jugular venipuncture intermittently for 24 h to determine WBC counts. Rectal temperatures and observations of behavioral/physical appearances were recorded hourly. After LPS, WBCs decreased the first hour (P = 0.0001) and rectal temperatures (P < 0.0001) increased through 4 h; both returned toward normal 6 h after challenge. Suffolk ewes exhibited greater changes in temperature (P = 0.03) and behavioral/physical responses (P < 0.0001) than Dorset ewes and had an enhanced acute-phase response demonstrated by increased concentrations of plasma haptoglobin (P = 0.04), as well as cortisol concentrations (P = 0.03). Real-time PCR was completed on buffy coat homogenates for expression of pro-inflammatory [CXCL8, IL-6, interferon gamma (IFNG), complement component 3 (C3), toll-like receptor 4 (TLR4), prostaglandin synthase 2 (PTGS2)] and anti-inflammatory [IL-10, superoxide dismutase 2 (SOD2), forkhead box P3 (FOXP3), peroxisome proliferator-activated receptor gamma (PPARG), mannose receptor C type 1 (MRC1), transforming growth factor β (TGFβ)] genes. After LPS treatment, gene expressions increased for CXCL8 (P = 0.0003), TLR4 (P = 0.004), SOD2 (P < 0.0001), and C3 (P = 0.003), while PPARG (P = 0.006) and MRC1 (P = 0.003) decreased. Overall, Dorset ewes had greater expression of TLR4 (P = 0.003), IL-10 (P = 0.045), PPARG (P = 0.002), FOXP3 (P = 0.001), and SOD2 (P = 0.0002), whereas Suffolk ewes had greater expression of IL-6 (P = 0.0007), IFNG (P = 0.02), PTGS2 (P = 0.0002), and C3 (P = 0.008). Suffolk ewes also displayed greater expression of IL-6 (P = 0.002) and C3 (P = 0.0004) in response to LPS. In conclusion, differences in gene expression may explain the enhanced inflammatory response in Suffolk ewes and may predispose Suffolk ewes to be more responsive to bacterial infection than Dorset ewes.
Group B coxsackieviruses and autoimmunity: focus on Type 1 diabetes (2011)

Group B coxsackieviruses (CVB) and/or their components have been found in the blood and pancreas of patients with Type 1 diabetes (T1D). CVB infections lead to the activation of the innate and adaptive immune systems, which can result in the induction or aggravation of autoimmune processes. Persistent and/or repeated infections of pancreas islet β cells with CVB and the resulting production of IFN-α and inflammatory mediators, combined with a predisposed genetic background, may induce bystander activation of autoimmune effector T cells and an autoreactive response to islet self-antigens through molecular mimicry. Moreover, the antibody-dependent enhancement of CVB infection of monocytes, as well as infection of the thymus can intervene in the pathogenesis of T1D. In contrast with the deleterious effect of CVB, it has been shown that these viruses can protect against the development of T1D under certain experimental conditions. The role of CVB in autoimmunity is complex, and therefore a better understanding of the inducer versus protective effects of these viruses in T1D will help to design new strategies to treat and prevent the disease.
Overview of the TREC 2020 deep learning track (2021)

This is the second year of the TREC Deep Learning Track, with the goal of studying ad hoc ranking in the large training data regime. We again have a document retrieval task and a passage retrieval task, each with hundreds of thousands of human-labeled training queries. We evaluate using single-shot TREC-style evaluation, to give us a picture of which ranking methods work best when large data is available, with much more comprehensive relevance labeling on the small number of test queries. This year we have further evidence that rankers with BERT-style pretraining outperform other rankers in the large data regime.
Differential regulation of growth and invasiveness of MCF-7 breast cancer cells by antiestrogens. (1988)

Estrogen increases the ability of the estrogen-dependent MCF-7 human breast cancer cell line to both proliferate and invade through an artificial basement membrane. In studying the response of MCF-7 cells to various antiestrogens, we found that 4-hydroxytamoxifen and tamoxifen inhibited cell proliferation but increased their invasiveness. In contrast, the structurally unrelated benzothiophene antiestrogens, LY117018 and LY156758, were potent antiproliferative agents which did not stimulate invasiveness. The differential effects of these antiestrogenic agents on invasion correlated with changes in production of collagenase IV, while no significant change was seen in the chemotactic activity of the cells. Invasiveness was increased by 17 beta-estradiol or 4-hydroxytamoxifen after a few hours of treatment and was rapidly lost when 17 beta-estradiol was withdrawn. Stimulation of invasiveness with 17 beta-estradiol was blocked by the antiestrogen, LY117018. Cells from the MDA-MB-231 line which lacks estrogen receptors were not affected by estrogen or antiestrogen in terms of proliferation or invasion. These studies indicate that the invasiveness of MCF-7 cells is regulated by antiestrogens through the estrogen receptor and may be mediated by collagenase IV activity. Antiestrogens which reduce both the proliferation and invasiveness of these cells may be interesting new candidates for clinical application.
Cytoskeleton Dynamics in Peripheral T Cell Lymphomas: An Intricate Network Sustaining Lymphomagenesis (2021)

Defects in cytoskeleton functions support tumorigenesis fostering an aberrant proliferation and promoting inappropriate migratory and invasive features. The link between cytoskeleton and tumor features has been extensively investigated in solid tumors. However, the emerging genetic and molecular landscape of peripheral T cell lymphomas (PTCL) has unveiled several alterations targeting structure and function of the cytoskeleton, highlighting its role in cell shape changes and the aberrant cell division of malignant T cells. In this review, we summarize the most recent evidence about the role of cytoskeleton in PTCLs development and progression. We also discuss how aberrant signaling pathways, like JAK/STAT3, NPM-ALK, RhoGTPase, and Aurora Kinase, can contribute to lymphomagenesis by modifying the structure and the signaling properties of cytoskeleton.
Study of comparison between the DCG-FGT and its equivalent circuit in MOS technology (2013)

In this paper, a comparison between the DCG-FGT (Dual-Control-Gate Floating-Gate Transistor) and its equivalent circuit composed of standard components is proposed. We demonstrate the DCG-FGT advantages with measurement and simulations under electrical simulator (ELDO). It is not easily to reproduce the DCG-FGT operating mode with standard MOS technology.
Low‐power‐consumption TFT‐LCD with dynamic memory embedded in the pixels (2002)

Abstract— A low‐power‐consumption thin‐film‐transistor liquid‐crystal display (TFT‐LCD) with dynamic memory cells embedded in each pixel using low‐temperature poly‐Si technology has been developed. By holding data in the memory, the operating rate of the data driver can be dramatically reduced to 4 Hz. Eight levels of gray scale with low power consumption can be achieved by using the area‐ratio gray‐scale method. This TFT‐LCD can be used for displaying fine still images, with low power consumption.