gebhart/patrepeval huggingface dataset:
Abstract 617: Inhibitors of Beta-Catenin Signaling Limit Growth of Vascular Smooth Muscle Cells (2017)

Smooth muscle cell (SMC) growth is essential for artery formation during development and significantly contributes to neointima formation after vascular injury in adulthood. We recently showed, using a tissue-specific deletion and knock-in of mutant alleles, that beta-catenin (b-ctn) signaling function is essential for SMC growth and artery formation; moreover, protein interactions mediated by its C-terminus domain are required for assembly of the arterial wall, while b-ctn N-terminus interactions are dispensable. Inhibitors of b-ctn have been developed, but their effects on vascular SMC growth have not been fully tested. We hypothesize that inhibitors that disrupt protein interactions mediated by the b-ctn C-terminus domain will impair b-ctn signaling and limit growth of vascular SMCs. We evaluated growth of mouse aortic SMCs and human coronary artery SMCs in culture using AlamarBlue after exposure to increasing concentrations (0.01 to 10 micromolar) of several validated b-ctn inhibitors or vehicle control: PKF118-310 (disrupts the b-ctn/TCF interaction), ICG001 (disrupts the b-ctn C-terminus/CBP interaction), XAV939 (promotes the b-ctn destruction complex), and carnosic acid (disrupts the b-ctn N-terminus/BCL9 interaction). We also evaluated the effect of these inhibitors on b-ctn transcriptional activity in SMCs using a TOPflash reporter system. We found that PKF118-310 (p&lt;0.05 vs. vehicle), ICG001 (p&lt;0.05 vs. vehicle), and XAV939 (p&lt;0.05 vs. vehicle), but not carnosic acid, limit mouse (n=16 independent cultures) and human (n=8 independent cultures) SMC growth in a dose-response manner. PKF118-310 exhibited the most potent inhibitory effect. We also found that PKF118-310, ICG001, and XAV939, but not carnosic acid, inhibit b-ctn transcriptional activity in arterial SMCs in culture. In conclusion, pharmacological inhibition of b-ctn signaling, particularly blocking the b-ctn C-terminus output, inhibits growth of vascular SMCs in culture, providing a rationale to test these inhibitors in models of vascular injury as they hold promise as novel therapies for cardiovascular disease.
The Electronic Assessment of the Longitudinal Course of Bipolar Disorder: The ChronoRecord Software (2003)

Longitudinal studies are the optimal approach when investigating the highly variable course of bipolar disorder, but such studies are expensive, prone to reporting errors and to missing data. Automation of data collection may reduce such errors and improve data quality. The ChronoRecord, validated software that patients can install on a home computer to report mood, medications, sleep, life events, weight and menstrual data, has been designed to achieve such automation. In the trial of the ChronoRecord reported here, 80 of 96 (83 %) patients with bipolar disorder showed high acceptance of this computer-based system for self-report, entering daily recordings for a period of 3-months. This new technology, in addition to providing an accurate longitudinal record for research purposes, also facilitates on-going patient feedback and accurate study monitoring.
NoncapsulatedKlebsiella pneumoniaeBearing Mannose-Containing O Antigens Is Rapidly Eradicated from Mouse Lung and Triggers Cytokine Production by Macrophages following Opsonization with Surfactant Protein D (2005)

To better understand the relationship between the surface polysaccharides of pulmonary pathogens and components of the lung innate immune system, we employed selected serotypes of Klebsiella pneumoniae expressing distinct capsular polysaccharides and/or O antigen in a murine model of K. pneumoniae infection. In addition, we examined the effect of surfactant protein D (SP-D) on the cytokine response of human monocyte-derived macrophages to these serotypes in vitro. Noncapsulated mannose-containing O3 serotypes (K50/n and K55/n), which react efficiently with SP-D in vitro, triggered high levels of interleukin-1beta (IL-1beta) and IL-6 production. In vivo, they were more efficiently cleared from the lungs of mice but not from macrophage-depleted mice. They also were more efficiently internalized by alveolar macrophages in vivo. In contrast, galactose-containing O1 serotypes (K2/n and K21a/n), which interact poorly with SP-D, exhibited significantly lower cytokine production and less efficient pulmonary clearance and were ineffectively internalized by alveolar macrophages. These findings are consistent with in vitro results showing that production of IL-1beta and IL-6 mRNA and IL-6 protein by human macrophages exposed to mannose-bearing Klebsiella O serotypes is significantly increased by SP-D. Thus, survival of inhaled bacteria in the lung depends partially on the lipopolysaccharide structure of the bacteria and their interactions with innate immunity components. We speculate that an imbalance of host SP-D and therefore cytokine levels may result in high susceptibility of the host to the pathogen.
Photolithographic Patterning of Cytop with Limited Contact Angle Degradation (2018)

Cytop is a commercially available amorphous fluoropolymer with excellent characteristics including electric insulation, water and oil repellency, chemical resistance, and moisture-proof property, making it an attractive material as hydrophobic layers in electrowetting-on-dielectric (EWOD) devices. However, its highly hydrophobic surface makes it difficult for photoresists to be directly coated on the surface. To pattern Cytop, plasma treatment prior to applying photoresists is required to promote the adhesion between the photoresist and the Cytop coating. This approach inevitably causes hydrophobicity loss in the final EWOD devices. Thus, a damage-reduced recipe for Cytop patterning is urgently needed. In this paper, we first characterized the damage caused by two categories of surface treatment methods: plasma treatment and metal treatment. Parameters such as plasma gas source (Ar/O₂), plasma treatment time (0⁻600 s), metal target (Al/Cu/Cr/Au), metal deposition process (magnetron sputtering or e-beam evaporation) were varied. Film thickness, wettability, and roughness were quantified by ellipsometry measurements, contact angle measurements, and atom force microscope (AFM), respectively. We then evaluated the effectiveness of annealing in damage reduction. Experimental results show that: (1) annealing is necessary in restoring hydrophobicity as well as smoothing surfaces; (2) specified film thickness can be obtained by controlling plasma treatment time; (3) "Ar/O₂ plasma treatment + an AZ5214 soft mask + annealing" is a feasible recipe; (4) "an Al/Cu/Cr/Au hard mask + annealing" is feasible as well.
Dimethyl Bromomalonate (2007)

(1; R = Me) [868-26-8] C5H7BrO4 (MW 211.02) InChI = 1S/C5H7BrO4/c1-9-4(7)3(6)5(8)10-2/h3H,1-2H3 InChIKey = NEMOJKROKMMQBQ-UHFFFAOYSA-N (2; R = Et) [685-87-0] C7H11BrO4 (MW 239.08) InChI = 1S/C7H11BrO4/c1-3-11-6(9)5(8)7(10)12-4-2/h5H,3-4H2,1-2H3 InChIKey = FNJVDWXUKLTFFL-UHFFFAOYSA-N (3; R = t-Bu) [15960-79-9] C11H19BrO4 (MW 295.20) InChI = 1S/C11H19BrO4/c1-10(2,3)15-8(13)7(12)9(14)16-11(4,5)6/h7H,1-6H3 InChIKey = MXQKZYBGLSKJNU-UHFFFAOYSA-N (cyclopropanation of Michael acceptors;1, 2 synthesis of vinylogous urethanes from thioamides via the Eschenmoser sulfide contraction3-5) Physical Data: (1) bp 112.5–113 °C/15 mmHg.6 (2) bp 150–152 °C/25 mmHg.6 (3) bp 120–125 °C/11 mmHg.7 Form Supplied in: (1) technical grade, ∼90% purity; (2) technical grade, 85–95% purity, contains varying amounts of diethyl malonate and diethyl dibromomalonate. Analysis of Reagent Purity: (1) 1H NMR (CDCl3) δ 3.85 (6H, s), 4.87 (1H, s);8 (2) 1H NMR (CCl4) δ 1.34 (6H, t, J = 7 Hz), 4.28 (4H, q, J = 7 Hz), 4.72 (1H, s); IR (CCl4) 1750 cm−1; (3) 1H NMR (CDCl3) δ 1.45 (18H, s), 4.6 (1H, s);9 13C NMR (CDCl3) δ 27.4, 45.4, 83.5, 163.3;9 IR (KBr) 1756 cm−1;9 IR (CCl4) 1765, 1740 cm−1;10 IR (film) 1735 cm−1.4 Preparative Methods: 1: by treatment of Malonic Acid with Bromine in diethyl ether followed by esterification with HCl in methanol;11 by electrolytic bromination of dimethyl malonate with Magnesium Bromide or Copper(II) Bromide and Sodium Methoxide in acetonitrile–water at 2–3 °C.12 2: by light-induced bromination of Diethyl Malonate with bromine in carbon tetrachloride;13 by treatment of diethyl malonate with bromotrichloromethane and 1,8‐Diazabicyclo[5.4.0]undec‐7‐ene in benzene at 0 °C.14 3: by bromination of Malonic Acid with bromine in diethyl ether at rt followed by sulfuric acid catalyzed esterification with Isobutene in diethyl ether at rt;7 by bromination of di-t-butyl malonate with bromine and Calcium Carbonate in chloroform at rt followed by reflux;7 by lithiation of di-t-butyl malonate with n‐Butyllithium in THF at −78 °C followed by addition of bromine and allowing reaction to warm to rt;10 by lithiation of di-t-butyl malonate with n-butyllithium in THF at −78 °C, addition of Chlorotrimethylsilane, warming to rt, and treatment of the resulting trimethylsilyl ketene acetal solution with bromine in carbon tetrachloride.4 4 Chloro, bromo, and iodo diethyl malonates have been prepared by microwave-induced α-halogenation of diethyl malonate in a one-pot, two-step reaction. The sequence involves MW α-tosylation of diethyl malonate using Koser's reagent [hydroxy(tosyloxy)iodo]benzene (HTIB) followed by reaction of the resulting tosylate under MW irradiation with MgX2 (X = Cl, Br, I).25
Superplastic Behavior of a Fine Grained AZ61 Alloy Processed by Large Strain Hot Rolling (2004)

A processing route based on conventional hot rolling has been recently developed to induce significant grain refinement in Mg alloys. The simplicity and rapidity of the processing route as well as the fact that conventional rolling is used, may allow it to be put into practice successfully in industry. This method consists of only two to three rolling passes, each producing a large thickness reduction, and intermediate annealings of 5 minutes duration. The resulting microstructure is mainly formed by very fine grains. Tensile tests at different temperatures and strain rates were performed in order to analyse the mechanical behaviour of the processed AZ61 alloy under different testing conditions. Microstructure and texture evolution during deformation were examined by optical microscopy (OM) and X-ray diffraction, respectively. It is shown that the microstructures developed by large strain hot rolling are capable of exhibiting significant superplastic elongations at moderate to low temperatures. Stress exponents close to 2 were measured during deformation under optimum superplastic conditions. Additionally, grains remained equiaxed and a significant decrease in the texture intensity is observed. This is consistent with the predominance of grain boundary sliding as the main deformation mechanism responsible for superplasticity
Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology (2022)

Identifying factors secreted by multiple myeloma (MM) cells that may contribute to MM tumor biology and progression is of the utmost importance. In this study, hepatoma-derived growth factor (HDGF) was identified as a protein present in extracellular vesicles (EVs) released from human MM cell lines (HMCLs). Investigation of the role of HDGF in MM cell biology revealed lower proliferation of HMCLs following HDGF knockdown and AKT phosphorylation following the addition of exogenous HDGF. Metabolic analysis demonstrated that HDGF enhances the already high glycolytic levels of HMCLs and significantly lowers mitochondrial respiration, indicating that HDGF may play a role in myeloma cell survival and/or act in a paracrine manner on cells in the bone marrow (BM) tumor microenvironment (ME). Indeed, HDGF polarizes macrophages to an M1-like phenotype and phenotypically alters naïve CD14+ monocytes to resemble myeloid-derived suppressor cells which are functionally suppressive. In summary, HDGF is a novel factor in MM biology and may function to both maintain MM cell viability as well as modify the tumor ME.
Tanshinone IIA Inhibits VEGF Secretion and HIF-1α Expression in Cultured Human Retinal Pigment Epithelial Cells under Hypoxia (2017)

Tanshinone IIA could be explored as a new potential candidate for treating wet AMD.
Using temporal detrending to observe the spatial correlation of traffic (2017)

This empirical study sheds light on the spatial correlation of traffic links under different traffic regimes. We mimic the behavior of real traffic by pinpointing the spatial correlation between 140 freeway traffic links in a major sub-network of the Minneapolis-St. Paul freeway system with a grid-like network topology. This topology enables us to juxtapose the positive and negative correlation between links, which has been overlooked in short-term traffic forecasting models. To accurately and reliably measure the correlation between traffic links, we develop an algorithm that eliminates temporal trends in three dimensions: (1) hourly dimension, (2) weekly dimension, and (3) system dimension for each link. The spatial correlation of traffic links exhibits a stronger negative correlation in rush hours, when congestion affects route choice. Although this correlation occurs mostly in parallel links, it is also observed upstream, where travelers receive information and are able to switch to substitute paths. Irrespective of the time-of-day and day-of-week, a strong positive correlation is witnessed between upstream and downstream links. This correlation is stronger in uncongested regimes, as traffic flow passes through consecutive links more quickly and there is no congestion effect to shift or stall traffic. The extracted spatial correlation structure can augment the accuracy of short-term traffic forecasting models.
Re‐engineering specificity in 1,3‐1, 4‐β‐glucanase to accept branched xyloglucan substrates (2010)

Family 16 carbohydrate active enzyme members Bacillus licheniformis 1,3-1,4-β-glucanase and Populus tremula x tremuloides xyloglucan endotransglycosylase (XET16-34) are highly structurally related but display different substrate specificities. Although the first binds linear gluco-oligosaccharides, the second binds branched xylogluco-oligosaccharides. Prior engineered nucleophile mutants of both enzymes are glycosynthases that catalyze the condensation between a glycosyl fluoride donor and a glycoside acceptor. With the aim of expanding the glycosynthase technology to produce designer oligosaccharides consisting of hybrids between branched xylogluco- and linear gluco-oligosaccharides, enzyme engineering on the negative subsites of 1,3-1,4-β-glucanase to accept branched substrates has been undertaken. Removal of the 1,3-1,4-β-glucanase major loop and replacement with that of XET16-34 to open the binding cleft resulted in a folded protein, which still maintained some β-glucan hydrolase activity, but the corresponding nucleophile mutant did not display glycosynthase activity with either linear or branched glycosyl donors. Next, point mutations of the 1,3-1,4-β-glucanase β-sheets forming the binding site cleft were mutated to resemble XET16-34 residues. The final chimeric protein acquired binding affinity for xyloglucan and did not bind β-glucan. Therefore, binding specificity has been re-engineered, but affinity was low and the nucleophile mutant of the chimeric enzyme did not show glycosynthase activity to produce the target hybrid oligosaccharides. Structural analysis by X-ray crystallography explains these results in terms of changes in the protein structure and highlights further engineering approaches toward introducing the desired activity.
Monodisperse Functional Colloidosomes with Tailored Nanoparticle Shells (2011)

We report the assembly of monodisperse colloidosomes containing a wide range of functional nanoparticles in the outer shell using a double emulsion templating method in a microfluidic device. By selecting nanoparticles of specific functionalities, hollow capsules with inert, magnetic, photocatalytic, and potentially biocompatible and piezoelectric shells are easily obtained. Proper control over the surface chemistry of the nanoparticles forming the shell and of the liquid interfaces involved is key to enable the assembly of colloidosomes using this double emulsification route.
Palladium‐Catalyzed, Ligand‐Controlled Chemoselective Oxidative Coupling Reactions of Benzene Derivatives with Acrylamides under an Oxygen Atmosphere (2012)

Under an oxygen umbrella: The Pd-catalyzed aerobic oxidative coupling of benzene derivatives with acrylates provides an efficient and atom-economical route to cinnamamides (see scheme). Readily available starting materials are used and molecular oxygen serves as the sole oxidant. By using this system, the chemoselective oxidative coupling reaction can provide either monoarylation or diarylation products simply by changing the molar ratio of Pd/acacH.
Effects of Social Factors and Team Dynamics on Adoption of Collaborative Robot Autonomy (2021)

As automation becomes more prevalent, the fear of job loss due to automation increases [22]. Workers may not be amenable to working with a robotic co-worker due to a negative perception of the technology. The attitudes of workers towards automation are influenced by a variety of complex and multi-faceted factors such as intention to use, perceived usefulness and other external variables [15]. In an analog manufacturing environment, we explore how these various factors influence an individual's willingness to work with a robot over a human co-worker in a collaborative Lego building task. We specifically explore how this willingness is affected by: 1) the level of social rapport established between the individual and his or her human co-worker, 2) the anthropomorphic qualities of the robot, and 3) factors including trust, fluency and personality traits. Our results show that a participant's willingness to work with automation decreased due to lower perceived team fluency (p=0.045), rapport established between a participant and their co-worker (p=0.003), the gender of the participant being male (p=0.041), and a higher inherent trust in people (p=0.018).
Primate physiologic data acquisition and analysis for space shuttle (1988)

More powerful and more flexible data acquisition, storage, and analysis systems are needed to gain a better understanding of animal (and thus human) physiology in the microgravity environment of space. In view of this, a physiologic acquisition and telemetry system (PATS), a multichannel data acquisition, telemetry, storage, and analysis system, is being developed. PATS is scheduled for use in the Rhesus Research Facility, a joint US/French experiment to be flown aboard Spacelab. PATS is designed to acquire data from units implanted in the abdominal cavities of rhesus monkeys carried in cages on board Spacelab. An implanted DATS (data acquisition and telemetry subsystem) unit permits physiologic parameters to be measured on the test animal with minimum physical restraints and eliminates the need for percutaneous leads that are often the source of infection and discomfort. To obtain feedback from the scientists using the flight version of PATS, a PATS simulator system (PATS-S), separate and distinct from the breadboard system, has been designed and fabricated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tissue Engineering in Dermatology (2009)

Editorial: Tissue Engineering: A Rapidly Growing Field of Skin Research: Lademann, J. Fluhr, J.W. Preface: Tissue Engineering in Dermatology: Fluhr, J.W. Elsner, P. Stem Cells and Tissue-Engineered Skin: Charruyer, A. Ghadially, R. Whole-Cell Bioprocessing of Human Fetal Cells for Tissue Engineering of Skin: Applegate, L.A. Scaletta, C. Hirt-Burri, N. Raffoul, W. Pioletti, D. Evaluation of Biocompatibility and Cytotoxicity Using Keratinocyte and Fibroblast Cultures: Wiegand, C. Hipler, U.-C. Tissue Engineering for Cutaneous Wounds: Selecting the Proper Time and Space for Growth Factors, Cells and the Extracellular Matrix: Macri, L. Clark, R.A.F. Skin Substitutes and Wound Healing: Auger, F.A. Lacroix, D. Germain, L. In vitro Irritation Models and Immune Reactions: Gibbs, S. Melanocytes: From Morphology to Application: Santiago-Walker, A. Li, L. Haass, N.K. Herlyn, M. Author Index Subject Index.
Smart Cloud Marketplace - Agent-Based Platform for Trading Cloud Services (2014)

Cloud computing services are rapidly gaining popularity with more and more businesses actively migrating to the cloud, and many new cloud providers emerging. In such circumstances, there is a need for a market platform that allows for automated trading of cloud services between numerous independent users. Therefore, in this paper we propose Smart Cloud Marketplace (SCM) as a platform for trading cloud services based on intelligent agent technology. Software agents represent the cloud service consumers and providers in the marketplace, and make intelligent decisions on their behalf. The platform enables participants to use different trading policies in order to automate and improve the efficiency of resource trading. Moreover, SCM supports multimarket trading, where different market mechanisms can be deployed. We have used the SCM platform to test different market mechanisms developed within our research group. Our experimental evaluation demonstrates that Smart Cloud Marketplace is a useful, flexible and effective platform for conducting experiments and ultimately for trading cloud services.
Comparative analysis of transcriptomes in aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing (2016)

Ephedra plants are taxonomically classified as gymnosperms, and are medicinally important as the botanical origin of crude drugs and as bioresources that contain pharmacologically active chemicals. Here we show a comparative analysis of the transcriptomes of aerial stems and roots of Ephedra sinica based on high-throughput mRNA sequencing by RNA-Seq. De novo assembly of short cDNA sequence reads generated 23,358, 13,373, and 28,579 contigs longer than 200 bases from aerial stems, roots, or both aerial stems and roots, respectively. The presumed functions encoded by these contig sequences were annotated by BLAST (blastx). Subsequently, these contigs were classified based on gene ontology slims, Enzyme Commission numbers, and the InterPro database. Furthermore, comparative gene expression analysis was performed between aerial stems and roots. These transcriptome analyses revealed differences and similarities between the transcriptomes of aerial stems and roots in E. sinica. Deep transcriptome sequencing of Ephedra should open the door to molecular biological studies based on the entire transcriptome, tissue- or organ-specific transcriptomes, or targeted genes of interest.
Gluten intolerance: chemistry, celiac-toxicity, and detection of prolamins in foods. (1990)

Cereal scientists and health scientists (including dietitians and gastroenterologists) mean different things when they refer to «gluten». This article sorts out for both groups the true situation regarding «gluten intolerance» in the context of celiac disease