gebhart/patrepeval huggingface dataset:
Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics   (2010)

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces beta-caryophyllene and alpha-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.
Representing Motion in a Static Image: Constraints and Parallels in Art, Science, and Popular Culture (2002)

Representing motion in a picture is a challenge to artists, scientists, and all other imagemakers. Moreover, it presents a problem that will not go away with electronic and digital media, because often the pedagogical purpose of the representation of motion is more important than the motion itself. All satisfactory solutions evoke motion-for example, dynamic balance (or broken symmetry), stroboscopic sequences, affine shear (or forward lean), and photographic blur-but they also typically sacrifice the accuracy of the motion represented, a solution often unsuitable for science. Vector representations superimposed on static images allow for accuracy, but are not applicable to all situations. Workable solutions are almost certainly case specific and subject to continual evolution through exploration by imagemakers.
Permeability characteristics of lipid bilayers from lipoic acid-derived phosphatidylcholines. Comparison of monomeric, crosslinked and noncrosslinked polymerized membranes (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPermeability characteristics of lipid bilayers from lipoic acid-derived phosphatidylcholines. Comparison of monomeric, crosslinked and noncrosslinked polymerized membranesJames. Stefely, Michael A. Markowitz, and Steven L. RegenCite this: J. Am. Chem. Soc. 1988, 110, 22, 7463–7469Publication Date (Print):October 1, 1988Publication History Published online1 May 2002Published inissue 1 October 1988https://pubs.acs.org/doi/10.1021/ja00230a030https://doi.org/10.1021/ja00230a030research-articleACS PublicationsRequest reuse permissionsArticle Views717Altmetric-Citations52LEARN 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
Murine 12/15-Lipoxygenase Regulates ATP-binding Cassette Transporter G1 Protein Degradation through p38- and JNK2-dependent Pathways (2009)

12/15-Lipoxygenase (12/15LO) plays a role in the pathogenesis of atherosclerosis and diabetes and has been implicated in low density lipoprotein oxidation. Murine macrophages express high levels of 12/15LO and are key cells involved in the accumulation and efflux of oxidized low density lipoprotein in the arterial wall. During this process, macrophages up-regulate scavenger receptors that regulate lipid uptake, and ATP-binding cassette (ABC) transporters, that regulate lipid efflux. We have previously demonstrated that 12/15LO enhances the turnover and serine phosphorylation of ABCG1. In the current study, we further elucidate the mechanisms by which 12/15LO regulates ABCG1. Proteasomal inhibitors blocked the down-regulation of ABCG1 expression and resulted in accumulation of phosphorylated ABCG1. Macrophages that lack 12/15LO have enhanced transporter expression, reduced ABCG1 phosphorylation, and increased cholesterol efflux. Conversely, macrophages that overexpress 12/15LO have reduced ABCG1 expression, increased transporter phosphorylation, and reduced cholesterol efflux. 12/15LO plays a key role in activating the MAPK pathway. Inhibition of the p38 or JNK pathways with pharmacological inhibitors or dominant negative constructs blocked 12S-hydroxyeicosatetranoic acid-mediated degradation of ABCG1. Moreover, we isolated macrophages from JNK1-, JNK2-, and MKK3-deficient mice to analyze the involvement of specific MAPK pathways. JNK2- and MKK3-, but not JNK1-deficient macrophages were resistant to the down-regulation of ABCG1 protein, reduction in efflux, and increase in serine phosphorylation by 12S-hydroxyeicosatetranoic acid. These findings provide evidence that 12/15LO regulates ABCG1 expression and function through p38- and JNK2-dependent mechanisms, and that targeting these pathways may provide novel approaches for regulating cholesterol homeostasis.
Quasistatic Treatment of Spatial Phenomena in Reactor Dynamics (1966)

(1966). Quasistatic Treatment of Spatial Phenomena in Reactor Dynamics. Nuclear Science and Engineering: Vol. 26, No. 4, pp. 563-565.
Colorimetric / fluorescent bacterial sensing by agarose-embedded lipid / polydiacetylene films (2007)

This work demonstrated a new simple chromatic platform for bacterial detection, based on the generation of easily recorded colour and fluorescence changes. The new bacterial detection scheme is highly generic and could be employed for varied practical uses, in which, rapid reporting on bacterial presence is required.
Cyanocarbon Chemistry. XVIII.<sup>1</sup> Tricyanovinylation of Hydrazones and Other Nucleophilic Substances (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyanocarbon Chemistry. XVIII.1 Tricyanovinylation of Hydrazones and Other Nucleophilic SubstancesJ. R. Roland and B. C. McKusickCite this: J. Am. Chem. Soc. 1961, 83, 7, 1652–1657Publication Date (Print):April 1, 1961Publication History Published online1 May 2002Published inissue 1 April 1961https://pubs.acs.org/doi/10.1021/ja01468a025https://doi.org/10.1021/ja01468a025research-articleACS PublicationsRequest reuse permissionsArticle Views127Altmetric-Citations23LEARN 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
Porous Liquids: A Promising Class of Media for Gas Separation (2014)

A porous liquid containing empty cavities has been successfully fabricated by surface engineering of hollow structures with suitable corona and canopy species. By taking advantage of the liquid-like polymeric matrices as a separation medium and the empty cavities as gas transport pathway, this unique porous liquid can function as a promising candidate for gas separation. Moreover, such a facile synthetic strategy can be further extended to the fabrication of other types of nanostructure-based porous liquid, opening up new opportunities for preparation of porous liquids with attractive properties for specific tasks.
Montelukast inhibition of resting and GM-CSF-stimulated eosinophil adhesion to VCAM-1 under flow conditions appears independent of cysLT1R antagonism (2008)

Montelukast (MLK) is a cysteinyl leukotriene receptor-1 (cysLT(1)R) antagonist with inhibitory effects on eosinophils, key proinflammatory cells in asthma. We assessed the effect of MLK on resting and GM-CSF-stimulated eosinophil adhesion to recombinant human (rh)VCAM-1 at different flow rates using our novel microflow system. At 1 or 2 dyn cm(-2), shear-stress unstimulated eosinophils tethered immediately to rhVCAM-1, "rolled" along part of the channel until they tethered, or rolled without tethering. At flow rates greater than 2 dyn cm(-2), adherent eosinophils began to be displaced from rhVCAM-1. MLK (10 nM and 100 nM) gave partial ( approximately 40%) but significant (P<0.05) inhibition of unstimulated eosinophil adhesion to rhVCAM-1 at 1 or 2 dyn cm(-2) shear stress. Once adhered, unstimulated eosinophils did not exhibit morphological changes, and GM-CSF-stimulated eosinophil adhesion under flow was characterized by greater cell flattening with significant (P<0.05) inhibition of adherent cell numbers by 100 nM MLK observed. This effect appeared specific for MLK, as the analog (E)-3-[[[3-[2-(7-chloro-2-quinolinyl)ethenyl]phenyl]-[[3-dimethylamino)-3-oxopropyl]thio]methyl]thio]-propanoic acid, sodium salt, had no significant effect on eosinophil adhesion to VCAM-1. The possibility that LTC(4), released from unstimulated or GM-CSF-treated eosinophils, contributed to their adhesion to VCAM-1 was excluded as the LT biosynthesis inhibitor 3-[1-(p-Chlorobenzyl)-5-(isopropyl)-3-t-butylthioindol-2-yl]-2,2-dimethylpropanoic acid had no inhibitory effect, and exogenously added LTC(4) did not enhance eosinophil adhesion. In contrast, LTD(4) enhanced eosinophil adhesion to VCAM-1, an effect blocked by MLK (10 and 100 nM). These findings demonstrate that MLK-mediated inhibition of unstimulated and GM-CSF-stimulated eosinophil adhesion to VCAM-1 under shear-stress conditions appears independent of cysLT(1)R antagonism.
Chemical functionalization of graphene (2008)

Experimental and theoretical results on chemical functionalization of graphene are reviewed. Using hydrogenated graphene as a model system, general principles of the chemical functionalization are formulated and discussed. It is shown that, as a rule, 100% coverage of graphene by complex functional groups (in contrast with hydrogen and fluorine) is unreachable. A possible destruction of graphene nanoribbons by fluorine is considered. The functionalization of infinite graphene and graphene nanoribbons by oxygen and by hydrofluoric acid is simulated step by step.
[An "atraumatic" universal needle for single-shot regional anesthesia: clinical results and a 6 year trial in over 30,000 regional anesthesias]. (1987)

The so-called "atraumatic" needle was developed by modification of two essential features of the Whitacre Spinal needle. The new atraumatic needle tip is universally suitable for all single-shot techniques of regional anesthesia. This is the result of a 6-year test period with 34,950 applications of 24- and 22-Gauge needles in spinal anesthesia, diagnostic lumbar puncture, peridural anesthesia, plexus anesthesia, peripheral nerve blocks with a Teflon-coated version (unipolar electrostimulation), and lumbar sympathetic and celiac plexus blocks. Postspinal headache was observed following 0.02% of punctures for anesthetic or diagnostic purposes. Transient monosymptomatic nerve damage occurred in 1 case after axillary block (0.009%). No permanent neurological sequelae were observed due to vascular, neural, or dural lesions. In comparison, 10 cases of persistent traumatic nerve damage were reported to be caused by conventional needles during the last decade. An analysis of these cases reveals some reasons for underestimating the risk of neurological sequelae after regional anesthesia. The routine clinical use of this type of atraumatic needle revealed no disadvantages with regard to efficacy of nerve blocks or training of anesthetists. Due to the extremely low incidence of postspinal headache, this needle has been used for spinal therapy and diagnostic lumbar punctures in outpatient pain therapy for 2 years. As of this time, the overall risk of outpatient lumbar puncture cannot be estimated. Our experience should encourage further controlled studies to evaluate criteria for excluding those patients unsuited for outpatient spinal anesthesia and lumbar puncture.
On the generation of non-Gaussian noise using the discrete-Fourier transform method (2002)

In this paper, specific time-domain noise signals with
predetermined statistical characteristics, are synthesized by means of
phase spectrum manipulations in the frequency domain. Each signal
maintains a constant magnitude frequency response. However, different
phase response distributions have been used to manipulate the phase
spectrum in order to obtain tailored statistical characteristics in the
time-domain. The sought characteristics include: kurtosis, skewness, and
crest factor. Simulation results are presented
A CMOS-Compatible Biological Transducer for Creatinine Detection: MIP-Gate ISFET (2009)

In this paper, it demonstrates a CMOS-compatible transducer for creatinine detection. Different with traditional application of ISFET (Ion Selective Field Effect Transistor), it is not for the hydrogen ion detection. To combine the CMOS MEMS platform with MIP (Molecular Imprinting Polymer) micro coating technologies, the developed MlP-gate ISFET could be used for the detecting of creatinine. The experiment results showed that the difference of response current was about 13? A when the concentration was varied from 0.199 mg/mL to 0.787 mg/mL. Beside, this paper successfully demonstrates the possibility of the liquid isolation and localized MIP coating technology.
EN EL MUNDO, 70 POR CIENTO DE LAS TIERRAS SECAS PRODUCTIVAS AMENAZADO POR LA DESERTIFICACION (1995)

ANTE EL ADVERSO PANORAMA QUE PRESENTAN LAS TIERRAS PRODUCTIVAS, OCASIONADO POR LA DESERTIFICACION COMO CONSECUENCIA DE LAS ACTIVIDADES HUMANAS, LA OFICINA REGIONAL DE LA FAO PARA AMERICA LATINA Y EL CARIBE Y EL PROGRAMA DE NACIONES UNIDAS PARA EL MEDIO AMBIENTE, EN COLABORACION CON EL JARDIN BOTANICO DE LA UNAM, ORGANIZARON EL PRIMER CURSO TALLER SOBRE TECNICAS APROPIADAS PARA LA PROPAGACION DE ESPECIES DE IMPORTANCIA ECONOMICA PARA LAS ZONAS ARIDAS Y SEMIARIDAS DE AMERICA LATINA Y EL CARIBE. EN LA INAUGURACION, EL DOCTOR JUAN IZQUIERDO, OFICIAL REGIONAL DE PRODUCCION VEGETAL DE LA FAO EN SANTIAGO DE CHILE, DEFINIO A LA DESERTIFICACION COMO UNA RUPTURA DEL FRAGIL EQUILIBRIO QUE HIZO POSIBLE EL DESARROLLO DE LA VIDA EN LAS ZONAS ARIDAS DEL PLANETA. EN ESTA RUPTURA, DIJO, SE DESENCADENAN UNA SERIE DE PROCESOS AUTODESTRUCTIVOS QUE SE TRADUCEN EN DISMINUCION DE LOS RENDIMIENTOS AGRICOLAS, PECUARIOS Y FORESTALES, ASI COMO EN LA PERDIDA DE LA DIVERSIDAD BIOLOGICA. COMO UNA ALTERNATIVA AL PROCESO DE DESERTIFICACION, EL DOCTOR IZQUIERDO SENALO A LA BIOTECNOLOGIA, YA QUE ESTA PERMITE ACELERAR EL PROCESO EN LA OBTENCION DE COPIAS FIELES DE DIVERSAS ESPECIES, AISLAR GENES DE ALTO VALOR ECONOMICO Y, CONSECUENTEMENTE, QUE LAS COMUNIDADES QUE VIVEN EN ZONAS ARIDAS AGREGUEN VALOR A SUS PLANTAS.
Cathode art (1949)

Patent attorneys continually refer to “one skilled in the art.” Somehow, this has an antique flavor. It smacks of wrinkles, recipes, and secret formulae, rather than of the firm basis we imagine must underlie our technological civilization. One would think of art, perhaps, in the case of the physician, who deals with a system as complicated and as little understood as the human body, but scarcely in connection with a matter of applied physics, involving old and well known phenomena of great commercial importance. A particular example should, however, convince the most skeptical that there is sometimes art where one would wish and hope for science. Lest it be too discouraging, the story that follows has, I believe, a happy ending, for it looks as if the physicists and chemists are at last reaching indisputable conclusions concerning the functioning of the oxide-coated thermionic cathode.
Quantitative herd-level evaluation of a commercially available vaccine for control of Salmonella in dairy cattle (2011)

Salmonella continues to threaten public health as well as negatively impact dairy producers on multiple levels. Efficacious solutions to control Salmonella among dairy cattle have long been sought to alleviate these problems. A novel vaccine technology has been developed based on purified siderophore receptors and porin proteins (SRP®) derived from Salmonella Newport. When vaccinated with these SRP® cattle are stimulated to produce antibodies which act in concert with host defenses to disrupt iron acquisition of pathogenic bacteria. To evaluate the effectiveness of this technology, a prospective cohort study was designed utilizing herds (n = 11) that practiced whole herd vaccination with the SRP® vaccine (vaccinated cohort) and herds (n = 11) that had not used the SRP® vaccine. Samples were collected during four rounds at approximately six week intervals from June through October 2009. Samples were transported to the laboratory at West Texas A&M University and cultured for the prevalence of Salmonella using selective enrichment methods. Salmonella isolates were evaluated for antimicrobial susceptibility and serotype. Data was analyzed using commercially available software to evaluate the herd-level effects of vaccination. Salmonella was ubiquitous throughout the Texas Panhandle and Eastern New Mexico, within-herd animal level estimates of prevalence ranged from 0.0 – 92%, over the length of the study period. Overall all rounds vaccinated herds had decreased (P = 0.012) Salmonella prevalence (15.3 vs. 27.5%). Vaccinated herds had numerically fewer Salmonella isolates belonging to the Newport serotype. Salmonella Typhimurium isolates were recovered approximately equally from vaccinated and non-vaccinated herds. Isolates from vaccinated herds were resistant to fewer antimicrobials throughout the study period. The ACSSuT(resistant to ampicillin, chloramphenicol, streptomycin, sulphisoxazole, and tetracycline) and MDR-AmpC (ACSSuT resistance plus resistance to ceftiofur and amoxicillin/clavulanate) resistant phenotypes were more frequently observed among non-vaccinated herds and none of the isolates from vaccinated or non-vaccinated herds were resistant to nalidixic acid, gentamicin, ciprofloxacin, or amikacin. These findings indicate vaccine efficacy for the reduction of Salmonella prevalence. Dairy operators along with herd veterinarians are encouraged to utilize this data with other herd specific factors in determining whether to use this specific vaccine.
Encoding Spike Patterns in Multilayer Spiking Neural Networks (2015)

Information encoding in the nervous system is supported through the precise spike-timings of neurons; however, an understanding of the underlying processes by which such representations are formed in the first place remains unclear. Here we examine how networks of spiking neurons can learn to encode for input patterns using a fully temporal coding scheme. To this end, we introduce a learning rule for spiking networks containing hidden neurons which optimizes the likelihood of generating desired output spiking patterns. We show the proposed learning rule allows for a large number of accurate input-output spike pattern mappings to be learnt, which outperforms other existing learning rules for spiking neural networks: both in the number of mappings that can be learnt as well as the complexity of spike train encodings that can be utilised. The learning rule is successful even in the presence of input noise, is demonstrated to solve the linearly non-separable XOR computation and generalizes well on an example dataset. We further present a biologically plausible implementation of backpropagated learning in multilayer spiking networks, and discuss the neural mechanisms that might underlie its function. Our approach contributes both to a systematic understanding of how pattern encodings might take place in the nervous system, and a learning rule that displays strong technical capability.
Nanoparticle Characterization by PCS: The Analysis of Bimodal Distributions (2008)

Photon correlation spectroscopy (PCS) is widely used for nanoparticle characterization, being particularly suited for the analysis of narrow distributions. However, because of its simplicity, it would be important to extend it to other situations, namely to wide particle size distributions and to bimodal samples. In this work an evaluation of the discriminating capability of the most common algorithms used in PCS to deconvolute the measured auto-correlation function, when analyzing bimodal samples, was performed. The results show that the CONTIN algorithm enables a better description of bimodal mixtures, though its performance is dependent on the characteristics of the sample and on operating conditions such as the sampling time. Additionally, a close analysis of the auto-correlation function revealed the existence of systematic deviations in the slope of the first section of that function when a bimodal sample is compared with the equivalent monomodal one (same average diameter). The results obtained indicate that the inspection of the first part of the auto-correlation function produces important information that can reveal the presence of more than one peak when an unknown sample is analyzed. This feature is rather important since the inversion process may mask one of the peaks due to the ill-conditioned nature of the problem. This prior information can be useful to alert the user to the need for an iterative adjustment of the parameters of the inversion process in order to better reveal all the peaks in the sample.
GD3 Synthase Overexpression Sensitizes Hepatocarcinoma Cells to Hypoxia and Reduces Tumor Growth by Suppressing the cSrc/NF-κB Survival Pathway (2009)

These findings underscore a role for GD3 in hypoxia susceptibility by disabling the c-Src/NF-kappaB survival pathway resulting in lower Mn-SOD expression, which may be of relevance in hepatocellular carcinoma therapy.