gebhart/patrepeval huggingface dataset:
Novel High-Throughput Detection Method To Assess Bacterial Surfactant Production (2010)

A novel biosurfactant detection assay was developed for the observation of surfactants on agar plates. By using an airbrush to apply a fine mist of oil droplets, surfactants can be observed instantaneously as halos around biosurfactant-producing colonies. This atomized oil assay can detect a wide range of different synthetic and bacterially produced surfactants. This method could detect much lower concentrations of many surfactants than a commonly used water drop collapse method. It is semiquantitative and therefore has broad applicability for uses such as high-throughput mutagenesis screens of biosurfactant-producing bacterial strains. The atomized oil assay was used to screen for mutants of the plant pathogen Pseudomonas syringae pv. syringae B728a that were altered in the production of biosurfactants. Transposon mutants displaying significantly altered surfactant halos were identified and further analyzed. All mutants identified displayed altered swarming motility, as would be expected of surfactant mutants. Additionally, measurements of the transcription of the syringafactin biosynthetic cluster in the mutants, the principal biosurfactant known to be produced by B728a, revealed novel regulators of this pathway.
Transmural Entry into Pancreatic Fluid Collections Using a Dedicated Aspiration Needle without Endoscopic Ultrasound Guidance (2006)

Purpose: Endoscopic drainage of pancreatic fluid collections (PFC) is increasingly being performed. A variety of techniques have been described to perform transmural entry, however, there is a lack of data on the technical success and safety of transmural entry using a single technique. We describe the largest experience in transmural entry of PFC's without EUS-guidance using a dedicated aspiration needle. Methods: All patients who underwent endoscopic transmural drainage of PFC from October 1998-May 2006 were identified from the endoscopy database. Data were abstracted from the endoscopic procedure report and the patient records and placed in a JMP drive. All drainages were performed without EUS guidance after visualization of an obvious intraluminal bulge using a dedicated large-bore aspiration needle (BAN-18, Cook Medical, Winston-Salem, NC). The transmural tract into the PFC was dilated using dilating balloons ranging from 6–20mm in diameter followed by subsequent placement of one-two 10-Fr double pigtail stents with or without nasocystic irrigation tubes. Successful entry was defined as entry allowing for placement of stents. Results: Table 1 summarizes the main results.Table 1: Results.1.No significant difference in the complication rate was observed when analyzed for the following variables: age, gender, balloon diameter, presence of endoscopic impression, drainage approach, size and type of fluid collection. Conclusions: Endoscopic transmural drainage of pancreatic fluid collections can be performed safely and effectively via the seldinger technique without endoscopic ultrasound guidance. This data will allow sample size calculations to be made if direct comparisons to this technique and others are undertaken.
Rapid Access to Orthogonally Functionalized Naphthalenes: Application to the Total Synthesis of the Anticancer Agent Chartarin (2016)

We report the synthesis of orthogonally functionalized naphthalenes from simple, commercially available indanones in four steps. The developed method proceeds through a two-step process that features a thermally induced fragmentation of a cyclopropane indanone with simultaneous 1,2-chloride shift. Migration of the chloride substituent occurs in a regioselective manner to preferentially afford the para-chloronaphthol substitution pattern. The obtained naphthols are versatile building blocks that can be selectively modified and used for the efficient construction of biologically active molecules. This has enabled the total synthesis of the potent anticancer natural product chartarin through a highly convergent retrosynthetic bond disconnection.
Rhodium Encapsulated within Silicalite‐1 Zeolite as Highly Efficient Catalyst for Nitrous Oxide Decomposition: From Single Atoms to Nanoclusters and Nanoparticles (2021)

Abstract The size of metal species plays a pivotal role in governing catalytic performance of supported metal catalysts. In this work, a series of Rh encapsulated within silicalite‐1 catalysts with different sizes were prepared by one‐pot hydrothermal method and employed to catalyze the decomposition of N 2 O. Detailed structure determinations by HAADF‐STEM, XPS and CO‐DRIFTS demonstrate that subtle modulation of the encapsulated Rh species were achieved easily from single‐atom to nanoclusters and nanoparticles by controlling the loading and reduction conditions of Rh. The turnover frequency (TOF) of N 2 O decomposition showed a typical volcano‐type dependence on Rh size. Kinetic studies revealed that this structure‐sensitive catalysis was related to the difference in N 2 O and O 2 adsorption/desorption for various Rh species. Furthermore, a Rh@S‐1 catalyst with a proper Rh size (ca. 1.6 nm) was identified as the best‐performing catalyst with a maximum TOF (ca. 95 h −1 ), showing much superior activity than other reported Rh‐based catalysts.
Variational Learning for Switching State-Space Models (2000)

We introduce a new statistical model for time series that iteratively segments data into regimes with approximately linear dynamics and learnsthe parameters of each of these linear regimes. This model combines and generalizes two of the most widely used stochastic time-series models -- hidden Markov models and linear dynamical systems -- and is closely related to models that are widely used in the control and econometrics literatures. It can also be derived by extending the mixture of experts neural network (Jacobs, Jordan, Nowlan, & Hinton, 1991) to its fully dynamical version, in which both expert and gating networks are recurrent. Inferring the posterior probabilities of the hidden states of this model is computationally intractable, and therefore the exact expectation maximization (EM) algorithm cannot be applied. However, we present a variational approximation that maximizes a lower bound on the log-likelihood and makes use of both the forward and backward recursions for hidden Markov models and the Kalman filter recursions for linear dynamical systems. We tested the algorithm on artificial data sets and a natural data set of respiration force from a patient with sleep apnea. The results suggest that variational approximations are a viable method for inference and learning in switching state-space models.
CARNITINE ESTERS PREVENT OXIDATIVE STRESS DAMAGE AND ENERGY DEPLETION FOLLOWING TRANSIENT FOREBRAIN ISCHAEMIA IN THE RAT HIPPOCAMPUS (2006)

1. The present study investigated whether propionyl-L-carnitine (PLC) has neuroprotective effects, similar to those reported for acetyl-L-carnitine (AC), against transient forebrain ischaemia-induced neuronal damage and biochemical derangement in the rat hippocampal CA1 region. 2. In total, 105 adult male Wistar albino rats were divided into seven groups of 15 animals each. The first three groups were injected i.p. with normal saline, AC (300 mg/kg) or PLC (300 mg/kg) for 7 successive days. The next three groups were injected i.p. with the same doses of normal saline, AC or PLC immediately after the induction of 10 min forebrain ischaemia and i.p. injections were continued for 7 successive days. Rats in the seventh group were subjected to sham-operated ischaemia and injected with normal saline for 7 successive days. 3. Seven days after treatment, animals were killed and their brains isolated for histopathological examination and biochemical studies. 4. Forebrain ischaemia resulted in a significant decrease in the number of intact neurons (77%), ATP concentration (51%) and glutathione content (32%), whereas there was a significant increase in the production of thiobarbituric acid-reactive substances (TBARS; 71%) and total nitrate/nitrite (NOx; 260%) in hippocampal tissues. 5. Administration of either AC or PLC attenuated forebrain ischaemia-induced neuronal damage, manifested by a greater number of intact neurons, ATP and glutathione, as well as a decrease in TBARS and NOx in hippocampal tissues. 6. Results from the present study suggest, for the first time, that PLC attenuates forebrain ischaemia-induced neuronal injury, oxidative stress and energy depletion in the hippocampal CA1 region. Propionyl-L-carnitine has neuroprotective effects similar to AC and could have a potential use in the treatment of neurodegenerative diseases. 7. The results of the present study will open up new perspectives for the use of PLC in the treatment of neurodegenerative diseases associated with, or secondary to, myocardial ischaemia-reperfusion injury and chronic circulatory failure.
Synthesis of Macrocyclic Dilactones through Lipases (2005)

We report herein a selective and efficient method to prepare macrocyclic dilactones in good yields from diols and succinic anhydride through a biocatalytic condensation reaction.
Chemical ordering in Cr3Al and relation to semiconducting behavior (2012)

Cr${}_{3}$Al shows semiconductor-like behavior which has been attributed to a combination of antiferromagnetism and chemical ordering of the Cr and Al atoms on the bcc sublattice. This article presents a detailed theoretical and experimental study of the chemical ordering in Cr${}_{3}$Al. Using density functional theory within the Korringa-Kohn-Rostoker (KKR) formalism, we consider five possible structures with the Cr${}_{3}$Al stoichiometry: a bcc solid solution, two-phase C11${}_{b}$ ${\mathrm{Cr}}_{2}\mathrm{Al}+\mathrm{Cr}$, off-stoichiometric C11${}_{b}$ Cr${}_{3}$Al, D0${}_{3}$ Cr${}_{3}$Al, and X-phase Cr${}_{3}$Al. The calculations show that the chemically ordered, rhombohedrally distorted X-phase structure has the lowest energy of those considered and should, therefore, be the ground state found in nature, while the D0${}_{3}$ structure has the highest energy and should not occur. While KKR calculations of the X phase indicate a pseudogap in the density of states, additional calculations using a full potential linear muffin-tin orbital approach and a plane-wave technique show a narrow band gap. Experimentally, thin films of Cr${}_{1\ensuremath{-}x}$Al${}_{x}$ were grown and the concentration, growth temperature, and substrate were varied systematically. The peak resistivity (2400 $\ensuremath{\mu}\ensuremath{\Omega}$-cm) is found for films with $x=0.25$, grown epitaxially on a 300 ${}^{\ensuremath{\circ}}$C MgO substrate. At this $x$, a transition between nonmetallic and metallic behavior occurs at a growth temperature of about 400 ${}^{\ensuremath{\circ}}$C, which is accompanied by a change in chemical ordering from X phase to C11${}_{b}$ Cr${}_{3}$Al. These results clarify the range of possible structures for Cr${}_{3}$Al and the relationship between chemical ordering and electronic transport behavior.
A Proposed Minimum Standard Set of Outcome Measures for Cataract Surgery (2015)

A minimum standard set of outcome measures for cataract surgery is important for meaningful comparison across contexts. The proposed data set is a compromise between all useful data and the practicalities of data collection.
[Cu(H2dped)](BF4)2(H2dped =N,N′-bis(2-(diphenylphosphino)phenyl)ethane-1,2-diamine): a stable phosphine complex of copper(II) (1994)

Controlled potential oxidation of [Cu(H2dped)]1+1 in 1,2-dichloroethane or reaction of [Cu(H2O)6](BF4)2 with H2dped in acetone affords the complex [Cu(H2dped)]2+2i.e. a CuII species stabilized by a soft–hard (P2N2) ligand set.
Visualizing human photoreceptor and retinal pigment epithelium cell mosaics in a single volume scan over an extended field of view with adaptive optics optical coherence tomography (2020)

Using adaptive optics optical coherence tomography, human photoreceptors and retinal pigment epithelium (RPE) cells are typically visualized on a small field of view of ∼1° to 2°. In addition, volume averaging is required for visualizing the RPE cell mosaic. To increase the imaging area, we introduce a lens based spectral domain AO-OCT system that shows low aberrations within an extended imaging area of 4°×4° while maintaining a high (theoretical) transverse resolution (at >7 mm pupil diameter) in the order of 2 µm. A new concept for wavefront sensing is introduced that uses light mainly originating from the RPE layer and yields images of the RPE cell mosaic in a single volume acquisition. The capability of the instrument for in vivo imaging is demonstrated by visualizing various cell structures within the posterior retinal layers over an extended field of view.
T cell independent Thy-1 allo-antibody response with the use of transgenic mice. (1986)

We have introduced a mouse Thy-1.1 gene into the germline of Thy-1.2 mice. The introduced gene was shown to be expressed at very high levels in thymocytes when compared with the endogenous gene. Transgenic thymocytes were shown to evoke a higher than normal primary anti-Thy-1.1 antibody response in plaque-forming cell (PFC) assays. This result suggests that a direct quantitative interaction of the Thy-1 antigen activates the B cell response.
Deep-learning-based cardiovascular risk stratification using coronary artery calcium scores predicted from retinal photographs (2021)

Yonsei University College of Medicine; Ministry of Health and Welfare, Korea Institute for Advancement of Technology, South Korea; Agency for Science, Technology, and Research; and National Medical Research Council, Singapore.
Metalloproteinase Inhibition and the Response to Angioplasty and Stenting in Atherosclerotic Primates (2002)

Determinants of restenosis after angioplasty include constrictive remodeling and intimal hyperplasia. Both processes require extensive matrix turnover, so matrix metalloproteinases (MMPs) have become potential targets of antirestenosis therapies. We studied the effects of RO113-2908, a broad-spectrum MMP inhibitor (MMPI), on the response to iliac artery angioplasty and stenting in atherosclerotic cynomolgus monkeys. Lumen diameter (LD) was measured angiographically, and artery wall geometry was assessed after perfusion-fixation at 4 weeks. Angiogenesis was measured in subcutaneous polyvinyl alcohol disks. Treatment provided significant, systemic MMP inhibitory activity (97±2.2% inhibition of 25 nmol/L MMP-12 by serum) and inhibited angiogenesis ( P =0.007). In contrast, loss of gain in LD ( P =0.73) and constrictive remodeling (external elastic lamina area ratio [injured/uninjured×100]: MMPI, 106.3±9.6% vs control, 119.9±7.2%; P =0.27) were not substantially improved 4 weeks after angioplasty. Treatment also failed to reduce intimal hyperplasia after angioplasty (intimal area [mm 2 ]: 1.4±0.3 vs 1.6±0.2, P =0.65) or stenting (2.4±0.2 vs 2.8±0.2, P =0.12). In summary, inhibition of MMP activity reduced angiogenesis but failed to prevent constrictive remodeling or intimal hyperplasia after angioplasty and stenting in atherosclerotic primates. Additional research is needed to define the spectrum of matrix-degrading proteases critical in healing atherosclerotic arteries after angioplasty.
Synthesis of polyesters by the polyaddition of bis(oxetane)s with active di(ester)s (2004)

Abstract The polyaddition of bis(oxetane)s 1,4‐bis[(3‐ethyl‐3‐oxetanylmethoxymethyl)]benzene (BEOB), 4,4′‐bis[(3‐ethyl‐3‐oxetanyl)methoxy]benzene (4,4′‐BEOBP), 1,4‐bis[(3‐ethy‐3‐oxetanyl)methoxy] ‐benzene (1,4‐BEOMB), 1,2‐bis[(3‐ethyl‐3‐oxetanyl)methoxy]benzene (1,2‐BEOMB), 4,4‐bis[(3‐ethyl‐3‐oxetanyl)methoxy]biphenyl (4,4′‐BEOMB), 3,3′,5,5′‐tetramethyl‐[4,4′‐bis(3‐ethyl‐3‐oxetanyl)methoxy]biphenyl (TM‐BEOBP) with active diesters di‐ s ‐phenylthioterephthalate (PTTP), di‐ s ‐phenylthioisoterephthalate (PTIP), 4,4′‐di( p ‐nitrophenyl)terephthalate (NPTP), 4,4′‐di( p ‐nitrophenyl)isoterephthalate (NPIP) were carried out in the presence of tetraphenylphosphonium chloride (TPPC) as a catalyst in NMP for 24 h, affording corresponding polyesters with M n 's in the range 2200–18,200 in 41–98% yields. The obtained polymers would soluble in common organic solvents and had high thermal stabilities. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 1528–1536, 2004
ChemInform Abstract: Self‐Assembly in Chemical Systems (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Effect of ammoniation and harvest method on waste and consumption of corn residue bales fed to cows in a round bale feeder (2020)

To determine the effects of harvest method and ammoniation (3.7% of dry matter) on consumption and waste of baled corn residue, a 6 × 6 Latin square with a 3 × 2 factorial treatment structure was conducted. Six treatments consisted of either nonammoniated or ammoniated residue, harvested one of three ways: conventional rake and bale (CONV), New Holland Cornrower with two rows of stem chopped into the windrow with tailings (2ROW), or EZBale system (EZB) with a disengaged combine spreader and tailings dropped in a windrow. Open cows were grouped by body weight to produce a light block of two pens (448 kg ± 49.6) and a heavy block of four pens (649 kg ± 65.9). One bale was fed to each pen during each of six 7-d periods using round bale ring feeders with closed bottom panels. Residue falling around (waste) and remaining in (refusals) the feeder was collected. The daily nutrient intake was estimated as the difference between what was offered and what remained (waste plus refusals). Crude protein (CP) of residue offered did not differ (<i>P</i> = 0.58) among harvest methods. The digestible organic matter (DOM) content of residue offered in 2ROW and EZB bales did not differ (<i>P</i> = 0.86) and was greater (<i>P</i> < 0.01) than CONV. Ammoniation increased (<i>P</i> < 0.01) CP and DOM content of the residue offered. Total wasted and refused residue did not differ (<i>P</i> = 0.12) between 2ROW (29%) and EZB (37%), while CONV (42%) was greater (<i>P</i> = 0.02) than 2ROW but did not differ (<i>P</i> = 0.34) from EZB. Ammoniation reduced (<i>P</i> = 0.03) total waste and refusals from 41% to 32%. The nutrient content of both waste and refusals did not differ (<i>P</i> ≥ 0.34) among harvest methods and, with the exception of CP, was not affected (<i>P</i> ≥ 0.15) by ammoniation. The CP content of the waste was greater (<i>P</i> = 0.02) and refusals tended to be greater (<i>P</i> = 0.08) from ammoniated bales. The CP intake of 2ROW was greater (<i>P</i> ≤ 0.02) than both EZB and CONV, while EZB tended (<i>P</i> = 0.06) to be greater than CONV. The CP intake of all ammoniated residues was greater (<i>P</i> < 0.01) than the nonammoniated residue. The DOM intake of nonammoniated 2ROW and EZB did not differ (<i>P</i> = 0.61) but was greater than nonammoniated CONV (<i>P</i> < 0.01). Ammoniation increased (<i>P</i> < 0.01) DOM intake. Overall, ammoniation had much larger effects than harvest method, resulting in reduced waste and refusals and greater intake of DOM and CP. However, the combination of both ammoniation and selective harvest (2ROW or EZB) was needed to result in energy and protein intakes that would meet the needs of a mature cow in mid-gestation.
Filtered Backprojection in Compton Imaging Using a Spherical Harmonic Wiener Filter With Pixelated CdZnTe (2020)

Filtered backprojection is an image reconstruction technique for Compton imaging that provides reasonably high resolution at much lower computational costs when compared to iterative methods. This work applies a Wiener filter that has been derived for spherical harmonics on Compton imaging using the OrionUM pixelated CdZnTe imaging spectrometer. To regularize the filter, an investigation is made into the power spectral density of the signal and noise to develop an appropriate spectral signal-to-noise ratio model for the restoration process. Experimental measurements were conducted with two <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">228</sup> Th sources placed 30° apart. The resulting filtered image of the two sources has an average full-width-at-half-maximum (FWHM) of 9.8° or 7.5° when using a mean squared error and structural similarity optimization approach, respectively, an improvement from the 29.0° FWHM image when using simple backprojection.
Optimizing Transmission Rate in NOMA via Block Diagonalization Beamforming and Power Allocation (2019)

In this paper, we propose a new transmission scheme, relying on user clustering, transmit beamforming and power allocation, for non-orthogonal multiple access (NOMA) in a downlink cellular framework. Assuming that channel state information is available at the base station, the users are first partitioned into small clusters based on a weighted multi-objective optimization, so that each cluster may be served by a single beamforming vector. The complete set of beamforming vectors is jointly designed to remove inter-cluster interference by taking advantage of block diagonalization along with maximum ratio transmission. Subsequently, the NOMA power allocation factors for the users in each cluster are determined by solving an optimization problem, where the aim is to maximize the transmission sum rate subject to power and SINR constraints. The performance of the proposed NOMA scheme is validated by means of numerical analysis. Compared to the benchmark approaches, the results show significant improvements in terms of spectral efficiency and interference cancellation.
Trading strategies in radio spectrum management (2008)

Radio resource management (RRM) is one of the most challenging and one of the most important aspects in the provisioning of quality of service (QoS) for wireless communication systems. With the ever increasing size of wireless mobile community and its demand for high-speed multimedia communications, efficient resource management becomes a paramount importance due to limited resources available such as spectrum and power availability. As radio spectrum is a finite resource, new approaches are therefore needed to maximize the existing spectrum to ensure the wireless users’ and network providers’ QoS requirements are met. In this paper we propose a novel radio spectrum trading via derivatives contracts as a means to address short-term demands for spectrum whilst ensuring end-to-end QoS is met.