gebhart/patrepeval huggingface dataset:
Methodology for Efficient and Biosecure Genetic Engineering of Biomedical Swine Models (2020)

The genetic proximity of swine to human, the overwhelming anatomical, physiological and pathophysiological similarities, and the ability to mimic external factors in a practical manner make swine the ideal preclinical model for many human diseases. While the value of swine in biomedical research is well recognized, their use has been limited by the lack of tools to easily edit the swine genome to model human disease, and the lack of facilities, resources and expertise at most institutions for supporting large‐scale swine research. The recent implementation of new genetic editing tools such as the CRISPR/Cas9 platform make the creation of novel genetic swine models possible and practical. However, conventional approaches to genetic engineering of swine rely on ova obtained from commercial abattoirs, significantly compromising biosecurity, and often offering little control over the background genetic of the swine breeds upon which the genomic editing is performed. Here, we describe methods and workflow that we have developed that allow for efficient genetic engineering of swine, while maintaining control over background genetics and minimizing the biosecurity risk to the animals and the facility. The process centrally relies on the refinement of reproductive cycle synchronization and superovulation of swine and time‐precise coordination of the entire genetic engineering workflow. Support or Funding Information The research was supported by the Biomedical &amp; Genomic Research Group Discretionary Fund (University of Wisconsin‐Madison), NF North Central, NF Network, and NF Team Foundation
Interaction of Minor-Groove-Binding Diamidine Ligands with an Asymmetric DNA Duplex. NMR and Molecular Modelling Studies (1995)

The aromatic diamidines berenil and propamidine bind reversibly to A+T-rich sites in the minor groove of B-form DNA duplexes. Based on extensive solution and crystallographic information we have designed a non-self-complementary double-stranded DNA sequence, d(GCAATGAGCG) d(CGCTCATTGC), that should contain a near-ideal binding site for berenil and a poorer site for the larger propamidine molecule, viz, d(AAT) d(ATT). H-1-NMR studies show that both ligands bind with 1:1 stoichiometry to the embedded 5'-AAT site, and induce numerous shifts of NMR resonances of DNA protons located in the minor groove. In addition, interactions with each strand can be distinguished by NOE spectroscopy due to the inherent asymmetry of the DNA. Detailed modelling based on experimental data show that no significant distortion of the B-DNA duplex is induced by either ligand. Sufficient NOE data were obtained to determine the position of the bound ligands in each complex. These conclusions are in agreement with predictions from molecular modelling calculations that provide a microscopic energy profile for interaction with the minor groove tract. Such calculations reveal an unexpected heterogeneous 5'-ATGA binding site that includes a spanned guanosine. This secondary binding site accounts for the extensive chemical shift perturbation induced by these ligands. The structures of the free DNA and the reversible complexes formed with each ligand molecule have been refined using an NOE-restrained isothermal annealing procedure. These structures confirm that the introduced ligands effect minimal perturbation of the helix, with binding to the 5'-AAT base sequence largely determined by specific non-bonded interactions.
Insights into the Rare cis-AB Blood Group: In Silico Genotyping and Analysis in the Indian Subcontinent (2023)

The rare blood groups reported from India include the Bombay phenotype, -D-/-D-, In (a+b-) and other weaker variants of ABH antigens. We report a case of cis-AB blood group, identified in an Indian patient whose blood grouping was performed by the column agglutination technique, conventional tube technique (CTT) after 15 minutes of incubation at room temperature as well as at 40C and subsequently whole exome sequencing for molecular analysis. The blood group was identified serologically as A2B3 and confirmed to be a cisAB phenotype by next-generation sequencing.
Sequential aggregate signatures for wireless routing protocols (2005)

Sequential aggregate signature, first introduced and formalized by A. Lysyanskaya et al. (see EUROCRYPT 2004, p.74-90, 2004), is emerging as a useful tool to ensure routing security and at the same time to improve performance. We propose a new mechanism to construct sequential aggregate signatures based on the cipher block chaining (CBC) mode, which is different from previous known results. We then construct an efficient sequential aggregate signature scheme and show that our construction is provably secure in the random oracle paradigm, assuming that the RSA problem is hard. Finally, we propose an interesting aggregate routing protocol for wireless ad hoc networks as an immediate application of our protocol.
TOI 564 b and TOI 905 b: Grazing and Fully Transiting Hot Jupiters Discovered by TESS (2020)

© 2020. The American Astronomical Society. All rights reserved. We report the discovery and confirmation of two new hot Jupiters discovered by the Transiting Exoplanet Survey Satellite (TESS): TOI 564 b and TOI 905 b. The transits of these two planets were initially observed by TESS with orbital periods of 1.651 and 3.739 days, respectively. We conducted follow-up observations of each system from the ground, including photometry in multiple filters, speckle interferometry, and radial velocity measurements. For TOI 564 b, our global fitting revealed a classical hot Jupiter with a mass of MJ and a radius of RJ. Also a classical hot Jupiter, TOI 905 b has a mass of MJ and radius of RJ. Both planets orbit Sun-like, moderately bright, mid-G dwarf stars with V ∼ 11. While TOI 905 b fully transits its star, we found that TOI 564 b has a very high transit impact parameter of, making it one of only ∼20 known systems to exhibit a grazing transit and one of the brightest host stars among them. Therefore, TOI 564 b is one of the most attractive systems to search for additional nontransiting, smaller planets by exploiting the sensitivity of grazing transits to small changes in inclination and transit duration over a timescale of several years.
Analysis of Fiber Based Emitting Head for Optical Wireless Communication (2019)

A fiber based emitting head for optical wireless communication (OWC) is proposed and experimentally evaluated. We analysed the characterization of emitting head by experiment and simulation software. The method of beam expanded was achieved by using an arc curvature design which was acted as a microlenses.
Strain tunability of dielectric and ferroelectric properties in epitaxial lead titanate thin films (2011)

Many distinguished properties of epitaxial ferroelectric thin films can be tunable through the misfit strain. The strain tunability of ferroelectric and dielectric properties in epitaxial lead titanate ultrathin films is numerically investigated by using a phase field model, in which the surface effect of polarization is taken into account. The response of polarization to the applied electric field in the thickness direction is examined with different misfit strains at room temperature. It is found that a compressive misfit strain increases the coercive field and the remanent polarization while a tensile misfit strain decreases both of them. The nonlinear dielectric constants of the thin films with tensile misfit strains are much larger than those of the thin films without misfit strains, which are attributed to the existence of the a/c/a/c multiple domains in the thin films under tensile misfit strains.
Accurate submicroampere controlled current source (1981)

A bipolar design technique for a submicroampere current-controlled current source which employs low value resistances and is integrable using standard monolithic processing is described. The circuit is self-starting and provides linear current/voltage control of the output current with higher accuracy and temperature stability than a recently reported technique.
Centrolobular Liver Fibrosis in the Hypercholesterolemic Rabbit (1996)

During a study on the development of atheromatous lesions in rabbits fed a diet with a low or high cholesterol supplement, we found a moderate to pronounced centrolobular liver fibrosis. This fibrosis developed in three stages. Early after supplementation of cholesterol, we observed increased immunoreactivity of collagen types I, III, and IV, and fibronectin, around central veins and in adjacent sinusoids. In the second stage, we observed further increase of collagen and fibronectin immunoreactivity, together with the appearance of alpha-smooth muscle actin (alpha-SM actin)-positive cells and anti-rabbit macrophage monoclonal antibody (RAM 11)-positive cells. In the third stage, we observed large numbers of alpha-SM actin-positive cells, together with heavy deposition of connective tissue proteins in pericentral sinusoids, in addition to focal atrophy of parenchymal cells. By transmission electron microscopy (TEM), fat-storing cells in the pericentral regions were shown to be enlarged, to lose their lipid-droplets, and to acquire dilated rough endoplasmic reticulum corresponding to an activated phenotype. Parenchymal cells were either normal or contained numerous small lipid-droplets. They sometimes were smaller and distorted. Northern hybridization performed on total RNA of whole liver showed an increased level of collagen alpha1(I), alpha1(III), and alpha1(IV) messenger RNA (mRNA) after 24 weeks of low dietary cholesterol supplementation. These data show enhanced expression of extracellular matrix proteins. We conclude that cholesterol overload induces pericentral liver fibrosis in rabbits. The diet clearly activates fat-storing cells to become fibrogenic effector cells. At present, we have no explanation why hypercholesterolemia induces phenotypic transition of fat-storing cells.
P2‐167: Influence of amyloid and APOE genotype on cognitive performance in a middle‐aged cohort (2015)

Previous studies have assessed the effects of amyloid and APOE genotype on cognition among elderly individuals, but few studies have examined this relationship among middle-aged individuals. We included 971 cognitively normal participants, mean [SD] age of 62.6 [5.5] years and 50% men, enrolled in the Mayo Clinic Study of Aging. All participants were test-naïve at baseline and completed multiple visits and cognitive assessments over 30 months of follow-up; 447 had PiB-PET amyloid imaging. Cognitive assessments included a standard neuropsychological battery and the CogState computerized battery. We used linear mixed models to examine the effects of amyloid, presence of an APOE ɛ4 allele, and their interaction on baseline cognition and on cognitive decline after controlling for age, sex, and education. Elevated amyloid was cross-sectionally associated with poorer performance on computerized tests of psychomotor speed and working memory, and was longitudinally predictive of declines on tests of attention/executive functions. The presence of an APOE ɛ4 allele was not associated with impaired cognition cross-sectionally or longitudinally. However, having both an APOE ɛ4 allele and higher amyloid was cross-sectionally associated with poorer performance on tests of psychomotor speed and spatial working memory. Longitudinally, having both an APOE ɛ4 allele and higher amyloid was associated with better episodic memory performance. Despite the modest associations between amyloid levels and cognition, elevated amyloidosis and APOE genotype does not appear to exert a dramatic influence on cognition in middle-age.
Slow Light in “Zero Thickness” Metamaterials (2008)

We show for the first time that a classical analogue of EIT can be realized in “zero thickness” planar metamaterials (meta-surfaces) resulting in substantial delay of propagating electromagnetic pulses.
Multiplex gene expression analysis for high-throughput drug discovery: screening and analysis of compounds affecting genes overexpressed in cancer cells. (2002)

Drug discovery strategies are needed that can rapidly exploit multiple therapeutic targets associated with the complex gene expression changes that characterize a polygenic disease such as cancer. We report a new cell-based high-throughput technology for screening chemical libraries against several potential cancer target genes in parallel. Multiplex gene expression (MGE) analysis provides direct and quantitative measurement of multiple endogenous mRNAs using a multiplexed detection system coupled to reverse transcription-PCR. A multiplex assay for six genes overexpressed in cancer cells was used to screen 9000 chemicals and known drugs in the human prostate cancer cell line PC-3. Active compounds that modulated gene expression levels were identified, and IC50 values were determined for compounds that bind DNA, cell surface receptors, and components of intracellular signaling pathways. A class of steroids related to the cardiac glycosides was identified that potently inhibited the plasma membrane Na(+)K(+)-ATPase resulting in the inhibition of four of the prostate target genes including transcription factors Hoxb-13, hPSE/PDEF, hepatocyte nuclear factor-3alpha, and the inhibitor of apoptosis, survivin. Representative compounds selectively induced apoptosis in PC-3 cells compared with the nonmetastatic cell line BPH-1. The multiplex assay distinguished potencies among structural variants, enabling structure-activity analysis suitable for chemical optimization studies. A second multiplex assay for five toxicological markers, Hsp70, Gadd153, Gadd45, O6-methylguanine-DNA methyltransferase, and cyclophilin, detected compounds that caused DNA damage and cellular stress and was a more sensitive and specific indicator of potential toxicity than measurement of cell viability. MGE analysis facilitates rapid drug screening and compound optimization, the simultaneous measurement of toxicological end points, and gene function analysis.
Wireless Body Area Networks: Where does energy go? (2012)

Wireless Body Area Networks (WBANs) promise to revolutionize health care in the near future. By integrating bio-sensors with a mobile phone it is possible to monitor an individual's health and related behaviors. Monitoring is done by analyzing the sensor data either on a mobile phone or on a remote server by relaying this information over a wireless network. However, the “wireless” aspect of WBAN is being limited by the battery life of the mobile phone. A WBAN designer has a range of options to trade-off limited battery with many important metrics. From the choice of programming languages to dynamically choosing between computation versus communication under varying signal strengths, there are several non-obvious choices that can have dramatic impact on battery life. In this research we use an in-field deployed WBAN called KNOWME to present a comprehensive quantification of a mobile phone's energy consumption. We quantify the energy impact of different programming paradigms, sensing modalities, data storage, and conflicting computation and communication demands. Based on the knowledge gained from the measurement studies, we propose an Active Energy Profiling strategy that uses short profiling periods to automatically determine the most energy efficient choices for running a WBAN.
[Recent advances in treatment and the future problems to be solved]. (2006)

The goal of the treatment of chronic heart failure is improvement of patient's prognosis and QOL. To achieve this goal, new pharmacological and nonpharmacological approaches have been developed. ACE inhibitor - and beta-blocker-treatment added to the standard therapy has been established to improve the prognosis, and ICD, cardiac resynchronization treatment (CRT) with biventricular pacing and LV assist device also contribute to the advances in the therapeutic progress. However, recent clinical trials for the new drugs which antagonize the endothelin receptors and TNF receptors failed to demonstrate the benefit of these new drugs. Establishment of the therapeutic strategies for treatment of diastolic heart failure is also another problem to be solved.
Efficient derivative-free optimization (2007)

The present paper considers the derivative-free optimization of expensive non-smooth functions. One of the most efficient algorithms for this class of problems is the surrogate-based optimization framework by Booker et al, 1999. Searches performed using this algorithm are restricted to points lying on an underlying grid to keep function evaluations far apart until convergence is approached. Once convergence on this discrete grid is obtained, the grid is refined and the process repeated. All previous implementations of this algorithm have been based on a Cartesian grid. However, Cartesian grids are not nearly as uniform at packing, covering, and quantizing parameter space as several alternatives that are well known in coding theory, referred to as "n-dimensional sphere packings" or "lattices". Also, the distribution of nearest-neighbor lattice points turns out to be far superior in these alternative lattices, further increasing the efficiency of the optimization algorithm. The present study illustrates how such lattices may be incorporated into the surrogate-based optimization framework.
Openness (2010)

This chapter presents an initial response to the problem of pluralism and uncertainty posed at the end of Chapter 1. The argument of this chapter is preliminary and incomplete, but it will serve as a template that will be progressively refined in subsequent chapters in response to questions and objections.
Conformational structure of cationic tetrahydropyran by one-photon vacuum ultraviolet mass-analyzed threshold ionization spectroscopy (2020)

Isolating and identifying the conformational forms of molecules are imperative processes to investigate the chemical reaction pathways of individual conformers. Herein, we explored the conformational structures of tetrahydropyran in the neutral (S0) and cationic (D0) states by varying the supersonic expansion conditions using one-photon vacuum ultraviolet mass-analyzed threshold ionization (VUV-MATI) spectroscopy. The constructed 2D potential energy surfaces associated with conformational interconversion between the chair and boat forms in the S0 and D0 states revealed that the ionic transitions observed in the MATI spectra correspond to the most stable chair conformer. Accordingly, based on the 0-0 band in the VUV-MATI spectrum supported by the VUV photoionization efficiency curve, the adiabatic ionization energy for the conversion of the chair conformer to a cationic state was determined to be 74 687 ± 4 cm-1 (9.2600 ± 0.0005 eV). Definitive vibrational assignment of the measured MATI spectra using Franck-Condon fitting revealed the cationic structure of the twisted chair conformer. The geometrical change upon ionization promoted the vibrational modes associated with ring inversion and deformation motions in the cationic state. This behavior, which was attributed to the effect of electron removal from the highest occupied molecular orbital (HOMO) consisting of the nonbonding orbital of the oxygen atom, reveals the role of electrons in the HOMO.
Application of a thermal rearrangement reaction to questions of structure of condensed dihydrodiazepinones. 4. Reexamination of the reactions of,2-diaminonaphthalene with ethyl acetoacetate and crotonic acid (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplication of a thermal rearrangement reaction to questions of structure of condensed dihydrodiazepinones. 4. Reexamination of the reactions of,2-diaminonaphthalene with ethyl acetoacetate and crotonic acidMervyn Israel and Estelle C. ZollCite this: J. Org. Chem. 1972, 37, 22, 3566–3567Publication Date (Print):November 1, 1972Publication History Published online1 May 2002Published inissue 1 November 1972https://pubs.acs.org/doi/10.1021/jo00795a051https://doi.org/10.1021/jo00795a051research-articleACS PublicationsRequest reuse permissionsArticle Views133Altmetric-Citations8LEARN 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
Fabrication and characterization of large-scale multifunctional transparent ITO nanorod films (2013)

In this study, large-scale multifunctional transparent ITO nanorod films that exhibit extreme wetting states (superhydrophobicity or superhydrophilicity), high transmittance, low resistivity to infer antistatic properties, antifogging, and self-cleaning were fabricated on 2-in. glass wafers and various substrates (glass, Si, Sus of 2.5 × 2.5 cm) via radio frequency (RF)-magnetron sputtering deposition. An ITO nanorod film prepared for 60 min at 500 °C exhibited excellent optical (∼85% transmittance at 500 nm) and electrical (sheet resistance of ∼90 Ω □−1, antistatic property, with a figure of merit of 2.2 × 10−3 Ω−1) properties. It also showed superhydrophilic property (with a water contact angle as low as 1°) and antifogging. After coating with fluoroalkylsilane, the ITO nanorod film exhibited strong and stable superhydrophobic characteristics, having a high water contact angle (172.1°), a near-zero sliding angle, and self-cleaning capabilities. It is expected that large-scale multifunctional transparent ITO nanorods will lead to further technological advancements in the area of novel optoelectrical applications and in future industrial applications.
Consideration of Silylation Contrast in an ArF Liquid-Phase Silylation Process (1997)

We have studied what determines the silylation contrast for the liquid-phase silylation process in ArF excimer laser lithography. In the liquid-phase silylation, the diffusion kinetics is dependent on the concentration of the diffusion promoter, which acts as the relaxation of the polymer film. The silylating condition of a proper concentration induces the equilibrium state of relaxation and diffusion: Case II diffusion. It was found that the Case II diffusion condition resulted in a higher silylation contrast. Next, attention was paid to the photo-crosslinking density for improving the silylation contrast. The soft-baking temperature had an influence on the crosslinking density. The densification of the polymer film by soft-baking increases the photo-crosslinking density, but an extreme densification decreases it, when the soft-baking temperature is near glass transition temperature ( T g ). It is considered that the arrangement of the polymer chains is closely linked with the efficiency of photo-crosslinking.
Evidence for Posterior Zonular Fiber Attachment on the Anterior Hyaloid Membrane (2006)

Contrary to the classic description, the majority of posterior zonular fibers are not attached directly to the posterior lens capsule, but are anchored to the anterior hyaloid membrane on their path from the ciliary body to the posterior capsule. This finding is in good agreement with several previous observations and models that suggest support of the posterior lens surface during accommodation.