gebhart/patrepeval huggingface dataset:
miRNA studies in<i>in vitro</i>and<i>in vivo</i>activated hepatic stellate cells (2011)

To understand which and how different miRNAs are implicated in the process of hepatic stellate cell (HSC) activation.
Phagocytosis of microbes: insights and prospects (1995)

one. For the adventurous in spirit, it combines the thrill of the chase with the capture and speedy demise of the villain. Computer buffs will find in the plasma membrane the cell’s motherboard, coordinating the flow of information from ligated surface receptors to the cell’s metabolic and motile machinery. Science fiction devotees will revel as invading microbial pathogens evade the cell’s outer defences and win the day by striking at a station along the endocytic pathway. The laid-back of all ages will appreciate the many ways prokaryotesform life-long, sometimes symbiotic, associations with the cells that phagocytose them. For cell biologists, the capacity of a bacterial or protozoan pathogen to affect a unique target in a higher eukaryotic cell is an opportunity to identify and probe otherwise undetectable regulatory pathways. Thatsome of these palhways are conserved in organisms whose evolutionary paths diverged millions of years ago (e.g. Legionella pneumophila forms similar r ibosome-studded vacuoles in fresh-water amoebae’ and in human macrophages’), indicates that lessons learned from lower eukaryotes (such as those described by Jeon in this issue) will be relevant to solving current problems of microbial pathogenesis and understanding pathways of host resistance (see for example Harding, and Selsted and Ouellette, this issue).
Probabilistic topic models (2011)

Probabilistic topic modeling provides a suite of tools for the unsupervised analysis of large collections of documents. Topic modeling algorithms can uncover the underlying themes of a collection and decompose its documents according to those themes. This analysis can be used for corpus exploration, document search, and a variety of prediction problems.
Automatic tagging using deep convolutional neural networks (2016)

We present a content-based automatic music tagging algorithm using fully convolutional neural networks (FCNs). We evaluate different architectures consisting of 2D convolutional layers and subsampling layers only. In the experiments, we measure the AUC-ROC scores of the architectures with different complexities and input types using the MagnaTagATune dataset, where a 4-layer architecture shows state-of-the-art performance with mel-spectrogram input. Furthermore, we evaluated the performances of the architectures with varying the number of layers on a larger dataset (Million Song Dataset), and found that deeper models outperformed the 4-layer architecture. The experiments show that mel-spectrogram is an effective time-frequency representation for automatic tagging and that more complex models benefit from more training data.
A Systems Biology Approach for Studying Heterotopic Ossification: Proteomic Analysis of Clinical Serum and Tissue Samples (2018)

Heterotopic ossification (HO) refers to the abnormal formation of bone in soft tissue. Although some of the underlying processes of HO have been described, there are currently no clinical tests using validated biomarkers for predicting HO formation. As such, the diagnosis is made radiographically after HO has formed. To identify potential and novel biomarkers for HO, we used isobaric tags for relative and absolute quantitation (iTRAQ) and high-throughput antibody arrays to produce a semi-quantitative proteomics survey of serum and tissue from subjects with (HO<sup>+</sup>) and without (HO<sup>-</sup>) heterotopic ossification. The resulting data were then analyzed using a systems biology approach. We found that serum samples from subjects experiencing traumatic injuries with resulting HO have a different proteomic expression profile compared to those from the matched controls. Subsequent quantitative ELISA identified five blood serum proteins that were differentially regulated between the HO<sup>+</sup> and HO<sup>-</sup> groups. Compared to HO<sup>-</sup> samples, the amount of insulin-like growth factor I (IGF1) was up-regulated in HO<sup>+</sup> samples, whereas a lower amount of osteopontin (OPN), myeloperoxidase (MPO), runt-related transcription factor 2 (RUNX2), and growth differentiation factor 2 or bone morphogenetic protein 9 (BMP-9) was found in HO<sup>+</sup> samples (Welch two sample t-test; P < 0.05). These proteins, in combination with potential serum biomarkers previously reported, are key candidates for a serum diagnostic panel that may enable early detection of HO prior to radiographic and clinical manifestations.
Spin-exchange-pumped<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">He</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>3</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">Xe</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>129</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>Zeeman masers (1994)

Steady-state noble gas Zeeman masers operating with $^{3}\mathrm{He}$ and $^{129}\mathrm{Xe}$ have been realized by spin exchange with laser optically pumped Rb. These masers can operate continuously for arbitrary lengths of time. For measurement intervals \ensuremath{\tau}=1000 to 10 000 s, frequency measurement precision for a phase locked $^{129}\mathrm{Xe}$ maser is shown to be better than 1\ifmmode\times\else\texttimes\fi{}${10}^{\mathrm{\ensuremath{-}}2}$${\mathrm{\ensuremath{\tau}}}^{\mathrm{\ensuremath{-}}3/2}$ Hz. Startup transients are used to study gain characteristics. In a two-cell setup maser conditions for both species can be optimized allowing a wide array of precision measurements.
Copper pathways in <i>Plasmodium falciparum</i> infected erythrocytes indicate an efflux role for the copper P-ATPase (2004)

Copper, like iron, is a transition metal that can generate oxygen radicals by the Fenton reaction. The Plasmodium parasite invades an erythrocyte host cell containing 20 microM copper, of which 70% is contained in the Cu/Zn SOD (cuprozinc superoxide dismutase). In the present study, we follow the copper pathways in the Plasmodium-infected erythrocyte. Metal-determination analysis shows that the total copper content of Percoll-purified trophozoite-stage-infected erythrocytes is 66% that of uninfected erythrocytes. This decrease parallels the decrease seen in Cu/Zn SOD levels in parasite-infected erythrocytes. Neocuproine, an intracellular copper chelator, arrests parasites at the ring-to-trophozoite stage transition and also specifically decreases intraparasitic levels of Cu/Zn SOD and catalase. Up to 150 microM BCS (2,9-dimethyl-4,7-diphenyl-1,10-phenanthrolinedisulphonic acid), an extracellular copper chelator, has no effect on parasite growth. We characterized a single copy PfCuP-ATPase (Plasmodium falciparum copper P-ATPase) transporter, which, like the Crypto-sporidium parvum copper P-ATPase, has a single copper-binding domain: 'Met-Xaa-Cys-Xaa-Xaa-Cys'. Recombinant expression of the N-terminal metal-binding domain reveals that the protein specifically binds reduced copper. Transcription of the PfCuP-ATPase gene is the highest at late ring stage/early trophozoite, and is down-regulated in the presence of neocuproine. Immunofluorescence and electron microscopy indicate the transporter to be both in the parasite and on the erythrocyte membrane. Both the decrease in total copper and the location of the PfCuP-ATPase gene indicate a copper-efflux pathway from the infected erythrocyte.
Multichannel transmission ellipsometer for characterization of anisotropic optical materials (1994)

We have developed a multichannel transmission ellipsometer to characterize the wavelength dependence of the optical characteristics of transparent, anisotropic solids. The source side of the instrument employs a broadband lamp in conjunction with a rotating polarizer. The light transmitted through the sample is analyzed by a stationary polarizer, a grating spectrograph, and a 1024-pixel photodiode array. The photodiode array collects irradiance spectra at several uniformly spaced values of the rotating polarizer angle P, and the irradiance registered at each pixel of the array is Fourier analyzed versus P. From this analysis one can characterize the change in polarization state induced by the sample as a continuous function of wavelength from 400 to 800 nm. The multichannel transmission ellipsometer can be applied in studies of linear and circular birefringence in new materials as well as in assessments of the spectroscopic performance of polarization modifying devices such as retarders. However, we also emphasize the application of the instrument as an educational tool for demonstrating polarization concepts in advanced undergraduate physics and optics laboratories. In this application anisotropies in common optical materials have been characterized, including circular birefringence in quartz and linear birefringence and dichroism in mica. Because high-precision data are collected continuously versus wavelength, the results represent a clear improvement over those obtained at discrete wavelengths.
Linearly polarized pumped passively Q-switched Nd:YVO<sub>4</sub>microchip laser for Ince–Gaussian laser modes with controllable orientations (2016)

A tilted, linearly polarized laser diode end-pumped Cr4+:YAG passively Q-switched a-cut Nd:YVO4 microchip laser for generating numerous Ince–Gaussian (IG) laser modes with controllable orientations has been demonstrated by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The same IG laser mode with different orientations has been achieved with the same absorbed pump power in a passively Q-switched Nd:YVO4 microchip laser under linearly polarized pumping when the incident pump power and the crystalline orientation of an a-cut Nd:YVO4 crystal are both properly selected. The significant improvement of pulsed laser performance of controllable IG modes has been achieved by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The maximum pulse energy is obtained along the a-axis of an a-cut Nd:YVO4 crystal and the highest peak power is achieved along the c-axis of an a-cut Nd:YVO4 crystal, respectively, which has potential applications on quantum computation and optical manipulation. The generation of controllable IG laser modes in microchip lasers under linearly polarized pumping provides a convenient and universal way to control IG laser mode numbers with anisotropic crystal as a gain medium.
Murine Immune Response to<i>Neisseria meningitidis</i>Group C Capsular Polysaccharide: Analysis of Monoclonal Antibodies Generated in Response to a Thymus-Independent Antigen and a Thymus-Dependent Toxoid Conjugate Vaccine (2000)

Antibody (Ab) responses to polysaccharides (PSs) such as Neisseria meningitidis group C PS (MCPS) are characterized as being thymus independent (TI) and are restricted with regard to clonotype and isotype expression. PS conjugated to proteins, e.g., MCPS coupled to tetanus toxoid (MCPS-TT), elicits a thymus-dependent (TD) response. In order to understand the influence of the form of a vaccine (TI versus TD) on the Ab repertoire, we generated monoclonal antibody (MAb) panels from mice immunized and boosted with MCPS or MCPS-TT in different ways. The panels of MAbs were examined for isotype, fine specificity, affinity, and V(H) gene family usage. The use of MCPS-TT resulted in a shift in the isotype from immunoglobulin M (IgM) and IgG3 elicited in response to the MCPS to primarily IgG1. This isotype shift was accompanied by a change in the fine specificity of the response to the conjugate compared to that of PS. New fine specificities and increased affinity were observed in response to the TD antigen (Ag). Dot blot and Northern analyses of MCPS MAbs revealed that V(H) gene family usage is dominated by V(H)J558, used by 23 of 39 MAbs. V(H)3609 was seen in three MAbs of restricted fine specificity. V(H)Q52, V(H)7183, and V(H)VGAM3-8 were seen in more than one MAb across these panels, while V(H)10 and V(H)X24 were detected only once in response to the TI-2 Ag. All MAbs in the panels utilized kappa light chains, and all functional J(kappa) genes were expressed.
A Simple and Efficient Route to Transparent Nanocomposites (2008)

The use of multicomponent solvent systems and multiply functionalized emulsifiers opens a versatile avenue to high-quality nanocomposites. Quantitative transfer of inorganic particles from an aqueous dispersion directly to hydrophobic solvent, where aggregation of the particles is fully suppressed, can be achieved on a large scale. Due to additional functionality on the surfaces, the particles can interact with a polymer matrix, allowing formation of homogeneous organic–inorganic hybrid materials.
Widely tunable continuous-wave mid-infrared laser source based on difference-frequency generation in AgGaS_2 (1998)

We demonstrate difference-frequency generation in the 6.8-12.5-mum range by mixing two high-power single-frequency laser diodes in a type II AgGaS(2) crystal. This compact all-solid-state scheme provides maximum output powers that exceed 1 muW and permits continuous adjustment-free scans larger than 2 cm(-1) across the entire tuning range.
A direct requirement for Hedgehog signaling for normal specification of all ventral progenitor domains in the presumptive mammalian spinal cord (2002)

The hedgehog signaling pathway organizes the developing ventral neural tube by establishing distinct neural progenitor fates along the dorsoventral axis. Smoothened (Smo) is essential for all Hedgehog (Hh) signaling, and genetic inactivation of Smo cells autonomously blocks the ability of cells to transduce the Hh signal. Using a chimeric approach, we examined the behavior of Smo null mutant neural progenitor cells in the developing vertebrate spinal cord, and we show that direct Hh signaling is essential for the specification of all ventral progenitor populations. Further, Hh signaling extends into the dorsal half of the spinal cord including the intermediate Dbx expression domain. Surprisingly, in the absence of Sonic hedgehog (Shh), we observe the presence of a Smo-dependent Hh signaling activity operating in the ventral half of the spinal cord that most likely reflects Indian hedgehog (Ihh) signaling originating from the underlying gut endoderm. Comparative studies of Shh, Smo, and Gli3 single and compound mutants reveal that Hh signaling acts in part to specify neural cell identity by counteracting the repressive action of Gli3 on p0, p1, p2, and pMN formation. However, whereas these cell identities are restored in Gli3/Smo compound mutants, correct stratification of the rescued ventral cell types is lost. Thus, Hh signaling is essential for organizing ventral cell pattern, possibly through the control of differential cell affinities.
A Radioimmunoassay for 1,25-Dihydroxycholecalciferol (1978)

1. 1alpha,25-Dihydroxy-25-hemisuccinate cholecalciferol has been synthesized and conjugated to bovine serum albumin. 2. This conjugate is immunogenic; when injected into rabbits antibodies of high affinity for 1alpha,25-dihydroxycholecalciferol were obtained. 3. Vitamin D metabolites lacking the 1alpha-hydroxy group were of lower cross-reactivity with the antibodies. 4. By using these antibodies and 1alpha,25-[23,24-3H]dihydroxycholecalciferol as tracer a sensitive radioimmunoassay has been developed capable of detecting 20 pg of 1alpha,25-dihydroxycholecalciferol.
Katalytische metallorganische Reaktionen von Ammoniak (2010)

Abstract Bis vor kurzem ging Ammoniak nur selten katalytische Transformationen in Gegenwart von Homogenkatalysatoren ein, und die Entwicklung derartiger Reaktionen, die unter milden Bedingungen selektiv nur ein Produkt ergeben, ist auf vielzählige Hindernisse gestoßen. Kürzlich entwickelte Katalysatoren ermöglichen es nun, über verschiedenartige Reaktionen Produkte mit stickstoffhaltigen funktionellen Gruppen aus Ammoniak herzustellen. Diese Reaktionen umfassen Hydroaminomethylierungen, reduktive Aminierungen, Alkylierungen, allylische Substitutionen, Hydroaminierungen und Kreuzkupplungen. Dieser Kurzaufsatz präsentiert Beispiele für solche Reaktionen ebenso wie die Faktoren, die die Katalysatoraktivität und ‐selektivität steuern.
Retrobiosynthetic NMR Studies with 13C-Labeled Glucose (1997)

The biosynthesis of gallic acid was studied in cultures of the fungus Phycomyces blakesleeanus and in leaves of the tree Rhus typhina. Fungal cultures were grown with [1-13C]glucose or with a mixture of unlabeled glucose and [U-13C6]glucose. Young leaves of R. typhina were kept in an incubation chamber and were supplied with a solution containing a mixture of unlabeled glucose and [U-13C6]glucose via the leaf stem. Isotope distributions in isolated gallic acid and aromatic amino acids were analyzed by one-dimensional 1H and 13C NMR spectroscopy. A quantitative analysis of the complex isotopomer composition of metabolites was obtained by deconvolution of the 13C13C coupling multiplets using numerical simulation methods. This approach required the accurate analysis of heavy isotope chemical shift effects in a variety of different isotopomers and the analysis of long range 13C13C coupling constants. The resulting isotopomer patterns were interpreted using a retrobiosynthetic approach based on a comparison between the isotopomer patterns of gallic acid and tyrosine. The data show that both in the fungus and in the plant all carbon atoms of gallic acid are biosynthetically equivalent to carbon atoms of shikimate. Notably, the carboxylic group of gallic acid is derived from the carboxylic group of an early intermediate of the shikimate pathway and not from the side chain of phenylalanine or tyrosine. It follows that the committed precursor of gallic acid is an intermediate of the shikimate pathway prior to prephenate or arogenate, most probably 5-dehydroshikimate. A formation of gallic acid via phenylalanine, the lignin precursor, caffeic acid, or 3,4, 5-trihydroxycinnamic acid can be ruled out as major pathways in the fungus and in young leaves of R. typhina. The incorporation of uniformly 13C-labeled glucose followed by quantitative NMR analysis of isotopomer patterns is suggested as a general method for biosynthetic studies. As shown by the plant experiment, this approach is also applicable to systems with low incorporation rates.
Recovering waste industrial heat efficiently (1983)

Organic Rankine Cycles (ORC's) are being used in the generation of electrical or mechanical power in situations where little demand exists for process steam. Using organic fluids in Rankine cycles improves the potential for economic recovery of waste heat. The right organic fluid can enhance the conversion efficiency by tailoring the ORC heat recovery cycle to the thermodynamic characteristics of the waste heat stream. The selection of the working fluid is affected by its flammability, toxicity, environmental impact, materials compatibility, and cost. Water, ethanol, 2-methyl Pyridine/H2O, Flourinol, Toluene, Freon R-11, and Freon R-113 are compared. An organic cycle using toluene as the working fluid is schematicized.
Improving the Centralized Control of Thermostatically Controlled Appliances by Obtaining the Right Information (2014)

This letter presents a performance enhancement for a previously developed direct load control scheme that controls (toggles on/off) thermostatically controlled appliances (TCAs) through two-way communication infrastructure for providing load balancing services. In addition to device operating temperature and on/off status (TCA states), two more pieces of information, rates of temperature increase and decrease (RTI/RTD), are calculated at each TCA and communicated to the central controller. By communicating the RTI/RTD to the central controller, the same or even better control performance can be achieved at 2-3 times longer sampling periods, showing significant reduction of the communication needs from each TCA to the central controller.
Investigating the ArF laser stability of CaF 2 at elevated fluences (2005)

Combined measurements of transmission T, absorption A and total scattering TS revealed the high accuracy of all applied measurement techniques by obtaining a sum T+A+TS+R = (100±0.3)% (R denotes the Fresnel reflection). In order to investigate CaF2 at high fluences, a variety of samples from high purity excimer grade to research grade was irradiated (80 ... 150 mJ/cm 2, 2*106 ...7*106 pulses) and characterized before and after irradiation by total scattering, laser induced fluorescence (LIF) and transmission measurements. Total scattering mappings showed negligible and measurable scattering in excimer grade and some research samples of minor purity, respectively. For the first time to our knowledge, laser induced fluorescence measurements revealed increasing (580nm, 740 nm) as well as decreasing (313 nm, 333 nm) emissions. The small increases of the linear absorption, obtained in all samples by transmission measurements, were used to distinguish high from minor quality material. For high quality samples the linear absorption change scales with NH3 (N: number of pulses), whereas for minor quality research samples a NH2-scaling was found.
Cloud-based mobile augmented reality, pitfalls and strategies in a realtime deployment (2014)

With the rise of Google Glass, etc., the era is now ripe for deeply context-aware Mobile Augmented Reality. With well-positioned cameras, 4G(+) connectivity, and public clouds, continuous (strong) computer vision is a possibility. Many research prototype mobile augmented reality systems assume and leverage a powerful backend system to alleviate resource-constrained mobile devices, often prescribed to be a ``cloud" service. This architecture, while promising and useful, introduces new complications to a practical deployment. For augmented reality, latency is a key limiting factor to the user's perception of quality. Latency, however, is nontrivial even with the massive, worldwide public cloud deployments available today. A second limiting factor is cost. Computational resources while ``cheap" in public clouds are not free. In this talk, I will discuss an example Mobile Augmented Reality system that deploys a realtime, latency-sensitive (AR) application with cloud backend processing in the critical path. In this system, we seek to dampen these challenging effects through a hybrid mobile-plus-cloud architecture that leverages both sensing and cloud-based strategies for mitigation.