gebhart/patrepeval huggingface dataset:
CmeABC Functions as a Multidrug Efflux System in Campylobacter jejuni (2002)

Campylobacter jejuni, a gram-negative organism causing gastroenteritis in humans, is increasingly resistant to antibiotics. However, little is known about the drug efflux mechanisms in this pathogen. Here we characterized an efflux pump encoded by a three-gene operon (designated cmeABC) that contributes to multidrug resistance in C. jejuni 81-176. CmeABC shares significant sequence and structural homology with known tripartite multidrug efflux pumps in other gram-negative bacteria, and it consists of a periplasmic fusion protein (CmeA), an inner membrane efflux transporter belonging to the resistance-nodulation-cell division superfamily (CmeB), and an outer membrane protein (CmeC). Immunoblotting using CmeABC-specific antibodies demonstrated that cmeABC was expressed in wild-type 81-176; however, an isogenic mutant (9B6) with a transposon insertion in the cmeB gene showed impaired production of CmeB and CmeC. Compared to wild-type 81-176, 9B6 showed a 2- to 4,000-fold decrease in resistance to a range of antibiotics, heavy metals, bile salts, and other antimicrobial agents. Accumulation assays demonstrated that significantly more ethidium bromide and ciprofloxacin accumulated in mutant 9B6 than in wild-type 81-176. Addition of carbonyl cyanide m-chlorophenylhydrazone, an efflux pump inhibitor, increased the accumulation of ciprofloxacin in wild-type 81-176 to the level of mutant 9B6. PCR and immunoblotting analysis also showed that cmeABC was broadly distributed in various C. jejuni isolates and constitutively expressed in wild-type strains. Together, these findings formally establish that CmeABC functions as a tripartite multidrug efflux pump that contributes to the intrinsic resistance of C. jejuni to a broad range of structurally unrelated antimicrobial agents.
Automatic registration of ICG images using mutual information and perfusion analysis (2005)

Introduction: Indocyanin green fundus angiographic images (ICGA) of the eyes is useful method in detecting and characterizing the choroidal neovascularization (CNV), which is the major cause of the blindness over 65 years of age. To investigate the quantitative analysis of the blood flow on ICGA, systematic approach for automatic registration of using mutual information and a quantitative analysis was developed. Methods: Intermittent sequential images of indocyanin green angiography were acquired by Heidelberg retinal angiography that uses the laser scanning system for the image acquisition. Misalignment of each image generated by the minute eye movement of the patients was corrected by the mutual information method because the distribution of the contrast media on image is changing throughout the time sequences. Several region of interest (ROI) were selected by a physician and the intensities of the selected region were plotted according to the time sequences. Results: The registration of ICGA time sequential images is required not only translate transform but also rotational transform. Signal intensities showed variation based on gamma-variate function depending on ROIs and capillary vessels show more variance of signal intensity than major vessels. CNV showed intermediate variance of signal intensity and prolonged transit time. Conclusion: The resulting registered images can be used not only for quantitative analysis, but also for perfusion analysis. Various investigative approached on CNV using this method will be helpful in the characterization of the lesion and follow-up.
Medial-Sided Ligamentous Injuries of the Athlete's Knee: Evaluation and Management (2023)

The superficial medial collateral ligament (sMCL) is the most commonly injured ligamentous structure in the knee. The other medial knee stabilizers include the deep medial collateral ligament, the posterior oblique ligament, and the medial meniscus. Medial collateral ligament injuries frequently occur in young athletes. As a result of the good healing capacity of the sMCL, the majority of acute medial-sided knee injuries can be treated nonoperatively with good outcomes. However, missed concomitant injuries can lead to residual laxity and instability of the knee when treated conservatively. When surgical management is warranted, numerous techniques exist, including repair, augmentation, and reconstruction. Recent anatomic and biomechanical studies defining the attachment sites and functional roles of the individual medial knee structures have led to advancements in diagnosis, treatment, and rehabilitation. These studies have allowed for the development of an anatomic reconstruction technique that restores the native stability and load-sharing relationships among the medial knee structures. The purpose of this narrative review is to summarize the recent updates in the anatomy, biomechanics, evaluation, and treatment of ligamentous injuries on the medial side of the athlete's knee.
Robbery in South Australia (1997)

This Information Bulletin examines trends in reported unarmed and armed robbery in South Australia during the past decade. It analyses such factors as the location and time when robbery occurs, the average value of goods stolen and the characteristics of victims. It also profiles those offenders apprehended for robbery, including some details of their past offending history and the penalties imposed by the Courts.
Modelling glucose/fructose isomerization with immobilized glucose isomerase in fixed and fluid bed reactors (1986)

Abstract Immobilized glucose isomerase is used to convert glucose to fructose in the production of “High Fructose Corn Syrup (HFCS)” by enzymatic starch hydrolysis. A reactor model was established analogous to heterogeneous catalytic reactor models, taking into account the effects of fluid/particle mass transfer, intraparticle transport, fluid bed expansion, backmixing and reversible kinetics. The kinetic data either for free enzymes and the biocatalyst particles were evaluated using laboratory scale stirred tank reactors. Fixed‐and fluid bed reactor experiments were performed. The comparison of calculated and experimental data show some deviation indicating that the correlations for mass transfer and back‐mixing for complex media, as used here, have to be checked.
Resonance Raman Spectra of TNT and RDX Using Vibronic Theory, Excited-State Gradient, and Complex Polarizability Approximations (2012)

Geometries, UV absorption bands, and resonance Raman (RR) cross sections of TNT and RDX are investigated using density functional theory (DFT) in conjunction with the Coulomb attenuated B3LYP exchange-correlation functional. The absorption and RR spectra are determined with use of vibronic (VB) theory, excited-state gradient, and complex polarizability (CPP) approximations. We examined low-energy isomers (two for TNT and four for RDX) whose energies differ by less than 1 kcal/mol, such that they would appreciably be populated at room temperature. The two TNT isomers differ by an internal rotation of the methyl group, while the four conformers of RDX differ by the arrangements of the nitro group relative to the ring. Our theoretical optical properties of the TNT and RDX isomers are in excellent agreement with experimental and recent CCSD-EOM results, respectively. For the two TNT isomers, the ultraviolet RR (UVRR) spectra are similar and in good agreement with recently measured experimental results. Additionally, the UVRR spectra computed using the excited-state and CPP approaches compare favorably with the VB theory results. On the other hand, the RR spectra of the RDX conformers differ from one another, reflecting the importance of the positioning of the NO2 groups with respect to the ring. In the gas phase or in solution, RDX would give a spectrum associated with a conformationally averaged structure. It is encouraging that the computed spectra of the conformers show similarities to recent measured RDX spectra in acetonitrile solution, and reproduce the 10-fold decrease in the absolute Raman cross sections of RDX compared to TNT for the observed 229 nm excitation. We show that in TNT and RDX vibrational bands that couple to NO2 or the ring are particularly resonance enhanced. Finally, the computed RDX spectra of the conformers present a benchmark for understanding the RR spectra of the solid-phase polymorphs of RDX.
In vitro testing of current spread during ventricular catheter coagulation using diathermy (2007)

The authors report on the development of an anterior cerebral artery pseudoaneurysm that hemorrhaged after monopolar coagulation for a ventricular catheter lodged in the interhemispheric fissure. After observing this complication, the authors developed a simple bench test that can be performed by any neurosurgeon to determine the safest coagulation parameters for any given diathermy unit. A modified grounding pad was placed in a beaker of a protein solution consisting of egg whites. Ventricular catheters were then placed in the solution, and a monopolar diathermy current was applied to a metal stylet at various wattages and for different durations of time. Inducing coagulation at 40 W with a diathermy unit produced flames emanating from around the pores of the catheter tip. Flash flames were also observed at 35 W, forming a coagulum of egg white for a distance of up to 1 cm from the catheter tip. All heat was dissipated through the holes of the first 16 mm of the catheter. At 20 W the flame was minimal and coagulation appeared adequate, whereas at 15 W only bubbles were seen around the tip together with suboptimal coagulum formation. This technique is a simple and effective means of determining the optimal setting for monopolar diathermy and can be used to figure the optimal catheter coagulation wattage for a given diathermy unit. Considering the results of this study, the authors have lowered the current for coagulation in ventricular catheters to 20 W.
Editorial (2012)

Innerhalb des kieferorthopädischen Anomalienspektrums beschäftigen uns Unterkieferrücklagen in der alltäglichen Praxis wahrscheinlich am häufigsten. Ihre Ätiologie, die diversen diagnostischen Möglichkeiten und vielfältigen Therapieansätze sind in der Literatur der letzten Jahrzehnte zahlreich beschrieben.
Hydrophobized Poly(Heptazine Imide) for Highly Effective Photocatalytic Hydrogen Peroxide Production in a Biphasic Fatty Alcohol-Water System (2022)

Light-driven production of hydrogen peroxide via selective dioxygen reduction is an attractive “green” alternative to the conventionally used anthraquinone process. One of the most promising classes of photocatalytic materials for this conversion that excels by high selectivity, chemical stability and low cost is represented by polymeric carbon nitrides, and particularly by various types of poly(heptazine imide) (PHI), i.e., ionic variants of carbon nitride. A crucial challenge highlighted by recent studies is the problem of separation of formed H2O2 from the reaction medium and especially from the suspended photocatalyst particles since photocatalytically generated H2O2 can undergo light-driven decomposition, as well as disproportionation on the surface of the photocatalyst in the dark. Herein, we report an elegant solution to this problem by implementing a biphasic reaction system in which the hydrophobic photocatalyst oxidizes a lipophilic electron donor in the organic phase, while the produced H2O2 is instantaneously extracted into the aqueous layer. To this end, we have achieved an effective hydrophobization of ionic carbon nitride (PHI) nanoparticles in the form of a composite with alkylated silica. The hydrophobized composite effectively photocatalyzes the reduction of dioxygen to H2O2 with concurrent oxidation of a model fatty alcohol (1-octanol) in the organic phase under visible light irradiation (406 nm LED), and enables, at the same time, facile separation of the high-value H2O2/water mixture from the reaction medium at H2O2 concentrations (~0.12 M) that are unprecedentedly high for light-driven systems reported in the literature. Notably, fatty alcohols are readily available from vegetable waxes and as pulping sub-products, and the products of their partial oxidation represent a valuable feedstock for the synthesis of pharmaceuticals and cosmetic products. This work thus showcases a rational design of a high-performance photocatalytic system for H2O2 production that enables easy separation of the product from electron donors and its recovery at high concentrations, and paves the way for sustainable and economically viable light-driven H2O2 production from easily available feedstock.
Subcellular partitioning of transcription factors during osteoblast differentiation: Developmental association of the AML/CBFα/PEBP2α‐related transcription factor‐NMP‐2 with the nuclear matrix (1997)

The subnuclear location of transcription factors may functionally contribute to the regulation of gene expression. Several classes of gene regulators associate with the nuclear matrix in a cell type, cell growth, or cell cycle related-manner. To understand control of nuclear matrix-transcription factor interactions during tissue development, we systematically analyzed the subnuclear partitioning of a panel of transcription factors (including NMP-1/YY-1, NMP-2/AML, AP-1, and SP-1) during osteoblast differentiation using biochemical fractionation and gel shift analyses. We show that nuclear matrix association of the tissue-specific AML transcription factor NMP-2, but not the ubiquitous transcription factor YY1, is developmentally upregulated during osteoblast differentiation. Moreover, we show that there are multiple AML isoforms in mature osteoblasts, consistent with the multiplicity of AML factors that are derived from different genes and alternatively spliced cDNAs. These AML isoforms include proteins derived from the AML-3 gene and partition between distinct subcellular compartments. We conclude that the selective partitioning of the YY1 and AML transcription factors with the nuclear matrix involves a discriminatory mechanism that targets different classes and specific isoforms of gene regulatory factors to the nuclear matrix at distinct developmental stages. Our results are consistent with a role for the nuclear matrix in regulating the expression of bone-tissue specific genes during development of the mature osteocytic phenotype. J. Cell. Biochem. 66:123–132, 1997. © 1997 Wiley-Liss, Inc.
Ultrafast Dynamics of Manganese(III), Manganese(II), and Free-Base Bacteriochlorin: Is There Time for Photochemistry? (2017)

Manganese(III) and manganese(II) complexes of halogenated sulfonamide tetraphenylbacteriochlorins were prepared for the first time via a transmetalation reaction and shown to be stable at room temperature. The behavior of the electronic states of the paramagnetic complexes is remarkably different from those of the metal-free bacteriochlorins or diamagnetic metallobacteriochlorins. The Mn<sup>3+</sup> complex exhibits eight electronic transitions between different states from 300 to 1100 nm, with a very prominent band (molar absorption coefficient of ca. 50000 M<sup>-1</sup> cm<sup>-1</sup>) at 829 nm. Ultrafast transient absorption showed the formation of an excited singquintet state that decays to a tripquintet state with a femtosecond lifetime. The tripquintet state decays in 5 ps, yielding a tripseptet state with a 570 ps lifetime. The electronic absorption of the Mn<sup>2+</sup> complex more closely resembles those of diamagnetic metallobacteriochlorins, but the longest decay lifetime is only ca. 8 ps. The intense photoacoustic waves generated with near-infrared excitation suggest the use of these complexes in photoacoustic tomography.
Increased Osseous 99mTc-DPD Uptake in End-Stage Ankle Osteoarthritis (2015)

Our findings suggest a pathologic bone-remodeling process in end-stage ankle OA areas with increased (99m)Tc-DPD uptake.
First Isolation of Hepatitis E Virus Genotype 4 in Europe through Swine Surveillance in the Netherlands and Belgium (2011)

Hepatitis E virus (HEV) genotypes 3 and 4 are a cause of human hepatitis and swine are considered the main reservoir. To study the HEV prevalence and characterize circulating HEV strains, fecal samples from swine in the Netherlands and Belgium were tested by RT-PCR. HEV prevalence in swine was 7-15%. The Dutch strains were characterized as genotype 3, subgroups 3a, 3c and 3f, closely related to sequences found in humans and swine earlier. The HEV strains found in Belgium belonged to genotypes 3f and 4b. The HEV genotype 4 strain was the first ever reported in swine in Europe and an experimental infection in pigs was performed to isolate the virus. The genotype 4 strain readily infected piglets and caused fever and virus shedding. Since HEV4 infections have been reported to run a more severe clinical course in humans this observation may have public health implications.
Test-time optimization in NOC-based manycore SOCs using multicast routing (2014)

A limitation of prior work on testing of network-on-chip (NOC)-based manycore SOCs is that cores are tested using unicast packets; this approach fails to exploit the homogeneity of cores in large manycore SOCs. By leveraging the capability of modern multicast routers to fork a flit to multiple destination ports simultaneously, we present two methods to minimize time to test cores in a homogeneous SOC with many identical cores. First, we formulate the test-time minimization problem in terms of integer linear programming. Next, we add a practical constraint, model the constrained problem in terms of grid partitioning, and apply dynamic programming (DP) to optimally solve it. We present results on synthetic NOC-based SOCs constructed using cores from the ITC'02 benchmarks to show that the proposed methods significantly outperform prior methods based on unicast, and demonstrate the scalability of the DP-based approach for an SOC consisting of more than 1,000 cores.
Multimodal Imaging in Rat Model Recapitulates Alzheimer's Disease Biomarkers Abnormalities (2017)

Imaging biomarkers are frequently proposed as endpoints for clinical trials targeting brain amyloidosis in Alzheimer's disease (AD); however, the specific impact of amyloid-β (Aβ) aggregation on biomarker abnormalities remains elusive in AD. Using the McGill-R-Thy1-APP transgenic rat as a model of selective Aβ pathology, we characterized the longitudinal progression of abnormalities in biomarkers commonly used in AD research. Middle-aged (9-11 months) transgenic animals (both male and female) displayed mild spatial memory impairments and disrupted cingulate network connectivity measured by resting-state fMRI, even in the absence of hypometabolism (measured with PET [<sup>18</sup>F]FDG) or detectable fibrillary amyloidosis (measured with PET [<sup>18</sup>F]NAV4694). At more advanced ages (16-19 months), cognitive deficits progressed in conjunction with resting connectivity abnormalities; furthermore, hypometabolism, Aβ plaque accumulation, reduction of CSF Aβ<sub>1-42</sub> concentrations, and hippocampal atrophy (structural MRI) were detectable at this stage. The present results emphasize the early impact of Aβ on brain connectivity and support a framework in which persistent Aβ aggregation itself is sufficient to impose memory circuits dysfunction, which propagates to adjacent brain networks at later stages.<b>SIGNIFICANCE STATEMENT</b> The present study proposes a "back translation" of the Alzheimer pathological cascade concept from human to animals. We used the same set of Alzheimer imaging biomarkers typically used in large human cohorts and assessed their progression over time in a transgenic rat model, which allows for a finer spatial resolution not attainable with mice. Using this translational platform, we demonstrated that amyloid-β pathology recapitulates an Alzheimer-like profile of biomarker abnormalities even in the absence of other hallmarks of the disease such as neurofibrillary tangles and widespread neuronal losses.
Site-Directed Mutagenesis Studies of Tn 5 Transposase Residues Involved in Synaptic Complex Formation (2007)

Transposition (the movement of discrete segments of DNA, resulting in rearrangement of genomic DNA) initiates when transposase forms a dimeric DNA-protein synaptic complex with transposon DNA end sequences. The synaptic complex is a prerequisite for catalytic reactions that occur during the transposition process. The transposase-DNA interactions involved in the synaptic complex have been of great interest. Here we undertook a study to verify the protein-DNA interactions that lead to synapsis in the Tn5 system. Specifically, we studied (i) Arg342, Glu344, and Asn348 and (ii) Ser438, Lys439, and Ser445, which, based on the previously published cocrystal structure of Tn5 transposase bound to a precleaved transposon end sequence, make cis and trans contacts with transposon end sequence DNA, respectively. By using genetic and biochemical assays, we showed that in all cases except one, each of these residues plays an important role in synaptic complex formation, as predicted by the cocrystal structure.
Noncovalent binding of 7.beta.,8.alpha.-dihydroxy-9.alpha.,10.alpha.-epoxytetrahydrobenzo[a]pyrene to DNA and its catalytic effect on the hydrolysis of the diol epoxide to tetrol (1982)

In the presence of native DNA the hydrolysis of benzo[a]pyrene-7,8-diol 9,10-epoxide (BPDE) to tetrols (BPT) is markedly accelerated (by a factor of up to approximately 80 at 25 degrees C, pH 7.0, in 5 mM sodium cacodylate buffer solution). When stopped-flow kinetic techniques are utilized, it is shown that the pseudo-first-order hydrolysis rate constant kH is smaller by a factor of approximately 3 in the presence of equivalent concentrations of denatured DNA, by a factor of 8-25 in the presence of nucleotides, and by a factor of 35-45 in the presence of nucleosides (depending on the nucleotide or nucleoside). In the presence of native DNa, kH increases with increasing DNA concentration and reaches a limiting value of kH = 0.684 +/- 0.04 s-1 at DNA concentrations in excess of approximately 5 x 10(-4) M (expressed in concentration of nucleotides). A kinetic model based on (1) rapid formation of a noncovalent BPDE-DNA complex followed by (2) slower hydrolysis of BPDE to BPT at these binding sites is consistent with the experimental data. It is shown furthermore that the DNA concentration dependence of kH and of noncovalent intercalative binding of BPDE to DNA is similar and that addition of magnesium ions (which is known to reduce intercalative binding of planar aromatic molecules to DNA) also reduces kH. These results suggest, but do not necessarily prove, that the DNA binding sites at which the hydrolysis of BPDE (to BPT) is catalyzed are intercalative in nature.
The flag taxonomy of open hypermedia systems (1996)

Article Free Access Share on The flag taxonomy of open hypermedia systems Authors: Kasper Østerbye Department of Computer Science, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg øst, Denmark Department of Computer Science, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg øst, DenmarkView Profile , Uffe Kock Wiil Department of Computer Science, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg øst, Denmark Department of Computer Science, Aalborg University, Fredrik Bajers Vej 7E, 9220 Aalborg øst, DenmarkView Profile Authors Info & Claims HYPERTEXT '96: Proceedings of the the seventh ACM conference on HypertextMarch 1996 Pages 129–139https://doi.org/10.1145/234828.234841Published:01 March 1996Publication History 52citation439DownloadsMetricsTotal Citations52Total Downloads439Last 12 Months19Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF