gebhart/patrepeval huggingface dataset:
Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to Bacillus subtilis (2006)

A Gram-positive, spore-forming bacillus was isolated from a sample taken from an approximately 2000-year-old shaft-tomb located in the Mexican state of Jalisco, near the city of Tequila. Tentative identification using conventional biochemical analysis consistently identified the isolate as Bacillus subtilis. DNA isolated from the tomb isolate, strain 10b(T), and closely related species was used to amplify a Bacillus-specific portion of the highly conserved 16S rRNA gene and an internal region of the superoxide dismutase gene (sodA(int)). Trees derived from maximum-likelihood methods applied to the sodA(int) sequences yielded non-zero branch lengths between strain 10b(T) and its closest relative, whereas a comparison of a Bacillus-specific 546 bp amplicon of the 16S rRNA gene demonstrated 99 % similarity with B. subtilis. Although the 16S rRNA gene sequences of strain 10b(T) and B. subtilis were 99 % similar, PFGE of NotI-digested DNA of strain 10b(T) revealed a restriction profile that was considerably different from those of B. subtilis and other closely related species. Whereas qualitative differences in whole-cell fatty acids were not observed, significant quantitative differences were found to exist between strain 10b(T) and each of the other closely related Bacillus species examined. In addition, DNA-DNA hybridization studies demonstrated that strain 10b(T) had a relatedness value of less than 70 % with B. subtilis and other closely related species. Evidence from the sodA(int) sequences, whole-cell fatty acid profiles and PFGE analysis, together with results from DNA-DNA hybridization studies, justify the classification of strain 10b(T) as representing a distinct species, for which the name Bacillus tequilensis sp. nov. is proposed. The type strain is 10b(T) (=ATCC BAA-819(T)=NCTC 13306(T)).
Protein Information and Knowledge Extractor: Discovering biological information from proteomics data (2010)

One of the main goals in proteomics is to solve biological and molecular questions regarding a set of identified proteins. In order to achieve this goal, one has to extract and collect the existing biological data from public repositories for every protein and afterward, analyze and organize the collected data. Due to the complexity of this task and the huge amount of data available, it is not possible to gather this information by hand, making it necessary to find automatic methods of data collection. Within a proteomic context, we have developed Protein Information and Knowledge Extractor (PIKE) which solves this problem by automatically accessing several public information systems and databases across the Internet. PIKE bioinformatics tool starts with a set of identified proteins, listed as the most common protein databases accession codes, and retrieves all relevant and updated information from the most relevant databases. Once the search is complete, PIKE summarizes the information for every single protein using several file formats that share and exchange the information with other software tools. It is our opinion that PIKE represents a great step forward for information procurement and drastically reduces manual database validation for large proteomic studies. It is available at http://proteo.cnb.csic.es/pike.
Generalization of Kirchhoff Law to Non Equilibrium (2021)

Planck's law of thermal radiation depends only on the temperature T and emissivity $\varepsilon$. It is one of the most fundamental discoveries about light-matter interaction that led to the development of quantum physics. Another basic property of a body is its ability to absorb incoming light, characterized by absorptivity $\alpha$. Kirchhoff's law of thermal radiation equals these two properties at thermodynamic equilibrium, i.e., $\varepsilon$=$\alpha$. The generalized Planck's equation extends Kirchhof's law out of equilibrium by scaling the absorptivity with the pump-dependent chemical potential $\mu$, obscuring emissivity as a material property. Quantum efficiency (QE) is a material property, defined out of equilibrium, describing the statistics of absorption followed by emission of a photon. Both emissivity and QE depend on the interplay between radiative and non-radiative rates. Here we theoretically and experimentally demonstrate a prime equation for emissivity as a material property in and out of equilibrium in the form of $\varepsilon$=$\alpha$(1-QE), which at equilibrium is reduced to Kirchhoff's law. Our work lays out the fundamental evolution of non-thermal emission with temperature, which is critical for the development of lighting and energy devices.
Fast-scanning spectroscopic method for the submillimeter: the FASSST spectrometer (1998)

A new FAst Scan Submillimeter Spectroscopic Technique (FASSST) is described. It uses voltage tunable Backward Wave Oscillators (BWOs) as primary sources of radiation. In contrast to the more traditional phase or frequency lock techniques, it uses fast scan (approximately 10<SUP>5</SUP> Doppler limited resolution elements/sec) and optical calibration methods. Its attributes include (1) absolute frequency calibration to approximately 1/10 of a Doppler limited linewidth (less than 0.1 MHz), (2) high sensitivity, (3) the ability to measure many thousands of lines/sec, and (4) simplicity. This system is made possible by (1) the excellent short term spectral purity of the broadly (approximately 100 GHz) tunable BWOs, (2) a very low noise, rapidly scannable high voltage power supply, (3) fast data acquisition, and (4) software capable of automated calibration and spectral line measurement.
1,3,5-2,4,6-Functionalized, Facially Segregated Benzenes—Exploitation of Sterically Predisposed Systems in Supramolecular Chemistry (2002)

In the present article, we introduce the unique steric features of 1,3,5-substituted triethylbenzenes as a design principle for host molecules and supramolecular systems. Due to steric gearing, all three functional substituents are disposed on the same side of the phenyl plane. The use of this benzene scaffold has lead to the synthesis of various receptor molecules for a wide range of different guest species. Furthermore, the facially segregated systems can be used as building blocks with a controlled conformation in the synthesis of macrocycles or self-assembled supramolecular systems.
Structural variation during hot rolling at lower temperature of aluminum alloys. (1991)

variation during hot rolling
Atomicity in electronic commerce (1998)

There is a tremendous demand to electronically buy and sell goods over networks. This field is called electronic commerce, and it has inspired a large variety of work. Unfortunately, much of this activity ignores traditional transaction processing concerns -chiefly atomicity. This paper discusses the role of atomicity in electronic commerce, pointing out various atomic flaws. Special attention is given to the atomicity problems of digital money proposals. Two examples of highly atomic electronic commerce systems, NetBill and cryptographic postage indicia, are presented.
Experimental Melanin-Induced Uveitis: Experimental Model of Human Acute Anterior Uveitis (2008)

Experimental melanin-protein-induced uveitis (EMIU), which is also known as experimental autoimmune anterior uveitis, was first described in 1993 by Broekhuyse et al. This experimental uveitis may be induced in certain inbred and outbred rat strains by immunization with bovine ocular melanin. The inflammation shares clinical features with human acute anterior uveitis. The duration of the first episode is approximately 1 month. Spontaneous recovery to a near normal clinical state is the rule, but multiple recurrences are common. Slit-lamp biomicroscopic examination reveals a florid anterior-chamber reaction, with formation of a retro-iridal empyema, fibrin clots and posterior synechiae. At a microscopic level, leukocytic infiltration is first observed in the anterior uvea. Although this tissue remains the site of maximum inflammation throughout an attack, in severe cases, limbitis, vitritis and choroiditis are also observed. Abrogation of EMIU occurs after treatment with anti-CD4 antibody, indicating that the uveitis is controlled by CD4-positive T cells. Several research groups have used EMIU to investigate various aspects of the pathogenesis of acute anterior uveal inflammation, including the participation of different leukocyte subsets, the expression of cell adhesion molecules, cytokines, chemokines and nitric oxide, the role of complement and the impact of apoptosis. In addition, EMIU has also been used to evaluate various biologic interventions with potential implications for the treatment of human disease.
Isolation of an aryloxyphenoxy propanoate (AOPP) herbicide-degrading strain Rhodococcus ruber JPL-2 and the cloning of a novel carboxylesterase gene (feh) (2015)

The strain JPL-2, capable of degrading fenoxaprop-P-ethyl (FE), was isolated from the soil of a wheat field and identified as Rhodococcus ruber. This strain could utilize FE as its sole carbon source and degrade 94.6% of 100 mg L(-1) FE in 54 h. Strain JPL-2 could also degrade other aryloxyphenoxy propanoate (AOPP) herbicides. The initial step of the degradation pathway is to hydrolyze the carboxylic acid ester bond. A novel esterase gene feh, encoding the FE-hydrolyzing carboxylesterase (FeH) responsible for this initial step, was cloned from strain JPL-2. Its molecular mass was approximately 39 kDa, and the catalytic efficiency of FeH followed the order of FE > quizalofop-P-ethyl > clodinafop-propargyl > cyhalofop-butyl > fluazifop-P-butyl > haloxyfop-P-methyl > diclofop-methy, which indicated that the chain length of the alcohol moiety strongly affected the hydrolysis activity of the FeH toward AOPP herbicides.
Nodes Having a Major Influence to Break Cooperation Define a Novel Centrality Measure: Game Centrality (2013)

Cooperation played a significant role in the self-organization and evolution of living organisms. Both network topology and the initial position of cooperators heavily affect the cooperation of social dilemma games. We developed a novel simulation program package, called 'NetworGame', which is able to simulate any type of social dilemma games on any model, or real world networks with any assignment of initial cooperation or defection strategies to network nodes. The ability of initially defecting single nodes to break overall cooperation was called as 'game centrality'. The efficiency of this measure was verified on well-known social networks, and was extended to 'protein games', i.e. the simulation of cooperation between proteins, or their amino acids. Hubs and in particular, party hubs of yeast protein-protein interaction networks had a large influence to convert the cooperation of other nodes to defection. Simulations on methionyl-tRNA synthetase protein structure network indicated an increased influence of nodes belonging to intra-protein signaling pathways on breaking cooperation. The efficiency of single, initially defecting nodes to convert the cooperation of other nodes to defection in social dilemma games may be an important measure to predict the importance of nodes in the integration and regulation of complex systems. Game centrality may help to design more efficient interventions to cellular networks (in forms of drugs), to ecosystems and social networks.
Electrochemical Annulation of Five‐Membered Rings Through Dearomatization of Furans and Thiophenes. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Deep Audio-Visual Learning: A Survey (2020)

Audio-visual learning, aimed at exploiting the relationship between audio and visual modalities, has drawn considerable attention since deep learning started to be used successfully. Researchers tend to leverage these two modalities either to improve the performance of previously considered single-modality tasks or to address new challenging problems. In this paper, we provide a comprehensive survey of recent audio-visual learning development. We divide the current audio-visual learning tasks into four different subfields: audio-visual separation and localization, audio-visual correspondence learning, audio-visual generation, and audio-visual representation learning. State-of-the-art methods as well as the remaining challenges of each subfield are further discussed. Finally, we summarize the commonly used datasets and performance metrics.
Characterizations of epitaxial Bi(Mg1/2Ti1/2)O3–Bi(Zn1/2Ti1/2)O3solid solution films grown by pulsed laser deposition (2014)

(111)-oriented epitaxial (1 − x)Bi(Mg1/2Ti1/2)O3–xBi(Zn1/2Ti1/2)O3 solid solution films were grown on (111)cSrRuO3/(111)SrTiO3 substrates by pulsed laser deposition, and their crystal structure and electrical properties were characterized. The solid solution films consisted of a perovskite single phase in the x range of 0–0.93. The coexistence region of rhombohedral and tetragonal phases was observed in the x range of 0.18–0.60, which differed from reported data for the powders synthesized at high temperatures and high pressures. The polarization–electric field hysteresis loops originating from ferroelectricity were observed at room temperature and 1 kHz in the x range of 0–0.33, and the remanent polarization monotonously decreased with increasing x. The relative dielectric constant measured at room temperature and 100 kHz and the apparent piezoelectric constant evaluated by piezoresponse force microscopy at room temperature and 5 Hz were maximum at approximately x = 0.14. These results suggest that these tendencies of the electrical and electromechanical properties were related to the volume fractions of the constituent phases in the solid solution films.
V1387: Laparoscopic Management of Vascular Complications in Urologic Surgery (2007)

You have accessJournal of UrologyVideo Session 5, Tuesday, May 22, 2007, 10:00 am - 12:00 pm1 Apr 2007V1387: Laparoscopic Management of Vascular Complications in Urologic Surgery Amar Singh, Mehrdad Alemozaffar, Kristian Novakovic, Manish A. Vira, Jonathan A. Coleman, and Peter A. Pinto Amar SinghAmar Singh More articles by this author , Mehrdad AlemozaffarMehrdad Alemozaffar More articles by this author , Kristian NovakovicKristian Novakovic More articles by this author , Manish A. ViraManish A. Vira More articles by this author , Jonathan A. ColemanJonathan A. Coleman More articles by this author , and Peter A. PintoPeter A. Pinto More articles by this author View All Author Informationhttps://doi.org/10.1016/S0022-5347(18)32185-2AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "V1387: Laparoscopic Management of Vascular Complications in Urologic Surgery." The Journal of Urology, 177(4S), p. 457 © 2016 by American Urological AssociationFiguresReferencesRelatedDetails Volume 177Issue 4SApril 2007Page: 457 Advertisement Copyright & Permissions© 2016 by American Urological AssociationMetricsAuthor Information Amar Singh More articles by this author Mehrdad Alemozaffar More articles by this author Kristian Novakovic More articles by this author Manish A. Vira More articles by this author Jonathan A. Coleman More articles by this author Peter A. Pinto More articles by this author Expand All Advertisement Loading ...
Selective in vivo removal of rheumatoid factor by an extracorporeal treatment device in rheumatoid arthritis patients (1991)

A prospective phase II trial was conducted to assess the feasibility, tolerance, and efficacy of a device designed for selective removal of rheumatoid factor from the plasma of rheumatoid arthritis patients. The device contained terpolymer hydrogel-coated plates with chemically attached, aggregated human immunoglobulin G, and it operated as an immunoaffinity column. Sixty-one patients aged 25 to 73 underwent weekly plasmapheresis treatments (the primary therapy phase). During the trial, patients continued current rheumatoid arthritis medications without dose adjustments. All patients received two to six treatments (primary therapy). Responding patients were eligible to continue apheresis treatment every 2 to 6 weeks (maintenance therapy). No serious, untoward side effects were noted in the course of this study; of 640 treatments, only 2 (in different patients) were aborted, one because of complaints of dizziness and angioedema and the other because of chest tightness and shortness of breath. Except for a significant (p less than 0.05) decrease in serum iron, no significant changes in complete blood count, serum electrolytes, renal and hepatic function tests, or serum C3 and C4 were noted. Although the trial was not designed to determine clinical efficacy, patients noted less morning stiffness, longer time to onset of fatigue, and improved global pain assessment (p less than 0.004); significant objective improvements were noted in joint pain, tenderness, swelling, and the number of affected joints (p less than 0.001). One-half of the treated patients had at least a 50 percent improvement in objective measures of antirheumatic activity.(ABSTRACT TRUNCATED AT 250 WORDS)
Transcriptional regulation of tyrosine hydroxylase by estrogen: opposite effects with estrogen receptors α and β and interactions with cyclic AMP (2005)

Reported effects of estrogen administration on tyrosine hydroxylase (TH) gene expression are confusing. Therefore, we studied the mechanism of regulation of TH transcription by estrogen with different estradiol receptor (ER) subtypes. PC12 cells, transiently co-transfected with expression vector for ERalpha or ERbeta, and luciferase gene under control of the TH promoter, were treated with 17 beta-estradiol (E2). E2 doubled luciferase activity with ERalpha; however, it was decreased with ERbeta. Mapping the TH promoter showed that the putative half estrogen response element (ERE) motif at - 675, as well as the activation protein 1 motif at - 205, were not required for response to E2 with either ER. The specificity protein 1/early growth response gene 1 (Egr 1) motif was required for the E2-elicited response with ERbeta, but not with ERalpha. Deletion of the cyclic AMP/Ca2+ response element (CRE/CaRE) nearly abolished E2-triggered responses with either ER. Further analysis revealed an imperfect canonical putative ERE overlapping with CRE/CaRE and Nurr1 response element. Oligonucleotides spanning this ERE displayed binding to ER, Cyclic AMP Response Element Binding Protein (CREB) and other proteins. Moreover, E2 attenuated the increase in TH transcription seen with cyclic AMP analogs. Thus, TH is transcriptionally regulated by estradiol in opposite directions depending on ER subtype. The overlapping ERE and CRE/CaRE may integrate interactions elicited by various regulators of TH transcription including cAMP and estrogens.
Involvement of miRNA in Erythroid Differentiation (2012)

miRNAs are a family of small ncRNAs that regulate gene expression by targeting mRNAs in a sequence-specific manner, inducing translational repression or mRNA degradation. In this review, we present and discuss the available literature on the expression of miRNAs in erythroid cells. There are several experimental systems that can be employed for studies focusing on the relationship between miRNAs and erythroid differentiation, including human embryonic stem cells forced to erythroid differentiation, K562 and UT-7 cells induced to hemoglobin production by chemical compounds, erythropoietin-treated erythroid precursor cells from normal subjects or patients affected by hematological disease and in vivo systems, such as zebrafish embryos. Several miRNAs were identified as deeply involved in the erythroid phenotype, including miR-15a, miR-16-1, miR-126, miR-144, miR-451 and miR-210. Several functions related with erythroid cells were demonstrated to be regulated by these miRNAs, including maturation and proliferation of early erythroid cells, expression of fetal γ-globin genes and enucleation. These identified erythroid specific miRNAs represent the starting point to develop new protocols for miRNA therapeutics, based on both anti-miR molecules or miRNA replacement.
Irs–2 Mediates the Antiapoptotic Effect of Insulin in Neonatal Hepatocytes (2004)

To assess the role of insulin action and inaction in the liver, immortalized hepatocyte cell lines have been generated from insulin receptor substrate (IRS)-2(-/-) and wild-type mice. Using this model, we have recently demonstrated that the lack of IRS-2 in neonatal hepatocytes resulted in insulin resistance. In the current study, we show that immortalized neonatal hepatocytes undergo apoptosis on serum withdrawal, with caspase-3 activation and DNA laddering occurring earlier in the absence of IRS-2. Insulin rescued wild-type hepatocytes from serum withdrawal-induced caspase-3 activation and DNA fragmentation in a dose-dependent manner, but it failed to rescue hepatocytes lacking IRS-2. In IRS-2(-/-) cells, insulin failed to phosphorylate Bad. Furthermore, in these cells, insulin was unable to translocate Foxo1 from the nucleus to the cytosol. Adenoviral infection of wild-type cells with constitutively active Foxo1 (ADA) induced caspase-8 and caspase-3 activities, proapoptotic gene expression, DNA laddering and apoptosis. Dominant negative Foxo1 regulated the whole pathway in an opposite manner. Prolonged insulin treatment (24 hours) increased expression of antiapoptotic genes (Bcl-xL), downregulated proapoptotic genes (Bim and nuclear Foxo1), and decreased caspase-3 activity in wild-type hepatocytes but not in IRS-2(-/-) cells. Infection of IRS-2(-/-) hepatocytes with adenovirus encoding IRS-2 reconstituted phosphatidylinositol 3-kinase (PI 3-kinase)/Akt/Foxo1 signaling, restored pro- and antiapoptotic gene expression, and decreased caspase-3 activity in response to insulin, thereby blocking apoptosis. In conclusion, IRS-2 signaling is specifically required through PIP3 generation to mediate the survival effects of insulin. Epidermal growth factor, via PIP3/Akt/Foxo1 phosphorylation, was able to rescue IRS-2(-/-) hepatocytes from serum withdrawal-induced apoptosis, modulating pro- and anti-apoptotic gene expression and downregulating caspase-3 activity.
Smartflex NiTi Wires for Shape Memory Actuators (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
A Swarm-Intelligence-Based Protocol for Data Acquisition in Networks with Mobile Sinks (2008)

This paper addresses the problem of data acquisition in ad hoc and sensor networks with mobile sinks and proposes a protocol based on swarm intelligence, SIMPLE, to route data in such environments. The proposed protocol is based on a swarm agent that integrates the residual energy of nodes into the route selection mechanism and maximizes the network's lifetime by evenly balancing the residual energy across nodes and minimizing the protocol overhead. The protocol is robust and scales well with both the network size and in the presence of multiple sinks. An information theoretic lower bound on the protocol overhead associated with the swarm agent advertisement is also obtained. SIMPLE is also shown to have a lower message complexity compared to similar algorithms previously proposed in literature. Simulation results are used to verify SIMPLE's performance and robustness and also to demonstrate its superior performance over existing algorithms.