gebhart/patrepeval huggingface dataset:
Superhydrophobic Surfaces as a Source of Airborne Singlet Oxygen through Free Space for Photodynamic Therapy (2020)

A superhydrophobic (SH) sandwich system has been developed to enable "contact-free" airborne singlet oxygen (<sup>1</sup>O<sub>2</sub>) delivery to a water droplet. The contact-free feature means that the sensitizer is physically separated from the droplet, which presents opportunities for photodynamic therapy (PDT). Trapping of airborne <sup>1</sup>O<sub>2</sub> in a H<sub>2</sub>O droplet residing on a lower SH surface was monitored with 9,10-anthracene dipropionate dianion by varying distances to an upper <sup>1</sup>O<sub>2</sub>-generating surface. Short distances of 20 μm efficiently delivered airborne <sup>1</sup>O<sub>2</sub> to the droplet in single-digit picomolar steady-state concentrations. Delivery decreases linearly with distance, but 50% of the <sup>1</sup>O<sub>2</sub> steady-state concentration is trapped at a distance of 300 μm from the generating surface. The 1270 nm luminescence intensity was measured within the SH sandwich system, confirming the presence of airborne <sup>1</sup>O<sub>2</sub>. Physical quenching of <sup>1</sup>O<sub>2</sub> to ground-state <sup>3</sup>O<sub>2</sub> by the water droplet itself and both physical and chemical quenching of <sup>1</sup>O<sub>2</sub> by the water droplet containing the trap 9,10-anthracene dipropionate dianion are observed. Unlike a majority of work in the field of PDT with dissolved sensitizers, where <sup>1</sup>O<sub>2</sub> diffuses short (hundreds of nanometers) distances, we show the delivery of airborne <sup>1</sup>O<sub>2</sub> via a superhydrophobic surface is effective through air in tenths of millimeters distances to oxidize an organic compound in water. Our results provide not only potential relevance to PDT but also surface bacterial inactivation processes.
The Flagellar Regulator TviA Reduces Pyroptosis by Salmonella enterica Serovar Typhi (2015)

To discern virulent from innocuous microbes, the innate immune system senses events associated with bacterial access to immunoprivileged sites such as the host cell cytosol. One such pathway is triggered by the cytosolic delivery of flagellin, the major subunit of the flagellum, by bacterial secretion systems. This leads to inflammasome activation and subsequent proinflammatory cell death (pyroptosis) of the infected phagocyte. In this study, we demonstrate that the causative agent of typhoid fever, Salmonella enterica serovar Typhi, can partially subvert this critical innate immune recognition event. The transcriptional regulator TviA, which is absent from Salmonella serovars associated with human gastroenteritis, repressed the expression of flagellin during infection of human macrophage-like (THP-1) cells. This mechanism allowed S. Typhi to dampen inflammasome activation, leading to reduced interleukin-1β (IL-1β) secretion and diminished cell death. Likewise, the introduction of the tviA gene in nontyphoidal Salmonella enterica serovar Typhimurium reduced flagellin-induced pyroptosis. These data suggest that gene regulation of virulence factors enables S. Typhi to evade innate immune recognition by concealing a pathogen-induced process from being sensed by the inflammasome.
Bacterial vaginosis – a microbiological and immunological enigma (2005)

The development of bacterial vaginosis (BV) among women of childbearing age and the resulting quantitative and qualitative shift from normally occurring lactobacilli in the vagina to a mixture of mainly anaerobic bacteria is a microbiological and immunological enigma that so far has precluded the formulation of a unifying generally accepted theory on the aetiology and clinical course of BV. This critical review highlights some of the more important aspects of BV research that could help in formulating new basic ideas respecting the biology of BV, not least the importance of the interleukin mediators of local inflammatory responses and the bacterial shift from the normally occurring lactobacilli species: L. crispatus, L. gasseri, L. jensenii, and L. iners to a mixed flora dominated by anaerobic bacteria.
Potent inhibition of human immunodeficiency virus type 1 in primary T cells and alveolar macrophages by a combination anti-Rev strategy delivered in an adeno-associated virus vector (1997)

The rate of viral replication appears to play a pivotal role in human immunodeficiency virus type 1 (HIV-1) pathogenesis and disease progression as it outstrips the capacity of the immune system to respond. Important cellular sites for HIV-1 production include T lymphocytes and tissue macrophages. Antiviral strategies, including newer treatment modalities such as gene therapy of HIV-1-susceptible cell populations, must be capable of engendering durable inhibitory effects to HIV-1 replication in both of these primary cell types in order to be effective. Among the potential genetic targets for intervention in the HIV-1 life cycle, the Rev regulatory system, consisting of Rev and its binding site, the Rev-responsive element (RRE), stands out as particularly attractive. Rev is essential for maintaining the stability of the viral genomic RNA as well as viral mRNAs encoding key structural and regulatory proteins. Moreover, it exhibits favorable threshold kinetics, in that Rev concentrations must rise above a critical level to exert their effect. To disable Rev function, primary T cells or macrophages were transduced with anti-Rev single-chain immunoglobulin (SFv) or RRE decoy genes either singly or in combination by employing adeno-associated virus vectors and then challenged with HIV-1. By directing both a protein and a nucleic acid against the normal interaction between Rev and the RRE, this genetic antiviral strategy effectively inhibited infection by either clinical or laboratory virus isolates. These results provide a framework for novel interventions to reduce virus production in the infected host.
A CELD‐fusion method for rapid determination of the DNA‐binding sequence specificity of novel plant DNA‐binding proteins (2005)

Summary The current focus of many functional genomic studies is on the elucidation of gene regulatory networks. The functional analyses of transcription factors and their DNA‐binding sites, in conjunction with genome‐wide expression profiling, are crucial in understanding of gene regulatory networks. This paper describes an efficient and easy method for characterizing the DNA‐binding sequence specificity of novel plant transcription factors. This new method is based on the fusion of a DNA‐binding protein (DBP) to 6×His‐tagged cellulase D (CELD), which serves both as a means for affinity purification of DBP‐DNA complex in the selection of binding sites from a pool of biotinylated random‐sequence oligonucleotides and as a reporter for measurement of DNA‐binding activity. Thus, it eliminates the use of radioactivity and gel electrophoresis techniques currently used for purification of DBP‐DNA complexes and assays of DNA‐binding activity. The effectiveness of this method was demonstrated by the success of simultaneous selection of the binding sites of nine plant DBPs from four superfamilies (AP2, bHLH, NAC and MYB). The high‐throughput capacity of CELD‐based DNA‐binding assays allows the quantitative analysis of the binding sequence specificity from a large number of DBP‐selected oligonucleotides. The binding sequence specificity of three novel transcription factors (rice OsbHLH66, wheat TaNAC69 and TaMYB80), determined with this method, is presented. This new method provides the capacity of high‐throughput analysis on the DNA‐binding sequence specificity of a large number of putative transcription factors, predicted on the basis of conserved DNA‐binding domains.
Phase Shifts of Potassium Uptake Rhythm in Lemna gibba G3 Due to Light, Dark or Temperature Pulses (1983)

Phase shifts in potassium uptake rhythm during continuous light in flow medium (FMC) and static (STC) culture of Lemna gibba G3, produced by various light and temperature pulses were examined. The phase responses were very similar to those known for a variety of circadian rhythms: A pulse of high temperature (39°C) shifted the phase in the same way as a light pulse inserted during darkness. A pulse of darkness, or of low temperature (5 or 10°C), however, caused a phase shift that was the inverse of that caused by a light pulse. A temperature pulse of definite timing erased the rhythm. Although the rhythms in the STC and FMC had essentially the same phase response, a highintensity light pulse was more effective in FMC and dark and temperature pulses in STC.
Studies on the anticoagulant, antimetastatic and heparin-binding properties of ghilanten-related inhibitors (1991)

The purpose of this study was to investigate the structure-activity relationships of ghilanten, an anticoagulant-antimetastatic protein of the South American leech Haementeria ghilianii. Five sequence-related variants of ghilanten, termed P1-P5, were purified and were shown to potently block the active-site hydrolysis of methoxycarbonyl-D-cyclohexylglycyl-glycyl-arginine-p-nitroanilide acetate by the human blood coagulation enzyme factor Xa; inhibition was rapid and stoichiometric. The amino acid sequence of P5 revealed a consensus sequence for heparin-binding at the carboxy-terminus. A synthetic peptide homologous to this region (93P-N-G-L-K-R-D-K-L-G-C-E-Y-C-E-C-R-P-K-R-K-L-I-P-R-L-S119) bound 125I-labelled heparin maximally at physiological pH and salt concentration. When administered intravenously to mice, the peptide suppressed lung metastases although less potentially than whole ghilanten. These findings suggest that the carboxy-terminal heparin-binding region may play a role in the antimetastatic action of the inhibitor.
Visible Reflectance Hyperspectral Imaging:  Characterization of a Noninvasive, in Vivo System for Determining Tissue Perfusion (2002)

We characterize a visible reflectance hyperspectral imaging system for noninvasive, in vivo, quantitative analysis of human tissue in a clinical environment. The subject area is illuminated with a quartz-tungsten-halogen light source, and the reflected light is spectrally discriminated by a liquid crystal tunable filter (LCTF) and imaged onto a silicon charge-coupled device detector. The LCTF is continuously tunable within its useful visible spectral range (525-725 nm) with an average spectral full width at half-height bandwidth of 0.38 nm and an average transmittance of 10.0%. A standard resolution target placed 5.5 ft from the system results in a field of view with a 17-cm diameter and an optimal spatial resolution of 0.45 mm. The measured reflectance spectra are quantified in terms of apparent absorbance and formatted as a hyperspectral image cube. As a clinical example, we examine a model of vascular dysfunction involving both ischemia and reactive hyperemia during tissue reperfusion. In this model, spectral images, based upon oxyhemoglobin and deoxyhemoblobin signals in the 525-645-nm region, are deconvoluted using a multivariate least-squares regression analysis to visualize the spatial distribution of the percentages of oxyhemoglobin and deoxyhemoglobin in specific skin tissue areas.
Deep Belief Networks Based Voice Activity Detection (2012)

Fusing the advantages of multiple acoustic features is important for the robustness of voice activity detection (VAD). Recently, the machine-learning-based VADs have shown a superiority to traditional VADs on multiple feature fusion tasks. However, existing machine-learning-based VADs only utilize shallow models, which cannot explore the underlying manifold of the features. In this paper, we propose to fuse multiple features via a deep model, called deep belief network (DBN). DBN is a powerful hierarchical generative model for feature extraction. It can describe highly variant functions and discover the manifold of the features. We take the multiple serially-concatenated features as the input layer of DBN, and then extract a new feature by transferring these features through multiple nonlinear hidden layers. Finally, we predict the class of the new feature by a linear classifier. We further analyze that even a single-hidden-layer-based belief network is as powerful as the state-of-the-art models in the machine-learning-based VADs. In our empirical comparison, ten common features are used for performance analysis. Extensive experimental results on the AURORA2 corpus show that the DBN-based VAD not only outperforms eleven referenced VADs, but also can meet the real-time detection demand of VAD. The results also show that the DBN-based VAD can fuse the advantages of multiple features effectively.
Bright Ideas for Chemical Biology (2008)

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.
One-step synthesis of 5′-azido-nucleosides (1980)

Regioselective azidation of unprotected or appropriately protected nucleosides was conducted by means of the reagent triphenylphosphine–carbon tetrabromide–lithium azide. By use of this reagent, 5′-azido-5′-deoxynucleosides were prepared conveniently in one step from nucleosides in high yields. Secondary hydroxy-groups of appropriately 5′-protected nucleosides were also converted by the reagent to azido-functions with complete inversion.
An Assisted User Interface for 3D EXAMINE Mode (2002)

Despite the rapid development of 3D technologies, controlling a viewpoint in a 3D environment remains a non-trivial or even difficult task for a novice user. Previous researches have shown that motion planning techniques can be use to assist user navigation in the so-called WALK mode for VRML browsers. In this paper we propose to use a motion-planning approach for assisting viewpoint control in the EXAMINE mode for 3D browsers. This approach uses a Reconfigurable Random Forest (RRF) structure to learn the 3D environment progressively as the viewpoint moves along. Unlike previous work that simplifies the workspace by projecting the environmental obstacles into 2D polygons, we have to deal with 3D motions and 3D obstacles. Efficiency of the planner becomes crucial in designing such an intelligent user interface with an acceptable frame rate. We have implemented and incorporated the planner into a Java3D-based VRML browser and tested it with several example scenarios with satisfactory results.
Scalable and fully self-aligned n-type carbon nanotube transistors with gate-all-around (2012)

While proven to provide high performance at sub-10 nm lengths, carbon nanotube (CNT) field-effect transistors (FETs) typically employ impractical gate geometries. Here we demonstrate fully self-aligned CNTFETs that include a gate-all-around (GAA) the nanotube channels - the ideal gate geometry for a 1D CNT. These GAA-CNTFETs have 30 nm channel lengths and exhibit n-type operation with high on-currents and good switching behavior that is explained by quantum transport (NEGF) simulations. This work is an important milestone showing that a technologically relevant self-aligned device can be realized with nanotubes.
Mechanism for membrane electroporation irreversibility under high-intensity, ultrashort electrical pulse conditions (2002)

An improved electroporation model is used to address membrane irreversibility under ultrashort electric pulse conditions. It is shown that membranes can survive a strong electric pulse and recover provided the pore distribution has a relatively large spread. If, however, the population consists predominantly of larger radii pores, then irreversibility can result. Physically, such a distribution could arise if pores at adjacent sites coalesce. The requirement of close proximity among the pore sites is more easily satisfied in smaller organelles than in outer cell membranes. Model predictions are in keeping with recent observations of cell damage to intracellular organelles (e.g., mitochondria), without irreversible shock at the outer membranes, by a nanosecond, high-intensity electric pulse. This mechanism also explains the greater damage from multiple electric shocks.
Intestinal dysfunction in Parkinson's disease: Lessons learned from translational studies and experimental models (2016)

The present review intends to provide an integrated and critical appraisal of the available knowledge on the alterations of enteric neuromuscular pathways regulating gut motor activity both in humans and preclinical models of PD. Moreover, we will discuss the possible involvement of neuro-immune mechanisms in the pathophysiology of aberrant gastrointestinal gut transit and neuromuscular activity in the small and large bowel.
Efficiency in Isotetronic Acid Synthesis via a Diamine−Acid Couple Catalyzed Ethyl Pyruvate Homoaldol Reaction (2005)

[reaction: see text] L-proline failed to act as an organocatalyst in the homoaldol reaction of ethyl pyruvate; however, it reacted with the ester to give an azomethine ylide that in turn underwent 1,3-dipolar cycloaddition with a second molecule of pyruvate. Direct catalytic homoaldol reaction of ethyl pyruvate was performed using an (S)-(+)-1-(2-pyrrodinylmethyl)pyrrolidine/trifluoroacetic acid combination as organocatalyst. The use of polymer-supported reagents allowed for the lactonization of the aldol and isolation of the isotetronic acid derivative in hydroxy-free form.
Speech Enhancement With Laplacian Speech Modeling (2007)

In this paper,a new speech enhancement system with Laplacian speech modeling is proposed.The clean speech com- ponents are estimated by Minimum-Mean-Square-Error(MMSE)estimator under the assumption that the clean speech DCT coefficients are modeled by a Laplaeian distribution and the noise DCT coefficients are modeled by a Gaussian distribution.Then,the MMSE esti- mator under speech presence uncertainty and a Laplaeian model is derived.Furthermore,the proper estimators of the statistical parame- ters are proposed.The speech Laplacian parameter is estimated by a decision-directed method and the noise power is estimated by the IMCRA algorithm with Laplacian model.The simulation results show that the proposed algorithm yields less residual noise and better speech quality than the Gaussian based speech enhancement algorithms proposed in recent years.
Scalable and robust internetwork routing for mobile hosts (2002)

This paper describes a new protocol for transparently routing packets to mobile hosts operating in a large internetwork. The protocol, called the Mobile Host Routing Protocol (MHRP), allows any host to become mobile at any time, yet there is no penalty for a host being "mobile capable", since the protocol automatically uses only the standard internetwork routing mechanisms and adds no overhead when a mobile host is currently connected to its home network. The paper concentrates on the design of MHRP as it applies to the Internet using IP. Mobile hosts use only their "home" IP addresses, regardless of their current location in the Internet. No changes are required in stationary hosts that communicate with mobile hosts, and no changes are required in mobile hosts above the IP level. MHRP introduces several new features to provide better robustness for routing to mobile hosts, and provides better scalability to very large numbers of mobile hosts than previous mobile host protocols.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
옵션가격결정이론에 기반한 실물자산의 투자시기 결정 (2010)

기업은 이익창출을 위해 자본과 비용을 투입하고 재무적 타당성을 분석하여 투자의 가부를 결정한다. 일반적으로 실물자산의 투자가 창출하는 현금흐름은 투자분석시의 결과와는 달리 불확실하게 변화하고 실물자산이 내포한 여러 경영상의 유연성이 유발하는 비대칭수익구조도 사업의 가치에 영향을 미친다. 실물자산의 투자가 수반하는 다양한 경영상의 유연성들 중, 경영진이 특정 기간 동안 투자를 지연할 수 있는 투자지연의 의사결정은 시장에서 새로운 정보가 유입되면 합리적인 대응을 가능케하여 사업의 가치를 증가시키는 것으로 알려져 왔으나 투자시기의 결정에 관한 연구는 부족해왔다. 그러므로 본 연구는 투자지연이 유효한 실물자산의 투자에서 합리적인 투자시기의 결정을 위해 투자지연에 의한 사업가치의 증분과 손실회복비용을 옵션가격결정 및 관련 금융?경제이론에 기반하여 추정하고 이를 수학적 변분원리를 이용하여 최적의 투자시기 탐색을 위한 이론 모델을 구성 한 후 부동산 실물자산인 REITs(Real Estate Investment Trusts)의 사례에 적용 및 분석함으로써 실물자산의 투자시기 결정을 위한 이론적인 틀을 제시하고자 한다.
Slow-release pesticide system. Polymers of lactic and glycolic acids as ecologically beneficial, cost-effective encapsulating materials (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSlow-release pesticide system. Polymers of lactic and glycolic acids as ecologically beneficial, cost-effective encapsulating materialsRichard G. SinclairCite this: Environ. Sci. Technol. 1973, 7, 10, 955–956Publication Date (Print):October 1, 1973Publication History Published online1 May 2002Published inissue 1 October 1973https://pubs.acs.org/doi/10.1021/es60082a011https://doi.org/10.1021/es60082a011research-articleACS PublicationsRequest reuse permissionsArticle Views385Altmetric-Citations28LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Histidine kinase activity of the ETR1 ethylene receptor from Arabidopsis (1998)

ETR1 represents a prototypical ethylene receptor. Homologues of ETR1 have been identified in Arabidopsis as well as in other plant species, indicating that ethylene perception involves a family of receptors and that the mechanism of ethylene perception is conserved in plants. The amino-terminal half of ETR1 contains a hydrophobic domain responsible for ethylene binding and membrane localization. The carboxyl-terminal half of the polypeptide contains domains with homology to histidine kinases and response regulators, signaling motifs originally identified in bacteria. The putative histidine kinase domain of ETR1 was expressed in yeast as a fusion protein with glutathione S-transferase and affinity purified. Autophosphorylation of the purified fusion protein was observed on incubation with radiolabeled ATP. The incorporated phosphate was resistant to treatment with 3 M NaOH, but was sensitive to 1 M HCl, consistent with phosphorylation of histidine. Autophosphorylation was abolished by mutations that eliminated either the presumptive site of phosphorylation (His-353) or putative catalytic residues within the kinase domain. Truncations were used to delineate the region required for histidine kinase activity. An examination of cation requirements indicated that ETR1 requires Mn2+ for autophosphorylation. These results demonstrate that higher plants contain proteins with histidine kinase activity. Furthermore, these results indicate that aspects of ethylene signaling may be regulated by changes in histidine kinase activity of the receptor.