gebhart/patrepeval huggingface dataset:
Targeting Retroviral Integration (1995)

Retroviral vectorsarecurrently themost widely used method ofgenetransfer ingene therapy, inpartbecause theretroviral integration systemprecisely links thetherapeutic sequencestothehost chromosome with neat covalent bonds. DNA integration, however, comes with aprice. Retroviral integration systemsshowlittle targetsite specificity, andhaphazard insertions into a patient's chromosomes can createproblems. Integration nearcellular proto-oncogenesmay lead toectopic gene activation andcancer,not a desirable outcome of gene therapy (1).Retroviral integration can also inactivate genes(2). Recent findings on site-specific DNA integration by retroviruses andretrotransposons suggesta strategyforretrovirusbased gene therapy thatavoids
Evaluation of the dimensioning and economical benefits of intelligent optical networks (2005)

In order to cope with the increasing capacity requirements in the optical backbone network, the introduction of optical cross connects (OXC) and intelligent optical networking (ION) capable components such as ASON (automatically switched optical networking) or GMPLS (generalized multi-protocol label switching) might become a necessity. In this paper we study the benefits of the introduction of such ION-capable components in the network, using a multi-purpose dimensioning tool (DT) developed within the scope of the ITEA TBONES (transparent optical backbone network simulator) project. The introduction of ION-capable components in the network allows to use the capacity in the network more efficiently, especially when considering a highly dynamic traffic. The enhanced flexibility of the ION-capable components also allows to optimize the capacity-usage in case of network-failures. Optimization of the logical topology could further reduce the capacity-requirements for incorporating a specific resilience scheme in the network. In the light of the ongoing traffic growth in the backbone network, these capacity savings could also result in network cost savings, depending on the moment and price for the introduction of a new OXC in each specific node. By optimizing this estimated cost of the network, an optimal schedule for the introduction of the OXCs can be proposed
Effects of water-absorption and thermal drift on a polymeric photonic crystal slab sensor (2018)

A photonic crystal slab (PCS) sensor is a universal refractive index sensor with possibilities and performance very similar to surface plasmon resonance (SPR), which represents the gold standard of biosensing. Cheap PCS sensors can be made vacuum-free entirely out of polymers, but come with additional challenges, besides those relating to temperature-variations, which must be considered in any refractive index based method: The polymeric waveguide core was found to swell by ∼0.3% as water absorbed into the waveguide core over ∼1.5 h. This was investigated by monitoring the wavelength of resonant reflection during absorption, by monitoring the release of water using ellipsometry, and by rigorous coupled-wave analysis (RCWA). The approach presented here enables monitoring of water uptake and thermal fluctuations, for drift-free, high-performance operation of a polymeric PCS sensor.
The Electrolytic Codeposition of Copper and Phosphorus (1989)

We report in this paper a recently patented process which permits the production of a low phosphorus content copper composite suitable for conversion to a commercial type phosphorized copper alloy. The research for this work was carried out on bench scale
Parathyroidectomy Is Associated with Reduced Mortality in Hemodialysis Patients with Secondary Hyperparathyroidism (2015)

Secondary hyperparathyroidism increases morbidity and mortality in hemodialysis patients. The Kidney Disease Outcomes Quality Initiative Guidelines recommend parathyroidectomy for patients with chronic kidney disease and parathyroid hormone concentrations exceeding 800 pg/mL; however, this concentration represents an arbitrary cut-off value. The present study was conducted to identify factors influencing mortality in hemodialysis patients with parathyroid hormone concentrations exceeding 800 pg/mL and to evaluate the effects of parathyroidectomy on outcome for these patients. Two hundred twenty-one hemodialysis patients with parathyroid hormone concentrations > 800 pg/mL from July 2004 to June 2010 were identified. 21.1% of patients (n = 60) received parathyroidectomy and 14.9% of patients (n = 33) died during a mean follow-up of 36 months. Patients with parathyroidectomy were found to have lower all-cause mortality (adjusted hazard ratio [aHR]: 0.34). Other independent predictors included age ≥ 65 years (aHR: 2.11) and diabetes mellitus (aHR: 3.80). For cardiovascular mortality, parathyroidectomy was associated with lower mortality (HR = 0.31) but with a marginal statistical significance (p = 0.061). In multivariate analysis, diabetes was the only significant predictor (aHR: 3.14). It is concluded that, for hemodialysis patients with parathyroid hormone concentrations greater than 800 pg/mL, parathyroidectomy is associated with reduced all-cause mortality.
Impaired dendritic-cell function in ectodermal dysplasia with immune deficiency is linked to defective NEMO ubiquitination (2006)

Ectodermal dysplasia with immune deficiency (EDI) is caused by alterations in NEMO (nuclear factor [NF]-kappaB essential modulator). Most genetic mutations are located in exon 10 and affect the C-terminal zinc finger domain. However, the biochemical mechanism by which they cause immune dysfunction remains undetermined. In this report, we investigated the effect of a cysteine-to-arginine mutation (C417R) found in the NEMO zinc finger domain on dendritic cell (DC) function. Following CD40 stimulation of DCs prepared from 2 unrelated patients with the NEMO C417R mutation, we found NEMO ubiquitination was absent, and this was associated with preserved RelA but absent c-Rel activity. As a consequence, CD40 stimulated EDI DCs failed to synthesize the c-Rel-dependent cytokine interleukin-12, had impaired up-regulation of costimulatory molecules, and failed to support allogeneic lymphocyte proliferation in vitro. In contrast, EDI DCs stimulated with the TLR4 ligand lipopolysaccharide (LPS) showed normal downstream NF-kappaB activity, DC maturation, and NEMO ubiquitination. These findings show for the first time how mutations in the zinc finger domain of NEMO can lead to pathway specific defects in NEMO ubiquitination and thus immune deficiency.
Weather-Based Damage Prediction Models for Electric Distribution Networks (2012)

From thunderstorms to hurricanes, electric distribution networks are subject to a wide range of warm weather storm events. Tropical Storm Irene (2011) and Hurricane Sandy (2012) are two events in recent memory that disrupted over half of The Connecticut Light and Power Company’s (CL&amp;P) service territory, which left some customers without power for up to eleven days. This research study investigates a damage prediction framework for both thunderstorms and hurricanes that combines two generalized linear models to probabilistically determine the occurrence and extent of damages, known as trouble spots, to the overhead power distribution network. The models are inputted with high-resolution weather simulations from the Weather and Research Forecasting (WRF) Model along with distributed information on CL&amp;P’s infrastructure, tree canopy density, and land cover data. The models were subjected to cross validation based on 30 major storm cases including the two tropical storms (Storm Irene and Hurricane Sandy), and exhibited a median percent error less than 30% for predicting the counts of trouble spots per event. Additionally, we explore an operational example of these models by using forecasts from 48 and 24 hours ahead of landfall by Hurricane Sandy to demonstrate how a real-time damage prediction system might operate.
In Vivo Application of Proton-Electron Double-Resonance Imaging (2017)

PEDRI has similarities with electron paramagnetic resonance imaging (EPRI) because both techniques observe the EPR signal, directly in the case of EPRI and indirectly with PEDRI. PEDRI provides information that is vital to research on homeostasis, development of diseases, or treatment responses in vivo. It is expected that the development of new EPR techniques will give insights into novel PEDRI applications and vice versa. Antioxid. Redox Signal. 28, 1345-1364.
An interdisciplinary framework for navigating social–climatic tipping points (2023)

Abstract To effectively navigate out of the climate crisis, a new interdisciplinary approach is needed to guide and facilitate research that integrates diverse understandings of how transitions evolve in intertwined social–environmental systems. The concept of tipping points, frequently used in the natural sciences and increasingly in the social sciences, can help elucidate processes underlying major social–environmental transitions. We develop the notion of interlinked ‘social–climatic tipping points’ in which desirability and intentionality are key constitutive features alongside stable states, feedbacks, reversibility and abruptness. We demonstrate the new insights that our interdisciplinary framework can provide by analysing the slowdown of the Atlantic Meridional Overturning Circulation and associated flooding of the Ahr Valley in Germany as a social–climatic tipping point. This framework can enable more sustainable and equitable futures by prioritising social–climatic tipping points for interdisciplinary research, identifying opportunities for action, and evaluating the nuanced desirability and acceptability of proposed solutions. Read the free Plain Language Summary for this article on the Journal blog.
GLIOMA EXTENT OF RESECTION AND ITS IMPACT ON PATIENT OUTCOME (2008)

Despite persistent limitations in the quality of data, mounting evidence suggests that more extensive surgical resection is associated with longer life expectancy for both low- and high-grade gliomas.
A single digital droplet PCR assay to detect multipleKITexon 11 mutations in tumor and plasma from patients with gastrointestinal stromal tumors (2018)

A single ddPCR assay for the detection of multiple exon 11 mutations in ctDNA is a feasible, promising tool for monitoring treatment response in patients with metastasized GIST and should be further evaluated in a larger cohort.
Rates and Mechanism of the Formation of Zerovalent Palladium Complexes from Mixtures of Pd(OAc)2 and Tertiary Phosphines and Their Reactivity in Oxidative Additions (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRates and Mechanism of the Formation of Zerovalent Palladium Complexes from Mixtures of Pd(OAc)2 and Tertiary Phosphines and Their Reactivity in Oxidative AdditionsChristian Amatore, Emmanuelle Carre, Anny Jutand, and Mohamed Amine M'BarkiCite this: Organometallics 1995, 14, 4, 1818–1826Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/om00004a039https://doi.org/10.1021/om00004a039research-articleACS PublicationsRequest reuse permissionsArticle Views4688Altmetric-Citations307LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Model-potential-based simulation of Si(100) surface reconstruction (1987)

We use recently derived empirical potentials of Stillinger and Weber, Tersoff, and Dodson to study Si(100) surface reconstruction employing molecular dynamics simulation. All of these potentials give symmetric dimers for the 2\ifmmode\times\else\texttimes\fi{}1 reconstruction on the Si(100) surface. Our calculated reconstruction energies are in good agreement with those given by total-energy density-functional calculations. We also use the model potentials to study the defect-reconstruction model of Pandey and the dimer-plus-chain model of Northrup. We find the Pandey defect reconstruction to be energetically comparable with the dimer reconstruction. Our simulations give much higher energies for the dimer-plus-chain reconstruction, making it energetically unfavorable on the Si(100) surface.
Excess Polarizability Reveals Exciton Localization/Delocalization Controlled by Linking Positions on Porphyrin Rings in Butadiyne-Bridged Porphyrin Dimers (2010)

We report direct measurements of the excess polarizability volumes of butadiyne-bridged zinc porphyrin dimers at singly beta-to-beta (1Zn) and doubly beta-to-beta (2Zn) positions using the transient dc photoconductivity (TDCP) technique. The excess polarizability volumes of the singlet exciton for 1Zn and 2Zn are 110 and 270 A(3), respectively, while those of the triplet exciton are approximately 100 A(3) for both dimers. Our measurements suggest that the singlet exciton is mainly localized on one porphyrin subunit for 1Zn, similar to the case for the porphyrin monomer. While the exciton is fully delocalized on two porphyrin subunits in the case of meso-to-meso linked dimer (3Zn), the extent of exciton localization/delocalization for doubly beta-to-beta linked dimer lies between those of singly beta-to-beta and meso-to-meso linked dimers. Electronic structure calculations show that the dramatically different extents of exciton localization/delocalization are the results of frontier orbital coefficients being small at beta positions but large at meso positions. Two butadiyne linkages between the porphyrins at beta positions (2Zn) clearly facilitate electronic communication between the two porphyrin subunits by virtue of stabilization of cumulenic charge resonance structures through enforced planarity.
Absence of Relationship Between Self-Reported Sleep Measures and Amyloid Load in Elderly Subjects (2019)

<b>Objective:</b> To determine the relationships between self-reported sleep profile and cortical amyloid load in elderly subjects without dementia. <b>Methods:</b> This cross-sectional study included 143 community-dwelling participants aged ≥70 years (median: 73 years [70-85]; 87 females) with spontaneous memory complaints but dementia-free. Sociodemographic characteristics, health status, neuropsychological tests, sleep, and <sup>18</sup>F-florbetapir (amyloid) PET data were collected. The clinical sleep interview evaluated nighttime sleep duration, but also daytime sleep duration, presence of naps, and restless leg syndrome (RLS) at time of study. Validated questionnaires assessed daytime sleepiness, insomnia, and risk of sleep apnea. The cortical standardized uptake value ratio (SUVr) was computed across six cortical regions. The relationship between sleep parameters and SUVr (cut-off ratio>1.17 and tertiles) was analyzed using logistic regression models. <b>Results:</b> Amyloid-PET was positive in 40.6% of participants. Almost 40% were at risk for apnea, 13.5% had RLS, 35.5% insomnia symptoms, 22.1% daytime sleepiness, and 18.8% took sleep drugs. No significant relationship was found between positive amyloid PET and nighttime sleep duration (as a continuous variable, or categorized into <6; 6-7; ≥7 h per night). Logistic regression models did not show any association between SUVr and daytime sleep duration, 24-h sleep duration, naps, RLS, daytime sleepiness, insomnia symptoms, and sleep apnea risk (before and after adjustment for APOEε4 and depressive symptoms). <b>Conclusion:</b> Our study did not confirm the association between amyloid-PET burden, poor sleep quantity/quality in elderly population, suggesting that the interplay between sleep, and amyloid is more complex than described.
Split Bregman Methods and Frame Based Image Restoration (2009)

Split Bregman methods introduced in [T. Goldstein and S. Osher, SIAM J. Imaging Sci., 2 (2009), pp. 323-343] have been demonstrated to be efficient tools for solving total variation norm minimization problems, which arise from partial differential equation based image restoration such as image denoising and magnetic resonance imaging reconstruction from sparse samples. In this paper, we prove the convergence of the split Bregman iterations, where the number of inner iterations is fixed to be one. Furthermore, we show that these split Bregman iterations can be used to solve minimization problems arising from the analysis based approach for image restoration in the literature. We apply these split Bregman iterations to the analysis based image restoration approach whose analysis operator is derived from tight framelets constructed in [A. Ron and Z. Shen, J. Funct. Anal., 148 (1997), pp. 408-447]. This gives a set of new frame based image restoration algorithms that cover several topics in image restorations, such as image denoising, deblurring, inpainting, and cartoon-texture image decomposition. Several numerical simulation results are provided. © 2009 Society for Industrial and Applied Mathematics.
Localization of 2‐[125I]Iodomelatonin Binding Sites in Mammalian Retina (1991)

Specific melatonin binding sites were localized in the mammalian retina using the selective radioligand 2-[125I]iodomelatonin. Frozen sections obtained from both pigmented and albino rabbit eyes and albino mouse eyes were incubated with 2-[125I]iodomelatonin in the absence and presence of competing agents. In eyecups from albino rabbits, the highest density of specific 2-[125I]iodomelatonin binding sites was localized over the inner plexiform layer. Approximately 40-60% of the binding was specific, as determined with both the agonist 6-chloromelatonin and the antagonist luzindole. A high density of binding sites was observed over the choroid and retinal pigmented epithelium, but no statistical difference between total and nonspecific binding was detected. Results were similar with eyecups from pigmented rabbits. Albino mice showed a significant extent of 2-[125I]iodomelatonin binding in both the inner plexiform and the outer and inner segment layers. The specific binding of 2-[125I]iodomelatonin in retinas from albino rabbits maintained in the light for 24 h before decapitation was increased in the inner retina compared with the control. The distribution of 2-[125I]iodomelatonin binding sites in the various layers of the mammalian retina is consistent with the described functions for this hormone in retinal physiology.
Immunoreactivity of Intact Virions of Human Immunodeficiency Virus Type 1 (HIV-1) Reveals the Existence of Fewer HIV-1 Immunotypes than Genotypes (2000)

In order to protect against organisms that exhibit significant genetic variation, polyvalent vaccines are needed. Given the extreme variability of human immunodeficiency virus type 1 (HIV-1), it is probable that a polyvalent vaccine will also be needed for protection from this virus. However, to understand how to construct a polyvalent vaccine, serotypes or immunotypes of HIV must be identified. In the present study, we have examined the immunologic relatedness of intact, native HIV-1 primary isolates of group M, clades A to H, with human monoclonal antibodies (MAbs) directed at epitopes in the V3, C5, and gp41 cluster I regions of the envelope glycoproteins, since these regions are well exposed on the virion surface. Multivariate analysis of the binding data revealed three immunotypes of HIV-1 and five MAb groups useful for immunotyping of the viruses. The analysis revealed that there are fewer immunotypes than genotypes of HIV and that clustering of the isolates did not correlate with either genotypes, coreceptor usage (CCR5 and CXCR4), or geographic origin of the isolates. Further analysis revealed distinct MAb groups that bound preferentially to HIV-1 isolates belonging to particular immunotypes or that bound to all three immunotypes; this demonstrates that viral immunotypes identified by mathematical analysis are indeed defined by their immunologic characteristics. In summary, these results indicate (i) that HIV-1 immunotypes can be defined, (ii) that constellations of epitopes that are conserved among isolates belonging to each individual HIV-1 immunotype exist and that these distinguish each of the immunotypes, and (iii) that there are also epitopes that are routinely shared by all immunotypes.
Strip interpolation in silicon and germanium strip detectors (2005)

The position resolution of double-sided strip detectors is limited by the strip pitch and a reduction in strip pitch necessitates more electronics. Improved position resolution would improve the imaging capabilities of Compton telescopes and PET detectors. Digitizing the preamplifier waveform yields more information than can be extracted with regular shaping electronics. In addition to the energy, depth of interaction, and which strip was hit, the digitized preamplifier signals can locate the interaction position to less than the strip pitch of the detector by looking at induced signals in neighboring strips. This allows the position of the interaction to be interpolated in three dimensions and improve the imaging capabilities of the system. In a 2 mm thick silicon strip detector with a strip pitch of 0.891 mm, strip interpolation located the interaction of 356 keV gamma rays to 0.3 mm FWHM. In a 2 cm thick germanium detector with a strip pitch of 5 mm, strip interpolation of 356 keV gamma rays yielded a position resolution of 1.5 mm FWHM.
Fractals in Biology and Medicine (1998)

In Interaction is devoted to the publication of advanced textbooks, monographs, and multi-authored volumes on mathematical concepts in the biological sCiences. It concentrates on truly interdisciplinary research presenting currently important biological fields and relevant methods of mathematical modelling and analysis. Emphasis will be put on mathemotical concepts and methods being developed and refined in close relation to problems and results relevant for experimental bioscientists.
Peculiarities of Electrochemical Behavior of Porous Carbon Electrodes of Supercapacitors in Aqueous Solutions of Salts of Alkali Metals (2018)

Electrochemical behavior of porous carbon electrodes with different densities (0.75 and 0.35 g/cm3) used in supercapacitors with aqueous solutions of lithium, sodium and potassium sulfates was studied. It was shown that Li2SO4 solution is the most suitable for high-density electrodes, whereas K2SO4 solution is better for low-density electrodes. Experimental data obtained by means of cyclic voltammetric and impedance curves demonstrate a mutual influence of the porous structure of the electrode materials and diameters of solvated and bare ions on the values of specific capacitance and resistance. This should be taken into account when an electrode/electrolyte system is chosen for high-efficiency energy storage devices.
Rejection of the Position Dependent Disturbance Torque of Motor System with Slowly Varying Parameters and Time Delays (2015)

This paper proposes an updating state dependent disturbance observer (USDDOB) to reject position dependent disturbances when parameters vary slowly, and input and output are time-delayed. To reject the effects of resultant slowly-varying position dependent disturbances, the USDDOB uses the control method of the state dependent disturbance observer (SDDOB) and time-invariance approximation. The USDDOB and a main proportional integral (PI) controller constitute a robust controller. Simulations and experiments using a 1-degree-of-freedom (1-DOF) tilted planar robot show the effectiveness of the proposed method.