gebhart/patrepeval huggingface dataset:
Functional Profiling Using the Saccharomyces Genome Deletion Project Collections (2016)

The ability to measure and quantify the fitness of an entire organism requires considerably more complex approaches than simply using traditional "omic" methods that examine, for example, the abundance of RNA transcripts, proteins, or metabolites. The yeast deletion collections represent the only systematic, comprehensive set of null alleles for any organism in which such fitness measurements can be assayed. Generated by the Saccharomyces Genome Deletion Project, these collections allow the systematic and parallel analysis of gene functions using any measurable phenotype. The unique 20-bp molecular barcodes engineered into the genome of each deletion strain facilitate the massively parallel analysis of individual fitness. Here, we present functional genomic protocols for use with the yeast deletion collections. We describe how to maintain, propagate, and store the deletion collections and how to perform growth fitness assays on single and parallel screening platforms. Phenotypic fitness analyses of the yeast mutants, described in brief here, provide important insights into biological functions, mechanisms of drug action, and response to environmental stresses. It is important to bear in mind that the specific assays described in this protocol represent some of the many ways in which these collections can be assayed, and in this description particular attention is paid to maximizing throughput using growth as the phenotypic measure.
An intraductal human-in-mouse transplantation model mimics the subtypes of ductal carcinoma in situ (2009)

The intraductal HIM transplantation model provides an invaluable tool that mimics human breast heterogeneity at the noninvasive stages and allows the study of the distinct molecular and cellular mechanisms of breast cancer progression.
The Family of Protein Kinase C: Its Molecular Heterogeneity and Differential Expression (1988)

Although protein kinase C (PKC) was once considered as a single entity (Nishizuka 1984), molecular cloning and enzymological analysis have revealed the existence of multiple subspecies of PKC in a number of mammalian tissues. These subspecies have a common structure closely related to, yet slightly different from, one another. The relative distribution of PKC subspecies varies markedly with different areas of tissues and cell types examined. It is tempting to surmise that each member of this family has a specific function in the various cellular processes that occur during cell-to-cell communication. The heterogeneity of the members of the PKC family is briefly summarized in this paper. The integrated nomenclature used herein for the multiple PKC subspecies reported from various laboratories is given in Table 1.
Effect of In Vitro Passaging on the Stem Cell-Related Properties of Tendon-Derived Stem Cells—Implications in Tissue Engineering (2011)

This study aimed to compare clonogenicity, proliferation, stem cell-related marker expression, senescence, and differentiation potential of rat patellar tendon-derived stem cells (TDSCs) at early (P5), mid (P10), and late (P20, P30) passages. The clonogenicity of the cells was assessed by colony-forming assay and their proliferative potential was assessed by bromodeoxyuridine assay. The surface expression of CD90 and CD73 was assessed by flow cytometry. The cellular senescence was assessed by β-galactosidase activity. The adipogenic, chondrogenic, and osteogenic differentiation potentials of TDSCs were assessed by standard assays after induction. The mRNA expression of tendon-related markers, scleraxis (Scx) and tenomodulin (Tnmd), was measured by quantitative real-time reverse transcription-polymerase chain reaction. Both the colony numbers and proliferative potential of TDSCs increased with passaging. Concomitantly, there was significant upregulation of β-galactosidase activity with TDSC passaging. The subculture of TDSCs downregulated the expression of CD90 and CD73. Lipid droplets were formed in the early and mid passages of TDSCs upon adipogenic induction, but were absent in the late passages. The expression of peroxisome proliferator activator receptor gamma 2 (PPARγ2) and CCAAT/enhancer binding protein alpha (C/EBPα) in TDSCs after adipogenic induction decreased with passaging. Chondrogenesis, proteoglycan deposition, collagen type II protein expression, collagen type 2A1 (Col2AI), and aggrecan (Acan) mRNA expression were less in pellets formed with later passages of TDSCs after chondrogenic induction. The expression of Scx and Tnmd was lower in the late, compared with early and mid, passages of TDSCs. However, matrix mineralization and expression of alkaline phosphatase (Alpl) and osteocalcin (Bglap) mRNA after osteogenic induction increased with TDSC passaging. Researchers and clinicians should consider the changes of stem cell-related properties of TDSCs when multiplying them in vitro for tissue engineering.
Synthesis and Pharmacological Screening of Several Aroyl and Heteroaroyl Selenylacetic Acid Derivatives as Cytotoxic and Antiproliferative Agents (2009)

The synthesis and cytotoxic activity of a series of twenty six aroyl and heteroaroyl selenylacetic acid derivatives of general formula Ar-CO-Se-CH(2)-COOH or Heterar-CO-Se-CH(2)-COOH are reported. The synthesis was carried out by reaction of acyl chlorides with sodium hydrogen selenide, prepared in situ, and this led to the formation of sodium aroylselenides that subsequently reacted with alpha-bromoacetic acid to produce the corresponding selenylacetic acid derivatives. All of the compounds were tested against a prostate cancer cell line (PC-3) and some of the more active compounds were assessed against a panel of four human cancer cell lines (CCRF-CEM, HTB-54, HT-29, MCF-7) and one mammary gland-derived non-malignant cell line (184B5). Some of the compounds exhibited remarkable cytotoxic and antiproliferative activities against MCF-7 and PC-3 that were higher than those of the reference compounds doxorubicin and etoposide, respectively. For example, in MCF-7 when Ar = phenyl, 3,5-dimethoxyphenyl or benzyl the TGI values were 3.69, 4.18 and 6.19 microM. On the other hand, in PC-3 these compounds showed values of 6.8, 4.0 and 2.9 microM. Furthermore, benzoylselenylacetic acid did not provoke apoptosis nor did it perturb the cell cycle in MCF-7.
Effecting change through the stream analysis process. (1989)

The growing nursing shortage requires immediate and compelling changes in the work environment for nurses. The author describes a method for effecting change that nursing administrators can use to plan and implement change within complex health care environments. Stream analysis ensures a comprehensive analysis of many interactive problems and a plan for change that is multidimensional, coordinated, and congruent with the goals of the institution and the professional goals for nursing practice.
Reducing the stigma of long acting injectable antipsychotics – current concepts and future developments (2018)

For both, clinicians and drug developers, drug adherence remains a major target for improving treatment outcomes.
Fusion d'images anatomiques (échographie) et fonctionnelles (tomoscintigraphie) rénales (1995)

Nous presentons une technique de mise en correspondance d'images tomoscintigraphiques et echographiques dans laquelle un systeme de reperage optique permet de suivre les mouvements de la sonde echographique a l'interieur du volume scintigraphique. Les images superposees sont presentees avec un effet de transparence. Des pathologies variees chez dix patients ont ete explorees. Les images multi-modalites s'averent conduire a une amelioration de l'information fournie et de l'interpretation.
Effect of Nitrite Concentration and pH on Steel Corrosion Induced by Chloride in Simulated Concrete Pore Environment (2012)

The influence of nitrite concentration on the corrosion of steel immersed in three simulated pH environments that really exist on the surface of steel in concrete has been investigated by comparing and analyzing the change of threshold level of Cl - and NO 2 - /Cl - mole ratio. The results indicate that with the presence of nitrite, the corrosion of steel can be inhibited effectively. Chloride threshold level increases with the increasing of nitrite concentration and highly alkaline environment plays an important role in assisting nitrite to inhibit corrosion. The use of NO 2 - /Cl - mole ratio as the parameter to guarantee the inhibition efficiency is suitable in highly alkaline environment, but not appropriate in weakly alkaline and neutral environments.
Transmission system of guide-wave for a pipe using a long distance wave guide (2015)

Nondestructive inspection of a high-temperature structure is required to guarantee its safety. However, there are no useful sensors for high-temperature structures. Some of them cannot work at temperatures over 50&deg;C.Another concern is that it is too expensive to use. Therefore, a sensing system, which can transmit and receive an ultrasonic wave and travel a long distance using a long waveguide, has been studied. This means that an ultrasonic sensor could be driven at atmospheric temperature. We could finally confirm that a guided ultrasonic wave generated by a trial electromagnetic acoustic transducer (EMAT) with a thin Ni sheet on the surface of the pipe can travel more than 10m using a thin bar with a 2mm diameter as the waveguide. However, we had difficulty in receiving a reflected ultrasonic wave from the bottom surface of a test specimen. We tried to improve the trial inspection system using an ultrasonic horn. Finally, an experiment in which the temperature of a test block was heated to about 500&deg;C has been done and the reflected ultrasonic wave from the bottom surface of it has been successfully detected using a long waveguide and the wave horn. Finally, we tried to transmit and receive a guided wave in a pipe using the developed system. It was determined that an additional one turn-shaped or wave-shaped waveguide attached to the surface of the pipe in the circumferential direction is useful.
Theory of mirror benchmarking and demonstration on a quantum computer (2021)

A new class of protocols called mirror benchmarking was recently proposed to measure the system-level performance of quantum computers. These protocols involve circuits with random sequences of gates followed by mirroring, that is, inverting each gate in the sequence. We give a simple proof that mirror benchmarking leads to an exponential decay of the survival probability with sequence length, under the uniform noise assumption, provided the twirling group forms a 2-design. The decay rate is determined by a quantity that is a quadratic function of the error channel, and for certain types of errors is equal to the unitarity. This result yields a new method for estimating the coherence of noise. We present data from mirror benchmarking experiments run on the Honeywell System Model H1. This data constitutes a set of performance curves, indicating the success probability for random circuits as a function of qubit number and circuit depth.
Fundamental Studies on 14MeV Neutron Streak Camera (1986)

The characteristics of the uranium oxide cathodes for a neutron streak tube have been experimentally evaluated, using a conventional streak tube with 2 MCP wafers whose photocathode is changed into an uranium oxide cathode. It has been confirmed from the neutron image on the output phosphor screen that the detection efficiency (fission event/neutron) is roughly between 10-6 and 10-7 and each fission produces a few hundreds electrons emitted into vacuum. The temporal spread of--14ps has been obtained from the streak image of emitted electron cloud per one fission. On the other hand, it has been found from the experiment that in the practical use, the noise generated in the MCPs becomes an obstacle.
Renyi Entanglement Entropy of Interacting Fermions Calculated Using the Continuous-Time Quantum Monte Carlo Method (2014)

We present a new algorithm for calculating the Renyi entanglement entropy of interacting fermions using the continuous-time quantum Monte Carlo method. The algorithm only samples the interaction correction of the entanglement entropy, which by design ensures the efficient calculation of weakly interacting systems. Combined with Monte Carlo reweighting, the algorithm also performs well for systems with strong interactions. We demonstrate the potential of this method by studying the quantum entanglement signatures of the charge-density-wave transition of interacting fermions on a square lattice.
Light emission is fundamentally tied to the quantum coherence of the emitting particle (2020)

Coherent emission of light by free charged particles is ubiquitous in many areas of physics and engineering, with the light's properties believed to be successfully captured by classical electromagnetism in all relevant experimental settings. The advent of interactions between light and free quantum matter waves brought about fundamental questions regarding the role of the particle wavefunction. Here we show that even in seemingly classical experimental regimes, light emission is fundamentally tied to quantum properties of the emitting particles, such as their quantum coherence and correlations. By employing quantum electrodynamics, we unveil the role of the particle's coherent momentum uncertainty, without which decoherence of light becomes dominant. As an example, we consider Cherenkov radiation, envisioned for almost a century as a shockwave of light. We find instead that the shockwave's duration is fundamentally bound from below by the particle's coherent momentum uncertainty due to the underlying entanglement between the particle and light. This quantum optical paradigm opens new capabilities in analytical electron microscopy, enabling the measurement of quantum correlations of shaped electron wavepackets. Our findings also have applications for Cherenkov detectors in particle physics. For example, by measuring spectral photon autocorrelations, one can unveil the particle's wavefunction size, shape and coherence. Such schemes are especially intriguing for many high-energy particles, where other techniques are not available.
DAMPs, PAMPs, and LAMPs in Immunity and Sterile Inflammation (2019)

Recognizing the importance of leukocyte trafficking in inflammation led to some therapeutic breakthroughs. However, many inflammatory pathologies remain without specific therapy. This review discusses leukocytes in the context of sterile inflammation, a process caused by sterile (non-microbial) molecules, comprising damage-associated molecular patterns (DAMPs). DAMPs bind specific receptors to activate inflammation and start a highly optimized sequence of immune cell recruitment of neutrophils and monocytes to initiate effective tissue repair. When DAMPs are cleared, the recruited leukocytes change from a proinflammatory to a reparative program, a switch that is locally supervised by invariant natural killer T cells. In addition, neutrophils exit the inflammatory site and reverse transmigrate back to the bloodstream. Inflammation persists when the program switch or reverse transmigration fails, or when the coordinated leukocyte effort cannot clear the immunostimulatory molecules. The latter causes inappropriate leukocyte activation, a driver of many pathologies associated with poor lifestyle choices. We discuss lifestyle-associated inflammatory diseases and their corresponding immunostimulatory lifestyle-associated molecular patterns (LAMPs) and distinguish them from DAMPs.
Geochemistry of Sulfur in Coal (1990)

This paper summarizes our understanding of the geochemistry of sulfur in coal in the following areas: 1) abundance of sulfur in coals of major coal basins in the U.S., 2) distribution of sulfur in coal lithotypes and macerals, 3) characteristics and geochemical significance of sulfur-containing organic compounds, 4) sulfur isotopic studies relating to the sources of sulfur in coal, and 5) sedimentary environments controlling the geochemistry of sulfur in coal. The evidence suggests that the sulfur in low-sulfur coal (≤1% S) is derived primarily from parent plant material. In medium-sulfur (>1 to <3% S) and high-sulfur (≥3% S) coal, there are two major sources of sulfur: 1) parent plant material, and 2) sulfate in seawater that flooded peat swamps. Compositional variations of sulfur in coal are largely controlled by sedimentary environments during peat accumulation and by postdepositional changes (diagenesis). A model of the formation of pyrite and organic sulfur compounds in high-sulfur coal is presented.
Autonomous jumping microrobots (2007)

An autonomous jumping microrobot has been designed, and its mechanical components have been fabricated and tested. Millimeter-scale autonomous mobile microrobots have potential applications in mobile sensor networks as well as search and exploration tasks. However, mobility is difficult at this scale due to rugged surfaces, obstacles and locomotion efficiency. Jumping has been proposed as a locomotion method to overcome these challenges. 
The microrobot design has been divided into four components: energy storage, high work density actuators, power, and control. Like its biological inspiration, the flea, a jumping microrobot requires an energy storage mechanism to store energy and release it quickly to jump. Small leg lengths require large accelerations to reach takeoff velocities required to jump 10s of cm. Silicone micro rubber bands have been fabricated and demonstrated to store and quickly release enough energy for a 10 mg robot to jump 17 cm straight up. 
To stretch these micro rubber bands, electrostatic inchworm motors have been designed and fabricated to provide high forces and large displacements with low input power requirements. Three key design innovations have been used to improve the force density of these motor designs 37x over previous efforts. First, a pre-biasing actuator reduces initial electrostatic gaps below lithographic limits. Second, a toothless, friction-based clutch allows for variable stop sizes and single drive actuator motors. Third, silicon nitride has been added to reduce motor sire. Initial motor designs using these three new features have been fabricated and tested. 
Finally, several prototypes have been built to integrate and test the four robot components. A small-scale version of the full robot with previously fabricated solar cells and an off-the-shelf microcontroller driving a small inchworm motor has been demonstrated. Separately, an inchworm motor has been used to store energy in a micro rubber band for quick release. It is hoped that many of the design and fabrication ideas presented in this work can be used to make autonomous mobile microrobots a reality.
Improved determination of hydrogen peroxide or lucigenin by measurement of lucigenin chemiluminescence in organised assemblies (1986)

Chemiluminescence (CL) from the reaction of 10,10′-dimethyl-9,9′-biacridinium dinitrate (lucigenin) with hydrogen peroxide in the presence of different organised assemblies has been evaluated as a means of improving the CL assay for the determination of hydrogen peroxide. If the assay is conducted in the presence of 3-(N-dodecyl-N,N-dimethylammonio)propane-1-sulphonate, hexadecyltrimethylammonium chloride or polyoxyethylene(23)dodecanol (Brij-35) micelles or β-cyclodextrin, improvements in the sensitivity by factors of 1.9–7.6 were observed relative to that in water. The best sensitivity is achieved in micellar Brij-35 in which the CL intensity is linearly proportional to hydrogen peroxide from 3.0 × 10–7 up to 1.0 × 10–3M(the highest concentration examined). The precision in Brij-35 is good with the relative deviation at the 95% confidence level being 3.2 ± 2.2%. The selectivity of the lucigenin CL assay for hydrogen peroxide is also improved in the Brij-35 medium. Additionally, the usable pH range in which analytically useful CL can be observed is extended in the Brij-35 or CTAC micellar systems relative to water. Preliminary data suggest that these advantages are also possible if one uses the reaction to quantitate lucigenin rather than hydrogen peroxide.
Metallography of advanced materials; Proceedings of the Twentieth Annual Technical Meeting of the International Metallographic Society, Monterey, CA, July 29, 30, 1987 (1988)

The present conference discusses topics in advanced electronic metallic materials and components, metal-matrix composites, novel alloy compositions and their performance characteristics, the processing of advanced ceramics, recent advancements insurface treatments and coatings, surface analysis techniques, and novel metallographic techniques. Attention is given to the catastrophic failure of hybrid leads, magnetic domain wall observations in Metglas 2605 SC, engineered microcomposites for special applications, the preparation of composites for microstructural analysis, the metallography of cavitation in a superplastic Al-Li alloy, plasma etching of Si/sub 3/N/sub 4/, laser surface treatment of (Fe-B-Ni)-M alloys, TEM analysis of microcrystalline metal boride layers, and a computer-controlled electropolishing system.
Inositol (1,4,5)-trisphosphate receptor links to filamentous actin are important for generating local Ca2+ signals in pancreatic acinar cells (2005)

We explored a potential structural and functional link between filamentous actin (F-actin) and inositol (1,4,5)-trisphosphate receptors (IP(3)Rs) in mouse pancreatic acinar cells. Using immunocytochemistry, F-actin and type 2 and 3 IP(3)Rs (IP(3)R2 and IP(3)R3) were identified in a cellular compartment immediately beneath the apical plasma membrane. In an effort to demonstrate that IP(3)R distribution is dependent on an intact F-actin network in the apical subplasmalemmal region, cells were treated with the actin-depolymerising agent latrunculin B. Immunocytochemistry indicated that latrunculin B treatment reduced F-actin in the basolateral subplasmalemmal compartment, and reduced and fractured F-actin in the apical subplasmalemmal compartment. This latrunculin-B-induced loss of F-actin in the apical region coincided with a reduction in IP(3)R2 and IP(3)R3, with the remaining IP(3)Rs localized with the remaining F-actin. Experiments using western blot analysis showed that IP(3)R3s are resistant to extraction by detergents, which indicates a potential interaction with the cytoskeleton. Latrunculin B treatment in whole-cell patch-clamped cells inhibited Ca(2+)-dependent Cl(-) current spikes evoked by inositol (2,4,5)-trisphosphate; this is due to an inhibition of the underlying local Ca(2+) signal. Based on these findings, we suggest that IP(3)Rs form links with F-actin in the apical domain and that these links are essential for the generation of local Ca(2+) spikes.
Native Valve Endocarditis Due to Enterococcus hirae (2002)

ABSTRACT Enterococcus hirae is a rare isolate in clinical specimens. We describe a case of native aortic-valve endocarditis that was caused by Enterococcus hirae in a 72-year-old man. This is the first reported case of endocarditis due to this organism.