gebhart/patrepeval huggingface dataset:
586Effects of maternal circulating amino acids on offspring birthweight: a Mendelian randomisation analysis (2021)

Abstract Background It is suggested amino acids are critical for fetal growth, but analyses assessing causality are lacking. Mendelian randomisation (MR) can be used to examine causal effects under instrumental variable (IV) assumptions. Methods We conducted a two-sample MR study utilizing summary data from genome-wide association studies (GWAS) of amino acids (sample 1, n = 86,507) and of offspring birthweight (sample 2, combined UK Biobank and Early Growth Genetics Consortium, n = 406,063). Seventy-five independent single nucleotide polymorphisms (SNPs) robustly associated with 18 amino acids (p &amp;lt; 4.9 × 10-10) were used as genetic instruments. Wald ratio and inverse variance weighted methods were used in MR main analysis. Sensitivity analyses were performed to explore IV assumption violations. To explore whether there was consistency between SNP-amino acid associations in pregnancy and in the GWAS, the latter were compared to associations in the Born in Bradford cohort. Results There was evidence of positive causal effects of maternal alanine (51.9 g birthweight increase per SD increase in amino acid level, 95% CI: 24.2, 79.5), glutamine (51.3 g, 95% CI: 33.5, 69.0), glycine (10.4 g, 95% CI: 1.3, 19.6) and serine (27.1 g, 95% CI: 11.2, 43.0) on birthweight and inverse causal effects of maternal isoleucine (-109.7 g, 95% CI: -194.6, -24.9) and histidine (-41.1 g, 95% CI: -78.5, -3.7) on birthweight. Sensitivity analyses to explore reverse causality and bias due to horizontal pleiotropy supported our findings. Conclusions Some maternal circulating amino acids have causal effects on birthweight. Key messages MR can be extended to probe effects of maternal nutrition on offspring development.
The ambrosia beetle, Gnathotrichus retusus (Coleoptera: Scolytidae) breeding in red alder, Alnus rubra (Betulaceae) (2000)

Brood adult ambrosia beetles recovered from well established galleries in a wind-thrown red alder, Alnlls rubra Bongard, on Burnaby Mountain, Burnaby, British Columbia, were identified as Cnalholrichlls retllslIS LeConte. The tree was attacked to a height of 25.8 m. Galleries penetrated up to 17.5 cm into the wood. The mean density of gallery entrance holes ( ± SE) was 120 ± 31.9 per m2 of the bark surface. The mean production of brood in five completely dissected galleries was 13.2 ± 5.5. These results show conclusively that C. relusus in British Columbia can breed successfully in an angiosperm host. Key Words: Cnalhotrichlls reilisus, Alnlls rubra, ambrosia beetle
Simulated Students and Classroom Use of Model-Based Intelligent Tutoring (2008)

Two educational uses of models and simulations: 1) Students create models and use simulations ; and 2) Researchers create models of learners to guide development of reliably effective materials. Cognitive tutors simulate and support tutoring - data is crucial to create effective model. Pittsburgh Science of Learning Center: Resources for modeling, authoring, experimentation. Repository of data and theory. Examples of advanced modeling efforts: SimStudent learns rule-based model. Help-seeking model: Tutors metacognition. Scooter uses machine learning detectors of student engagement.
Chelate-stabilised tetrahydrofuran complexes of platinum(II). Crystal structure of [PtCl(Ph2PCH2C4H7O)(Ph2PCH2C4H7O)][PF6] (1989)

The platinum(II) complexes cis- and trans-[PtCl2(PPh2CH2[graphic omitted])2](2) and (3) are described. The cis isomer (2) reacts with K[PF6] to give the monochelate cis-[[graphic omitted])-(Ph2PCH2[graphic omitted])[PF6](4a). Complex (2) also reacts with AgClO4 to give the bis chelate cis-[[graphic omitted])2][ClO4]2(5a). The tetrahydrofuran (thf) complexes (4a) and (5a) are compared with closely related alcohol and linear ether complexes and it is deduced that the trans influence of the neutral O-donors is in the order ROH > thf > R2O. The X-ray structure (R= 0.039 for 5 730 diffractometer observed reflections) of complex (4a) confirms the structural assignment; the Pt–O bond length [2.142(4)Å] is somewhat longer than found for covalent Pt–O bonds.
Ventilator-associated pneumonia caused by Pseudomonas aeruginosa (2012)

Departments of Microbiology and Immunology and Medicine, Northwestern University, Chicago, IL *See also p. 2320. Supported, in part, by grants R01AI053674 and R01AI075191 from the National Institutes of Health. The author collaborates on two grants with Microbiotix, Inc., on the development of inhibitors of Pseudomonas aeruginosa type III secretion.
Use of adenoviruses encoding CD40L or IL‐2 against B cell lymphoma (2004)

Some B cell lymphomas lack important costimulatory properties that could prevent them from being used as cell based vaccines. Infection of A20 B lymphoma cells with a replication-defective adenovirus encoding murine (m) CD40L, but not mIL-2, produces an antigen presentation phenotype with upregulation of MHC Class I/II, induction of B7-1/2 molecules and production of MIL-12 and MIP-1alpha. Subcutaneous vaccination with irradiated Ad-mCD40L-infected- or Ad-mIL-2-infected-A20 cells generated A20-specific CD8+ T cell responses and cross reactive A20 Ig antibodies. Only vaccination with Ad-mCD40L-infected A20 cells produced a significant delay in tumor growth and long-term survival (p = 0.0039). Stronger protective immunity to A20 challenge was generated by intravenous priming with A20 cells infected with Ad-mCD40L, Ad-mIL-2 or their combination followed by a boost immunization with A20 cells activated with syngeneic fibroblasts expressing CD40L. Compared to Ad-LacZ-infected A20 priming, the combination priming was most effective followed by Ad-mCD40L and Ad-mIL-2 (p = 0.0027, p = 0.0027, p = 0.0163 respectively). Significant A20-specific CD8+ T cell-mediated cytotoxicity was only demonstrated in splenocytes from these groups of vaccinated animals. By contrast, ELISPOT assay of splenocytes from all A20 prime/boosted vaccinated groups demonstrated increases in gamma-interferon release by T cells elicited by in vitro stimulation either with A20 cells or another syngeneic 2PK-3 lymphoma, indicating the presence of cross reactive immunity. Similarly anti-A20 immunoglobulin antibodies generated after vaccination were not necessarily A20 idiotype-specific. Direct therapy of pre-established tumors was achieved with the combination of Ad-mCD40L and Ad-mIL-2 given at Days 4 and 8 at the tumor site with a significant long-term survival of 85% of tumor-bearing mice (p = 0.0001). Our study strongly supports the use of Ad-CD40L and Ad-IL-2 combination therapy for the treatment of patients with B cell lymphoma.
Multi-frame example-based super-resolution using locally directional self-similarity (2015)

This paper presents a multi-frame example-based super-resolution (SR) algorithm using locally directional self-similarity. Existing example-based super-resolution algorithms generate patches using multiple training images or single self-image. On the other hand the proposed method minimizes the patch mismatching error by generating a patch dictionary in a local region of multiple, adjacent frames. As a result, the proposed algorithm can remove interpolation artifacts based on a degradation model of low-resolution images. The dictionary is classified by the orientation of patches for fast searching. The proposed algorithm consists of two steps: i) dictionary generation based on the image degradation model and ii) multi-frame image reconstruction for super-resolution. Experimental results show that the proposed SR algorithm provides better reconstructed images with less undesired artifacts than existing methods.
Protein Kinase C Phosphorylation: An Introduction (2003)

The constitutive, lipid-dependent protein kinase activity of purified protein kinase C (PKC) delayed the realization that phosphorylation of the PKCs themselves played a fundamental role in their catalytic activities. With the clarity of hindsight, it is evident that the proteins originally purified from tissue sources and indeed those recombinant proteins derived from baculovirus infection of insect cells were already highly phosphorylated (1). The requirement for modification was thus not obvious.
Targeted Attacks on Teleoperated Surgical Robots: Dynamic Model-Based Detection and Mitigation (2016)

This paper demonstrates targeted cyber-physical attacks on teleoperated surgical robots. These attacks exploit vulnerabilities in the robot's control system to infer a critical time during surgery to drive injection of malicious control commands to the robot. We show that these attacks can evade the safety checks of the robot, lead to catastrophic consequences in the physical system (e.g., sudden jumps of robotic arms or system's transition to an unwanted halt state), and cause patient injury, robot damage, or system unavailability in the middle of a surgery. We present a model-based analysis framework that can estimate the consequences of control commands through real-time computation of robot's dynamics. Our experiments on the RAVEN II robot demonstrate that this framework can detect and mitigate the malicious commands before they manifest in the physical system with an average accuracy of 90%.
Genres as a tool for understanding and analyzing user experience in games (2004)

HCI has profoundly changed the way people work with computers, it also has the potential to help shape the way people entertain in the digital age. As a popular entertainment form, games are poised to become the next frontier for HCI research. However, the broader HCI community only has limited knowledge of games. The intent of this demo is to paint a broad picture of today's games. We employ genre theory, which has been widely used in film study, as a framework to introduce a variety of games, analyze different interface metaphors and user experiences of games, and present innovative interaction techniques and devices used in games.
Heat-Treated Lysozyme Hydrochloride: A Study on Its Structural Modifications and Anti-SARS-CoV-2 Activity (2023)

Lysozyme (E.C. 3.2.1.17), an about 14 kDa protein and pI 11, widely spread in nature, is present in humans mainly in milk, saliva, and intestinal mucus as a part of innate defense mechanisms. It is endowed with antimicrobial activity due to its action as an N-acetylmuramidase, cleaving the 1-4β glycosidic linkage in the peptidoglycan layer of Gram-positive bacteria. This antimicrobial activity is exerted only against a limited number of Gram-negative bacteria. Different action mechanisms are proposed to explain its activity against Gram-negative bacteria, viruses, and fungi. The antiviral activity prompted the study of a possible application of lysozyme in the treatment of SARS-CoV-2 infections. Among the different sources of lysozyme, the chicken egg albumen was chosen, being the richest source of this protein (c-type lysozyme, 129 amino acids). Interestingly, the activity of lysozyme hydrochloride against SARS-CoV-2 was related to the heating (to about 100 °C) of this molecule. A chemical-physical characterization was required to investigate the possible modifications of native lysozyme hydrochloride by heat treatment. The FTIR analysis of the two preparations of lysozyme hydrochloride showed appreciable differences in the secondary structure of the two protein chains. HPLC and NMR analyses, as well as the enzymatic activity determination, did not show significant modifications.
Alpha-tocotrienol is the most abundant tocotrienol isomer circulated in plasma and lipoproteins after postprandial tocotrienol-rich vitamin E supplementation (2012)

Bio-discrimination between vitamin E isomers in humans reduces the rate of T3 absorption and affects their incorporation into lipoproteins. Although low absorption of T3 into circulation may impact some of their physiological functions in humans, T3 have biological functions well below concentration noted in this study.
The BTB-ZF transcription factor Zbtb20 is driven by Irf4 to promote plasma cell differentiation and longevity (2014)

The transcriptional network regulating antibody-secreting cell (ASC) differentiation has been extensively studied, but our current understanding is limited. The mechanisms of action of known "master" regulators are still unclear, while the participation of new factors is being revealed. Here, we identify Zbtb20, a Bcl6 homologue, as a novel regulator of late B cell development. Within the B cell lineage, Zbtb20 is specifically expressed in B1 and germinal center B cells and peaks in long-lived bone marrow (BM) ASCs. Unlike Bcl6, an inhibitor of ASC differentiation, ectopic Zbtb20 expression in primary B cells facilitates terminal B cell differentiation to ASCs. In plasma cell lines, Zbtb20 induces cell survival and blocks cell cycle progression. Immunized Zbtb20-deficient mice exhibit curtailed humoral responses and accelerated loss of antigen-specific plasma cells, specifically from the BM pool. Strikingly, Zbtb20 induction does not require Blimp1 but depends directly on Irf4, acting at a newly identified Zbtb20 promoter in ASCs. These results identify Zbtb20 as an important player in late B cell differentiation and provide new insights into this complex process.
Improved time to publication in Journal of Geophysical Research‐Atmospheres (2012)

Timely publication of manuscripts is important to authors and readers. AGU has significantly accelerated both the review and production processes for the Journal of Geophysical Research‐Atmospheres (JGR‐Atmospheres). Via a number of mechanisms (e.g., shortening the time allotted for reviewer selection, manuscript reviews, and revisions), the mean time to first decision has been decreased from 98 days in 2007 to 50 days in 2011, and the mean time to final decision has been decreased from 132 days in 2007 to 71 days in 2011. By implementing a new content management system, adjusting the workflow for improved efficiency, requesting authors to proofread their manuscripts quicker, and improving monitoring and follow‐up to author and vendor queries, the mean production time from manuscript acceptance to publication has been decreased from 128 days in 2010 to only 56 days in 2012. Thus, in the past few years the mean time to publication of JGR‐Atmospheres has been cut in half. These milestones have been achieved with no loss of quality of presentation or content. In addition, online posting of “papers in press” on JGR‐Atmosphere's home page typically occurs within a few days after acceptance. JGR‐Atmospheres editors thank manuscript reviewers, authors, and AGU staff who have greatly contributed to the more timely review and publication processes. This information will be updated periodically on the JGR‐Atmospheres home page. A chart showing the average time from acceptance to publication for all of AGU's journals is available at http://www.agu.org/pubs/pdf/31May2012_Timeliness_Chart.pdf .
Catalytic deoxygenation on transition metal carbide catalysts (2016)

We highlight the evolution and tunability of catalytic function of transition metal carbides under oxidative and reductive environments for selective deoxygenation reactions.
Protein kinase C epsilon translocation and phosphorylation by cis-diamminedichloroplatinum(II) (CDDP): potential role in CDDP-mediated cytotoxicity. (1998)

Phorbol ester-like protein kinase C (PKC) activators, such as 12-O-tetradecanoylphorbol-13-acetate, and perturbation of some growth factor receptors have been reported to alter the cytotoxicity of cis-diamminedichloroplatinum(II) (CDDP). To study the mechanism of this alteration, we have examined the effect of CDDP per se on PKC isozymes. The SKBR-3 human breast carcinoma cell line exhibits at least six different PKC isozymes (PKC alpha, betaI, betaII, delta, epsilon, and zeta). After exposure to 10-100 microM CDDP for 3 h, only PKC epsilon translocated from the plasma membrane to the nuclear membrane and to the cytosolic fraction. This translocation was observed in a time- and dose-dependent manner by Western blot and confocal microscopy. CDDP also decreased the mobility of PKC epsilon in the nuclear membrane fraction, an effect that was blocked by protein phosphatase 2A, suggesting drug-mediated isozyme phosphorylation. This translocation and phosphorylation were also induced by the cisplatin analogue carboplatin but not with the anticancer agents Adriamycin and Taxol. Antisense oligodeoxynucleotides against PKC epsilon down-regulated isozyme content, blocked drug-induced translocation, and reduced cisplatin-mediated cytotoxicity 3-fold compared to that of sense-treated cells. Antisense PKC epsilon also decreased SKBR-3 cell sensitivity to carboplatin but not to Adriamycin and Taxol. These data support a role for PKC epsilon translocation and phosphorylation on CDDP-mediated toxicity.
Harmonic coupling analysis of a multi-drive system with slim DC-link drive (2017)

One of the problems with slim dc-link adjustable speed drive is the difficulties to analyze the harmonic coupling when it is integrated into a multi-drive system. The traditional methods analyze this harmonic issue by neglecting the harmonic coupling, and base on the linear time-invariant methods. Its disadvantages include the time consumption and large computer memory. This paper proposes to do harmonic analysis by using the harmonic state-space modeling method by using the linear time-periodic theory. By using the proposed model, the harmonic couplings, between dc-link and point of common coupling in different drives, are all analyzed in the multi-drive system. In the meantime, the effects of the small film dc-link capacitance and the nonlinear characteristic of the diode rectifier are considered. The detailed modeling procedure, the simulations and the lab experiment on a two-drive system including two cases, i.e. “conventional ° slim” and “slim ° slim”, are carried out to verify the proposed analysis method.
Cytosolic Ca2+ signalling in inflammatory neutrophils: implications for rheumatoid arthritis (Review). (1998)

Recognition of the ways in which neutrophil behaviour is regulated may be crucial for a full understanding of their role in inflammation and in rheumatoid arthritis. Although it is well established that changes in cytosolic free Ca2+ play a central role in triggering neutrophil responses, only recently has evidence accumulated which points strongly to the existence of two distinct Ca2+ pathways in neutrophils. One pathway is mediated by conventional agonists, such as formylated peptides, IL-8, C5a and PAF, and the other by cross-linking and immobilisation of surface receptors, such as integrins, and the Fc receptors, CD32 and CD16. In this review, we give evidence for these two signalling pathways in neutrophils, highlighting the roles of two Ca2+ storage and release organelles, one centrally located and stationary, and the other peripheral and mobile. We point out the significance of these two routes of Ca2+ signalling for the correct sequence of neutrophil responses, and suggest that aberration of this sequence could result in pathogenic neutrophil activation.
Sparse representations in unions of bases (2003)

The purpose of this correspondence is to generalize a result by Donoho and Huo and Elad and Bruckstein on sparse representations of signals in a union of two orthonormal bases for R/sup N/. We consider general (redundant) dictionaries for R/sup N/, and derive sufficient conditions for having unique sparse representations of signals in such dictionaries. The special case where the dictionary is given by the union of L/spl ges/2 orthonormal bases for R/sup N/ is studied in more detail. In particular, it is proved that the result of Donoho and Huo, concerning the replacement of the /spl lscr//sup 0/ optimization problem with a linear programming problem when searching for sparse representations, has an analog for dictionaries that may be highly redundant.
Neuropeptide imaging in rat spinal cord with MALDI-TOF MS: Method development for the application in pain-related disease studies (2017)

Spinal cord as a connection between brain and peripheral nervous system is an essential material for studying neural transmission, especially in pain-related research. This study was the first to investigate pain-related neuropeptide distribution in rat spinal cord using a matrix-assisted laser desorption ionization-time of flight imaging mass spectrometry (MALDI TOF MS) approach. The imaging workflow was evaluated and showed that MALDI TOF MS provides efficient resolution and robustness for neuropeptide imaging in rat spinal cord tissue. The imaging result showed that in naive rat spinal cord the molecular distribution of haeme, phosphatidylcholine, substance P and thymosin beta 4 were well in line with histological features. Three groups of pain-related neuropeptides, which are cleaved from prodynorphin, proenkephalin and protachykinin-1 proteins were detected. All these neuropeptides were found predominantly localized in the dorsal spinal cord and each group had unique distribution pattern. This study set the stage for future MALDI TOF MS application to elucidate signalling mechanism of pain-related diseases in small animal models.
A New Synthetic Compound, 2-OH, Enhances Interleukin-2 and Interferon-γ Gene Expression in Human Peripheral Blood Mononuclear Cells (2009)

A new synthetic compound, 6-hydroxy-2-tosylisoquinolin-1(2H)-one (2-OH), was selected for immunopharmacological activity tests. The effects of 2-OH on human peripheral blood mononuclear cell (PBMC) proliferation were determined by tritiated thymidine uptake. Compared to phytohemagglutinin (PHA; 5 microg/mL) stimulation, 2-OH significantly enhanced PBMC proliferation in a dose-dependent manner. The 50% enhancement activity (EC(50)) for 2-OH was 4.4+/-0.1 microM. In addition, effects of 2-OH on interleukin-2 (IL-2) and interferon-gamma (IFN-gamma) production in PBMC were determined by enzyme immunoassay. Results demonstrated that 2-OH stimulated IL-2 and IFN-gamma production in PBMC. Data from reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR indicated that IL-2 and IFN-gamma mRNA expression in PBMC could be induced by 2-OH. Therefore, 2-OH enhanced IL-2 and IFN-gamma production in PBMC by modulation their gene expression. We suggest that 2-OH may be an immunomodulatory agent.
Hydrolysis of ATP in chemical models. (1981)

Hydrolysis of ATP was found to be accelerated by the addition of hexadecyltrimethylammonium chloride (CTAC). The high acceleration was observed in the concentration below rather than above the critical micell concentration of CTAC. The catalytic effect was observed at pH's 5 and 8, while not significantly at pH 3.