gebhart/patrepeval huggingface dataset:
Numerical Study of InGaN Pattern Formation Caused by Phase Separation (2000)

We performed a numerical study of the two-dimensional pattern formation of InGaN driven by a phase separation using the cell dynamical system (CDS) approach to reveal the detailed nature of a self-assembled InGaN dot-like structure showing characteristic optical properties. We calculated two-dimensional pattern formations under various conditions. First, over a wide In compositional range (0&lt;In&lt;0.6), a dot-like structure appears arising from a phase separation as well as due to the effects of strains and defects. These results are consistent with those in the case of experimentally observed structures reported earlier. Thus, we can conclude that in the present study, the pattern formation by a phase separation affects the emission mechanism of InGaN-based semiconductor light-emitting device because of a compositional fluctuation of In. Second, the calculated results suggest that the pattern formations depend on the experimental parameters, such as growth temperature, the average and local fluctuation of In composition, the lattice mismatch of InGaN and GaN, and defects.
The damage mechanism in borosilicate glass generated by nanosecond pulsed laser at 1.064 μm (2012)

We studied theoretically the laser-plasma interaction, and performed experiments to investigate the mechanisms giving rise to optical damage in Borosilicate glass using nanosecond laser pulses at wavelength 1064 nm. Our experimental result shows that the optical damage process generated by nanosecond laser pulses is the result of an optically induced plasma. The plasma is initiated when the laser irradiance frees electrons from the glass. Although it may be debated, the electrons are likely freed by multi-photon absorption and the number density grows via impact ionization. Later when the electron gas density reaches the critical density, the electron gas resonantly absorbs the laser beam through collective excitation since the laser frequency is equal to the plasma frequency. The laser energy absorbed through the collective excitation is much larger than the energy absorbed by multi-photon ionization and impact ionization. Our experimental result also shows the plasma survives until the end of the laser pulse and the optical damage occurs after the laser pulse ceases. The plasma decay releases heat to the lattice. This heat causes the glass to be molten and soft. It is only as the glass cools and solidifies that stresses induced by this process cause the glass to fracture and damage. We also show the experimental evidence of the change of the refractive index of the focusing region as the density of the electron gas changes from sub-critical to overcritical, and the reflection of the over-critical plasma. This reflection limits the electron gas density to be not much larger than the critical density.
Distributive mixing characteristics of a Dulmage-type screw for a single-screw extruder: Experimental and numerical evaluation (2021)

The mixing characteristics of a Dulmage-type screw, a kind of distributive mixing element, in single-screw extrusion were investigated. To evaluate the mixing ability, a melt-mixing extrusion experiment diluting a masterbatch with its base polymer and a numerical polymer melt flow simulation were performed. The experimental and simulation results revealed that the screw mixing performance oscillates with respect to N/Q, where N and Q are the screw rotation speed and the mass flow rate, respectively. The simulation results demonstrated that the screw mixing progresses by repeating the circumferential mixing in the ring zones and the radial redistribution in the fin zone slots. Based on these mixing kinetics, the number of swirling movements in the fin zone slots that determines the radial redistribution was found to govern the N/Q dependence of the global mixing. This study provides an essential guide for optimizing Dulmage-type screw mixing operations and Dulmage-type screw structure improvements.
Absorption and emission behavior of bis(2,2′-bipyridine)[2-(2-pyridyl)benzimidazole]ruthenium(ii) doped in silica gel matrices (1999)

Silica gels doped with bis(2,2′-bipyridine)[2-(2-pyridyl)benzimidazole]ruthenium(II), [Ru(bpy)2(pbimH)]2+, which dissociates a proton from the imino group upon light irradiation, were prepared by the sol–gel method under both acidic and basic conditions. Changes in the absorption spectra of the [Ru(bpy)2(pbimH)]2+-doped silica sols and gels prepared under basic conditions with the transition from sols to wet gels were similar to those of [Ru(bpy)2(pbimH)]2+ in methanol–water solution with a change from basic to acidic conditions. Therefore, the acid–base equilibrium is shifted from the deprotonated form, [Ru(bpy)2(pbim)]+, to the protonated form, [Ru(bpy)2(pbimH)]2+, during the sol–gel transition. At the gelation point, the wavelength of the emission maximum under basic conditions was shorter than that under acidic conditions, indicating that the mobility of the Ru complex in silica gels was more strongly restricted under basic conditions than under acidic conditions.
SCAD Journal Volume 5, Issue 1 (2014)

SCAD Journal Volume 5, Issue 1, First pages
Effect of Surface Heat Exchange Intensifier Geometry on Heat Transfer Tube Strength (2019)

Experimental studies of the tensile and compression strength as well as the strength at three-point bending of heat exchange tubes with various types of surface intensifiers, were made. The effect of intensifier geometry on sample strength is shown. The ranges of geometric parameters of intensifiers, which provide high-performance characteristics of heat exchange tubes, and possibilities to improve the maintenance reliability, are given.
Genome-wide cell-free DNA (cfDNA) methylation signatures and effect on tissue of origin (TOO) performance. (2019)

3049 Background: For multi-cancer detection using cfDNA, TOO determination is critical to enable safe and efficient diagnostic follow-up. Previous array-based studies captured &lt; 2% of genomic CpGs. Here, we report genome-wide fragment-level methylation patterns across 811 cancer cell methylomes representing 21 tumor types (97% of SEER cancer incidence), and define effects of this methylation database on TOO prediction within a machine learning framework. Methods: Genomic DNA from 655 formalin-fixed paraffin-embedded (FFPE) tumor tissues and 156 isolated cells from tumors was subjected to a prototype 30x whole-genome bisulfite sequencing (WGBS) assay, as previously reported in the Circulating Cell-free Genome Atlas (CCGA) study (NCT02889978). Two independent TOO models, one with and one without the methylation database, were fitted on training samples; each was used to predict on the test set. A WGBS classifier was used to detect cancer at 98% specificity; reported TOO results reflect percent agreement between predicted and true TOO among those detected cancers (166 cases: 81 stage I-III, 69 stage IV, 16 non-informative). Results: Genome-wide methylation data generated from this database allowed fragment-level analysis and coverage of ~30 million CpGs across the genome (~60-fold greater than array-based approaches). Incorrect TOO assignments decreased by 35% (20% to 13%) after incorporating methylation database information into TOO classification. Improvement was observed across all cancer types and was consistent in early-stage cancers (stage I-III). Respective performances in breast cancer (n = 23) were 87% vs 96%; in lung cancer (n = 32) were 85% vs 88%; in hepatobiliary (n = 10) were 70% vs 90%; and in pancreatic cancer (n = 17) were 94% vs 100%. Results using an optimized approach informed by these results in a large cohort of CCGA participants will be reported. Conclusions: Incorporating data from a large methylation database improved TOO performance in multiple cancer types. This supports feasibility of this methylation-based approach as an early cancer detection test across cancer types. Clinical trial information: NCT02889978.
Insights into amyloid disease from fly models (2014)

The formation of amyloid aggregates is a feature of most, if not all, polypeptide chains. In vivo modelling of this process has been undertaken in the fruitfly Drosophila melanogaster with remarkable success. Models of both neurological and systemic amyloid diseases have been generated and have informed our understanding of disease pathogenesis in two main ways. First, the toxic amyloid species have been at least partially characterized, for example in the case of the Aβ (amyloid β-peptide) associated with Alzheimer's disease. Secondly, the genetic underpinning of model disease-linked phenotypes has been characterized for a number of neurodegenerative disorders. The current challenge is to integrate our understanding of disease-linked processes in the fly with our growing knowledge of human disease, for the benefit of patients.
Simulating low vision in high dynamic range scenes (2004)

environment is vast • absolute range: ~100,000,000:1 (sunlight to starlight) • dynamic range: >10,000:1 (highlights to shadows) Abstract: Previous work [Peli91] has demonstrated the value of using digital techniques to simulate the appearance of images to low vision observers. However unlike images, real scenes often have high dynamic ranges of intensities that can produce serious visual impairments in people with low vision. Existing simulation techniques do not account for these effects. In this work we present a new algorithm for simulating the appearance of high dynamic range scenes to normal and low vision observers. As input, the algorithm takes a stream of high dynamic range images captured by a digital camera or generated by a computer graphics system. The images are processed through a computational model of vision that accounts for the changes in glare, contrast and color sensitivity, visual acuity, and dark adaptation that occur under varying illumination conditions for normal and low vision observers. The output is a stream of low dynamic range images that simulate for a display observer what the scene looks like to the scene observer. To demonstrate the utility of the method we generate image sequences that simulate the dramatic differences in glare susceptibility and dark adaptation that are experienced by young and old observers in high dynamic range scenes. Simulating low vision in high dynamic range scenes Piti Irawan, James A. Ferwerda, Stephen R. Marschner Program of Computer Graphics, Cornell University
Robust sensorless control strategy with enhanced dynamics (2017)

A new sensorless control strategy applied to nonlinear system has been developed in order to reach better dynamic performances. Indeed in current sensorless control strategies, the speed of the control is limited by the speed of the estimation of the state variables. The main asset of this new control strategy is to determine the control vector in parallel of the estimation of the state variables, which allows the control dynamics to get closer to the dynamics of the estimation. Compared to a classic control strategy put afterwards the variable estimation performed with an extended Kalman filter, this new strategy presented in this paper shows good results.
6-Thioguanine inhibits rotavirus replication through suppression of Rac1 GDP/GTP cycling (2018)

Rotavirus infection has emerged as an important cause of complications in organ transplantation recipients and might play a role in the pathogenesis of inflammatory bowel disease (IBD). 6-Thioguanine (6-TG) has been widely used as an immunosuppressive drug for organ recipients and treatment of IBD in the clinic. This study aims to investigate the effects and mode-of-action of 6-TG on rotavirus replication. Human intestinal Caco2 cell line, 3D model of human primary intestinal organoids, laboratory rotavirus strain (SA11) and patient-derived rotavirus isolates were used. We have demonstrated that 6-TG significantly inhibits rotavirus replication in these intestinal epithelium models. Importantly, gene knockdown or knockout of Rac1, the cellular target of 6-TG, significantly inhibited rotavirus replication, indicating the supportive role of Rac1 for rotavirus infection. We have further demonstrated that 6-TG can effectively inhibit the active form of Rac1 (GTP-Rac1), which essentially mediates the anti-rotavirus effect of 6-TG. Consistently, ectopic over-expression of GTP-Rac1 facilitates but an inactive Rac1 (N17) or a specific Rac1 inhibitor (NSC23766) inhibits rotavirus replication. In conclusion, we have identified 6-TG as an effective inhibitor of rotavirus replication via the inhibition of Rac1 activation. Thus, for transplantation patients or IBD patients infected with rotavirus or at risk of rotavirus infection, the choice of 6-TG as a treatment appears rational.
VXTe Deepwater Tree Development – Cost and Risk Reduction Through New and Advanced Technology (2020)

Abstract The oil and gas industry continues to face low energy prices, which has pushed manufacturers to re-think conventional designs and methods that may not be at the efficiency levels required to operate under today’s environmental and economic conditions. This paper describes the development of a new and advanced subsea tree technology that reduces equipment cost and installation time, thereby reducing risk and adding significant value to the end user. Traditional completion systems have become increasingly complex as efforts were made to address individual problems as they arose. These challenges included wellhead interfaces capable of handling the stack-up tolerances of casing hangers, and a need to orient the tubing hanger relative to a flowline connection system. The solution utilized by most conventional systems was the incorporation of a tubing head spool or some other elaborate means of orienting within the BOP, which created the need for temporary well barriers, required costly workover riser systems and wireline trips, and ultimately led to concentric bore systems with annulus valves located on a tubing head spool. The VXTe subsea tree system solves the problems associated with wellhead stack-up tolerances and orientation of the tubing hanger, in a simple, robust and elegant manner. The simplicity of the system allows the tubing hanger to be installed like a casing hanger. In this way, the drilling and completion operations may be undertaken without the cost and safety concerns normally associated with temporary well suspensions or BOP trips, and the orientation requirements for flowline connections are completely decoupled from the tubing hanger installation. The requirement for well barriers is also eliminated, thereby trimming the costs of additional spools, and further eliminating leak paths and failure modes. By eliminating the cumbersome solutions employed by conventional systems, our system also eliminates the need for the extensive SIT testing required to validate working interfaces. The VXTe system is a simple, robust and elegant answer to the industry's most pressing subsea tree challenges and aligns with the IOGP requirements agreed upon by most of the major operators. The VXTe system has undergone a number of verification analysis and validation testing adhering to API standards. In addition to meeting applicable API testing requirements, additional cycle testing was performed to validate the performance of the system over the anticipated life cycle. This included installation and removal cycle testing in addition to pressure and temperature testing. The design details, analysis, and test results will be presented.
Purpose-Driven Reconciliation of Approaches to Estimate Chemical Releases (2018)

A framework is presented to address the toolbox of chemical release estimation methods available for manufacturing processes. Although scientists and engineers often strive for increased accuracy, the development of fit-for-purpose release estimates can speed results that could otherwise delay decisions important to protecting human health and the environment. A number of release estimation approaches are presented, with the newest using decision trees for regression and prediction. Each method is evaluated in a case study for cumene production to study the reconciliation of data quality concerns and requirements for time, resources, training, and knowledge. The evaluation of these decision support criteria and the lessons learned are used to develop a purpose-driven framework for estimating chemical releases.
&lt;title&gt;Three-dimensional stereotactic neurosurgical planner/simulator&lt;/title&gt; (1995)

We have designed and implemented a computer-based system for three-dimensional stereotactic planning of minimally invasive neurosurgical procedures. The system integrates rapid acquisition of digital medical images, segmentation, multi-modality registration, and three-dimensional planning capabilities. Emphasis on real-time planning is central to our system: imaging, pre-processing and planning are performed on the morning of surgery in clinically useful times. We have tested the system on procedures such as needle biopsies, depth electrode placements, pallidotomies, thalamotomies and craniectomies for arteriovenous malformations, aneurysms and tumors. We describe in this paper the core algorithms of our system, and discuss issues related to implementation, validation and user acceptance.
45 CD11c-hi T-bet+ B cells contribute to the pathogenesis of SLE through generation of autoreactive plasma cells (2019)

<h3>Background</h3> The etiology of systemic lupus erythematosus (SLE) is unclear, though dysregulated B cells play a key role. Several unconventional B cell subsets that associate with autoantibodies have been described in SLE. The aim of this study was to further evaluate B cell subsets in SLE and their connection to autoreactive specificities and disease manifestations. <h3>Methods</h3> The frequency and phenotype of CD11c+Tbet+B cells were determined by flow cytometry. Autoantibodies were measured at the UT Southwestern core facility. The presence of CD11c+B cells in nephritic kidney was determined with IHC. IgH repertoires and mutational frequencies as well as transcriptome profile of CD11c+B cells were analyzed from RNA isolated from CD11c+B cells from SLE patients and compared to other B cell subsets from the same individual. Purified B cells from HD or SLE donors were cultured with either CD3-activated T cells or IL-21 co-stimulation and evaluated for B cell phenotype or production of auto-antibodies. <h3>Results</h3> We found a CD11c hi T-bet +B cell subset highly expanded in SLE with a unique expression profile including chemokine receptors consistent with migration to target tissues. Notably, these cells were enriched for autoreactive specificities, present in nephrotic kidney and significantly correlated with specific clinical manifestations. IL-21 was a potent inducer of CD11c hi T-bet +B cells that further promoted the differentiation of these cells into Ig-secreting plasma cells. IgH repertoire analysis showed CD11c hi T-bet +B cells displayed a diverse repertoire with high levels of somatic hypermutation similar to memory B cells and plasma cells. This diverse repertoire suggests that CD11c hi T-bet +B cells accumulate in response to a plethora of antigens overtime, including self-antigens in SLE. <h3>Conclusions</h3> These results show that CD11c-hi T-bet +B cells are polyclonally expanded, and highly somatically hypermutated in SLE. Furthermore, IL-21 may be involved in their expansion and differentiation into autoreactive plasma cells, which in turn may contribute to autoimmune manifestations in SLE. <h3>Funding Source(s):</h3> This research was supported in part by the Intramural Research Program of the NIH, National Institute on Aging and National Institute of Arthritis and Musculoskeletal and Skin Diseases and MedImmune, LLC.
Interferon-α Subtypes in an Ex Vivo Model of Acute HIV-1 Infection: Expression, Potency and Effector Mechanisms (2015)

HIV-1 is transmitted primarily across mucosal surfaces and rapidly spreads within the intestinal mucosa during acute infection. The type I interferons (IFNs) likely serve as a first line of defense, but the relative expression and antiviral properties of the 12 IFNα subtypes against HIV-1 infection of mucosal tissues remain unknown. Here, we evaluated the expression of all IFNα subtypes in HIV-1-exposed plasmacytoid dendritic cells by next-generation sequencing. We then determined the relative antiviral potency of each IFNα subtype ex vivo using the human intestinal Lamina Propria Aggregate Culture model. IFNα subtype transcripts from the centromeric half of the IFNA gene complex were highly expressed in pDCs following HIV-1 exposure. There was an inverse relationship between IFNA subtype expression and potency. IFNα8, IFNα6 and IFNα14 were the most potent in restricting HIV-1 infection. IFNα2, the clinically-approved subtype, and IFNα1 were both highly expressed but exhibited relatively weak antiviral activity. The relative potencies correlated with binding affinity to the type I IFN receptor and the induction levels of HIV-1 restriction factors Mx2 and Tetherin/BST-2 but not APOBEC3G, F and D. However, despite the lack of APOBEC3 transcriptional induction, the higher relative potency of IFNα8 and IFNα14 correlated with stronger inhibition of virion infectivity, which is linked to deaminase-independent APOBEC3 restriction activity. By contrast, both potent (IFNα8) and weak (IFNα1) subtypes significantly induced HIV-1 GG-to-AG hypermutation. The results unravel non-redundant functions of the IFNα subtypes against HIV-1 infection, with strong implications for HIV-1 mucosal immunity, viral evolution and IFNα-based functional cure strategies.
A dual-polarized broadband planar antenna and channelizing filter bank for millimeter wavelengths (2013)

We describe the design, fabrication, and testing of a broadband log-periodic antenna coupled to multiple cryogenic bolometers. This detector architecture, optimized here for astrophysical observations, simultaneously receives two linear polarizations with two octaves of bandwidth at millimeter wavelengths. The broad bandwidth signal received by the antenna is divided into sub-bands with integrated in-line frequency-selective filters. We demonstrate two such filter banks: a diplexer with two sub-bands and a log-periodic channelizer with seven contiguous sub-bands. These detectors have receiver efficiencies of 20%–40% and percent level polarization isolation. Superconducting transition-edge sensor bolometers detect the power in each sub-band and polarization. We demonstrate circularly symmetric beam patterns, high polarization isolation, accurately positioned bands, and high optical efficiency. The pixel design is applicable to astronomical observations of intensity and polarization at millimeter through sub-millimeter wavelengths. As compared with an imaging array of pixels measuring only one band, simultaneous measurements of multiple bands in each pixel has the potential to result in a higher signal-to-noise measurement while also providing spectral information. This development facilitates compact systems with high mapping speeds for observations that require information in multiple frequency bands.
Supplementary Figures 1-2 from ABCA3 as a Possible Cause of Drug Resistance in Childhood Acute Myeloid Leukemia (2023)

Supplementary Figures 1-2 from ABCA3 as a Possible Cause of Drug Resistance in Childhood Acute Myeloid Leukemia