gebhart/patrepeval huggingface dataset:
Liver Regeneration and Bioengineering - The Emergence of Whole Organ Scaffolds (2012)

Every year an estimated two million people die of advanced liver disease. The World Health Organization estimates that over six hundred and fifty million people worldwide are affected by some form of liver disease, including thirty million Americans. On a worldwide base, the bleak cenario of one to two million deaths are accounted to liver related diseases annually. From all the countries, China has the world’s largest population of Hepatitis B patients (approx. 120 million) with five hundred thousand people dying of the liver disease every year(1, 2). In the US alone, there are around five hundred thousand critical episodes of liver problems every year requiring hospitalization with a huge burden to the patients and an enormous cost to the health care system. In the European Union and United States of America alone, over eighty one thousand and twenty six thousand people died of chronic liver disease in 2006, respectively(1, 3). For these patients, liver transplantation is currently the only therapy proven to extend survival for end-stage liver disease, as it is also the only treatment for severe acute liver failure and the some forms of inborn errors of metabolism. However, the waiting list for liver transplants is extensive and many on the list will not receive an organ due to a dramatic shortage of donors or not being eligible(1).
Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB fromBacillus stearothermophilusBR219 (2006)

Class II extradiol-cleaving catecholic dioxygenase, a key enzyme of aromatic compound degradation in bacteria, cleaves the aromatic ring of catechol by adding two O atoms. PheB is one of the class II extradiol-cleaving catecholic dioxygenases and shows a high substrate specificity for catechol derivatives, which have one aromatic ring. In order to reveal the mechanism of the substrate specificity of PheB, PheB has been crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The space group of the obtained crystal was P2(1)2(1)2(1), with unit-cell parameters a = 65.5, b = 119.2, c = 158.7 A. The crystal diffracted to 2.3 A resolution.
Engineered Production of Short Chain Fatty Acid in Escherichia coli Using Fatty Acid Synthesis Pathway (2016)

Short-chain fatty acids (SCFAs), such as butyric acid, have a broad range of applications in chemical and fuel industries. Worldwide demand of sustainable fuels and chemicals has encouraged researchers for microbial synthesis of SCFAs. In this study we compared three thioesterases, i.e., TesAT from Anaerococcus tetradius, TesBF from Bryantella formatexigens and TesBT from Bacteroides thetaiotaomicron, for production of SCFAs in Escherichia coli utilizing native fatty acid synthesis (FASII) pathway and modulated the genetic and bioprocess parameters to improve its yield and productivity. E. coli strain expressing tesBT gene yielded maximum butyric acid titer at 1.46 g L-1, followed by tesBF at 0.85 g L-1 and tesAT at 0.12 g L-1. The titer of butyric acid varied significantly depending upon the plasmid copy number and strain genotype. The modulation of genetic factors that are known to influence long chain fatty acid production, such as deletion of the fadD and fadE that initiates the fatty acid degradation cycle and overexpression of fadR that is a global transcriptional activator of fatty acid biosynthesis and repressor of degradation cycle, did not improve the butyric acid titer significantly. Use of chemical inhibitor cerulenin, which restricts the fatty acid elongation cycle, increased the butyric acid titer by 1.7-fold in case of TesBF, while it had adverse impact in case of TesBT. In vitro enzyme assay indicated that cerulenin also inhibited short chain specific thioesterase, though inhibitory concentration varied according to the type of thioesterase used. Further process optimization followed by fed-batch cultivation under phosphorous limited condition led to production of 14.3 g L-1 butyric acid and 17.5 g L-1 total free fatty acid at 28% of theoretical yield. This study expands our understanding of SCFAs production in E. coli through FASII pathway and highlights role of genetic and process optimization to enhance the desired product.
Structure-Dependent Reactivity of Semiconducting Single-Walled Carbon Nanotubes with Benzenediazonium Salts (2008)

The addition of diazonium salts to single-walled carbon nanotubes (SWCNTs) in aqueous surfactant suspensions quenches the intrinsic near-infrared fluorescence of semiconducting SWCNTs through sidewall chemical reactions. Spectrally resolved fluorescence spectroscopy of mixed SWCNT samples has been used to measure structure-dependent relative reactivities in the initial stages of these reactions. For several 4-substituted benzenediazonium salts, Ar-R (Ar = N 2 (+)-C 6H 4 and R = Cl, NO 2, OMe), reactivities at pH 10 were found to be greatest for SWCNTs having the largest band gaps. The magnitude of this band gap dependence varies according to the R-group of the salt, with R = OMe showing the strongest variation. For R = OH, acidification of the sample to pH 5.5 results in reversal of the structural trend, as smaller band gap SWCNTs show slightly greater reactivities. The derivatization reactions observed here proceed concurrently, although at different rates, for semiconducting and metallic SWCNT species. These results therefore provide insight into the difficulties of separating metallic and semiconducting SWCNTs through selective reaction schemes and underscore the need for fluorescence spectroscopy to be used in assessing semiconducting SWCNT reactions.
Morpholino spin-labeling for base-pair sequencing of a 3'-terminal RNA stem by proton homonuclear Overhauser enhancements: yeast ribosomal 5S RNA (1987)

Base-pair sequences for 5S and 5.8S RNAs are not readily extracted from proton homonuclear nuclear Overhauser enhancement (NOE) connectivity experiments alone, due to extensive peak overlap in the downfield (11-15 ppm) proton NMR spectrum. In this paper, we introduce a new method for base-pair proton peak assignment for ribosomal RNAs, based upon the distance-dependent broadening of the resonances of base-pair protons spatially proximal to a paramagnetic group. Introduction of a nitroxide spin-label covalently attached to the 3'-terminal ribose provides an unequivocal starting point for base-pair hydrogen-bond proton NMR assignment. Subsequent NOE connectivities then establish the base-pair sequence for the terminal stem of a 5S RNA. Periodate oxidation of yeast 5S RNA, followed by reaction with 4-amino-2,2,6,6-tetramethylpiperidinyl-1-oxy (TEMPO-NH2) and sodium borohydride reduction, produces yeast 5S RNA specifically labeled with a paramagnetic nitroxide group at the 3'-terminal ribose. Comparison of the 500-MHz 1H NMR spectra of native and 3'-terminal spin-labeled yeast 5S RNA serves to identify the terminal base pair (G1 . C120) and its adjacent base pair (G2 . U119) on the basis of their proximity to the 3'-terminal spin-label. From that starting point, we have then identified (G . C, A . U, or G . U) and sequenced eight of the nine base pairs in the terminal helix via primary and secondary NOE's.
In vivo and 3D Visualization of Coronary Artery Development by Optical Coherence Tomography (2007)

One of the most critical but poorly understood processes during cardiovascular development is the establishment of a functioning coronary artery (CA) system. Due to the lack of suitable imaging technologies, it is currently impossible to visualize this complex dynamic process on living human embryos. Furthermore, due to methodological limitations, this intriguing process has not been unveiled in living animal embryos, too. We present here, to the best of our knowledge, the first in vivo images of developing CAs obtained from the hearts of chick embryos grown in shell-less cultures. The in vivo images were generated by optical coherence tomography (OCT). The OCT system used in this study is a mobile fiber-based time-domain real-time OCT system operating with a center wavelength of 1330 nm, an A-scan rate of 4 kHz, and a typical frame rate of 8 frames/s. The axial resolution is 17 μm (in tissue), and the lateral resolution is 30 μm. The OCT system is optimized for in vivo chick heart visualization and enables OCT movie recording with 8 frames/s, full-automatic 3D OCT scanning, and blood flow visualization, i.e., Doppler OCT imaging. Using this OCT system, we generated in vivo OCT recordings of chick embryo hearts to study the process of connection of the future right coronary artery (RCA) to the aorta. Recordings were made at three critical stages during development: day 8 (no clear connection yet), day 9 (established connection of RCA with the aorta with clear blood flow) and day 10 (further remodeling of the established RCA).
Supported Ionic Metallocene Polymerization Catalysts (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTSupported Ionic Metallocene Polymerization CatalystsGregory G. Hlatky and David J. UptonView Author Information Exxon Chemical Company, Baytown Polymers Center, P.O. Box 5200, Baytown, Texas 77522Cite this: Macromolecules 1996, 29, 24, 8019–8020Publication Date (Web):November 18, 1996Publication History Received19 June 1996Revised10 September 1996Published online18 November 1996Published inissue 1 January 1996https://doi.org/10.1021/ma960889xCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views433Altmetric-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 InReddit Read OnlinePDF (71 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Hydrocarbons,Polymers,Sandwich compounds,Silica Get e-Alerts
Using mobile network data to color epidemic risk maps (2022)

In this paper we propose a method for using mobile network data to detect potential COVID-19 hospitalizations and derive corresponding epidemic risk maps. We apply our methods to a dataset from more than 2 million cellphones, collected over the months of March and April in 2020 by a British mobile network provider. The method consists of different algorithms, including detection, filtering, validation and fine-tuning. The approach detected over 2,800 potentially hospitalized individuals, yielding a 98.6% agreement with released public records of patients admitted to NHS hospitals. Analyzing the mobility pattern of these individuals prior to their potential hospitalization, we present a series of risk maps. Compared with census-based maps, our risk maps indicate that the areas of highest risk are not necessarily the most densely populated ones. We also show that the areas of highest risk may change from day to day. Finally, we observe that hospitalized individuals tended to have a higher average mobility than non-hospitalized ones. Overall, we conclude that the rich spatio-temporal information extracted from mobile network data may benefit both the mobile-based technologies and the policies that are being developed against existing and future epidemics.
Avaliação do sistema de entrega e estabilidade de uma vacina de DNA contendo o gene ssiv DE Brucella abortus, encapsulada em nanopartículas de quitosana. (2017)

Made available in DSpace on 2017-11-09T18:16:05Z (GMT). No. of bitstreams: 1\nAvaliacaodosistemadeentregaeestabilidade.pdf: 69296 bytes, checksum: 00e9a3f9c89c3f34427cc6c293a1b240 (MD5)\n Previous issue date: 2017-11-09
Microwave-assisted synthesis of palladium nanoparticles supported on copper oxide in aqueous medium as an efficient catalyst for Suzuki cross-coupling reaction (2018)

We report here a reliable green method for the synthesis of palladium nanoparticles supported on copper oxide as a highly active and efficient catalyst for Suzuki cross-coupling reaction. The experimental synthetic approach is based on microwave-assisted chemical reduction of an aqueous mixture of palladium and copper salt simultaneously using hydrazine hydrate as reducing agent. The catalyst was fully characterized using various techniques showing well-dispersed palladium nanoparticles. The catalytic activity and recyclability of the prepared catalyst were experimentally explored in the ligand-free Suzuki cross-coupling reaction with a diverse series of functionalized substrates. The synthesized Pd/CuO catalyst shows many advantages beside its high catalytic efficiency such as the recyclability of up to five times with negligible loss of catalytic activity, short reaction times, use of environmentally benign solvent systems, and mild reaction conditions.
Evaluation of commercial latex reagents for identification of O157 and H7 antigens of Escherichia coli (1996)

Agglutination reactions obtained with three commercial latex reagents for detecting Escherichia coli O157 antigen (Oxoid Diagnostic Reagents, Hampshire, England; Pro-Lab Inc., Richmond Hill, Ontario, Canada; and Remel Microbiology Products, Lenexa, Kans.) and one for detecting H7 antigen (Remel) were compared with those obtained by standard serologic methods by using the Centers for Disease Control and Prevention (CDC) reference antisera for O157 and H7 antigens. For 159 strains of E. coli and related organisms, the Oxoid, Pro-Lab, and Remel O157 latex reagents each had a sensitivity and specificity of 100% compared with the CDC reference antiserum. For 106 strains of E. coli and related organisms that were not enhanced for motility through semisolid medium, the Remel H7 latex reagent had a sensitivity of 96% and a specificity of 100% compared with the standard tube agglutination method with CDC H7 antiserum. Measures to enhance motility were needed for some strains to detect the H7 antigen. Our findings demonstrate that the commercial latex reagents are good alternatives to standard serologic methods for identifying the O157 and H7 antigens of E. coli.
Aerobic and anaerobic ammonium oxidizers in the Cariaco Basin: distributions of major taxa and nitrogen species across the redoxcline (2017)

AME Aquatic Microbial Ecology Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials AME 79:31-48 (2017) - DOI: https://doi.org/10.3354/ame01817 Aerobic and anaerobic ammonium oxidizers in the Cariaco Basin: distributions of major taxa and nitrogen species across the redoxcline Sara Cernadas-Martín1,*, Elizabeth A. Suter1, Mary I. Scranton1, Yrene Astor2, Gordon T. Taylor1 1School of Marine and Atmospheric Sciences, 145 Endeavour Hall, Stony Brook University, Stony Brook, New York 11794-5000, USA 2Estacion de Investigaciones Marinas de Margarita, Fundación la Salle de Ciencias Naturales, Apartado 144, Punta de Piedras, Estado Nueva Esparta 06318, Venezuela *Corresponding author: sara.cernadas@stonybrook.edu ABSTRACT: Depth distributions of cells and functional gene copies from anaerobic ammonium-oxidizing (anammox) bacteria, aerobic ammonium-oxidizing bacteria (AOB) and archaea (AOA) in the Cariaco Basin, Venezuela were obtained using FISH and q-PCR assays. These distributions were compared to concentrations of dissolved ammonium (NH4+), nitrite (NO2-), nitrate (NO3-), hydrogen sulfide (H2S) and oxygen (O2) along the redoxcline during 3 cruises. Cell counts of anammox bacteria and copies of their nitrite reductase gene (Scalindua-nirS) were consistently observed in 2 distinct layers: the suboxic zone (≤1.1 × 106 cells l-1) and the upper euxinic zone (≤4.7 × 106 cells l-1). We hypothesize that anammox bacteria vertically organize in response to NO2- sources, with NO2- for the shallower assemblage supplied by nitrification and for the deeper assemblage by denitrification. Peaks in AOA cell abundances (up to 14.8 × 106 cells l-1) consistently coincided with copy numbers of archaeal ammonia monooxygenase subunit A gene (archaeal amoA) in the lower oxic zone. Peak abundances of beta- and gammaproteobacterial AOB cells (up to 24.0 × 106 cells l-1) and one of their ammonia monooxygenase genes (β-amoA) overlapped above the shallow anammox peak. Our results suggest that anammox bacteria AOB, AOA and denitrifiers are metabolically interdependent and ultimately controlled by vertical fluxes of O2, NO3-, NO2-, and NH4+ in the Cariaco Basin. KEY WORDS: Anammox · Ammonium oxidation · Cariaco · q-PCR · FISH · Nutrient flux Full text in pdf format PreviousNextCite this article as: Cernadas-Martín S, Suter EA, Scranton MI, Astor Y, Taylor GT (2017) Aerobic and anaerobic ammonium oxidizers in the Cariaco Basin: distributions of major taxa and nitrogen species across the redoxcline. Aquat Microb Ecol 79:31-48. https://doi.org/10.3354/ame01817 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in AME Vol. 79, No. 1. Online publication date: April 07, 2017 Print ISSN: 0948-3055; Online ISSN: 1616-1564 Copyright © 2017 Inter-Research.
Towards a service composition language for heterogeneous service environments (2011)

In this paper we provide an outline and characteristics of a language that allows the design of compositions within a heterogeneous service landscape. Heterogeneous refers to services from various industries and application domains like for example telecommunication, enterprise, web 2.0 and general IT. The language shall enable to use services from all these domains within a single service composition. We propose general requirements for this new language and we also offer an analysis of existing languages and their specific application domains. Finally, we discuss and propose extensions to an already existing standardized workflow language that enables heterogeneous compositions.
A longitudinal-torsional mode ultrasonic needle for deep penetration into bone (2022)

This work presents a longitudinal-torsional (L-T) composite mode ultrasonic needle device for deep bone penetration. The L-T needle is a geometrically modified version of an L-mode needle whose efficacy as a prototype ultrasonic bone biopsy device has been previously demonstrated by the authors. Finite element analysis (FEA) aided in the design of the L-T needle, with the aim of maximising the achievable torsional displacement while matching the longitudinal displacement achieved by the L-mode needle. Experimental modal analysis (EMA) of the fabricated ultrasonic device was used to identify the modal parameters and validate the FEA model. Harmonic analysis then provided an insight into how the inherent nonlinearities of the high-power transducer are affected by incorporating the geometrical features that degenerate the L mode into an L-T mode. High power characterisation shows that the longitudinal displacement amplitude of the L-T mode needle is larger than that of the L-mode needle. Comparative penetration tests in fresh Wistar rat skull were evaluated by investigating cell death and cell survival. The region of statistically significant cell death was small for both devices, with the combined axial and shear motion of the L-T device causing increased osteocyte necrosis within this region. Nevertheless, the results suggest a promising environment for post-operative healing. It is shown how this technology offers a potential technique for a surgical approach to the petrous apex, an application that requires a deep penetration into bone.
CMOS-3D Smart Imager Architectures for Feature Detection (2012)

This paper reports a multi-layered smart image sensor architecture for feature extraction based on detection of interest points. The architecture is conceived for 3-D integrated circuit technologies consisting of two layers (tiers) plus memory. The top tier includes sensing and processing circuitry aimed to perform Gaussian filtering and generate Gaussian pyramids in fully concurrent way. The circuitry in this tier operates in mixed-signal domain. It embeds in-pixel correlated double sampling, a switched-capacitor network for Gaussian pyramid generation, analog memories and a comparator for in-pixel analog-to-digital conversion. This tier can be further split into two for improved resolution; one containing the sensors and another containing a capacitor per sensor plus the mixed-signal processing circuitry. Regarding the bottom tier, it embeds digital circuitry entitled for the calculation of Harris, Hessian, and difference-of-Gaussian detectors. The overall system can hence be configured by the user to detect interest points by using the algorithm out of these three better suited to practical applications. The paper describes the different kind of algorithms featured and the circuitry employed at top and bottom tiers. The Gaussian pyramid is implemented with a switched-capacitor network in less than 50 μs, outperforming more conventional solutions.
Neural-network-based calibration of a mini-spectrophotometer (2003)

A new method for calibration of mini-spectrophotometers is proposed. The method is designed to overcome two important drawbacks of existing methods, viz. their inability to deal with the problems implied by insufficiency of the number of output data and the effects of light polarization. It is based on the use of a tunable laser for acquisition of calibration data, and an RBF (radial basis function) neural network for modeling the polarization effects. The results of a preliminary study of this method, based on semi-synthetic data, are given.
The Eurasian Steppe is an important goat propagation route: A phylogeographic analysis using mitochondrial DNA and Y‐chromosome sequences of Kazakhstani goats (2018)

Goats (Capra hircus) were domesticated in the Fertile Crescent and propagated all over the world. The Silk Road through the Eurasian Steppe belt is a possible propagation route for domestic goats to Central Asia. Kazakhstan is in close geographical proximity to domestication centers and covers the majority of the Eurasian Steppe belt. In this study, we examined the genetic diversity and phylogeographic structure of Kazakhstani goats. The mtDNA sequences of 141 Kazakhstani goats were categorized into haplogroups A, C, and D, of which haplogroup A was predominant (97%), whereas haplogroups C and D were detected at low frequencies (1.4% each). The Kazakhstani haplotypes C were thzen categorized into Asian mtDNA type. Sequence analysis of the SRY gene on the Y-chromosome in 67 male Kazakhstani goats revealed two haplotypes: Y1A (64%) and Y2A (36%). Analysis of the distribution of mtDNA haplogroups and SRY haplotypes from Eurasia and Africa demonstrated genetic similarity among animals from Kazakhstan, Mongolia, and Northwest China located on the Eurasian Steppe belt. These phylogeographic results suggested that the Eurasian Steppe belt was an important propagation route for goats to Central Asia.