gebhart/patrepeval huggingface dataset:
Accurate in vitro, translesion synthesis by Escherichia coli DNA polymerase I (large fragment) on a site-specific, aminofluorenemodified oligonucleotide (1991)

We have measured the accuracy of in vitro synthesis by DNA polymerase I (large fragment) during translesion synthesis past an aminofluorene (AF) adduct. These studies were carried out using a site-specifically modified template which contained a single AF adduct. The template was prepared by first modifying the lone guanine in a 17 base long oligonucleotide and extensively purifying and characterizing this product. The modified 17mer was then ligated to a synthetic duplex to produce a 31 nucleotide long template strand containing the AF adduct annealed to a 14mer, such that the 3'-hydroxyl primer terminus was four nucleotides before the modified guanine. Synthesis on this template by DNA polymerase I efficiently bypassed the AF adduct and produced full-length duplex 31mers. T7 DNA polymerase, on the other hand, was unable to utilize the AF-modified template though it was active on an identical unmodified one. The strand synthesized by DNA polymerase I was then separated from the modified strand, annealed to a complementary oligonucleotide, and the resulting heteroduplex cloned into M13. Each of the 49 clones isolated had sequences which indicated that cytidine had been incorporated opposite the AF-modified guanine.
Ultracompact hermetic laser diode modules for harsh environment (2018)

We report on a high brightness fiber coupled single element laser diode and its assessment on various harsh conditions. The Ultra Compact Hermetic (UCH) modules (0.7 cm<sup>3</sup>) are manufactured using a totally glue free process owing to proprietary weld processes and a controlled inner atmosphere. They deliver up to 10W out of the fiber at 25 &deg;C and more than 8W at 60&deg; C for &lambda;&equals;940nm. UCH modules emitting at 830nm also deliver more than 4.8W at 25&deg;C. We report on the robust behavior of the UCH modules in harsh environment such as vibrations and exposure to radiations
The association of short-term effects of air pollution and sleep disorders among elderly residents in China (2019)

TPS 732: Neurological effects in adults, Exhibition Hall, Ground floor, August 27, 2019, 3:00 PM - 4:30 PM Background: Sleep disorders are a main symptom of mental and neurological disorders in elderly and have been previously linked to short-term exposures to air pollution. Here we assessed such associations in China where air pollution exposures are high and the proportion of elderly in the population is growing. We assessed association between short-term air pollutants exposures and hospital visits for sleep disorders among elderly Chinese in Ningbo, China. Methods: We utilized a regional health information database in China (2008-2017) that collected information on hospital visits for sleep disorders among the elderly (age 60+). Measures of daily air pollution concentrations including nitrogen dioxide (NO2), sulfur dioxide (SO2), ozone (O3), inhalable particles (PM10), and ambient fine particulate matter (PM2.5) were generated from seven environmental air quality monitoring sites in the study area. We used a generalized additive model to evaluate associations between hospital visits for sleep disorders and short-term air pollution exposures for up to 7 days prior to a hospital visit. Results: Short-term exposure to multiple air pollutants was associated with hospital visits for sleep disorders in an elderly population; with the strongest associations during 2-3 days prior to a clinic visits for traffic-related pollutants including air quality index (AQI), PM2.5, PM10, and NO2 and for SO2 and O3 for 5 days prior to the visits. Effect estimates for females and younger residents (<75 years) were somewhat stronger. Conclusions: Our study based on large health care record system suggested that short-term air pollution exposures are associated with sleep disorders in the elderly. Future studies with individual level data and an ability to evaluate the severity of sleep disorders and their relation to mental and physical health in general and air pollution are needed.
From psychology to physicality: how nerve growth factor transduces early life stress into gastrointestinal motility disorders later in life (2019)

Environmental stressors in early childhood can have a detrimental impact later in life, manifesting in functional gastrointestinal disorders including irritable bowel syndrome (IBS). The phenomenon is also observed in rodents, where neonatal-maternal separation, a model of early life stress, induces phenotypes similar to IBS; however, the underlying mechanisms remain unelucidated. Our recent study provided a mechanism for the pathogenesis in the gut, demonstrating that increased visceral hyperalgesia resulted from the expansion of the intestinal stem cell compartment leading to increased differentiation and proliferation of serotonin (5-hydroxytryptamine/5-HT)-producing enterochromaffin cells. Moreover, it identified nerve growth factor (NGF) as a key mediator of the pathogenesis; surprisingly, it exerts its effect via cross talk with Wnt/β-catenin signaling. This article addresses the roles of NGF in driving IBS and its potential clinical implications, outstanding questions in how psychological stimuli are transduced into physical phenotypes, as well as future directions of our findings. <b>Abbreviations</b>: 5-HT: 5-hydroxytryptamine/serotonin; BDNF: brain-derived neurotrophic factor; CRF: corticotrophin-releasing factor; EC: enterochromaffin; ENS: enteric nervous system; GI: gastrointestinal; GPCR: G-protein-coupled receptor; IBS (-D): irritable bowel syndrome (diarrhea predominant); LRP5/6: low-density lipoprotein receptor-related protein 5/6; MAPK: mitogen-activated protein kinase; NGF: nerve growth factor; NMS: neonatal-maternal separation; PI3K: phosphoinositode3-kinase; PLCγ: phospholipase c, gamma subtype; TrkA: tropomyosin receptor kinase A.
Design and Testing of a Prototype Slow Positron Beam at the NC State University PULSTAR Reactor (2005)

Slow positrons have proven to be a powerful tool for the analysis of materials. This nondestructive probe is capable of reconstructing the electronic environment below the surface of materials utilizing the conservation of energy and momentum on the annihilation quanta. Radioactive sources are capable of producing slow positron rates on the order of 10⁶ Hz, but the pair production mechanism is necessary to produce more intense beams. The environment in the vicinity of nuclear reactor cores is capable of producing copious amounts of photons with energy above the threshold for the pair production mechanism.\n\n\tMCNP simulations were performed which modeled North Carolina State University's PULSTAR reactor to calculate the photon flux above the pair production threshold energy. It was determined that the addition of cadmium to the end of the beam port would enhance the photon flux by a factor of 3. Further simulations demonstrated that core optimization could increase the flux by an additional factor of 2.\n\n\t A positron beam was designed to focus positrons produced in the vicinity of the core into a solenoid which would allow transport through the biological shield. SIMION simulations were performed to demonstrate the effectiveness of the proposed beam and concluded that the beam design could focus positrons with a wide range of energies.\n\n\tA prototype beam was completed and placed within a beam port of the PULSTAR reactor. Tests immediately demonstrated the production and control of slow positrons. Additional tests established the dependence of the count rate on the axial magnetic field of the solenoid, with a maximum count rate achieved by the prototype beam being 33x10⁷ slow positrons per second.\n\n\tThe knowledge gained from the prototype can be applied to future work to improve the overall beam effectiveness. Future works includes the bending of the solenoid and implementation of core optimizations. The size of the moderator can also be increased from that of the prototype to increase the beam intensity.
Scaleup of Cu(InGa)Se2Thin Film Coevaporative Physical Vapor Deposition Process, 1. Evaporation Source Model Development (2009)

Even though rapid advances have been made in improving Cu(InGa)Se2 thin-film-based solar cell efficiencies, the breakthroughs have been limited to the laboratory scale. Most commercially viable thin-film technologies reside at the premanufacturing development stage and scaleup has proven to be much more difficult than expected. Elemental in-line evaporation on flexible substrates in a roll-to-roll configuration is a commercially attractive process for the manufacture of large-area CuInSe2-based photovoltaics. At the University of Delaware’s Institute of Energy Conversion (IEC), such a process is being investigated, at the pilot scale, for a polyimide web substrate. The process works well for 6-in.-wide substrates and for short deposition runtimes. However, a commercially viable process is required to produce large-area, high-quality films at a much-higher throughput. Specifically, the desired film thickness (∼2 μm) and composition uniformity must be achieved continuously and reproducibly on large-area (12-in.-wide) substrates at translation speeds (∼1 ft/min) much higher than those currently used in pilot-scale processes. Although achievement of the desired film thickness and composition setpoints is best addressed by proper control system design, the film thickness uniformity is determined by the source design and individual nozzle effusion rates. The nozzle effusion rates, in turn, are dependent on the melt surface temperature profile and, thus, on the source design itself. Therefore, proper source design is critical in achieving film thickness uniformity. We have identified two modeling requirements for effective thermal evaporation source design: (i) a detailed three-dimensional thermal model of the evaporation source, to predict the melt surface temperature accurately, and (ii) a nozzle effusion model, to predict the effusion rate and the vapor flux distribution for a given nozzle geometry (length and diameter), melt surface temperature, and evaporant. To meet the first requirement, we have developed a first-principles three-dimensional electrothermal model using COMSOL Multiphysics software; the Direct Simulation Monte Carlo (DSMC) method has been used for effusion modeling. In this paper, which is the first of a two-part series, we present the details of the two models and their experimental validation.
Spatial- and Range- ISLR Trade-Off in MIMO Radar Via Waveform Correlation Optimization (2021)

This paper aims to design a set of transmit waveforms in cognitive colocated Multi-Input Multi-Output (MIMO) radar systems considering the simultaneous minimization of spatial- and the range- Integrated Sidelobe Level Ratio (ISLR). The design problem is formulated as a bi-objective Pareto optimization under practical constraints on the waveforms, namely total transmit power, peak-to-average-power ratio (PAR), constant modulus, and discrete phase alphabet. A Coordinate Descent (CD) based approach, called UNIQUE, is proposed in which at every single variable update of the algorithm we obtain the solution of the uni-variable optimization problems. The novelty of the paper comes from deriving a flexible waveform design problem applicable for the emerging 4D imaging MIMO radars with application to automotive radar systems. The simultaneous optimization leads to a trade-off between the two ISLRs and the simulation results illustrate significantly improved trade-off offered by the proposed methodologies.
Tissue healing response following hyperthermic vapor ablation in the porcine longissimus muscle (2015)

As the use of hyperthermic ablation technologies has increased, so too has the need to understand their effects on tissue and their healing responses. This study was designed to characterize tissue injury and healing following hyperthermic vapor ablation in the <i>in vivo </i>porcine longissimus muscle model. The individual ablations were performed using the NxThera Vapor Delivery System (<i>NxThera Inc., Minneapolis, MN</i>). To assess the vapor ablation’s evolution, the swine were euthanized post-treatment on Day 0, Day 3, Day 7, Day 14, Day 28, Day 45 and Day 90. Triphenyltetrazolium chloride viability staining (<i>TTC staining</i>) was used to macroscopically assess the extent of each vapor ablation within the tissue. The ablation associated healing responses were then histologically evaluated for acute inflammation, chronic inflammation, foreign body reaction and fibrosis. Two zones of tissue injury were initially identified in the ablations: 1) a central zone of complete coagulative necrosis and 2) an outer “transition zone” of viable and non-viable cells. The ablations initially increased in size from Day 0 to Day 7 and then progressively decreased in size though Day 45. The initial Day 3 healing changes originated in the transition zone with minimal acute and chronic inflammation. As time progressed, granulation tissue began to form by Day 7 and peaked around Day 14. Collagen formation, deposition and remodeling began in the adjacent healthy tissue by Day 28, replaced the ablation site by Day 45 and reorganized by Day 90. In conclusion, this vapor ablation technology provided a non-desiccating form of hyperthermic ablation that resulted in coagulative necrosis without a central thermally/heat-fixed tissue component, followed a classical wound healing pathway, and healed with minimal associated inflammation.
ChemInform Abstract: THE NATURE OF THE LAMBDA263 CHROMOPHORE IN THE PALYTOXINS (1975)

Abstract Die Natur des Chromophors K2 63 aus Palytoxinen wird zu Teilstücken der Art (I) und (II) bestimmt.
Repurposing FDA-Approved Drugs for COVID-19 Using a Data-Driven Approach (2020)

&lt;p&gt;There have been more than 116,000 recorded deaths worldwide to-date caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the etiological agent of the Coronavirus Disease 2019 (COVID-19), and over 1.8 million individuals are currently infected. Although there are now hundreds of clinical trials for COVID-19, there are currently no effective licensed treatments, while the numbers of infected individuals continue to rise at an exponential rate in many parts of the world. Here, we used a data-driven approach utilizing connectivity mapping and the transcriptional signature of lung carcinoma cells infected with SARS-CoV-2, to search for drugs across the spectrum of medicine that have repurposing potential for treating COVID-19. We also performed chemoinformatic analyses to test whether the identified compounds were predicted to physically interact with the SARS-CoV-2 RNA-dependent RNA polymerase or main protease enzymes. Our study identified commonly prescribed FDA-approved molecules as important candidates for drug repositioning against COVID-19, including flupentixol, reserpine, fluoxetine, trifluoperazine, sunitinib, atorvastatin, raloxifene, butoconazole, and metformin. These drugs should not be taken for treating or preventing COVID-19 without a doctor’s advice, as further research and clinical trials are now needed to elucidate their efficacy for this purpose.&lt;/p&gt;
Fourier Domain Beamforming: The Path to Compressed Ultrasound Imaging (2013)

Sonography techniques use multiple transducer elements for tissue visualization. Signals detected at each element are sampled prior to digital beamforming. The sampling rates required to perform high resolution digital beamforming are significantly higher than the Nyquist rate of the signal and result in considerable amount of data, that needs to be stored and processed. A recently developed technique, compressed beamforming, based on the finite rate of innovation model, compressed sensing (CS) and Xampling ideas, allows to reduce the number of samples needed to reconstruct an image comprised of strong reflectors. A drawback of this method is its inability to treat speckle, which is of significant importance in medical imaging. Here we build on previous work and extend it to a general concept of beamforming in frequency. This allows to exploit the low bandwidth of the ultrasound signal and bypass the oversampling dictated by digital implementation of beamforming in time. Using beamforming in frequency, the same image quality is obtained from far fewer samples. We next present a CS-technique that allows for further rate reduction, using only a portion of the beamformed signal's bandwidth. We demonstrate our methods on in vivo cardiac data and show that reductions up to 1/28 over standard beamforming rates are possible. Finally, we present an implementation on an ultrasound machine using sub-Nyquist sampling and processing. Our results prove that the concept of sub-Nyquist processing is feasible for medical ultrasound, leading to the potential of considerable reduction in future ultrasound machines size, power consumption and cost.
A view of visual adaptation from a different position (1997)

Purpose: To examine the effect of adaptation upon perceived visual location of luminance-defined and texture-defined stimuli.



Methods: We describe an illusion in which 5 sec of adaptation to an antisymmetric Gaussian stimulus results in a marked perceived misalignment in a subsequently-viewed 3-Gaussian blob stimulus. The magnitude of perceived misalignment was established for various levels of adapting and test contrast.



Results: The effect of varying the contrast of the adapting and test stimuli depends only upon the ratio of adapting/test contrast. Adaptation effects for luminance- and texture-defined stimuli differ in terms of inter-ocular transfer and rate of decay. Whilst adapting and testing to the same type of stimulus (luminance- or texture-defined) produces large shifts in perceived position, little or no crossover was found. The data are accounted for by a model in which the centroid of the linear combination of after-image and test stimulus is extracted.



Conclusion: The perceived location of both luminance- and texture-defined stimuli can be strongly influenced by appropriate adapting stimuli. However, the adaptation processes for both types of stimuli remain independent and demonstrate different characteristics.
Self-pulsing and fast excitable response in micropillar and nano-lasers with saturable absorber (2013)

We present recent experimental and theoretical results on the nonlinear dynamics of semiconductor micro and nano-lasers. First, fast excitable, neuron-like, dynamics is experimentally evidenced in a micropillar laser with intracavity saturable absorber with fast response times in the 200ps range. We study also the refractory time in this system and show the existence of a relative refractory period, analogue to what is found in neurons. Second, we propose a scheme for achieving self-pulsing in nanolasers based on asymmetrically coupled cavities and study theoretically its implementation in a photonic-crystal based system. Short pulses with duration as short as 35ps with multi-GHz repetition rates are found, as well as a region giving rise to a chaotic dynamics. We also predict a parameter region where the self-pulsing bifurcation can lead to ultra-fast excitable dynamics in such a nanolaser.
A perceptual metric for blind measurement of blocking artifacts with applications in transform-block-based image and video coding (2008)

In this paper, we analyze the formation of blocking artifacts as a result of quantization of the discrete cosine transform (DCT) coefficients. These artifacts are known to be the dominant distortion of lossy block-based hybrid image and video coding schemes when operating at very low data rates. Our analysis is carried out based on the theory of edge detection and by means of a mathematical framework to model the properties of receptive fields, which are known to be the main mechanism for sensing intensity contrasts and edges. Based on our analysis we propose a metric to quantify the blocking artifact distortion. The proposed distortion metric considers the susceptibility of a region in a reconstructed (decoded) image to the formation of blocking artifacts via a probabilistic model, which quantifies the possibility of a detected edge to be a distortion.
Suppl. Fig. 2: Workflow of imaging data co-registration. from Combined PET Imaging of the Inflammatory Tumor Microenvironment Identifies Margins of Unique Radiotracer Uptake (2023)

&lt;p&gt;PET and CT images were co-registered using three CT-detectable, molecular sieve spheres (# 1-3) rinsed in radiotracer solution. After segmentation of spheres in the CT image (arrows), PET and CT images were superimposed by using the automated "Landmark tool" provided by the Vinci software. The "Magic tool" was applied for minor corrections of co-registrations. The resulting resliced PET image was saved for further processing. In a second step, MR and CT images were superimposed using the "Fusion- and Magic tool". For illustration MR is pseudocolored in red, while the CT was inverted in color (black). The CT contour was further superimposed to demonstrate co-registration accuracy. Selected bone structures were used as additional quality measures of image registration. The resliced CT image was saved with the new transformation matrix. In a last step, the before mentioned transformation of the CT (CTMR) was transferred to the PET, resulting in co-registration of PET/MR/CT. This workflow was repeated for every PET scan per mouse.&lt;/p&gt;
Toward Clinical X-ray Phase-Contrast CT (2010)

Our results demonstrate the huge potential of phase-contrast CT for clinical investigations of human specimens and, potentially, of humans. Because the applied technique works efficiently with conventional x-ray tubes and detectors, it is suitable for the realization of preclinical and clinical phase-contrast CT systems.
Low Antibody Levels against Cell Wall–Attached Proteins ofStreptococcus pyogenesPredispose for Severe Invasive Disease (2004)

Acute-phase serum samples from 70 patients with group A streptococcal (GAS) invasive disease were analyzed for IgG antibodies against 6 recently characterized GAS virulence factors (SclA, SclB, GRAB, MtsA, EndoS, and IdeS) and SpeB. Antibody levels against the cell wall-attached GAS antigens SclA, SclB, and GRAB were significantly lower in patients with severe invasive disease (streptococcal toxic shock syndrome [STSS] and/or necrotizing fasciitis [NF]; n=35), compared with levels in patients with nonsevere GAS bacteremia (n=35). Among patients with severe invasive disease, significantly lower antibody levels against GRAB were found in patients with STSS (n=10) than in patients with NF (n=17). Antibody levels against SpeB in patients with severe bacteremia were similar to those in patients with nonsevere bacteremia, and levels in patients with STSS were similar to those in patients with NF. The data indicate that immunity to cell wall-attached proteins may play a role in the protection against severe invasive disease and that antibodies against GRAB may be of importance in the pathogenesis of STSS.