gebhart/patrepeval huggingface dataset:
Molecular Profiling of the<i>Clostridium leptum</i>Subgroup in Human Fecal Microflora by PCR-Denaturing Gradient Gel Electrophoresis and Clone Library Analysis (2006)

A group-specific PCR-based denaturing gradient gel electrophoresis (DGGE) method was developed and combined with group-specific clone library analysis to investigate the diversity of the Clostridium leptum subgroup in human feces. PCR products (length, 239 bp) were amplified using C. leptum cluster-specific primers and were well separated by DGGE. The DGGE patterns of fecal amplicons from 11 human individuals revealed host-specific profiles; the patterns for fecal samples collected from a child for 3 years demonstrated the structural succession of the population in the first 2 years and its stability in the third year. A clone library was constructed with 100 clones consisting of 1,143-bp inserts of 16S rRNA gene fragments that were amplified from one adult fecal DNA with one forward universal bacterial primer and one reverse group-specific primer. Eighty-six of the clones produced the 239-bp C. leptum cluster-specific amplicons, and the remaining 14 clones did not produce these amplicons but still phylogenetically belong to the subgroup. Sixty-four percent of the clones were related to Faecalibacterium prausnitzii (similarity, 97 to 99%), 6% were related to Subdoligranulum variabile (similarity, approximately 99%), 2% were related to butyrate-producing bacterium A2-207 (similarity, 99%), and 28% were not identified at the species level. The identities of most bands in the DGGE profiles for the same adult were determined by comigration analysis with the 86 clones that harbored the 239-bp group-specific fragments. Our results suggest that DGGE combined with clone library analysis is an effective technique for monitoring and analyzing the composition of this important population in the human gut flora.
Fundamental Physical Constants and Conversion Factors (1995)

This section provides a summary of important units for geomagnetism and geoelectricty. In addition, a summary of conversion factors and fundamental units of relevance to earth and planetary science are presented for reference. Despite the sentiment expressed above by Vigoureux, it still seems that plenty of us slave over SI units in geomagnetism. There is probably no other scientific discipline in which the topic of units generates so much endless discussion and confusion than in magnetism. Before the late 1970’s, practically all the geophysical literature in geomagnetism and paleomagnetism used the Gaussian CGS system of units. The CGS system is a perfectly sound, intemally consistent, system of units, but, like all systems of units and dimensions, is totally arbitrary. As the name implies, the cgs system is based on three base units: centimeter, gram, and second. All other units are derived from these three. The Gaussian cgs system is based on two earlier systems, the electrostatic units (esu) and electromagnetic units (emu). Electrostatic units were defined by Coulomb’s law describing the force between two electrical charges. Similarly, electromagnetic units were defined by the force between two magnetic charges or two current-carrying wires. One consequence of this dichotomy is that the dimen-
High-speed interlaced spin-echo magnetic resonance imaging (2000)

A new method is introduced for increasing the efficiency in multislice single spin-echo MRI. The method interlaces the excitation and measurement of different slices, resulting in an effective use of the echo delay time between RF excitation and reception. Under certain conditions, the method allows for scan time reduction compared to standard single spin-echo MRI, in particular for long echo times. The technique is demonstrated in examples of brain scans, indicating that a substantial increase is scan speed can be achieved without loss in image signal-to-noise ratio or contrast. Potential applications include perfusion imaging using T(2)-contrast agents, as well as BOLD-based functional imaging. Magn Reson Med 43:905-908, 2000. Published 2000 Wiley-Liss, Inc.
Nucleotide sequence of the structural genes for an anion pump. The plasmid-encoded arsenical resistance operon. (1986)

The structural genes for the arsenical pump of the conjugative R-factor R773 contained on a HindIII fragment of 4.3 kilobase pairs were cloned into bacteriophage M13. A series of ordered deletions was created using Bal31 digestion, and the nucleotide sequence of the operon determined. Three open reading frames for genes arsA, arsB, and arsC were found. The arsA gene encodes a hydrophilic protein of 63,169 Da with two potential adenylate-binding sites. The arsB gene encodes a potentially membrane protein of 45,577 Da. The arsC gene encodes a 15,811-Da hydrophilic protein. The arsA and arsC gene products correspond to cytosolic proteins previously identified from minicell experiments. Isolated ArsA protein was shown to bind to dye-agarose columns which act as affinity resins for nucleotide-binding proteins. A model is proposed in which these gene products form an anion translocating ATPase for extrusion of arsenite and arsenate from resistant cells.
Simple Coupling of Gas Chromatography to Electrospray Ionization Mass Spectrometry (2008)

A simple method for direct coupling of gas chromatography (GC) with electrospray ionization mass spectrometry (ESI/MS) has been developed. The outlet of the GC capillary column was placed between the ESI needle and the atmospheric pressure ionization (API) source of a mass spectrometer. The ionization occurs via dissolution of neutral compounds into the charged ESI droplet followed by ion evaporation or via a gas-phase proton transfer reaction between a protonated solvent molecule and an analyte. The mass spectra of organic volatile compounds showed abundant protonated molecules with little fragmentation, being very similar to those produced by normal liquid ESI. The quantitative performance of the system was evaluated by determining the limit of detection (LOD), linearity ( r (2)), and repeatability (RSD). The GC-ESI/MS method was shown to be stable, providing high sensitivity and good quantitative performance.
Iron uptake in ferritin is blocked by binding of [Cr(TREN)(H <sub>2</sub> O)(OH)] <sup>2+</sup> , a slow dissociating model for [Fe(H <sub>2</sub> O) <sub>6</sub> ] <sup>2+</sup> (2002)

Ferritin concentrates iron as a hydrous ferric oxide in a protein cavity (8 nm in diameter) by using eight pores along the threefold symmetry axes of the octahedral supramolecular structure. The role of ligand exchange in the entry of Fe(II) hexahydrate into ferritin protein has been studied with [Cr(TREN)(H(2)O)(OH)](2+) [TREN = N(CH(2)CH(2)NH(2))(3)], a model for Fe(H(2)O)(6)2+ with only two exchangeable ligands. The results show that five different ferritin proteins, varying in pore structure, oxidation sites, and nucleation sites, bind Cr(TREN) at functional protein sites, based on inhibition of iron mineralization and oxidation. Properties of Cr(TREN)-ferritin adducts include an increased isoelectric point, a shift in the Cr(TREN) UV/vis spectrum consistent with exchange of water for protein carboxylate or thiolate ligands, binding affinities of 50-250 microM, and a slow rate of dissociation (k = 4 x 10(-6) sec(-1)). The relationship of Cr(TREN) inhibition of iron oxidation and mineralization by Cr(TREN) to the known structures of the various ferritins tested suggests that Cr(TREN) plugs the ferritin pores, obstructing Fe(II) entry in folded and unfolded pores. Because only two exchangeable waters are sufficient for pore binding of Cr(TREN), the physiological Fe(II) donor must bind to the pore with few exchangeable ligands. These results show the advantage of using stable model complexes to explore properties of transient Fe-protein complexes during Fe mineralization in ferritin.
Calendaring for wide area networks (2014)

Datacenter WAN traffic consists of high priority transfers that have to be carried as soon as they arrive alongside large transfers with pre-assigned deadlines on their completion (ranging from minutes to hours). The ability to offer guarantees to large transfers is crucial for business needs and impacts overall cost-of-business. State-of-the-art traffic engineering solutions only consider the current time epoch and hence cannot provide pre-facto promises for long-lived transfers. We present Tempus, an online traffic engineering scheme that exploits information on transfer size and deadlines to appropriately pack long-running transfers across network paths and time, thereby leaving enough capacity slack for future high-priority requests. Tempus builds on a tailored approximate solution to a mixed packing-covering linear program, which is parallelizable and scales well in both running time and memory usage. Consequently, Tempus is able to quickly and effectively update its solution when new transfers arrive or unexpected changes happen. These updates involve only small edits to existing transfers. Therefore, as experiments on traces from a large production WAN show, Tempus can offer and keep promises to long-lived transfers well in advance of their actual deadline; the promise on minimal transfer size is comparable with an offline optimal solution and outperforms state-of-the-art solutions by 2-3X.
Impaired FANCD2 monoubiquitination and hypersensitivity to camptothecin uniquely characterize Fanconi anemia complementation group M (2009)

FANCM is a component of the Fanconi anemia (FA) core complex and one FA patient (EUFA867) with biallelic mutations in FANCM has been described. Strikingly, we found that EUFA867 also carries biallelic mutations in FANCA. After correcting the FANCA defect in EUFA867 lymphoblasts, a "clean" FA-M cell line was generated. These cells were hypersensitive to mitomycin C, but unlike cells defective in other core complex members, FANCM(-/-) cells were proficient in monoubiquitinating FANCD2 and were sensitive to the topoisomerase inhibitor camptothecin, a feature shared only with the FA subtype D1 and N. In addition, FANCM(-/-) cells were sensitive to UV light. FANCM and a C-terminal deletion mutant rescued the cross-linker sensitivity of FANCM(-/-) cells, whereas a FANCM ATPase mutant did not. Because both mutants restored the formation of FANCD2 foci, we conclude that FANCM functions in an FA core complex-dependent and -independent manner.
Detection of P and T-waves in Electrocardiogram (2008)

Abstract — Electrocardiogram (ECG) is characterized by a recurrent wave sequence of P, QRS and T- wave associated with each beat. This paper presents a new method for the detection of P and T-waves in 12-lead ECG using Support Vector Machine (SVM). Digital filtering techniques are used to remove power line interference and base line wander present in the ECG signal. SVM is used as a classifier for the detection of P and T-waves. The performance of the algorithm is evaluated using 50, original simultaneously recorded 12-lead ECG recordings from the standard CSE ECG database. Significant detection rate is achieved. The method successfully detects monophasic as well as biphasic waves. Index Terms — ECG, SVM, QRS complex, P-wave, T-wave. I.
Distributed neural system for general intelligence revealed by lesion mapping (2010)

General intelligence (g) captures the performance variance shared across cognitive tasks and correlates with real-world success. Yet it remains debated whether g reflects the combined performance of brain systems involved in these tasks or draws on specialized systems mediating their interactions. Here we investigated the neural substrates of g in 241 patients with focal brain damage using voxel-based lesion-symptom mapping. A hierarchical factor analysis across multiple cognitive tasks was used to derive a robust measure of g. Statistically significant associations were found between g and damage to a remarkably circumscribed albeit distributed network in frontal and parietal cortex, critically including white matter association tracts and frontopolar cortex. We suggest that general intelligence draws on connections between regions that integrate verbal, visuospatial, working memory, and executive processes.
Receptivity of three-dimensional boundary-layers to localized wall roughness and suction (2000)

The receptivity of three-dimensional, incompressible, boundary-layer flows to localized roughness or suction is studied theoretically and numerically. Three-dimensional boundary-layer flows have a strong “nonparallel” component due to the curvature of the potential-flow streamlines. Our theoretical model extends the Fourier-transform methodology to nonparallel flows using a Taylor expansion of the laminar mean-flow at the location of the roughness. Both the near-field and the far-field solutions are contained in the model. Additionally, the use of MacLaurin expansions in the complex plane leads quickly to the receptivity factors of eigenmodes. The theoretical results are validated with solutions to the linearized Navier–Stokes equations efficiently obtained by replacing the actual wall forcing with a smoother, but equivalent, forcing. We find that the far-field response is proportional to both H̃(αe) and dH̃(αe)/dα, where H̃(α) is the Fourier transform of the forcing distribution, and αe is the eigenmode’s wave number. The receptivity coefficient for H̃(αe) decreases when nonparallelism is included in our models, while that for dH̃(αe)/dα increases.
Mixed-architecture process scheduling on tightly coupled reconfigurable computers (2014)

The design and implementation of a multitasking runtime system for mixed-architecture applications on a tightly coupled FPGA-CPU platform is presented. The runtime environment and the user applications assume an underlying machine that encompasses multiple computing architectures within a unified machine model. Using this model, a unified process scheduling mechanism was developed that enables concurrent execution of multiple mixed-architecture processes. Scheduling and allocation strategies, including blocking and preemption, were implemented and evaluated with respect to performance and fairness on a Xilinx Zynq platform using a mix of synthetic workloads.
Determination of volatile halogenated hydrocarbons in water by gas chromatography (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetermination of volatile halogenated hydrocarbons in water by gas chromatographyKlaus L. E. Kaiser and Barry G. OliverCite this: Anal. Chem. 1976, 48, 14, 2207–2209Publication Date (Print):December 1, 1976Publication History Published online1 May 2002Published inissue 1 December 1976https://pubs.acs.org/doi/10.1021/ac50008a039https://doi.org/10.1021/ac50008a039research-articleACS PublicationsRequest reuse permissionsArticle Views154Altmetric-Citations38LEARN 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
Secretion of the <i>Rhizobium leguminosarum</i> nodulation protein NodO by haemolysin‐type systems (1992)

The Rhizobium leguminosarum biovar viciae nodulation protein NodO is partially homologous to haemolysin of Escherichia coli and, like haemolysin, is secreted into the growth medium. The NodO protein can be secreted by a strain of E. coli carrying the cloned nodO gene plus the haemolysin secretion genes hlyBD, in a process that also requires the outer membrane protein encoded by tolC. The related protease secretion genes, prtDEF, from Erwinia chrysanthemi also enable E. coli to secrete NodO. The Rhizobium genes encoding the proteins required for NodO secretion are unlinked to nodO and are unlike other nod genes, since they do not require flavonoids or NodO for their expression. Although proteins similar to NodO were not found in rhizobia other than R. leguminosarum bv. viciae, several rhizobia and an Agrobacterium strain containing the cloned nodO gene were found to have the ability to secrete NodO. These observations indicate that a wide range of the Rhizobiaceae have a protein secretion mechanism analogous to that which secretes haemolysin and related toxins and proteases in the ENterobacteriaceae.
Cortical Hierarchies Perform Bayesian Causal Inference in Multisensory Perception (2015)

To form a veridical percept of the environment, the brain needs to integrate sensory signals from a common source but segregate those from independent sources. Thus, perception inherently relies on solving the "causal inference problem." Behaviorally, humans solve this problem optimally as predicted by Bayesian Causal Inference; yet, the underlying neural mechanisms are unexplored. Combining psychophysics, Bayesian modeling, functional magnetic resonance imaging (fMRI), and multivariate decoding in an audiovisual spatial localization task, we demonstrate that Bayesian Causal Inference is performed by a hierarchy of multisensory processes in the human brain. At the bottom of the hierarchy, in auditory and visual areas, location is represented on the basis that the two signals are generated by independent sources (= segregation). At the next stage, in posterior intraparietal sulcus, location is estimated under the assumption that the two signals are from a common source (= forced fusion). Only at the top of the hierarchy, in anterior intraparietal sulcus, the uncertainty about the causal structure of the world is taken into account and sensory signals are combined as predicted by Bayesian Causal Inference. Characterizing the computational operations of signal interactions reveals the hierarchical nature of multisensory perception in human neocortex. It unravels how the brain accomplishes Bayesian Causal Inference, a statistical computation fundamental for perception and cognition. Our results demonstrate how the brain combines information in the face of uncertainty about the underlying causal structure of the world.
An Experimental Study of Voltage, Current, and Charge Controlled Stimulation Front-End Circuitry (2007)

We have developed an experimental 4-channel stimulator prototype capable of performing voltage controlled stimulation (VCS), current controlled stimulation (CCS), and switched capacitor based stimulation (SCS) all on the same platform for neurological experiments. The stimulator allows changing main stimulation parameters such as amplitude, pulse width, pulse frequency, and output channels in real-time either wirelessly or hardwired. The stimulator was used to objectively evaluate the power efficiencies of each stimulation strategy using platinum epilepsy electrodes with 2.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> exposed area in saline solution. We measured 92%, 65%, and 77% efficiencies for VCS, CCS, and SCS, respectively, on a 962Ω - 810 nF resistive-capacitive load. The motivation behind this research is to find the most power efficient stimulation front-end (SFE) circuitry for implantable neurological stimulators (INS).
Three-Dimensional Blood Flow Dynamics: Spiral/Helical Laminar Flow (2011)

The Methodist DeBakey Cardiovascular Journal provides timely updates on important topics in cardiovascular medicine with quarterly, thematic review-article issues. Each issue is curated by subject-matter-expert guest editors and includes invited reviews along with case reports, interesting multimodality images, and humanities submissions. Additional case reports, images, CME quizzes, and editorials are published on a continuous basis online. MDCVJ is geared towards cardiologists, cardiovascular surgeons, general practitioners, and CV residents and fellows and is indexed in PubMed and MEDLINE.MDCVJ is published by Houston Methodist DeBakey Heart & Vascular Center as part of DeBakey CV Education, an epicenter for cardiovascular academic and clinical education programs located in the heart of the Texas Medical Center. Along with the Journal, DeBakey CV Education offers online and hands-on training for cardiovascular healthcare professionals at all stages in their careers. DeBakey CV Education’s vast YouTube library features hundreds of training videos and live webcasts, including Journal features. Subscribe to the YouTube channel today and sign up for newsletter updates about training opportunities.
A Saturated <i>N</i>‐Acylethanolamine Other than <i>N</i>‐Palmitoyl Ethanolamine with Anti‐inflammatory Properties: a Neglected Story… (2008)

N-acylethanolamines, which include the endocannabinoid anandamide and the cannabinoid receptor-inactive saturated compounds N-palmitoyl ethanolamine and N-stearoyl ethanolamine, are ethanolamines of long-chain fatty acids degraded by fatty acid amide hydrolase (FAAH) known to accumulate in degenerating tissues and cells. Whilst much evidence supports a protective anti-inflammatory role of both anandamide and N-palmitoyl ethanolamine, very little information is available with regard to the bioactivity of N-stearoyl ethanolamine. Employing a murine model of passive IgE-induced cutaneous anaphylaxis, we have found that N-stearoyl ethanolamine is endowed with marked anti-inflammatory properties in vivo, supporting the hypothesis that endogenous N-stearoyl ethanolamine is, in analogy to N-palmitoyl ethanolamine, a bioactive signalling lipid capable of downregulating allergic inflammation in the skin. This effect, although mimicked by synthetic, non-selective, CB(1)/CB(2) receptor agonists, such as WIN55, 212-2, was not sensitive to CB(1) or CB(2) receptor antagonists, but rather was fully reversed by capsazepine, a competitive antagonist of the TRPV1 receptor. Moreover, CB(1) receptor antagonists, although effective in antagonising the WIN55,212-2-induced hypothermia, did not reduce the anti-inflammatory effect of WIN55,212-2, whilst CB(2) receptor antagonists, per se inactive, potentiated the WIN55,212-2 effect, suggesting an involvement of non-CB(1)/CB(2) receptors in the anti-inflammatory action of WIN55,212-2. All this, together with demonstration of FAAH as a major regulator of the in vivo concentrations of saturated N-stearoyl ethanolamine, in addition to N-palmitoyl ethanolamine, raise the speculation that pharmacological treatments with saturated N-acylethanolamines such as N-stearoyl ethanolamine, or alternatively FAAH inhibitors able to increase their local concentration, rather than selective CB receptor agonists, might be of promising therapeutic benefit in reducing allergic inflammation in the skin.