gebhart/patrepeval huggingface dataset:
Arhodomonas sp. Strain Seminole and Its Genetic Potential To Degrade Aromatic Compounds under High-Salinity Conditions (2014)

Arhodomonas sp. strain Seminole was isolated from a crude oil-impacted brine soil and shown to degrade benzene, toluene, phenol, 4-hydroxybenzoic acid (4-HBA), protocatechuic acid (PCA), and phenylacetic acid (PAA) as the sole sources of carbon at high salinity. Seminole is a member of the genus Arhodomonas in the class Gammaproteobacteria, sharing 96% 16S rRNA gene sequence similarity with Arhodomonas aquaeolei HA-1. Analysis of the genome predicted a number of catabolic genes for the metabolism of benzene, toluene, 4-HBA, and PAA. The predicted pathways were corroborated by identification of enzymes present in the cytosolic proteomes of cells grown on aromatic compounds using liquid chromatography-mass spectrometry. Genome analysis predicted a cluster of 19 genes necessary for the breakdown of benzene or toluene to acetyl coenzyme A (acetyl-CoA) and pyruvate. Of these, 12 enzymes were identified in the proteome of toluene-grown cells compared to lactate-grown cells. Genomic analysis predicted 11 genes required for 4-HBA degradation to form the tricarboxylic acid (TCA) cycle intermediates. Of these, proteomic analysis of 4-HBA-grown cells identified 6 key enzymes involved in the 4-HBA degradation pathway. Similarly, 15 genes needed for the degradation of PAA to the TCA cycle intermediates were predicted. Of these, 9 enzymes of the PAA degradation pathway were identified only in PAA-grown cells and not in lactate-grown cells. Overall, we were able to reconstruct catabolic steps for the breakdown of a variety of aromatic compounds in an extreme halophile, strain Seminole. Such knowledge is important for understanding the role of Arhodomonas spp. in the natural attenuation of hydrocarbon-impacted hypersaline environments.
Amyloid‐Beta Interaction with Mitochondria (2011)

Mitochondrial dysfunction is a hallmark of amyloid-beta(Aβ)-induced neuronal toxicity in Alzheimer's disease (AD). The recent emphasis on the intracellular biology of Aβ and its precursor protein (AβPP) has led researchers to consider the possibility that mitochondria-associated and/or intramitochondrial Aβ may directly cause neurotoxicity. In this paper, we will outline current knowledge of the intracellular localization of both Aβ and AβPP addressing the question of how Aβ can access mitochondria. Moreover, we summarize evidence from AD postmortem brain as well as cellular and animal AD models showing that Aβ triggers mitochondrial dysfunction through a number of pathways such as impairment of oxidative phosphorylation, elevation of reactive oxygen species (ROS) production, alteration of mitochondrial dynamics, and interaction with mitochondrial proteins. In particular, we focus on Aβ interaction with different mitochondrial targets including the outer mitochondrial membrane, intermembrane space, inner mitochondrial membrane, and the matrix. Thus, this paper establishes a modified model of the Alzheimer cascade mitochondrial hypothesis.
MARS WAS WET (2004)

RETURN TO ISSUEPREVNewsNEXTMARS WAS WETResults from rover Opportunity show almost unequivocal signs of waterELIZABETH WILSONCite this: Chem. Eng. News 2004, 82, 10, 7Publication Date (Print):March 8, 2004Publication History Published online14 November 2010Published inissue 8 March 2004https://pubs.acs.org/doi/10.1021/cen-v082n010.p007https://doi.org/10.1021/cen-v082n010.p007newsACS PublicationsCopyright © 2004 AMERICAN CHEMICAL SOCIETYArticle Views12Altmetric-Citations-LEARN 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 options SUBJECTS:Planets,Water Get e-Alerts
Cellulase-catalysed, stereoselective synthesis of oligosaccharides (1993)

Oligosaccharides are synthesised enzymatically using β-lactosyl fluoride as glycosyl donor and a variety of mono-, di-and tri-saccharides as acceptors; the nature of the active site of the catalyst cellulase is discussed on the basis of these reactions.
The transdermal administration of fentanyl in the treatment of postoperative pain: pharmacokinetics and pharmacodynamic effects (1989)

A transdermal formulation of fentanyl (TTS-fentanyl, Alza Corp., Palo Alto, CA) was evaluated in 13 surgical patients after an abdominal operation. An intraoperative dose of fentanyl (100-200 micrograms i.v.) was administered at the same time as the TTS-fentanyl systems (50-125 micrograms/h) were applied to the antero-lateral chest wall. The TTS-fentanyl systems remained in situ for 24 h and were then removed and a second lot of systems were applied to the contra-lateral chest wall. There was a mean (S.D.) delay time of 12.7 (9.6) h before minimum effective blood fentanyl concentrations (MEC) were obtained from the systems and pseudo-steady state was reached between 36 and 48 h. There was a decay time of 16.1 (7.1) h after the systems were removed for the blood fentanyl concentration to decrease to less than the mean MEC for the control of postoperative pain. There was marked variability between patients in the actual hourly fentanyl dose rate determined from the residual amount of fentanyl remaining in the system and the duration of application. Significantly more supplementary pethidine was administered for inadequate postoperative analgesia between 0 and 12 h compared to the 12-24, 24-36 and 36-48 h periods; this was consistent with the observed delay time. Three patients required a reduction in the hourly fentanyl dose rate because of bradypnoea while 1 patient required an increase in dose because of inadequate pain relief. Nausea was the most frequently reported side effect (85% of patients) while bradypnoea, drowsiness, unpleasant dreams and headache were also reported. These effects were due to the combined effects of a sustained blood fentanyl concentration and the intermittent supplementary pethidine doses. Side effects due to the topical formulation were transient and included erythema (8 patients) and a minor rash (2 patients) in the area occluded by the systems. The TTS-fentanyl systems provided a significant contribution to postoperative pain control but, at the TTS dose rates used, supplementary doses of pethidine were required by all patients probably to control 'incident' pain.
Contrast-enhanced Magnetic Resonance Imaging in Pediatric Patients: Review and Recommendations for Current Practice (2013)

Magnetic resonance imaging (MRI), frequently with contrast enhancement, is the preferred imaging modality for many indications in children. Practice varies widely between centers, reflecting the rapid pace of change and the need for further research. Guide-line changes, for example on contrast-medium choice, require continued practice reappraisal. This article reviews recent developments in pediatric contrast-enhanced MRI and offers recommendations on current best practice. Nine leading pediatric radiologists from internationally recognized radiology centers convened at a consensus meeting in Bordeaux, France, to discuss applications of contrast-enhanced MRI across a range of indications in children. Review of the literature indicated that few published data provide guidance on best practice in pediatric MRI. Discussion among the experts concluded that MRI is preferred over ionizing-radiation modalities for many indications, with advantages in safety and efficacy. Awareness of age-specific adaptations in MRI technique can optimize image quality. Gadolinium-based contrast media are recommended for enhancing imaging quality. The choice of most appropriate contrast medium should be based on criteria of safety, tolerability, and efficacy, characterized in age-specific clinical trials and personal experience.
Experimental ultrasound characterization of red blood cell aggregation using the structure factor size estimator (2007)

The frequency dependence of the ultrasonic backscattering coefficient (BSC) was studied to assess the level of red blood cell (RBC) aggregation. Three monoelement focused wideband transducers were used to insonify porcine blood sheared in a Couette flow from 9 to 30 MHz. A high shear rate was first applied to promote disaggregation. Different residual shear rates were then used to promote formation of RBC aggregates. The structure factor size estimator (SFSE), a second-order data reduction model based on the structure factor, was applied to the frequency-dependent BSC. Two parameters were extracted from the model to describe the level of aggregation at 6% and 40% hematocrits: W, the packing factor, and D the aggregate diameter, expressed in number of RBCs. Both parameters closely matched theoretical values for nonaggregated RBCs. W and D increased during aggregation with stabilized values modulated by the applied residual shear rate. Furthermore, parameter D during the kinetics of aggregation at 6% hematocrit under static conditions correlated with an optical RBC aggregate size estimation from microscopic images (r(2)=0.76). To conclude, the SFSE presents an interesting framework for tissue characterization of partially correlated dense tissues such as aggregated RBCs.
Carbon-hydrogen vs. carbon-carbon bond cleavage of 1,2-diarylethane radical cations in acetonitrile-water (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbon-hydrogen vs. carbon-carbon bond cleavage of 1,2-diarylethane radical cations in acetonitrile-waterDonald M. Camaioni and James A. FranzCite this: J. Org. Chem. 1984, 49, 9, 1607–1613Publication Date (Print):May 1, 1984Publication History Published online1 May 2002Published inissue 1 May 1984https://pubs.acs.org/doi/10.1021/jo00183a023https://doi.org/10.1021/jo00183a023research-articleACS PublicationsRequest reuse permissionsArticle Views1018Altmetric-Citations40LEARN 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
The Outer Membrane Proteins of Gram-Negative Bacteria: Biosynthesis, Assembly, and Functions (1978)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Reactions of methyl-substituted cyclopentanones with lithium aluminum hydride and methyllithium. Structural determinations and proton nuclear magnetic resonance study of the reaction products (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReactions of methyl-substituted cyclopentanones with lithium aluminum hydride and methyllithium. Structural determinations and proton nuclear magnetic resonance study of the reaction productsMin-Hon ReiCite this: J. Org. Chem. 1978, 43, 11, 2173–2178Publication Date (Print):May 1, 1978Publication History Published online1 May 2002Published inissue 1 May 1978https://pubs.acs.org/doi/10.1021/jo00405a020https://doi.org/10.1021/jo00405a020research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-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
Phrase-Indexed Question Answering: A New Challenge for Scalable Document Comprehension (2018)

We formalize a new modular variant of current question answering tasks by enforcing complete independence of the document encoder from the question encoder. This formulation addresses a key challenge in machine comprehension by requiring a standalone representation of the document discourse. It additionally leads to a significant scalability advantage since the encoding of the answer candidate phrases in the document can be pre-computed and indexed offline for efficient retrieval. We experiment with baseline models for the new task, which achieve a reasonable accuracy but significantly underperform unconstrained QA models. We invite the QA research community to engage in Phrase-Indexed Question Answering (PIQA, pika) for closing the gap. The leaderboard is at: nlp.cs.washington.edu/piqa
Neutrophil Elastase Mediates Innate Host Protection against <i>Pseudomonas aeruginosa</i> (2008)

According to the widely accepted view, neutrophil elastase (NE), a neutrophil-specific serine protease, is a major contributor to Pseudomonas aeruginosa infection-associated host tissue inflammation and damage, which in severe cases can lead to death. Herein, we provide for the first time compelling evidence that the host rather employs NE to protect itself against P. aeruginosa infection. Using a clinically relevant model of pneumonia, targeted deficiency in NE increased the susceptibility of mice to P. aeruginosa. We found that NE was required for maximal intracellular killing of P. aeruginosa by neutrophils. In investigating the mechanism of NE-mediated killing of P. aeruginosa, we found that NE degraded the major outer membrane protein F, a protein with important functions, including porin activity, maintenance of structural integrity, and sensing of host immune system activation. Consistent with this, the use of an isogenic mutant deficient in outer membrane protein F negated the role of NE in host defense against P. aeruginosa infection.
Effect of single subconjunctival injection of bevacizumab on primary pterygium: clinical, histopathological and immunohistochemical study (2018)

The use of single intra lesional injection of Avastin in pterygium decreased vascularity and decreased VEGF expression in injected pterygium after one month. Our study proved the effect of single intra lesional injection of Avastin on pterygium. Further studies may enable limiting the need for surgery and improve quality of life for patients with pterygia.
Effect of Selective Doping on the Emission Characteristics of a Heavily Si-Doped GaAs/AlGaAs Quantum Well (1987)

Spontaneous emission characteristics in a heavily doped active layer have successfully been improved by using a selective doping structure. It is observed that at a sheet carrier density of 1.6×10 13 cm -2 a selectively Si-doped GaAs/AlGaAs multiple quantum-well has a higher radiative recombination rate than a uniformly doped structure with a recombination lifetime of 0.6 ns. Spatial separation of impurities from recombining majority and minority carriers has eliminated the formation of band tail and the impurity-related nonradiative centers from the well layer.
Effect of Ti<sup>3+</sup> on TiO<sub>2</sub>-Supported Cu Catalysts Used for CO Oxidation (2012)

In this paper, we have shown that Cu/TiO(2) catalysts are highly active in CO oxidation. For instance, a 3.4% Cu/TiO(2) catalyst exhibits a higher turnover rate for the effective removal of CO in air than 3-5% Pt/TiO(2) and 20% Cu/ZnO/Al(2)O(3) catalysts. A small amount of Cu(+) species is formed during the calcination treatment at 225 °C, which is the main active phase for the CO oxidation. However, it is proposed that some highly dispersed CuO can also form in the TiO(2) lattice during the calcination treatment. Furthermore, a strong electron interaction between Cu(2+) in highly dispersed CuO and Ti(3+) on rutile TiO(2) (Cu(2+)+Ti(3+)→Cu(+)+Ti(4+)) has been shown to occur. Overall, the reduction of Cu(+) is a major factor that contributes to the reaction rate of the CO oxidation.
Strategies That Work (2023)

Since the first publication of Strategies That Work, numerous new books on reading comprehension have been published and more educators than ever are teaching comprehension. In this third edition of their groundbreaking book, authors Stephanie Harvey and Anne Goudvis bring you Strategies That Work: Teaching Comprehension for Understanding, Engagement, and Building Knowledge. This new edition is organized around three section: Part I: Starting with the Foundation of Meaning, these chapters provide readers with a solid introduction to reading comprehension instruction, including principles that guide practice, suggestions for text selection, and a review of recent research Part II: Part II contains lessons to put these principles into practices for all areas of reading comprehension Part III: This section shows you how to integrate comprehension instruction across the curriculum and the school day, with a focus on science and social studies. In addition, this new version includes updated bibliographies, including the popular Great Books for Teaching Content, online resources, and fully revised chapters focusing on digital reading, strategies for integrating comprehension and technology, and comprehension across the curriculum. Harvey and Goudvis tackle close reading, close listening, text complexity, and critical thinking and demonstrate how your students can build knowledge through thinking-intensive reading and learning. This third edition is a must-have resource for a generation of new teachers – and a welcome refresher for those with dog-eared copies of this timeless guide to reading comprehension.
Histograms of Categorized Shapes for 3D ear detection (2010)

We introduce a novel shape-based feature set, termed the Histograms of Categorized Shapes (HCS), for robust Three-Dimensional (3D) object recognition. By adopting the sliding window approach and a linear Support Vector Machine (SVM) classifier, the efficacy of the HCS feature is assessed on a 3D ear detection task. Experimental results demonstrate that the approach achieves a perfect detection rate, i.e., a 100% detection rate with a 0% false positive rate, on a validation set consisting of 142 range profile images from the University of Notre Dame (UND) 3D ear biometrics database. It is to the best of our knowledge that the detection rate achieved here outperforms those reported in the literature for the given dataset. The proposed detector is also extremely efficient in both training and detection due to the simplicity of the feature extraction and speed of the classification process, suggesting that the method is suitable for practical use in 3D ear biométrie applications.
T<sub>1</sub> Shortening in the Cerebral Cortex after Multiple Administrations of Gadolinium-based Contrast Agents (2016)

We report a 34-year-old male who manifested T<sub>1</sub> shortening of the cerebral cortices after more than 86 contrast-enhanced MRI studies. We observed high-signal intensity (SI) on T<sub>1</sub>-weighted images (T<sub>1</sub>WIs) not only in the globus pallidus, dentate nucleus, and pulvinar of thalamus, but also in the cortices of the pre- and post-central gyri and around the calcarine sulcus. High SI in the cerebral cortices was not clearly demonstrated on T<sub>1</sub>WI scans performed 11 years earlier. The high SI we observed in these areas of the brain corresponded to areas with a normal iron-deposition predilection. Gadolinium deposition in the brain may be associated with the iron metabolism.
Mechanical–Electrical Measurements and Relevant Test Structures for Sensing Interconnect Stress Effects in CMOS Technology (2012)

For CMOS technology, the increase of interconnects metal density is responsible for heterogeneous mechanical stress fields in active regions of silicon. Coupled mechanical–electrical measurements are performed to evaluate the impact of stress at circuit and device levels. This mismatch originated by interconnects metal lines stress is measured through the use of piezoresistive test structures. Local mechanical stress can thus be monitored in a simple process control compatible approach.
Characterization of Ehp, a Secreted Complement Inhibitory Protein from Staphylococcus aureus (2007)

We report here the discovery and characterization of Ehp, a new secreted Staphylococcus aureus protein that potently inhibits the alternative complement activation pathway. Ehp was identified through a genomic scan as an uncharacterized secreted protein from S. aureus, and immunoblotting of conditioned S. aureus culture medium revealed that the Ehp protein was secreted at the highest levels during log-phase bacterial growth. The mature Ehp polypeptide is composed of 80 residues and is 44% identical to the complement inhibitory domain of S. aureus Efb (extracellular fibrinogen-binding protein). We observed preferential binding by Ehp to native and hydrolyzed C3 relative to fully active C3b and found that Ehp formed a subnanomolar affinity complex with these various forms of C3 by binding to its thioester-containing C3d domain. Site-directed mutagenesis demonstrated that Arg(75) and Asn(82) are important in forming the Ehp.C3d complex, but loss of these side chains did not completely disrupt Ehp/C3d binding. This suggested the presence of a second C3d-binding site in Ehp, which was mapped to the proximity of Ehp Asn(63). Further molecular level details of the Ehp/C3d interaction were revealed by solving the 2.7-A crystal structure of an Ehp.C3d complex in which the low affinity site had been mutationally inactivated. Ehp potently inhibited C3b deposition onto sensitized surfaces by the alternative complement activation pathway. This inhibition was directly related to Ehp/C3d binding and was more potent than that seen for Efb-C. An altered conformation in Ehp-bound C3 was detected by monoclonal antibody C3-9, which is specific for a neoantigen exposed in activated forms of C3. Our results suggest that increased inhibitory potency of Ehp relative to Efb-C is derived from the second C3-binding site in this new protein.