gebhart/patrepeval huggingface dataset:
Structural and Dynamic Features of F-recruitment Site Driven Substrate Phosphorylation by ERK2 (2015)

The F-recruitment site (FRS) of active ERK2 binds F-site (Phe-x-Phe-Pro) sequences found downstream of the Ser/Thr phospho-acceptor on cellular substrates. Here we apply NMR methods to analyze the interaction between active ERK2 (ppERK2), and a 13-residue F-site-bearing peptide substrate derived from its cellular target, the transcription factor Elk-1. Our results provide detailed insight into previously elusive structural and dynamic features of FRS/F-site interactions and FRS-driven substrate phosphorylation. We show that substrate F-site engagement significantly quenches slow dynamics involving the ppERK2 activation-loop and the FRS. We also demonstrate that the F-site phenylalanines make critical contacts with ppERK2, in contrast to the proline whose cis-trans isomerization has no significant effect on F-site recognition by the kinase FRS. Our results support a mechanism where phosphorylation of the disordered N-terminal phospho-acceptor is facilitated by its increased productive encounters with the ppERK2 active site due to docking of the proximal F-site at the kinase FRS.
Inclusive Decision-Making (2019)

As urban areas face uncertain climate futures, leaders are challenged with making decisions to mitigate the effects of climate events on vulnerable populations. However, these populations have historically been excluded from many parts of the decision-making process. To promote more equitable decision-making, an inclusive, data-driven decision support methodology was developed to include the needs and voices of populations in economically and culturally marginalized areas. The approach was applied by the Sustainable Cities Decision-Making research team at Iowa State University in collaboration with local civic, non-profit, and residential partners in Des Moines, Iowa. The team identified evidence-based approaches for the integration of human behavior data, building energy use characteristics, future climate scenarios, and near-building microclimate data to inform decisions about how to adapt their city and its neighborhoods to changing climate conditions. Using this methodology, best practices were developed to gather data from community members and stakeholders. The data were then used in models, visualizations, and action projects that closed the loop between data gathering and results dissemination to benefit the local community. This work can be used to inform decisions being made by individuals and policymakers. Importantly, the process is iterative: after decisions are made, the cycle may begin again with data collection to evaluate the outcomes of these actions.
Simulink Libraries for Visual Programming of VTK and ITK (2010)

We have created open-source Simulink block libraries for ITK and VTK that allow pipelines for these toolkits to be built in a visual, drag-and-drop style within MATLAB. Each block contains an instance of an ITK or VTK class. Any block connections and parameters that the user makes within MATLAB’s Simulink visual environment are converted into connections and parameters for the ITK and VTK pipelines. In addition, we provide conversion of images to and from MATLAB arrays to allow MATLAB image processing blocks to be mixed with ITK and VTK blocks. The code for our block libraries is generated automatically from XML descriptions of the inputs, outputs, and parameters of the ITK and VTK classes. We have used these block libraries to build some example pipelines and believe that they will be useful for developing applications in image analysis and image-guided therapy.
Colonic Polyps and Colon Cancer (2010)

Globally, more than 1 million new cases of colorectal cancer (CRC) are diagnosed each year and CRC accounts for 10% of all cancer deaths. Symptoms (i.e., hematochezia, melena, change in bowel habits, etc.) and signs (i.e., anemia, positive fecal occult blood test, etc.) of CRC can be subtle and non-specific, but often indicate relatively advanced-stage disease. Since prognosis is inversely associated with CRC stage, early detection of premalignant adenomas or locally-invasive cancers is a clinical priority. Therapy for invasive malignancy is multi-modal and can involve surgery, chemotherapy and radiation therapy. Although not universally applied, guidelines have been developed for post-therapeutic CRC surveillance to detect recurrent and metachronous lesions.
&lt;title&gt;Photorefractive keratectomy at 193 nm using an erodible mask&lt;/title&gt; (1992)

Clinical experience with more than ten thousand sighted eyes has demonstrated great promise for correcting myopia with photorefractive keratectomy (PRK). Previously reported techniques have incorporated computer-controlled irises, diaphragms, and apertures to regulate the desired distribution of 193 nm radiation onto the eye. This paper reports on an entirely new approach for performing PRK which utilizes an erodible mask to control the shape transfer process. Compared to the more traditional techniques, the erodible mask offers promise of correcting a broad range of refractive errors. In this paper the erodible mask and associated hardware are described in detail. We describe the shape transfer experiments used to predict the functional relationship between the desired refractive correction and the mask shape. We report on early clinical results from five patients with myopic astigmatism. We conclude that the early shape transfer experiments overestimated the spherical component of the correction by 1.25 diopters and underestimated the cylindrical component by approximately 0.85 diopters. The data suggest there may be biological effects which evoke different healing responses when myopic PRK corrections are performed with and without astigmatism. Clinical trials are proceeding with the mask shapes adjusted for these observations.
40 Elucidating genetic pathways in sle and stratifying patients via whole genome sequencing (2017)

<h3>Background and aims</h3> Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Twin studies indicate a strong genetic contribution to lupus, yet often the pathogenic variant remains unknown. A better understanding of the individual genetic causes of SLE will enable personalised therapies. Using next generation sequencing technologies (WES/WGS) it is now possible to identify rare/novel gene variants that cause disease. <h3>Methods</h3> We have used WES/WGS to identify rare genetic variants with strong effects that contribute to SLE and complex autoimmunity. The effect of variants on protein function were evaluated using <i>in vitro</i> biochemical and over-expression assays. Immunophenotyping of patient PBMCs and the use of bespoke mouse models engineered by CRISPR/Cas9 to harbour patient-specific variants were used to dissect disease mechanisms. <h3>Results</h3> We identified a genetic variant in TREX1 as a cause of cerebral SLE, providing proof of principle that rare genetic variants do contribute to complex autoimmunity. The patient was revealed to be a prime candidate for tailored therapies targeting type-I interferons. Using our validated bioinformatics pipeline and methodology, we have now identified two other cohorts of patients with genetic variants that impair thymic tolerance and T1-IFN signalling, respectively. Biochemical assays confirmed the variants impair protein function. Furthermore, flow cytometry identified immunophenotypes in the patients’ PBMCs that may explain disease pathogenesis. The mechanisms by which they drive SLE pathogenesis are being evaluated in patient-specific mice mouse models. <h3>Conclusions</h3> By understanding the precise genetic mechanisms that contribute to SLE pathogenesis, our data is able to stratify patients and, through a personalised approach, identify tailored therapeutic options.
Development and Function of Invariant Natural Killer T Cells Producing TH2- and TH17-Cytokines (2012)

There is heterogeneity in invariant natural killer T (iNKT) cells based on the expression of CD4 and the IL-17 receptor B (IL-17RB), a receptor for IL-25 which is a key factor in T(H)2 immunity. However, the development pathway and precise function of these iNKT cell subtypes remain unknown. IL-17RB⁺iNKT cells are present in the thymic CD44⁺/⁻ NK1.1⁻ population and develop normally even in the absence of IL-15, which is required for maturation and homeostasis of IL-17RB⁻iNKT cells producing IFN-γ. These results suggest that iNKT cells contain at least two subtypes, IL-17RB⁺ and IL-17RB⁻ subsets. The IL-17RB⁺iNKT subtypes can be further divided into two subtypes on the basis of CD4 expression both in the thymus and in the periphery. CD4⁺ IL-17RB⁺iNKT cells produce T(H)2 (IL-13), T(H)9 (IL-9 and IL-10), and T(H)17 (IL-17A and IL-22) cytokines in response to IL-25 in an E4BP4-dependent fashion, whereas CD4⁻ IL-17RB⁺iNKT cells are a retinoic acid receptor-related orphan receptor (ROR)γt⁺ subset producing T(H)17 cytokines upon stimulation with IL-23 in an E4BP4-independent fashion. These IL-17RB⁺iNKT cell subtypes are abundantly present in the lung in the steady state and mediate the pathogenesis in virus-induced airway hyperreactivity (AHR). In this study we demonstrated that the IL-17RB⁺iNKT cell subsets develop distinct from classical iNKT cell developmental stages in the thymus and play important roles in the pathogenesis of airway diseases.
P11.22 Radiotherapy effects in GBM Rat model CNS1 (2019)

Abstract BACKGROUND CNS1 is a syngeneic glioma model in Lewis Rats. It is an aggressive infiltrating tumor cell line that mimics important aspects of human GBM such as rapid growth, dispersal along blood vessels and white matter, pseudopallisading cells with features of hemorrhage and necrosis. CNS1 tumors are infiltrated with macrophages and T-cells, and were studied in the context of immunotherapy and gene therapy, extracellular matrix and invasion, but CNS1 response to radiation has not yet been described. If we wish to combine novel immune-based therapies with existing GBM protocols that include radiation and chemotherapy, we will need models that respond to these protocols. As a first step in this direction, we sought to describe CNS1 response to radiation in vitro and in vivo. MATERIAL AND METHODS In vitro, survival of irradiated CNS1 cells was assessed with clonogenic assay. Radiation varied in dose from 0 to 10 Gy and was delivered via Kimtron Polaris X-ray generator. In vivo, male Lewis rats were intra-cranially inoculated with 0.5*106 CNS1 tumor cells and monitored for survival. Treated rats (N=6) were subjected to a single 20Gy whole-head radiation treatment under full anesthesia, delivered five days post-inoculation. Control rats (N=5) were anesthetized but not irradiated. Tumor size was monitored using contrast enhanced T1-weighted MRI in both treated and control rats at several time points (4, 6, 11, 18 and 32 days post tumor inoculation). RESULTS CNS1 cells are sensitive to radiation in vitro, as cell survival decreased after exposure to increasing amounts of radiation. In vivo, while initial tumor size did not significantly differ between groups, rats treated with radiation survived significantly longer than control rats (23.8 ± 5.0 days vs. 11 ± 4.1 days, p&lt;0.005). Growth arrest following irradiation in vivo was not detected 1d after treatment but was observed 6d post-irradiation. Growth arrest was recorded in half of the treated rats, showing no increase in tumor size (N=2) or reduction in tumor volume (N=1) relative to 1d post-irradiation. Tumor growth rates were lower in all irradiated rats relative to control rats. Survival time was negatively correlated with initial tumor size in the control group but not in the treatment group. CONCLUSION CNS1 rat model of GBM is a valid model of radiotherapy effects on GBM tumors. Further studies combining radiation and chemotherapy are the next step. Support for this work was provided by Israel Cancer Association.
Detecting Loose Regolith in Lunar Craters Using Thermal Imaging (2016)

Robotic missions could soon explore permanently shadowed craters on the lunar poles in order to characterize ice accumulation beneath the surface. However, the regolith in these craters is hypothesized to be very loose and could endanger a rover mission. This work analyzes the ability of thermal imaging to detect hazardous, low-density regolith in shadowed regions on the lunar poles. A series of simulations was conducted to estimate the surface temperature of lunar regolith as a function of density in polar craters. A generalized lunar crater model was used, and thermal properties of regolith were taken from experiments on Apollo samples. Results showed that in most situations there is a difference in temperature between nominal and loose regolith samples. This effect is most consistent at night in the absence of solar radiation and generally causes temperature differences between 2 K and 3 K. Based on comparisons to the capabilities of the DIVINER lunar radiometer, it is likely that regolith density differences would be detectable by a rover-mounted instrument.
Integrating Mobile-Based Systems with Healthcare Databases (2011)

In this chapter, we discuss issues related to e-health and focus on two major challenges in distributed healthcare database management: database heterogeneity and user mobility. We designed and prototyped a mobile-agent-based mobile data-access system framework that can address these challenges. It applies a thesaurus-based hierarchical database federation to cope with database heterogeneity and utilizes the mobile-agent technology to respond to the complications introduced by user mobility and wireless networks. The functions provided by this system are described in detail and a performance evaluation is also provided.Request access from your librarian to read this chapter's full text.
A New Pulsed 404 nm Laser Source for Biomedical Applications (2008)

We report frequency doubling in a new external cavity configuration with pulsed output up to 720 mW using an 808 nm tapered diode laser as pump source. The laser is used for fluorescence diagnostics applications.
Alternative Synthetic Routes to Epoxy Polymer – Clay Nanocomposites using Organic or Mixed‐Ion Clays Modified by Protonated Di/Triamines (Jeffamines) (2008)

Abstract The use of homoionic organic clays and mixed‐ion organic/inorganic clays modified by di‐ or triamines (Jeffamines), which are being used as epoxy resin curing agents, in the synthesis of polymer nanocomposites has been studied in this work. Our aim is to enhance polymer crosslinking and interfacial adhesion in the nanocomposite structure by utilizing the functionality of the di/triamines on the surface of clay nanolayers and by reducing the organic modifier via formation of homostructured mixed‐ion organic/inorganic clays. The results show that the use of homoionic organic clays exchanged with relatively short chain di‐ or triamines and mixed‐ion organic/inorganic clays partially exchanged (ca. 35%) with long chain diamines resulted in intercalated structures with enhanced thermo‐mechanical properties (Young's Modulus, Storage Modulus). On the other hand, homoionic organic clays exchanged with long chain diamines and triamines resulted in exfoliated nanocomposites but with compromised mechanical properties due to the plasticizing effect of the long chain amine modifiers.
Optical Engineering (2004)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text T. Z. Kosc, K. L. Marshall, A. Trajkovska-Petkoska, R. Varshneya, and S. D. Jacobs, "Optical Engineering," Optics & Photonics News 15(12), 33-33 (2004) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
CONFISCA: An SIMD-Based Concurrent FI and SCA Countermeasure with Switchable Performance and Security Modes (2021)

CONFISCA is the first generic SIMD-based software countermeasure that can concurrently resist against Side-Channel Attack (SCA) and Fault Injection (FI). Its promising strength is presented in a PRESENT cipher case study and compared to software-based Dual-rail with Pre-charge Logic concurrent countermeasure. It has lower overhead, wider usability, and higher protection. Its protection has been compared using Correlation Power Analysis, Welch’s T-Test, Signal-to-Noise Ratio and Normalized Inter-Class Variance testing methods. CONFISCA can on-the-fly switch between its two modes of operation: The High-Performance and High-Security by having only one instance of the cipher. This gives us the flexibility to trade performance/energy with security, based on the actual critical needs.
CCDC 1009347: Experimental Crystal Structure Determination (2016)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Octave-spanning coherent supercontinuum generation in a silicon nitride waveguide (2015)

We demonstrate the generation of a supercontinuum spanning more than 1.4 octaves in a silicon nitride waveguide using sub-100-fs pulses at 1 μm generated by either a 53-MHz, diode-pumped ytterbium (Yb) fiber laser or a 1-GHz, Yb:CaAlGdO(4) (Yb:CALGO) laser. Our numerical simulations show that the broadband supercontinuum is fully coherent, and a spectral interference measurement is used to verify that the supercontinuum generated with the Yb:CALGO laser possesses a high degree of coherence over the majority of its spectral bandwidth. This coherent spectrum may be utilized for optical coherence tomography, spectroscopy, and frequency metrology.
Solubilization of Cs and K from Tetraphenylborate Precipitates in Highly Alkaline Environments (2017)

Precipitated Cs tetraphenylborate, along with K tetraphenylborate and aqueous alkaline supernate, is present in certain high-level waste tanks at the Savannah River Site. Two possible processes for transferring the Cs+ (and K+) into the aqueous phase are described. One consists of displacement of the heavy alkalis from the solid tetraphenylborate by adding a tetraalkylammonium hydroxide. Almost 100% solubilization is obtained at ambient temperature using tetra-n-butylammonium hydroxide. The other consists of oxidative decomposition of the tetraphenylborate using persulfate. The extent of solubilization is found to increase with increasing temperature and persulfate:tetraphenylborate ratio. High yields of tetraphenylborate decomposition are obtained at elevated temperatures (55–90°C), and these yields increase with rising persulfate:tetraphenylborate ratios. The decomposition yields are lowered in the presence of nitrite, which is a component of the alkaline supernate, but are still significant, especially at elevated temperatures and high persulfate:tetraphenylborate ratios. The adverse effect of nitrite can be greatly reduced by lowering the pH.
Hybrid multiple wavelength reference using fiber gratings and molecular absorption (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text W. C. Swann, M. A. Hubbard, and S. L. Gilbert, "Hybrid multiple wavelength reference using fiber gratings and molecular absorption," in Bragg Gratings, Photosensitivity, and Poling in Glass Waveguides, T. Erdogan, E. Friebele, and R. Kashyap, eds., Vol. 33 of OSA Trends in Optics and Photonics Series (Optica Publishing Group, 1999), paper BC9. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
A theoretical foundation for location secrecy (2017)

Sharing users' positional information is often required for high accuracy localization, which is a cornerstone for numerous wireless applications in commercial, military, and social sectors. This raises a concern of leaking positional information to adversaries during the localization process. This paper establishes a mathematical foundation for location secrecy. In particular, we determine the location secrecy metric (LSM) for a localization network in which an eavesdropper has a generic measurement capability. We obtain a simple and closed-form expression of the LSM for the case where the eavesdropper's measurement of a user's position is corrupted by a Gaussian noise. We further extend this result to a more general measurement model, and design location secrecy protection strategies based on the insights gained from our analysis. The performance of the proposed algorithms is verified through numerical simulation.
Cerium Oxide Nanoparticle Conjugated with MicroRNA-146a Decreases Lung Inflammation and Fibrosis in Bleomycin Murine Model (2019)

Introduction Bronchopulmonary dysplasia and chronic lung disease due to prematurity are significant sources of morbidity and mortality in former pre-term infants. Central to the pathogenesis of bronchopulmonary dysplasia is the presence of chronic inflammation and increased oxidative stress which lead to pulmonary fibrosis. We hypothesized that a novel therapeutic directed at reducing inflammation and oxidative stress may also reduce fibrosis and the long-term sequela these infants face. MicroRNAs are short, non-coding RNAs that post-transcriptionally regulate gene activity. MicroRNA-146a is a key regulatory molecule in the NFkB mediated inflammatory response, with downstream effects on pro-inflammatory cytokines including IL-6. MicroRNA-146a was conjugated to cerium oxide nanoparticles (CNP146a), which are scavengers of reactive oxygen species and rapidly taken up by epithelial cells. The aim of this project was to evaluate intratracheal delivery of CNP146a at the time of bleomycin injury and examine its effects on decreasing pulmonary inflammation and subsequent fibrosis. Methods Using an established murine model, 29 juvenile (10 week) male and female C57BL/6 mice, underwent intratracheal instillation of bleomycin (3units/kg), PBS (as a control), or bleomycin and a single dose of CNP146a (10uM). Animals were euthanized either 7 days post-injury for bronchial alveolar lavage and tissue harvest or 14 days post-injury for lung inflation and tissue harvest. Results Histologic analysis 14 days post-injury (Figure 1) shows significant lung injury with bleomycin, including the presence of alveolar hemorrhage, increased collagen deposition, and an abundance of CD45+ cells when compared to PBS treated controls. The study group treated with CNP146a at the time of bleomycin injury showed less mucosal sloughing/hemorrhage, decreased CD45+inflammatory cells, and markedly decreased lung fibrosis. Bronchial alveolar lavage (BAL) specimens were processed for cell viability. There were no viable cells observed in the BAL obtained from the bleomycin treated group at 7 days (0.0% cell viability compared to 32.04% cell viability in the PBS controls). The CNP146a treated group had improved cell viability, equivalent to the control animals (35.92% cell viability). Conclusions CNP-146a is a new therapeutic that may possess applications for the prevention and treatment of chronic pulmonary disease in former pre-term infants at risk of developing bronchopulmonary dysplasia or chronic lung disease. Histology 14 days post-injury demonstrates decreased inflammation, hemorrhage, and fibrosis the CNP146a treated group. Further, the BAL samples show improved cell viability in the CNP-146a treated group. These results indicate that CNP146a decreases the inflammation and fibrosis associated with the bleomycin induced model of pulmonary fibrosis and may be an effective therapy in the mitigation of chronic pulmonary disease.