gebhart/patrepeval huggingface dataset:
Siderophore-Microcins in Escherichia coli: Determinants of Digestive Colonization, the First Step Toward Virulence (2020)

Siderophore-microcins are antimicrobial peptides produced by enterobacteria, especially <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> strains. The antibiotic peptide is post-translationally modified by the linkage of a siderophore moiety. Therefore, it can enter and kill phylogenetically related bacteria by a "Trojan Horse" stratagem, by mimicking the iron-siderophore complexes. Consequently, these antimicrobial peptides are key determinants of bacterial competition within the intestinal niche, which is the reservoir for pathogenic <i>E. coli</i>. The most frequent extraintestinal infections caused by <i>E. coli</i> are urinary tract infections. Uropathogenic <i>E. coli</i> (UPEC) can produce many virulence factors, including siderophore-microcins. Siderophore-microcins are chromosomally encoded by small genomic islands that exhibit conserved organization. In UPEC, the siderophore-microcin gene clusters and biosynthetic pathways differ from the "archetypal" models described in fecal strains. The gene cluster is shorter. Thus, active siderophore-microcin production requires proteins from two other genomic islands that also code for virulence factors. This functional and modular synergy confers a strong selective advantage for the domination of the colonic niche, which is the first step toward infection. This optimization of genetic resources might favor the selection of additional virulence factors, which are essential in the subsequent steps of pathogenesis in <i>E. coli</i> infection.
Impact of Endoluminal Treatment on Small Abdominal Aortic Aneurysm: Aneurysm Sac Regression and Secondary Interventions With 5 Years of Follow-Up (2007)

Does early repair of small abdominal aortic aneurysms (AAAs) lead to faster aneurysm sac regression or less secondary intervention? Computed tomography scans and reconstructions from M2S of all patients undergoing endovascular AAA repair at our institution from 1996 to 2006 were retrospectively reviewed. A small aneurysm is defined as an aneurysm sac to renal diameter ratio of less than 2. There were 374 patients with endovascular AAA repair that had complete imaging studies. There were 75 patients (20%) with small AAAs; of those, 19 patients (25.3%) had endoleak compared with 108 patients (36.1%) with a large aneurysm ( P = .1). Over a mean follow-up time of 42 months (range, 1-109), 11 small AAAs (14.7%) had secondary interventions compared with 58 (19.4%) of the large AAAs (P = .41). Small AAAs at 5 years had a 2.5% volume sac regression but a 3.0% increase in diameter. Those with a large aneurysm had a slight increase in sac volume and diameter at 1 month (3.3%, 1.4%) and then steadily decreased to -13.4% and -8.8% at 5 years. Patients with Endologix (Endologix Inc., Irvine, Calif) devices have the most regression when compared with patients with AneuRx (Medtronic Inc., Minneapolis, Minn) and Talent (Medtronic Inc., Minneapolis, Minn) devices. Early endovascular intervention in small AAAs does not result in faster aneurysm sac regression or secondary intervention. Aneurysm sac regression is significantly affected by endoleak, aneurysm size, and device used.
A Diurnal Rhythm in Brown Adipose Tissue Causes Rapid Clearance and Combustion of Plasma Lipids at Wakening (2018)

Many favorable metabolic effects have been attributed to thermogenic activity of brown adipose tissue (BAT). Yet, time of day has rarely been considered in this field of research. Here, we show that a diurnal rhythm in BAT activity regulates plasma lipid metabolism. We observed a high-amplitude rhythm in fatty acid uptake by BAT that synchronized with the light/dark cycle. Highest uptake was found at the onset of the active period, which coincided with high lipoprotein lipase expression and low angiopoietin-like 4 expression by BAT. Diurnal rhythmicity in BAT activity determined the rate at which lipids were cleared from the circulation, thereby imposing the daily rhythm in plasma lipid concentrations. In mice as well as humans, postprandial lipid excursions were nearly absent at waking. We anticipate that diurnal BAT activity is an important factor to consider when studying the therapeutic potential of promoting BAT activity.
Discussion on Production Process of 1:10000 DLG (2007)

This paper takes production of the 1: 10000 Sangzhi DLG as an example,and discusses data processing and quality control on Geoway platform in the medium and small-scaled project.Also,it gropes some produce experience and provides the reference for the mapping department and the correlation worker.
Degradation characteristics of oil-immersed pressboard samples induced by partial discharges under DC voltage (2017)

To investigate partial discharge-induced degradation characteristics of oil-immersed pressboard under DC voltage, an experimental platform with needle-plane oil-pressboard insulation model is established. The surface condition and DC breakdown voltage of pressboard samples after PD pretreatment are observed and measured. In addition, a fitting formula to evaluate the degradation extent of pressboard samples is proposed. The results show that under constant PD pretreatments, surface roughness of pressboard samples decreases first and increases afterwards. The changing rate is positively correlated with PD intensity. During PD pretreatment, a “whitish-colored circular region” appears at samples' surface and grows with PD intensity. For PD pretreatments of 500 pC and 1000 pC, DC breakdown voltage of pressboard samples remains unchanged. The breakdown spot has no clear carbonization nor creepage trace. For PD pretreatments of 2000 pC and 3000 pC, DC breakdown voltage decreases. The breakdown spot is obviously carbonized and creepage paths emerge around spots. Further analysis indicates that degradation of oil-immersed pressboard samples due to DC PDs is the result of motion activation process induced by electrical and thermal effects under DC electric field.
Terahertz spectroscopy for the isothermal detection of bacterial DNA by magnetic bead-based rolling circle amplification (2017)

The demand for rapid and sensitive bacterial detection is continuously increasing due to the significant requirements of various applications. In this study, a terahertz (THz) biosensor based on rolling circle amplification (RCA) was developed for the isothermal detection of bacterial DNA. The synthetic bacterium-specific sequence of 16S rDNA hybridized with a padlock probe (PLP) that contains a sequence fully complementary to the target sequence at the 5' and 3' ends. The linear PLP was circularized by ligation to form a circular PLP upon recognition of the target sequence; then the capture probe (CP) immobilized on magnetic beads (MBs) acted as a primer to initialize RCA. As DNA molecules are much less absorptive than water molecules in the THz range, the RCA products on the surface of the MBs cause a significant decrease in THz absorption, which can be sensitively probed by THz spectroscopy. Our results showed that 0.12 fmol of synthetic bacterial DNA and 0.05 ng μL<sup>-1</sup> of genomic DNA could be effectively detected using this assay. In addition, the specificity of this strategy was demonstrated by its low signal response to interfering bacteria. The proposed strategy not only represents a new method for the isothermal detection of the target bacterial DNA but also provides a general methodology for sensitive and specific DNA biosensing using THz spectroscopy.
Direct-Acting Antivirals for Hepatitis C Virus (HCV): The Progress Continues (2015)

Treatment for hepatitis C virus (HCV) infection has progressed at remarkable speed. From poorly tolerated injectable therapy with very low cure rates, treatment has moved to highly effective well-tolerated all oral direct-acting antiviral therapies with cure rates above 90% for almost all patients populations. Direct-acting antivirals have developed out of an improved understanding of the viral lifecycle with recognition of targets that could be inhibited by small molecules. To date protease inhibitors, non-structural 5a inhibitors and nucleotide and non-nucleotide polymerase inhibitors have been developed. These agents have been used initially with peginterferon and ribavirin and subsequently in combination without the need for interferon. Rational combinations have overcome the major challenge of rapid emergence of drug resistance and second-generation agents in each class have improved safety and efficacy profiles with fewer drug-drug interactions and very few adverse effects. The progress of direct-acting antiviral development is outlined with a review of each class of agent as well as a discussion of challenges for the future.
Cyclic voltammetry of diphenylpicrylhydrazyl in tetrahydrofuran (1968)

Cyclic voltammetry has revealed four reversible single electron transfer processes in the oxidation and reduction of diphenylpicrylhydrazyl (DPPH) in tetrahydrofuran (THF). These are associated with a cation, a free radical, a monoanion, a dianion radical, and a trianion of DPPH.THF is a good solvent for cyclic voltammetry as evidenced by the stability of the products generated at the electrodes. It is also one of the few excellent solvents for anionic polymerization and is therefore a remarkably suitable medium for studies of electropolymerization phenomena.
Small incision lenticule extraction (SMILE) history, fundamentals of a new refractive surgery technique and clinical outcomes (2014)

This review summarizes the current status of the small incision lenticule extraction (SMILE) procedure. Following the early work by Sekundo et al. and Shah et al., SMILE has become increasingly popular. The accuracy of the creation of the lenticule with the VisuMax femtosecond laser (Carl Zeiss Meditec) has been verified using very high-frequency (VHF) digital ultrasound and optical coherence tomography (OCT). Visual and refractive outcomes have been shown to be similar to those achieved with laser in situ keratomileusis (LASIK), notably in a large population reported by Hjortdal, Vestergaard et al. Safety in terms of the change in corrected distance visual acuity (CDVA) has also been shown to be similar to LASIK. It was expected that there would be less postoperative dry eye after SMILE compared to LASIK because the anterior stroma is disturbed only by the small incision, meaning that the anterior corneal nerves should be less affected. A number of studies have demonstrated a lower reduction and faster recovery of corneal sensation after SMILE than LASIK. Some studies have also used confocal microscopy to demonstrate a lower decrease in subbasal nerve fiber density after SMILE than LASIK. The potential biomechanical advantages of SMILE have been modeled by Reinstein et al. based on the non-linearity of tensile strength through the stroma. Studies have reported a similar change in Ocular Response Analyzer (Reichert) parameters after SMILE and LASIK, however, these have previously been shown to be unreliable as a representation of corneal biomechanics. Retreatment options after SMILE are discussed. Tissue addition applications of the SMILE procedure are also discussed including the potential for cryo-preservation of the lenticule for later reimplantation (Mohamed-Noriega, Angunawela, Lim et al.), and a new procedure referred to as endokeratophakia in which a myopic SMILE lenticule is implanted into a hyperopic patient (Pradhan et al.). Finally, studies reporting microdistortions in Bowman's layer and corneal wound healing responses are also described.
Fluorescent GPCR Ligands as New Tools in Pharmacology-Update, Years 2008- Early 2014 (2014)

The robust of fluorescent techniques to study the ligand-receptor interaction followed by rapidly developing fluorescence imaging techniques resulted in a burst of the novel fluorescent ligands development. Taking into consideration not only ligand's high affinity to the receptor, but also their fluorescent properties to visualize the interaction even in the single cell level, gives the researchers a strong impulse to investigate that field of GPCR ligands. Moreover, paying attention to the "non pharmacological" advantages of these ligands, as well as the techniques to be used, fluorescent ligands become commonly used pharmacological tools to study GPCRs. Herein we report on the results described in the literature since late 2007 in the field of the fluorescent GPCR small, non-peptide ligands according the receptor affinity, fluorophores that has been used to tag the molecules and their fluorescent properties as well as their application in GPCR research.
Liposomal resiquimod for the treatment of Leishmania donovani infection (2013)

FDA-approved resiquimod, in a liposomal formulation, displays promising results in treating visceral leishmaniasis.
Mitigating ocean random medium effects in array processing by using a cross-correlator beamformer instrumentation (2022)

Ocean random medium effects such as internal waves can cause distortions to signal wave fronts that are highly detrimental to detecting and localizing signals with acoustic arrays. Motivated by the lucky imaging techniques used in astronomy [1], we have previously found evidence in real array data that when the data are looked at a much finer time scales, there can be brief moments when the wave front has little distortion [2]. However, the challenge has been developing metrics for ranking the quality of the data frames in order to exploit these lucky scintillations. In this paper, we propose a simple frame quality metric based on a cross-correlator instrumentation of the delay-sum beamformer [3] evaluated by arithmetically averaging the higher-order spatial correlation lags along the time delay trajectory corresponding to the beamformer focal location and then utilizing only the highest ranked frames in the localization. We connect this metric to beamformer focus sharpness by showing that the main lobe curvature increases monotonically with the number of lags used and demonstrate the approach on real underwater acoustic array data. [1] https://www.ast.cam.ac. uk/research/lucky [2] I.P. Kirsteins, JASA 143, 1976 (2018). [3] E. Ruigrok et al., “Cross-correlation beamforming,” J. Seismol. 21, 495–508 (2017).
Effects of aging on baroreflex regulation of sympathetic activity in humans (1992)

Arterial baroreflexes contribute importantly to blood pressure regulation through their influence on parasympathetic outflow to the sinus node and sympathetic outflow to the peripheral circulation. Baroreflex control of heart rate is known to be diminished in older individuals. Whether advancing age is associated with a parallel attenuation in baroreflex control of sympathetic outflow to the peripheral circulation has not been studied in humans. To provide such information, we made direct measurements of muscle sympathetic nerve activity (MSNA) in healthy males who ranged in age from 18 to 71 yr. The subjects were arbitrarily divided into three groups: younger (18-34 yr; n = 35), middle aged (35-50 yr; n = 15), and older (51-71 yr; n = 16). Although basal levels of MSNA were higher in older subjects than in younger and middle-aged subjects, the gains of baroreflex control of MSNA were the same in the older, middle-aged, and younger subjects (-4.6 +/- 0.6, -4.8 +/- 0.9, -5.1 +/- 0.5 U/mmHg, P greater than 0.10). In contrast, the gains of baroreflex control of cardiac intervals were attenuated in the older and middle-aged subjects compared with the younger subjects (9.8 +/- 1.2, 13.6 +/- 1.4, 21.7 +/- 1.3 ms/mmHg, P less than 0.05). Our data indicate that although the parasympathetic component of the arterial baroreflex becomes impaired with advancing age, the sympathetic component can be well maintained in healthy individuals even into the seventh decade.
POLARIZATION-LOCKED VECTOR SOLITONS IN A FIBER LASER (1999)

The vectorial nature of light is often ignored in the discussions of optical solitons because typically it does not drastically alter the behavior of solitons. When a soliton propagates in homogeneously birefringent fiber polarization effects have to be taken into account [1,2].
Deep Brain Stimulation, Neuroethics, and the Minimally Conscious State (2009)

We briefly review the motivation, ethical framing, and results of a recent single-subject study of central thalamic deep brain stimulation (DBS) in a patient remaining in the chronic minimally conscious state (MCS). In the study, a severely brain-injured human subject showed behavioral improvements in attentive responsiveness, limb control, recovery of oral feeding, and spoken language following central thalamic DBS. 1 These findings are placed into the context of, and contrasted with, prior efforts applying thalamic brain stimulation to patients in the vegetative state (VS). Efforts to develop DBS for recovery of function in the setting of disorders of consciousness must meet several challenges presented by the expected wide variance of underlying brain injuries and need to carefully identify potential goals of therapeutic intervention. Although the study involved only a single subject, the results demonstrate a causal relationship between brain stimulation and cognitive recovery. The generalizability of these findings is completely unknown and the complexity of the problem will require careful and systematic research to move forward.
A Mouse Model for the Study of Contact-Dependent Transmission of Influenza A Virus and the Factors That Govern Transmissibility (2012)

Influenza A virus transmission by direct contact is not well characterized. Here, we describe a mouse model for investigation of factors regulating contact-dependent transmission. Strains within the H3N2 but not H1N1 subtype of influenza virus were transmissible, and reverse-engineered viruses representing hybrids of these subtypes showed that the viral hemagglutinin is a determinant of the transmissible phenotype. Transmission to contact mice occurred within the first 6 to 54 h after cohousing with directly infected index mice, and the proportion of contacts infected within this period was reduced if the index mice had been preinfected with a heterologous subtype virus. A threshold level of virus present in the saliva of the index mice was identified, above which the likelihood of transmission was greatly increased. There was no correlation with transmission and viral loads in the nose or lung. This model could be useful for preclinical evaluation of antiviral and vaccine efficacy in combating contact-dependent transmission of influenza.
PtO2/PTSA system catalyzed regioselective hydration of internal arylalkynes bearing electron withdrawing groups (2018)

A highly efficient PtO<sub>2</sub>/PTSA catalyst system for the hydration of a wide array of alkynes was developed. This method proved to be compatible with a large range of functional groups and the ketone products were obtained in high yields. The scope of this methodology was also extended to the synthesis of 3-aryl-isochromenones, -indoles and -benzofurans.
Multivessel intervention and placement of a percutaneous right ventricular assist device in a patient with acute myocardial infarction complicated by cardiac arrest. (2011)

We present a case of a 66-year-old male who presented with ST elevation myocardial infarction and complicated by cardiac arrest. The patient underwent emergent multivessel revascularization. However, the patient developed right ventricular failure with persistent and recalcitrant hemodynamic instability. Placement of a TandemHeart™ right ventricular assist device™ (Cardiac Assist, Pittsburgh, Pennsylvania) was undertaken to allow for right ventricular recovery. The device was removed after several days and the patient has had no further events one year after arrest.
Generation and characterization of soybean and marker‐free tobacco plastid transformants over‐expressing a bacterial 4‐hydroxyphenylpyruvate dioxygenase which provides strong herbicide tolerance (2006)

Plant 4-hydroxyphenylpyruvate dioxygenase (HPPD) is part of the biosynthetic pathway leading to plastoquinone and vitamin E. This enzyme is also the molecular target of various new bleaching herbicides for which genetically engineered tolerant crops are being developed. We have expressed a sensitive bacterial hppd gene from Pseudomonas fluorescens in plastid transformants of tobacco and soybean and characterized in detail the recombinant lines. HPPD accumulates to approximately 5% of total soluble protein in transgenic chloroplasts of both species. As a result, the soybean and tobacco plastid transformants acquire a strong herbicide tolerance, performing better than nuclear transformants. In contrast, the over-expression of HPPD has no significant impact on the vitamin E content of leaves or seeds, quantitatively or qualitatively. A new strategy is presented and exemplified in tobacco which allows the rapid generation of antibiotic marker-free plastid transformants containing the herbicide tolerance gene only. This work reports, for the first time, the plastome engineering for herbicide tolerance in a major agronomic crop, and a technology leading to marker-free lines for this trait.
Crystallization and preliminary X-ray study of recombinant betaine–homocysteineS-methyltransferase from rat liver (2002)

Betaine-homocysteine S-methyltransferase is one of the three enzymes involved in homocysteine catabolism. It uses betaine as the methyl donor to convert homocysteine into methionine, also producing dimethylglycine. Recombinant BHMT from rat liver was crystallized by the vapour-diffusion method in both native and seleniomethionyl-labelled forms. Crystals belong to space group P2(1), with unit-cell parameters a = 57.8, b = 149.3, c = 96.2 A, beta = 92.9 degrees. Data from native, seleniomethionine-labelled and two heavy-atom derivatives were collected using synchrotron sources. Self-rotation function and sedimentation-velocity experiments suggest that the enzyme is tetrameric with 222 symmetry.
Trace-driven HW/SW cosimulation using virtual synchronization technique (2005)

Poor performance of HW/SW cosimulation is mainly caused by synchronization requirement between component simulators. Virtual synchronization technique was proposed to remove the need of synchronization in cycle accurate cosimulation. But the previous execution-driven simulation based on virtual synchronization has limitations in the application area. In this paper, we propose a novel trace-driven HW/SW cosimulation using virtual synchronization technique. Through OS modeling and channel modeling, the proposed cosimulation technique could be applied more widely while improving the simulation performance further. Experiments with a DIVX player example prove the viability of the proposed technique.