gebhart/patrepeval huggingface dataset:
Manipulating the chloroplast genome of Chlamydomonas: Present realities and future prospects (1992)

Biotechnology is being applied in vitro modification and stable reintroduction of chloroplast genes in Chlamydomonas reinhardtii and Nicotiana tabacum by homologous recombination. We are attempting the function analyses of plastid encoded proteins involved in photosynthesis, characterization of sequences which regulate expression of plastid genes at the transcriptional and translational levels, targeted disruption of chloroplast genes and molecular analysis of processes involved in chloroplast recombination.
The role of circumcision, tobacco, and alcohol use in genital human papillomavirus infection among men from Denmark (2021)

It is crucial to understand the natural history of genital human papillomavirus (HPV) infection in men to prevent the increasing male HPV-related disease burden. We evaluated the associations between HPV infection and circumcision, smoking, and alcohol use after accounting for sexual behavior. The study included 2331 male personnel from Danish barracks. Penile swabs were tested for HPV DNA with a polymerase chain reaction assay, INNO-LiPA. All men completed a self-administered questionnaire providing data on potential risk factors for HPV such as lifestyle and sexual habits. Using multivariable logistic regression, associations between potential risk factors and HPV infection were estimated and expressed as odds ratios (ORs) with 95% confidence intervals (CI). Current cigarette smoking was associated with increased odds of HPV detection (OR = 1.2; 95% CI: 1.0-1.4), but we found no association with alcohol use in the analysis adjusted for sexual behavior. Circumcision reduced the odds of a prevalent HPV infection (OR = 0.7; 95% CI: 0.5-1.0) although not statistically significantly. Strong associations with lifetime and recent number of female sex partners were observed, but in contrast to uncircumcised men, increasing number of sex partners was not associated with higher HPV prevalence in circumcised men. In conclusion, smoking was associated with increased odds of penile HPV in men from the general population in Denmark, whereas circumcision seemed to reduce the risk. Moreover, our results indicated that there might be differences in the viral susceptibility between circumcised and uncircumcised men.
Synthesis of monoclinic<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>IrT</mml:mi><mml:msub><mml:mi mathvariant="normal">e</mml:mi><mml:mn>2</mml:mn></mml:msub></mml:mrow></mml:math>under high pressure and its physical properties (2015)

In a pressure-temperature $(P\text{\ensuremath{-}}T)$ diagram for synthesizing $\mathrm{IrT}{\mathrm{e}}_{2}$ compounds, the well-studied trigonal $(H)$ phase with the $\mathrm{Cd}{\mathrm{I}}_{2}$-type structure is stable at low pressures. The superconducting cubic $(C)$ phase can be synthesized under higher temperatures and pressures. A rhombohedral phase with the crystal structure similar to the $C$ phase can be made at ambient pressure; but the phase contains a high concentration of Ir deficiency. In this paper we report that a rarely studied monoclinic $(M)$ phase can be stabilized in narrow ranges of pressure and temperature in this $P\text{\ensuremath{-}}T$ diagram. The peculiar crystal structure of the $M\text{\ensuremath{-}}\mathrm{IrT}{\mathrm{e}}_{2}$ eliminates the tendency to form Ir-Ir dimers found in the $H$ phase. The $M$ phase has been fully characterized by structural determination and measurements of electrical resistivity, thermoelectric power, DC magnetization, and specific heat. These physical properties have been compared with those in the $H$ and $C$ phases of $\mathrm{I}{\mathrm{r}}_{1\ensuremath{-}x}\mathrm{T}{\mathrm{e}}_{2}$. Moreover, magnetic and transport properties and specific heat of the $M\text{\ensuremath{-}}\mathrm{IrT}{\mathrm{e}}_{2}$ can be fully justified by calculations with the density-functional theory presented in this paper.
Multiwavelength Transmission Spectroscopy Revisited for the Characterization of the Protein and Polystyrene Nanoparticle Mixtures (2013)

Multiwavelength Transmission (MWT) UV-Vis-NIR spectroscopy, an effective technique often underutilized for the characterization of processes involving particulates, such as protein aggregation, is systematically explored using bovine serum albumin and a set of NIST-traceable particle size (PS) standards having certified particle diameters over the nominal size range of 30 to 100 nm. The PS standards are used as surrogates for protein aggregates and other contaminants such as oils and microbubbles. Therefore, the standards can be used to quantitatively modify the optical properties of protein solutions and thus observe the effect of the presence of aggregates and other particulates on their wavelength-dependent transmission spectra. The experimental results demonstrate that the changes induced in the optical density spectra of proteins due to the presence of PS particles are detectable and consistent with the expectations set by light scattering theory. It is demonstrated that the size and relative concentrations of the particle populations present in the protein samples can be quantified. Because of the considerable dynamic range of MWT UV-Vis-NIR spectroscopy for particle analysis and its real-time measurement capabilities, this type of spectroscopy can be effectively used for the characterization of protein aggregates and for the continuous real-time monitoring of aggregation processes and for the identification and quantification of contaminants in protein-based products.
Additional file 14: of [18F]tetrafluoroborate as a PET tracer for the sodium/iodide symporter: the importance of specific activity (2016)

Expanded view of 11B NMR spectrum of boric acid. (PDF 12.5 KB).
A Validated High-Performance Liquid Chromatography-Ultraviolet Method for Quantification of the CCR5 Inhibitor Maraviroc in Plasma of HIV-Infected Patients (2010)

Maraviroc is the first commercialized CCR5 inhibitor for HIV therapy. A new high-performance liquid chromatography-ultraviolet method to quantify maraviroc concentrations in human plasma was developed and validated. The method is based on a protein precipitation procedure, with an acidic solution of acetonitrile (trifluoroacetic acid 0.1%) and quinoxaline as internal standard. The analytes were eluted using a gradient run in 15 minutes on an analytical C18 Luna column (150 mm x 4.6 mm ID) with a particle size of 5 mum. Maraviroc and internal standard were detected by UV at 193 nm and 352 nm, respectively. The calibration curve was linear up to 2500 ng/mL. The mean recovery of maraviroc was 96%. All validation data were in accordance with U.S. Food and Drug Administration requirements. The new high-performance liquid chromatography-ultraviolet method reported here could be used routinely to monitor plasma concentrations of maraviroc in healthy volunteers and HIV-infected patients.
Zigbee performance during severe interruptions in electric power systems (2011)

The goal of this paper is to investigate the reliability of ZigBee based wireless sensor networks in transforming existing power systems into future smart grids. The performance of the communication network for specific propagation environment and frequency band is investigated. The interrupting RF signals generated from harsh normal and abnormal operating conditions in power system environment are investigated. High noise level in 13 to 16kV HV systems, impulsive transients of 10 to 34kV according to IEEE Std. 792 turn-to-turn tests as well as partial discharge activities in 4 to 24kV free space are tested using real laboratory data. The interruption limits of ZigBee coordinator and device units during these conditions are defined.
Effectiveness of elastic band-type ankle&amp;ndash;foot orthoses on postural control in poststroke elderly patients as determined using combined measurement of the stability index and body weight-bearing ratio (2015)

Based on our outcomes, we recommend the prescription of E-AFOs as part of a physiotherapy rehabilitation program to promote recovery of postural stability poststroke. When possible, therapeutic outcomes should be documented using the Biodex Balance System and foot pressure system, as used in our study, to provide evidence needed to support the development of a larger controlled trial to generate high-quality evidence on the effectiveness of E-AFOs.
Leakage of signal function with reused keys in RLWE key exchange (2017)

In this paper, we show that the signal function used in Ring-Learning with Errors (RLWE) key exchange could leak information to find the secret s of a reused public key p = as+2e. This work is motivated by an attack proposed in [1] and gives an insight into how public keys reused for long term in RLWE key exchange protocols can be exploited. This work specifically focuses on the attack on the KE protocol in [2] by initiating multiple sessions with the honest party and analyze the output of the signal function. Experiments have confirmed the success of our attack in recovering the secret.
The Zebrafish Swimbladder: A Simple Model for Lung Elastin Injury and Repair (1999)

In this communication we offer data to suggest that the zebrafish swimbladder may provide a simple model of elastin injury and repair which is amenable to genetic analysis and pertinent to lung physiology. In situ hybridization of zebrafish embryos illustrated that elastin gene expression is evident in the developing gut tract prior to swimbladder morphogenesis. Northern blot analysis demonstrated that the major zebrafish elastin mRNA is 2.0 kb which is significantly smaller than its higher vertebrate counterpart. Amino acid analysis of alkali-resistant protein from the anterior chamber of the adult zebrafish swimbladder showed a composition similar to higher vertebrate elastins including significant amounts of desmosine crosslinks. Electron microscopic investigations of the swimbladder wall indicate a simple structure with an inner layer of elastin fibers. Elastase delivery to the swimbladder in vitro resulted in significant fragmentation of elastin in the anterior chamber providing an environment for studying elastin repair within the tissue.
Latency and consistent flow migration: relax for lossless updates (2019)

Consistency in network updates is a nascent research area, especially in the context of traffic engineering or Software Defined Networks. Various approaches have been proposed and implemented in the problem space of flow migration and congestion, primarily focusing on different flows not breaking the bandwidth capacities of the used links during updates. However, current network update techniques overlook the effect of flows congesting their own path during a network update due to latency on the links. Furthermore, while congestion will be resolved eventually after the network update, the buffers of the affected routers can be filled for a long time period, leading to the following paradox: a flow is moved to a path with less latency, but the latency stays the same! As flows are often migrated because of latency concerns, this is highly undesirable. We show that these effects occur already in a small topology in practice, causing packet loss due to overfull buffers. Furthermore, we prove that finding a lossless flow migration is NP-hard, already for a single (splittable) flow on directed acyclic graphs. Nonetheless, we can relax latency requirements to still obtain lossless flow migration. To this end, we show how to adapt current systems such as SWAN or Dionysus [SIGCOMM’13/’14], also developing our own polynomial time schedule algorithm, and discussing future consistent flow migration technique adaptations.
Analysis of the Specification Influence on the Efficiency of an Optimized Test Flow for ADCs (2003)

International audience
Plasmon-enhanced terahertz emission in self-assembled quantum dots by femtosecond pulses (2014)

A scheme for terahertz (THz) generation from intraband transition in a self-assembled quantum dot (QD) molecule coupled to a metallic nanoparticle (MNP) is analyzed. The QD structure is described as a three-level atom-like system using the density matrix formalism. The MNP with spherical geometry is considered in the quasistatic approximation. A femtosecond laser pulse creates a coherent superposition of two subbands in the quantum dots and produces localized surface plasmons in the nanoparticle which act back upon the QD molecule via dipole-dipole interaction. As a result, coherent THz radiation with a frequency corresponding to the interlevel spacing can be obtained, which is strongly modified by the presence of the MNP. The peak value of the terahertz signal is analyzed as a function of nanoparticle's size, the MNP to QD distance, and the area of the applied laser field. In addition, we theoretically demonstrate that the terahertz pulse generation can be effectively controlled by making use of a train of femtosecond laser pulses. We show that by a proper choice of the parameters characterizing the pulse train a huge enhancement of the terahertz signal is obtained.
Osteoblasts Generate Testosterone From DHEA and Activate Androgen Signaling in Prostate Cancer Cells (2020)

Bone metastasis is a complication of prostate cancer in up to 90% of men afflicted with advanced disease. Therapies that reduce androgen exposure remain at the forefront of treatment. However, most prostate cancers transition to a state whereby reducing testicular androgen action becomes ineffective. A common mechanism of this transition is intratumoral production of testosterone (T) using the adrenal androgen precursor dehydroepiandrosterone (DHEA) through enzymatic conversion by 3β- and 17β-hydroxysteroid dehydrogenases (3βHSD and 17βHSD). Given the ability of prostate cancer to form blastic metastases in bone, we hypothesized that osteoblasts might be a source of androgen synthesis. RNA expression analyses of murine osteoblasts and human bone confirmed that at least one 3βHSD and 17βHSD enzyme isoform was expressed, suggesting that osteoblasts are capable of generating androgens from adrenal DHEA. Murine osteoblasts were treated with 100 nM and 1 μM DHEA or vehicle control. Conditioned media from these osteoblasts were assayed for intermediate and active androgens by liquid chromatography-tandem mass spectrometry. As DHEA was consumed, the androgen intermediates androstenediol and androstenedione were generated and subsequently converted to T. Conditioned media of DHEA-treated osteoblasts increased androgen receptor (AR) signaling, prostate-specific antigen (PSA) production, and cell numbers of the androgen-sensitive prostate cancer cell lines C4-2B and LNCaP. DHEA did not induce AR signaling in osteoblasts despite AR expression in this cell type. We describe an unreported function of osteoblasts as a source of T that is especially relevant during androgen-responsive metastatic prostate cancer invasion into bone. © 2021 American Society for Bone and Mineral Research (ASBMR). This article has been contributed to by US Government employees and their work is in the public domain in the USA.
BASIC STUDY ON RELATION BETWEEN FLATNESS OF END OF HIGH STRENGTH CONCRETE SPECIMEN AND COMPRESSIVE STRENGTH (2010)

In this research, the relation between the flatness of the end of the high strength concrete specimen and its compressive strength was examined. The results of the examination are shown as follows. (1) The flatness of the end of the specimen can be evaluated by measuring 17 points with a device shown in JIS A 5308. (2) Flatness of the end of the specimen will change with the time passing. Therefore, specimens should be ground just before the strength test. (3) Every flatness of the end of the grounded specimen was within the limits regulated in JIS A 1132. (4) In this experiment, compressive strength decreased as the roughness of the end of the specimen increased. (5) In this experiment, the influence of the flatness on the strength reduction rate increased with the rise of the compressive strength level.
E-selectin engages PSGL-1 and CD44 through a common signaling pathway to induce integrin αLβ2-mediated slow leukocyte rolling (2010)

In inflamed venules, neutrophils rolling on E-selectin induce integrin alpha(L)beta(2)-dependent slow rolling on intercellular adhesion molecule-1 by activating Src family kinases (SFKs), DAP12 and Fc receptor-gamma (FcRgamma), spleen tyrosine kinase (Syk), and p38. E-selectin signaling cooperates with chemokine signaling to recruit neutrophils into tissues. Previous studies identified P-selectin glycoprotein ligand-1 (PSGL-1) as the essential E-selectin ligand and Fgr as the only SFK that initiate signaling to slow rolling. In contrast, we found that E-selectin engagement of PSGL-1 or CD44 triggered slow rolling through a common, lipid raft-dependent pathway that used the SFKs Hck and Lyn as well as Fgr. We identified the Tec kinase Bruton tyrosine kinase as a key signaling intermediate between Syk and p38. E-selectin engagement of PSGL-1 was dependent on its cytoplasmic domain to activate SFKs and slow rolling. Although recruiting phosphoinositide-3-kinase to the PSGL-1 cytoplasmic domain was reported to activate integrins, E-selectin-mediated slow rolling did not require phosphoinositide-3-kinase. Studies in mice confirmed the physiologic significance of these events for neutrophil slow rolling and recruitment during inflammation. Thus, E-selectin triggers common signals through distinct neutrophil glycoproteins to induce alpha(L)beta(2)-dependent slow rolling.
Ethylene Production of Heat-treated Stem Tissues of Red-osier Dogwood at Several Growth Stages (1993)

Ethylene production in stem tissues of red-osier dogwood (Cornus sericea L.) following heat treatment was determined at several growth stages. Ethylene production of heat-stressed stem tissue depended on the stage of development and was a function of the degree of stress. During active growth and early endodormancy, heat stress of stem tissues stimulated ethylene production, reaching a peak at 40C, followed by a steady decrease at higher temperatures. Highest ethylene levels from stressed tissues occurred in May, July, September, and March. Only a trace amount of ethylene was produced during endodormancy to ecodormancy (late October to January) from stressed and nonstressed stem tissues. Applying ACC to stem segments at late endodormancy (December) or applying methionine and IAA to stem segments at maximum endodormancy (November) enhanced ethylene production of both nonstressed and heat-stressed stem tissues. Chemical names used: 1 H- indole-3-acetic acid (IAA); 1-aminocyclopropane-1-carboxylic acid (ACC).
A feature-based, robust, hierarchical algorithm for registering pairs of images of the curved human retina (2002)

This paper describes a robust hierarchical algorithm for fully-automatic registration of a pair of images of the curved human retina photographed by a fundus microscope. Accurate registration is essential for mosaic synthesis, change detection, and design of computer-aided instrumentation. Central to the algorithm is a 12-parameter interimage transformation derived by modeling the retina as a rigid quadratic surface with unknown parameters. The parameters are estimated by matching vascular landmarks by recursively tracing the blood vessel structure. The parameter estimation technique, which could be generalized to other applications, is a hierarchy of models and methods, making the algorithm robust to unmatchable image features and mismatches between features caused by large interframe motions. Experiments involving 3,000 image pairs from 16 different healthy eyes were performed. Final registration errors less than a pixel are routinely achieved. The speed, accuracy, and ability to handle small overlaps compare favorably with retinal image registration techniques published in the literature.
<sup>15</sup>N Solid State NMR Spectroscopic Study of Surface Amine Groups for Carbon Capture: 3-Aminopropylsilyl Grafted to SBA-15 Mesoporous Silica (2017)

Materials composed of high-porosity solid supports, such as SBA-15, containing amine-bearing moieties inside the pores, such as 3-aminopropylsilane (APS), are envisioned for carbon dioxide capture; solid-state <sup>15</sup>N NMR can be highly informative for studying chemisorption reactions. Two <sup>15</sup>N-enriched samples with different APS loadings were studied to probe the identity of the pendant molecules and structure of the chemisorbed CO<sub>2</sub> species. <sup>15</sup>N cross-polarization magic-angle spinning NMR provides unique information about the amines, whether they are rigid or dynamic, by measuring contact time curves and rotating frame, T<sub>1ρ</sub>(<sup>15</sup>N), relaxation. Both carbamate and carbamic acid are formed; carbamic acid is shown to be less stable than carbamate. After desorption, a steady state for the chemisorbed reaction product is reached, leaving behind carbamate. <sup>15</sup>N NMR monitors the evolution of the species over time. During desorption, APS is regenerated, but the ammonium propylsilane intensity does not change, leading us to conclude that carbamic acid desorbs, while carbamate (to which ammonium propylsilane is ion paired) persists. A secondary ditehtered amine present does not react with CO<sub>2</sub>, and we posit this may be due to its rigidity. These findings demonstrate the versatility of solid-state NMR to provide information about these complex CO<sub>2</sub> reactions with solid amine sorbents.
Crystal structure of carbonyl[tri(<i>p</i>-chlorophenyl)phosphine] (η<sup>5</sup>-pentamethylcyclopentadienyl)iridium(I),(CO)[<i>p</i>-ClC<sub>6</sub>H<sub>4</sub>)<sub>3</sub>P][η<sup>5</sup>-C<sub>5</sub>(CH<sub>3</sub>)<sub>5</sub>]Ir (1997)

Article Crystal structure of carbonyl[tri(p-chlorophenyl)phosphine] (η5-pentamethylcyclopentadienyl)iridium(I),(CO)[p-ClC6H4)3P][η5-C5(CH3)5]Ir was published on March 1, 1997 in the journal Zeitschrift für Kristallographie - Crystalline Materials (volume 212, issue 3).
A dual-wavelength single particle aerosol fluorescence monitor (2005)

Laser diodes and light-emitting diodes capable of continuous sub-300 nm radiation emission will ultimately represent optimal excitation sources for compact and fieldable bio-aerosol monitors. However, until such devices are routinely available and whilst solid-state UV lasers remain relatively expensive, other low-cost sources of UV can offer advantages. This paper describes one such prototype that employs compact xenon discharge UV sources to excite intrinsic fluorescence from individual particles within an ambient aerosol sample. The prototype monitor samples ambient air via a laminar sheathed-flow arrangement such that particles within the sample flow column are rendered in single file as they intersect the beam from a continuous-wave 660nm diode laser. Each individual particle produces a scattered light signal from which an estimate of particle size (down to ~1 um) may be derived. This same signal also initiates the sequential firing (~10 us apart) of two xenon sources which irradiate the particle with UV pulses centred upon ~280 nm and ~370 nm wavelength, optimal for excitation of bio-fluorophores tryptophan and NADH respectively. For each excitation wavelength, fluorescence is detected across two bands embracing the peak emissions of the same bio-fluorophores. Thus, for each particle, a 2-dimensional fluorescence excitation-emission matrix is recorded together with an estimate of particle size. Current measurement rates are up to ~125 particles/s (limited by the xenon recharge time), corresponding to all particles for concentrations up to ~2 x 10<sup>4</sup> particles/l. Developments to increase this to ~500 particles/s are in hand. Analysis of results from aerosols of E.coli, BG spores, and a variety of non-biological materials are given.