gebhart/patrepeval huggingface dataset:
Human Serum Albumin Bearing Covalently Attached Iron(II) Porphyrins as O2-Coordination Sites (2004)

Tetrakis{(alpha,alpha,alpha,alpha-o-pivalamido)phenyl}porphinatoiron(II) with a bifunctional tail possessing an axially coordinated imidazolyl group and a protein attachable succinimidyl(glutamyl) group (FeP-GluSu) has been synthesized. It can efficiently react with the lysine residues of recombinant human serum albumin (rHSA), giving a new albumin-heme conjugate [rHSA(FeP-Glu)]. MALDI-TOFMS showed a distinct molecular ion peak at m/z 70 643, which indicates that three FeP-Glu molecules were covalently linked to the rHSA scaffold. The binding number of FeP-Glu is approximately three (mol/mol) and independent of the mixing ratio. The CD spectrum and Native PAGE revealed that the albumin structure remained unaltered after the covalent bonding of the hemes. This rHSA(FeP-Glu) conjugate can bind and release O2 reversibly under physiological conditions (pH 7.3, 37 degrees C) in the same manner as hemoglobin and myoglobin. The O2-adduct complex had a remarkably long lifetime (tau(1/2): 5 h). The O2-binding affinity [P(1/2)O2: 27 Torr] was identical to that of human red cells. Laser flash photolysis experiments gave the O2- and CO-association rate constants and suggested that there are two different geometries of the imidazole binding to the central ion.
Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening (2015)

Janus kinase inhibitors represent a promising opportunity for the pharmaceutical intervention of various inflammatory and oncological indications. Subtype selective inhibition of these enzymes, however, is still a very challenging goal. In this study, a novel, customized virtual screening protocol was developed with the intention of providing an efficient tool for the discovery of subtype selective JAK2 inhibitors. The screening protocol involves protein ensemble-based docking calculations combined with an Interaction Fingerprint (IFP) based scoring scheme for estimating ligand affinities and selectivities, respectively. The methodology was validated in retrospective studies and was applied prospectively to screen a large database of commercially available compounds. Six compounds were identified and confirmed in vitro, with an indazole-based hit exhibiting promising selectivity for JAK2 vs JAK1. Having demonstrated that the described methodology is capable of identifying subtype selective chemical starting points with a favorable hit rate (11%), we believe that the presented screening concept can be useful for other kinase targets with challenging selectivity profiles.
Introduction To Fluorescence And Photophysics (2003)

Emission of light in the form of fluorescence often accompanies deactivation of an electronically excited species. Fluorescence is defined as the radiative transition between two electronic states of the same spin multiplicity. Most organic molecules have paired electrons in their ground state molecular orbital configuration. The spins are balanced (e.g., s, = +5 and s2 = —5, S = £s = 0) and the spin multiplicity (Ms = 2S + 1 = 1) is singlet. Alternatively, inversion of the spin of the excited electron results in the two unpaired electrons having the same spin orientation. The overall spin S is 1 (s, = +i, s2 = +5), the spin multiplicity (Ms = 2S + 1) is 3, and a triplet state results. Most commonly, fluorescence refers to singlet-singlet transitions, especially the transition between the lowest, or first, excited singlet state (SO and the ground state (S0). Other types of less common fluorescence processes do occur, such as that from the second (S2) excited singlet state, and the doublet-doublet fluorescence exhibited in the radiative relaxation between excited and ground state free radicals (one unpaired electron, S = 5, Ms = 2S 41 = 2). However, this introduction will focus on S,-S0 fluorescence, which is by far the most common type.
Phenotyping and Genotyping of Antibiotic-Resistant Escherichia coli Isolated from a Natural River Basin (2008)

Scientists have become increasingly concerned about the occurrence of antibacterial resistance in the environment. In this study, Escherichia coli resistant to one or more antibiotics among nine antibiotics was screened from Wenyu River Basin in Beijing, China, with mean frequency of 48.7 +/- 8.7% of 388 isolates in summer and 47 +/- 6% of 236 isolates in winter. The mean multiantibiotic resistance (MAR) index in summer was 0.11 +/- 0.03, slightly lower than that (0.14 +/- 0.04) in winter. Most frequent resistance appeared for sulfonamides, tetracycline, and ampicillin. The distribution of 20 tetracycline, three sulfonamide, and three beta-lactam resistance genes was assessed in the resistant isolates. While 97% of the ampicillin (AMP) resistant mechanism could be explained by the resistance gene TEM, 90% of the tetracycline (TC) and 96% of the sulfonamide (SXT) resistances could be explained by tet(A), tet(B), tet(M), and their combinations and sul(I), sul(II), sul(III), and their combinations, respectively. tet(M), a tetracycline-resistant gene originally detected in Gram-positive bacteria, and its combinations with tet(A) or tet(B) were first detected in E. coli isolated from a natural river basin, suggesting that tet(M) in E. coli might have been transferred from other bacterial species through horizontal gene transfer, which was supported by the fact that no tet(M) was detected in the isolates of human and chicken sources, except for only one isolate from swine. The source of sulfonamide-resistant E. coli in the river was supposed to be mainly from humans, based on a comparison of the sulfonamide resistance genotypes in animals and humans.
ChemInform Abstract: A General Method for Suzuki—Miyaura Coupling Reactions Using Lithium Triisopropyl Borates. (2012)

Abstract The title borates are used as nucleophiles for the coupling reaction.
Glucose depletion activates mmu-miR-466h-5p expression through oxidative stress and inhibition of histone deacetylation (2012)

MicroRNAs (miRNAs) are involved in the regulation of multiple cellular processes. Changes of miRNA expression have been linked to the development of various diseases including cancer, but the molecular events leading to these changes at different physiological conditions are not well characterized. Here we examined the intracellular events responsible for the miR-466h-5p activation in mouse cells exposed to glucose deprivation. MiR-466h-5p is a member of the miR-297-669 cluster located in intron 10 of Sfmbt2 gene on mouse chromosome 2 and has a pro-apoptotic role. We showed that the time-dependant activation of miR-466h-5p, miR-669c and the Sfmbt2 gene followed the inhibition of histone deacetylation caused by glucose deprivation-induced oxidative stress. This oxidative stress causes the accumulation of reactive oxygen species (ROS) and depletion of reduced glutathione (GSH) that together inhibited histone deacetylases (HDACs) activity, reduced protein levels of HDAC2 and increased acetylation in miR-466h-5p promoter region, which led to the activation of this miRNA. Based on this study and previous work, we suggest a possible role of miR-466h-5p (and miR 297-669 cluster) in the cells during toxic metabolites accumulation. Improved characterization of the molecular events that lead to the activation of miR-466h-5p may provide a better understanding of the relation between cellular environment and miRNA activation.
Mast Cell Protease 5 Mediates Ischemia-Reperfusion Injury of Mouse Skeletal Muscle (2005)

Ischemia with subsequent reperfusion (IR) injury is a significant clinical problem that occurs after physical and surgical trauma, myocardial infarction, and organ transplantation. IR injury of mouse skeletal muscle depends on the presence of both natural IgM and an intact C pathway. Disruption of the skeletal muscle architecture and permeability also requires mast cell (MC) participation, as revealed by the fact that IR injury is markedly reduced in c-kit defective, MC-deficient mouse strains. In this study, we sought to identify the pathobiologic MC products expressed in IR injury using transgenic mouse strains with normal MC development, except for the lack of a particular MC-derived mediator. Histologic analysis of skeletal muscle from BALB/c and C57BL/6 mice revealed a strong positive correlation (R(2) = 0.85) between the extent of IR injury and the level of MC degranulation. Linkage between C activation and MC degranulation was demonstrated in mice lacking C4, in which only limited MC degranulation and muscle injury were apparent. No reduction in injury was observed in transgenic mice lacking leukotriene C(4) synthase, hemopoietic PGD(2) synthase, N-deacetylase/N-sulfotransferase-2 (enzyme involved in heparin biosynthesis), or mouse MC protease (mMCP) 1. In contrast, muscle injury was significantly attenuated in mMCP-5-null mice. The MCs that reside in skeletal muscle contain abundant amounts of mMCP-5 which is the serine protease that is most similar in sequence to human MC chymase. We now report a cytotoxic activity associated with a MC-specific protease and demonstrate that mMCP-5 is critical for irreversible IR injury of skeletal muscle.
Floral gene resources from basal angiosperms for comparative genomics research (2005)

Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways.
Electrochemiluminescent Cells Based on Zeolite‐Encapsulated Host–Guest Systems: Encapsulated Ruthenium Tris‐bipyridyl (2007)

An electrochemiluminescent cell has been developed that has an active layer consisting of ruthenium tris-bipyridyl encapsulated inside zeolite Y supercages. Operation of the cell requires the addition of polyethylene glycol as the solid electrolyte. The cell, which exhibits electrical conductivity behavior typical of a semiconductor, has an optimum operating voltage of 3 V. Ion exchange of sodium by cesium and vapor deposition of calcium metal inside the zeolite pores enhance the electrochemiluminescent efficiency of the cell by a factor of 4.
A search for new physics in dijet mass and angular distributions inppcollisions at \sqrt{s}=7 TeV measured with the ATLAS detector (2011)

A search for new interactions and resonances produced in LHC proton-proton (pp) collisions at a centre-of-mass energy √s = 7 TeV was performed with the ATLAS detector. Using a dataset with an integrated luminosity of 36 pb -1, dijet mass and angular distributions were measured up to dijet masses of ∼3.5TeV and were found to be in good agreement with Standard Model predictions. This analysis sets limits at 95% CL on various models for new physics: an excited quark is excluded for mass between 0.60 and 2.64 TeV, an axigluon hypothesis is excluded for axigluon masses between 0.60 and 2.10 TeV and quantum black holes are excluded in models with six extra space-time dimensions for quantum gravity scales between 0.75 and 3.67 TeV. Production cross section limits as a function of dijet mass are set using a simplified Gaussian signal model to facilitate comparisons with other hypotheses. Analysis of the dijet angular distribution using a novel technique simultaneously employing the dijet mass excludes quark contact interactions with a compositeness scale A below 9.5 TeV.
OP-VENT (2022)

A mechanical ventilator keeps a patient with respiratory failure alive by pumping precisely controlled amounts of air (or an air/O2 mixture) at controlled pressure into the patient's lungs [3, 5]. During intake (inspiration), the ventilator meters the flow of air and the duration of the flow to deliver a controlled tidal volume of air (typically 50 to 800 mL). During the exhaust (expiration) phase, the flow is turned off and a path is opened to allow the patient to exhale to the atmosphere - possibly with a positive pressure maintained at the end of the expiratory period (PEEP). The timing of the breaths can be entirely managed by the ventilator, or a new breath can be initiated by the patient.
ChemInform Abstract: SULFUR AS A REGIOCHEMICAL CONTROL ELEMENT. CYCLOADDITIONS OF 2‐ALKOXY(ACYLOXY)‐3‐ALKYL(ARYL)THIOBUTA‐1,3‐DIENES (1980)

Abstract Der Einfluß von Sund O, Substituenten sowie von Lewissäure‐Katalysatoren (Silicagel, BF 3 ‐Et2O, MgBr 2 ) auf die Regioselektivität der Produktverteilung bei verschiedenen Diels‐Alder‐Additionen wird untersucht.
Does laser surface texturing really have a negative impact on the fatigue lifetime of mechanical components? (2021)

Abstract Laser surface texturing (LST) has been proven to improve the tribological performance of machine elements. The micro-scale patterns manufactured by LST may act as lubricant reservoirs, thus supplying oil when encountering insufficient lubrication. However, not many studies have investigated the use of LST in the boundary lubrication regime, likely due to concerns of higher contact stresses that can occur with the increasing surface roughness. This study aims to examine the influence of LST on the fatigue lifetime of thrust rolling bearings under boundary lubrication. A series of periodic patterns were produced on the thrust rolling bearings, using two geometrically different designs, namely cross and dimple patterns. Base oil ISO VG 100 mixed with 0.05 wt% P of zinc dialkyldithiophosphate (ZDDP) was supplied. The bearings with cross patterns reduce the wear loss by two orders of magnitude. The patterns not only retain lubricant in the textured pockets but also enhance the formation of an anti-wear tribofilm. The tribofilm generation may be improved by the higher contact stresses that occur when using the textured surface. Therefore, in contrast to the negative concerns, the ball bearings with cross patterns were instead found to increase the fatigue life by a factor of three.
EOSC-Life A common environment that can run cross-RIs workflows (2022)

Research in the communities behind the BMS RIs relies on a large and diverse set of software tools and computational workflows that are often not easily reusable outside their domain or community of origin. The core purpose of WP2 is to make these tools and workflows Findable, Accessible, Interoperable and Reusable (FAIR) in the European Open Science Cloud (EOSC), so that users across the BMS RIs, as well as the broad scientific community, can take full advantage of the EOSC through a common set of resources and environment. This deliverable reports on the implementation of the WP2 roadmap to create such an environment supporting the deployment of tools and workflows from different domains of the life sciences in the EOSC.
Model-Driven Sensing-Node Selection and Power Allocation for Tracking Maneuvering Targets in Perceptive Mobile Networks (2023)

Maneuvering target tracking will be an important service of future wireless networks to assist innovative applications such as intelligent transportation. However, tracking maneuvering targets by cellular networks faces many challenges. For example, the dense network and high-speed targets make the selection of the sensing nodes (SNs) and the associated power allocation very challenging. Existing methods demonstrated engaging performance, but with high computational complexity. In this paper, we propose a model-driven deep learning (DL)-based approach for SN selection. To this end, we first propose an iterative SN selection method by jointly exploiting the majorization-minimization (MM) framework and the alternating direction method of multipliers (ADMM). Then, we unfold the iterative algorithm as a deep neural network and prove its convergence. The proposed method achieves lower computational complexity, because the number of layers is less than the number of iterations required by the original algorithm, and each layer only involves simple matrix-vector additions/multiplications. Finally, we propose an efficient power allocation method based on fixed point (FP) water filling and solve the joint SN selection and power allocation problem under the alternative optimization framework. Simulation results show that the proposed method achieves better performance than the conventional optimization-based methods with much lower computational complexity.
In Vivo Evidence of Angiogenesis Induced by Transcription Factor Ets-1 (2004)

The present study demonstrated that ets-1 regulated angiogenesis through the induction of angiogenic growth factors (VEGF and HGF). Overexpression of ets may provide a new therapeutic strategy to treat peripheral arterial disease.
Myogenesis in primary cell cultures from larvae of the abalone, Haliotis rufescens. (1994)

Myogenesis culminating in the differentiation of contracting myocytes occurs in primary cell cultures derived from premyogenic trochophore and early veliger larvae of Haliotis rufescens (red abalone, gastropod mollusc). No detectable muscle cells were present at the start of the primary cultures. Onset and organization of myofibrillogenesis in culture (revealed by histochemical and immunohistochemical detection of filamentous actin, myosin, and desmin) generally paralleled those of smooth muscle development in vivo, although development of cells with striated sarcomeres was occasionally observed in culture, but not in the intact larvae. Most of the muscle cells that developed in culture were mononucleate, although some multinucleate syncytia were observed. Dissociated larval cells remained viable up to 12 weeks, exhibiting an average of one to two divisions in the first six days, and attachment of approximately 6 to 8% of the original population. Cell culture and in vitro myogenesis of Haliotis myoblasts and myocytes will facilitate studies of the molecular mechanisms controlling early muscle development, and should provide a useful model system for biotechnological improvement of the abalone.
Excimer laser micropatterning of freestanding thermo-responsive hydrogel layers for cells-on-chip applications (2012)

We report a novel reliable and repeatable technologic manufacturing protocol for the realization of micro-patterned freestanding hydrogel layers based on thermo-responsive poly-(N-isopropyl)acrylamide (PNIPAAm), which have potential to be employed as temperature-triggered smart surfaces for cells-on-chip applications. PNIPAAm-based films with controlled mechanical properties and different thicknesses (100–300 µm thickness) were prepared by injection compression moulding at room temperature. A 9 × 9 array of 20 µm diameter through-holes is machined by means of the KrF excimer laser on dry PNIPAAm films which are physically attached to flat polyvinyl chloride (PVC) substrates. Machining parameters, such as fluence and number of shots, are optimized in order to achieve highly resolved features. Micro-structured freestanding films are then easily obtained after hydrogels are detached from PVC by gradually promoting the film swelling in ethanol. In the PNIPAAm water-swollen state, the machined holes' diameter approaches a slight larger value (30 µm) according to the measured hydrogel swelling ratio. Thermo-responsive behaviour and through-hole tapering characterization are carried out by metrology measurements using an optical inverted and confocal microscope setup, respectively. After the temperature of freestanding films is raised above 32 °C, we observe that the shrinkage of the whole through-hole array occurs, thus reducing the holes' diameter to less than a half its original size (about 15 µm) as a consequence of the film dehydration. Different holes' diameters (10 and 30 µm) are also obtained on dry hydrogel employing suitable projection masks, showing similar shrinking behaviour when hydrated and undergone thermo-response tests. Thermo-responsive PNIPAAm-based freestanding layers could then be integrated with other suitable micro-fabricated thermoplastic components in order to preliminary test their feasibility in operating as temperature-activated components in the frame of the development of microfluidic devices in multilayer hybrid materials.
1st international workshop on user modeling from social media (2012)

Massive amounts of data are being generated on social media sites, such as Twitter and Facebook. People from all walks of life share data about social events, express opinions, discuss their interests, publicize businesses, recommend products, and, explicitly or implicitly, reveal personal information. This workshop will focus on the use of social media data for creating models of individual users from the content that they publish. Deeper understanding of user behavior and associated attributes can benefit a wide range of intelligent applications, such as social recommender systems and expert finders, as well as provide the foundation in support of novel user interfaces (e.g., actively engaging the crowd in mixed-initiative question-answering systems). These applications and interfaces may offer significant benefits to users across a wide variety of domains, such as retail, government, healthcare and education. User modeling from public social media data may also reveal information that users would prefer to keep private. Such concerns are particularly important because individuals do not have complete control over the information they share about themselves. For example, friends of a user may inadvertently divulge private information about that user in their own posts. In this workshop we will also discuss possible mechanisms that users might employ to monitor what information has been revealed about themselves on social media and obfuscate any sensitive information that has been accidentally revealed.
Position/Force Control of Multi-Axis Robot Manipulator based on the TDOF Robust Servo Controller for Each Joint (1992)

The aim of this paper is mainly to demonstrate the efficacy of our robot control method without using non-linear compensation using the inverse dynamics. This method is based on the modern Two-Degrees-Of-Freedom (TDOF) robust position servosystem for each joint which has extremely high servo stiffness. We will show the experimental results of various kinds of robot motion controls using the lifesize 6-axis manipulator and DSP based controller.
Radical Cyclizations of Acylgermane Oxime Ethers and Hydrazones:  Direct Routes to Cyclic Hydrazones and Oximes (1998)

Efficient syntheses of ω-halo-, phenylseleno-, and vinylacylgermane hydrazones and oxime ethers have been developed, and the radical cyclizations of these substrates have been studied. The preparation of substituted triphenylacylgermanes has been improved through a copper-mediated coupling of acid chlorides and LiGePh3. Condensation of various acylgermanes with O-benzyl hydroxylamine or N,N-dimethylhydrazine efficiently generates the new acceptor systems, which undergo 5-exo cyclizations in good yields. The acylgermane hydrazone and -oxime ether radicals have cyclization rate constants of about 107 s-1 and are thus better acceptors than the parent acylgermanes.
Macroscopic Origin of Circular Dichroism Effects by Alignment of Self‐Assembled Fibers in Solution (2007)

In Reih' und Glied: Durch Konvektion werden in klaren, nichtviskosen verdünnten Lösungen supramolekulare Aggregate gebildet (siehe Bild). Die Ausrichtung erzeugt einen Lineardichroismus, der zu Artefakten in Circulardichroismusmessungen führt.