gebhart/patrepeval huggingface dataset:
Reducing <i>Staphylococcus aureus</i> resistance to lysostaphin using CRISPR‐dCas9 (2019)

Bacteriolytic enzymes (cell lytic enzymes) are promising alternatives to antibiotics especially in killing drug-resistant bacteria. However, some bacteria slowly become resistant to various classes of peptidoglycan hydrolases, for reasons not well studied, in the presence of growth-supporting nutrients, which are prevalent at sites of infection. Here, we show that Staphylococcus aureus, a human and animal pathogen, while susceptible to the potent staphylolytic enzyme lysostaphin (Lst) in buffered saline, is highly resistant in the rich medium tryptic soy broth (TSB). Through a series of biochemical analysis, we identified that the resistance was due to prevention of Lst-cell binding mediated by the wall teichoic acids (WTAs) present on the cell surface. Inhibition or deletion of the gene tarO responsible for the first step of WTA biosynthesis greatly reduced S. aureus resistance to Lst in TSB. To overcome the resistance, we took advantage of the gene regulation potential of CRISPR-dCas9 and demonstrated that downregulation of tarO, tarH, and/or tarG gene expression, the latter two encoding enzymes that anchor WTAs in the outer layer of cell wall peptidoglycan, sensitized S. aureus to Lst and enabled eradication of the bacterium in TSB in 24 hr. As a result, we elucidate a key mechanism of Lst resistance in metabolically active S. aureus and provide a potential approach for treating life-threatening or hard-to-treat infections caused by Gram-positive pathogens.
Role of PPAR-δ in the development of zymosan-induced multiple organ failure: an experiment mice study (2010)

In this study, we have shown that GW0742 attenuates the degree of zymosan-induced non-septic shock in mice.
Endovascular stent graft repair of aortic aneurysms (1997)

Vascular surgeons are increasingly encountering older patients with large aneurysms associated with severe comorbid conditions. This situation can increase operative morbidity and elevate the mortality rate of aortic surgery over 60%. With some frequency many patients will represent a prohibitive risk for conventional graft replacement. The endoluminal treatment of 110 patients has proved to be feasible and may represent an alternative solution. One hundred six of the patients had an abdominal aortic aneurysm and in four patients, the thoracic aorta was involved. All of them underwent endoluminal repair for the aortic pathology using the combination of stents and grafts in aorto-aortic or aorto-iliac position, with straight, tapered, or bifurcated stent-graft devices. The results are as follows: Initial success was 84% in aorto-aortic abdominal devices and 100% in aorto-aortic thoracic devices. In aorto-iliac devices, initial success was 75%. Late success rates were 62% of the initial group and 80% of the initially successful group.
Prediction of Ras-effector interactions using position energy matrices (2007)

Supplementary data are available at Bioinformatics online.
<i>In situ</i> resistance measurements of epitaxial cobalt silicide nanowires on Si(110) (2005)

We have performed in situ resistance measurements for individual epitaxial CoSi2 nanowires (NWs) (approximately 60 nm wide and 5μm long) formed on a Si(110) surface. Two- and four-point probe measurements were done with a multitip scanning tunneling microscope at room temperature. The NWs were well isolated from the substrate by a Schottky barrier with zero-bias resistance of 107Ω. The resistivity of the NWs was 30μΩcm, which is similar to that for high-quality epitaxial films. The NW resistance was essentially unchanged after exposure to air.
Visual Art and Self-Construction (2023)

"Visual Art and Self-Construction." Journal of the British Society for Phenomenology, 54(3), pp. 320–321
Measurement of prompt <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si1.svg"><mml:msubsup><mml:mrow><mml:mi mathvariant="normal">D</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="normal">s</mml:mi></mml:mrow><mml:mrow><mml:mo linebreak="badbreak" linebreakstyle="after">+</mml:mo></mml:mrow></mml:msubsup></mml:math>-meson production and azimuthal anisotropy in Pb–Pb collisions at <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" altimg="si2.svg"><mml:msqrt><mml:mrow><mml:msub><mml:mrow><mml:mi>s</mml:mi></mml:mrow><mml:mrow><mml:mi mathvariant="normal">NN</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:msqrt><mml:mo linebreak="goodbreak" linebreakstyle="after">=</mml:mo><mml:mn>5.02</mml:mn><mml:mspace width="0.25em"/><mml:mtext>TeV</mml:mtext></mml:math> (2022)

The production yield and angular anisotropy of prompt Ds+ mesons were measured as a function of transverse momentum (pT) in Pb–Pb collisions at a centre-of-mass energy per nucleon pair sNN=5.02TeV collected with the ALICE detector at the LHC. Ds+ mesons and their charge conjugates were reconstructed at midrapidity (|y|<0.5) from their hadronic decay channel Ds+→ϕπ+, with ϕ→K−K+, in the pT intervals 2<pT<50GeV/c and 2<pT<36GeV/c for the 0–10% and 30–50% centrality intervals. For pT>10GeV/c, the measured Ds+-meson nuclear modification factor RAA is consistent with the one of non-strange D mesons within uncertainties, while at lower pT a hint for a Ds+-meson RAA larger than that of non-strange D mesons is seen. The enhanced production of Ds+ relative to non-strange D mesons is also studied by comparing the pT-dependent Ds+/D0 production yield ratios in Pb–Pb and in pp collisions. The ratio measured in Pb–Pb collisions is found to be on average higher than that in pp collisions in the interval 2<pT<8GeV/c with a significance of 2.3σ and 2.4σ for the 0–10% and 30–50% centrality intervals. The azimuthal anisotropy coefficient v2 of prompt Ds+ mesons was measured in Pb–Pb collisions in the 30–50% centrality interval and is found to be compatible with that of non-strange D mesons. The main features of the measured RAA, Ds+/D0 ratio, and v2 as a function of pT are described by theoretical calculations of charm-quark transport in a hydrodynamically expanding quark–gluon plasma including hadronisation via charm-quark recombination with light quarks from the medium. The pT-integrated production yield of Ds+ mesons is compatible with the prediction of the statistical hadronisation model.
Ultra-low voltage wideband inductorless balun LNA with high gain and high IP2 for sub-GHz applications (2016)

The design of an ultra-low voltage CMOS wideband LNA topology operating under a 0.6 V power supply with high gain and high IP2 is presented in this paper. The circuit performance is targeted towards use in direct conversion receivers, where a high IP2 is required. The LNA operates in sub-1 GHz applications reaching frequencies as low as 50 MHz, as it is required by IEEE 802.22 standard. The topology proposed here is based on the resistive-feedback inverter with a cascaded auxiliary amplifier to implement noise canceling. This cascaded amplifier is composed by a common-source (CS) amplifier and a very linear buffer at the output of the cascade. The high IP2 is obtained by a proper transistor biasing and by combining diodes with the load of the amplifiers with the highest non-linearity. This topology also works as a balun to comply with single-ended input from antennas and differential mixers as output loads. The post-layout simulations included bondwire inductances and pad capacitances parasitics. The results show a bandwidth of 50 MHz-1 GHz, voltage gain > 18 dB, NF <; 3.8 dB, S <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">11</sub> <; -13 dB and maximum IP2 of 38 dBm. The LNA power consumption is just 6.7 mW, excluding pad buffers.
Composition of secondary alcohols, ketones, alkanediols, and ketols in Arabidopsis thaliana cuticular waxes (2009)

Arabidopsis wax components containing secondary functional groups were examined (i) to test the biosynthetic relationship between secondary alcohols and ketols and (ii) to determine the regiospecificity and substrate preference of the enzyme involved in ketol biosynthesis. The stem wax of Arabidopsis wild type contained homologous series of C(27) to C(31) secondary alcohols (2.4 microg cm(-2)) and C(28) to C(30) ketones (6.0 microg cm(-2)) dominated by C(29) homologues. In addition, compound classes containing two secondary functional groups were identified as C(29) diols (approximately 0.05 microg cm(-2)) and ketols (approximately 0.16 microg cm(-2)). All four compound classes showed characteristic isomer distributions, with functional groups located between C-14 and C-16. In the mah1 mutant stem wax, diols and ketols could not be detected, while the amounts of secondary alcohols and ketones were drastically reduced. In two MAH1-overexpressing lines, equal amounts of C(29) and C(31) secondary alcohols were detected. Based on the comparison of homologue and isomer compositions between the different genotypes, it can be concluded that biosynthetic pathways lead from alkanes to secondary alcohols, and via ketones or diols to ketols. It seems plausible that MAH1 is the hydroxylase enzyme involved in all these conversions in Arabidopsis thaliana.
Data Appendix for "Alignment of data sharing practices in biomedical data repositories with open, FAIR, citable and trustworthy principles" (2020)

Fiona Murphy, Michael Bar-Sinai, Maryann E. Martone This directory contains the data collected for this paper, both raw and processed. Content: Raw interview transcripts, produced by PolicyModelsServer (https://github.com/IQSS/DataTaggingServer) AMP-T2D.xml CIL.xml FlCy.xml (for Flow Cytometry) IDR.xml MassIVE.xml MetabolomicsWorkbench.xml NIHFigshare.xml Zenodo.xml <em>Summary directory</em><br> Human-readable versions of the above XML transcripts. AMP-T2D.xml.txt CIL.xml.txt FlCy.xml.txt IDR.xml.txt MassIVE.xml.txt MetabolomicsWorkbench.xml.txt NIHFigshare.xml.txt Zenodo.xml.txt * summary-coordinate.tsv: Tab-separated summary - coordinates of each repository<br> * summary.json: JSON summary of the coordinates of each repository, and the policy space itself<br> * summary-transcript.tsv: Tab-separated summary - interview answers for each repository
Detection of arterial emboli using Doppler ultrasound in rabbits. (1991)

The purpose of this study was to develop an animal model that could be used to test the ability of Doppler ultrasound to detect arterial emboli composed of materials that are often involved in cerebral emboli. Emboli introduced into the rabbit aorta via the left renal artery consisted of clotted whole blood, platelets, atheromatous material, fat, or air. The ultrasound examination was carried out continuously during the studies using a multifrequency transcranial Doppler apparatus with a 2-MHz probe, a sample volume of 15 mm, at a depth of 15 mm. The intensity of the Doppler spectrum was measured and displayed as a 15-shade color scale, each shade representing a 3-dB difference. The diameter of the aorta at the site of the ultrasound examination was similar to the diameter of the middle cerebral artery in humans. All 125 emboli introduced were clearly detected because they caused a Doppler signal at least 15 dB greater than that of the surrounding blood. These results show that the potential for emboli detection using Doppler ultrasound in the clinical situation is now considerable.
Application of Artificial Neural Networks to Wave Nowcasting (2010)

In this paper the Artificial Neural Networks (ANN) are used to produce a reliable short term (up to 100 s) prediction of the actual sea surface elevation, named “wave nowcasting”. This is of primary importance to support marine operations of vessels in Offshore Engineering. The present study proposes a combined application of ANN and wavegrouping analysis based on the Hilbert transform. The observations of empirical time series are used to verify the performance of this model and to find the best configuration. The results indicate that the radial basis function networks provide an effective and accurate tool to forecast the arrival of wave groups at the vessel location.
Managing home routers from the cloud using Software Defined Networking (2016)

Software Defined Networking (SDN) is increasingly being applied to the management and orchestration of data center networks, wide-area networks, and enterprise networks. In this work we demonstrate the benefits of cloud-based SDN management of home routers. We install open-source firmware (OpenWRT and OpenVSiwtch) on off-the-shelf gateways, and deliver new services to consumers via our software in the cloud. Our service allows users to see their household devices and respective bandwidth usage in real-time, impose a download quota on a per-device basis, and impose time-based parental controls on specific household devices. By removing control from the home gateway to the cloud, we show that new services can be delivered rapidly via easy-to-use interfaces suitable for technically unsophisticated users.
Rift Valley fever virus MP-12 vaccine encoding Toscana virus NSs retains neuroinvasiveness in mice (2013)

Rift Valley fever is a mosquito-borne zoonotic disease endemic to sub-Saharan Africa. Rift Valley fever virus (RVFV; genus Phlebovirus, family Bunyaviridae) causes high rates of abortion and fetal malformation in pregnant ruminants, and haemorrhagic fever, neurological disorders or blindness in humans. The MP-12 strain is a highly efficacious and safe live-attenuated vaccine candidate for both humans and ruminants. However, MP-12 lacks a marker to differentiate infected from vaccinated animals. In this study, we originally aimed to characterize the efficacy of a recombinant RVFV MP-12 strain encoding Toscana virus (TOSV) NSs gene in place of MP-12 NSs (rMP12-TOSNSs). TOSV NSs promotes the degradation of dsRNA-dependent protein kinase (PKR) and inhibits interferon-β gene up-regulation without suppressing host general transcription. Unexpectedly, rMP12-TOSNSs increased death in vaccinated outbred mice and inbred BALB/c or C57BL/6 mice. Immunohistochemistry showed diffusely positive viral antigens in the thalamus, hypothalamus and brainstem, including the medulla. No viral antigens were detected in spleen or liver, which is similar to the antigen distribution of moribund mice infected with MP-12. These results suggest that rMP12-TOSNSs retains neuroinvasiveness in mice. Our findings demonstrate that rMP12-TOSNSs causes neuroinvasion without any hepatic disease and will be useful for studying the neuroinvasion mechanism of RVFV and TOSV.
A New Methodology for Incorporating Chiral Linkers into Stapled Peptides (2017)

Stapled peptides have arisen as a new class of chemical probe and potential therapeutic agents for modulating protein-protein interactions. Here, we report the first two-component i,i+7 stapling methodology that makes use of two orthogonal, on-resin stapling reactions to incorporate linkers bearing a chiral centre into a p53-derived stapled peptide. Post-stapling modifications to the chain were performed on-resin and enabled rapid access to various peptide derivatives from a single staple. The stapled peptides have increased helicity, protease stability and in vitro binding affinities to MDM2 compared to the equivalent unstapled peptide. This approach can be used to generate a library of diverse stapled peptides with different properties starting from a single stapled peptide, with scope for much greater functional diversity than that provided by existing stapling methodologies.
Omega-3 Fatty Acid Supplementation Reduces Intervertebral Disc Degeneration (2019)

BACKGROUND Intervertebral disc (IVD) degeneration is a common cause of lower back pain, which carries substantial morbidity and economic cost. Omega-3 fatty acids (n-3 FA) are known to reduce inflammatory processes with a relatively benign side effect profile. This study aimed to investigate the effect of n-3 FA supplementation on IVD degeneration. MATERIAL AND METHODS Two non-contiguous lumbar discs of 12 Sprague Dawley rats were needle-punctured to induce disc degeneration. Post-surgery, rats were randomly assigned to either a daily n-3 FA diet (530 mg/kg/day of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) in a 2: 1 ratio, administered in sucrose solution) or control diet (sucrose solution only), which was given for the duration of the study. After 1 month, blood serum arachidonic acid/eicosapentaenoic acid (AA/EPA) ratios were analyzed. After 2 months, micro-MRI (magnetic resonance imaging) analysis and histological staining of disc explants were performed to analyze the IVD. RESULTS A reduction of blood AA/EPA ratios from 40 to 20 was demonstrated after 1 month of daily supplementation with n-3 FA. Micro-MRI analysis showed an injury-induced reduction of IVD hydration, which was attenuated in rats receiving n-3 FA. Histological evaluation demonstrated the destruction of nucleus pulposus tissue in response to needle puncture injury, which was less severe in the n-3 FA diet group. CONCLUSIONS The results of this study suggest that n-3 FA dietary supplementation reduces systemic inflammation by lowering AA/EPA ratios in blood serum and has potential protective effects on the progression of spinal disc degeneration, as demonstrated by reduced needle injury-induced dehydration of intervertebral discs and reduced histological signs of IVD degeneration.
A new metals passivator in fluid catalytic cracking (1988)

Chevron's new metal passivation process based on bismuth additives has been extensively tested in bench scale experiments, pilot plant studies and commercial trials. This technology offers process benefits equivalent to antimony-based additives without the use of, or production of, products or by-products which contain materials on the EPA list of hazardous materials.
Results (correlation coëfficient and p-value) of the Spearman's rank correlation analyses between the remaining dysregulated AMPs after treatment in responders, &lt;i&gt;VIL1&lt;/i&gt; and &lt;i&gt;IL8&lt;/i&gt;, and between alpha-defensins and &lt;i&gt;PLA2G2A&lt;/i&gt;, using the microarray log2 normalized expression values of the probe sets representing these genes. (2015)

&lt;p&gt;Results (correlation coëfficient and p-value) of the Spearman's rank correlation analyses between the remaining dysregulated AMPs after treatment in responders, &lt;i&gt;VIL1&lt;/i&gt; and &lt;i&gt;IL8&lt;/i&gt;, and between alpha-defensins and &lt;i&gt;PLA2G2A&lt;/i&gt;, using the microarray log2 normalized expression values of the probe sets representing these genes.&lt;/p&gt;
Experimental Veriflcation of RFI Mitigation with a Focal Plane Array Feed (2007)

We demonstrate the use of spatial filtering algorithms for radio frequency interference (RFI) mitigation in conjunction with a focal plane array of electrically small elements. The array consists of a seven-element hexagonal arrangement of thickened dipole antennas with 1600 MHz designed center frequency backed by a circular ground plane at the focal plane of a 3 m parabolic reflector. Rooftop-mounted signal sources were used to simulate a weak signal of interest at boresight and a strong, broadband interferer in the reflector sidelobes. Using an adaptive beamformer, the amplitude of the interfering signal was reduced sufficiently to recover the signal of interest. For an interference to noise ratio of 15 dB as measured at the center array element, the interferer was suppressed to the level of the fluctuations of the 10-second integrated noise floor (the minimum detectable signal level was interference-limited and no longer decreases after 10 s integration). Similar cancellation performance was demonstrated for a nonstationary interferer moving at an angular velocity of 0.1◦ per second. Pattern rumble due to beamformer adaptation was observed and quantified. For a moving RFI source, the degree of pattern rumble was found to be unacceptably large in terms of its effects on the maximum stable integration time and receiver sensitivity. An array feed with more elements together with specialized signal processing algorithms designed to suppress pattern rumble will likely be required in order to use adaptive spatial filtering for astronomical observations.
Nickel Complexes with Oxazoline-Based <i>P</i>,<i>N</i>-Chelate Ligands:  Synthesis, Structures, and Catalytic Ethylene Oligomerization Behavior (2004)

The phosphinooxazoline ligands 9−12 have been prepared and used to examine and compare the catalytic properties of their corresponding Ni(II) complexes in ethylene oligomerization. The molecular structure of rac-2-[1‘-(diphenylphosphanyl)ethyl]-4,4-dimethyl-4,5-dihydrooxazole (10) has been determined by X-ray diffraction. The paramagnetic Ni(II) complexes [NiX(μ-X)(P,N)]2 (19, X = Br, P,N = 2-[(diphenylphosphanyl)methyl]-4,4-dimethyl-4,5-dihydrooxazole (9)); 20, X = Cl, P,N = 9; 21, X = Cl, P,N = 10); 22, X = Cl; P,N = 2-[(diphenylphosphanyl)methyl]-4-(R)-phenyl-4,5-dihydrooxazole (12)); 23, X = Br, P,N = 12) and [NiCl2(P,N)] (24; P,N = 2-[1‘-(diphenylphosphanyl)-1‘-methylethyl]-4,4-dimethyl-4,5-dihydrooxazole (11)) were prepared in yields of 79−90%, and 19 and 24 have been characterized by X-ray diffraction. The former is a dinuclear complex with distorted-trigonal-bipyramidal geometry around the Ni(II) centers, whereas 24 is a mononuclear, tetrahedral complex, which underlines the strong influence of a substituent on the carbon atom α to P. The metal coordination sphere in complexes 19−24 was determined in solution by the Evans method to be trigonal bipyramidal for 19−23 and tetrahedral for 24. Whereas complexes 19−23 and [NiCl2(PCy3)2] were inactive for ethylene polymerization in the presence of methylaluminoxane (MAO), the mononuclear complex 24 gave a TOF of 7900 mol of C2H4/((mol of Ni) h) with a selectivity for 1-butene of 38%. Complexes 19, 20, and 22 were inactive for the oligomerization of ethylene in the presence of NaBH4, but 19, 21, and 24 were active with AlEtCl2 as a cocatalyst. Activities and selectivities were compared to those of [NiCl2(PCy3)2], a typical precatalyst used in the dimerization of α-olefins. Complex 19 yielded a turnover frequency of 36 300 mol of C2H4/((mol of Ni) h) in the presence of 14 equiv of AlEtCl2. In the presence of only 6 equiv of cocatalyst, the Ni complexes 21 and 24 showed TOF values of 38 100 and 45 900 mol of C2H4/((mol of Ni) h), respectively, higher than that of 27 200 mol of C2H4/((mol of Ni) h) obtained with [NiCl2(PCy3)2].