gebhart/patrepeval huggingface dataset:
Intrahost Selection Pressure Drives Equine Arteritis Virus Evolution during Persistent Infection in the Stallion Reproductive Tract (2019)

Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a reproductive and respiratory disease of horses. Following natural infection, 10 to 70% of infected stallions can become carriers of EAV and continue to shed virus in the semen. In this study, sequential viruses isolated from nasal secretions, buffy coat cells, and semen of seven experimentally infected and two naturally infected EAV carrier stallions were deep sequenced to elucidate the intrahost microevolutionary process after a single transmission event. Analysis of variants from nasal secretions and buffy coat cells lacked extensive positive selection; however, characteristics of the mutant spectra were different in the two sample types. In contrast, the initial semen virus populations during acute infection have undergone a selective bottleneck, as reflected by the reduction in population size and diversifying selection at multiple sites in the viral genome. Furthermore, during persistent infection, extensive genome-wide purifying selection shaped variant diversity in the stallion reproductive tract. Overall, the nonstochastic nature of EAV evolution during persistent infection was driven by active intrahost selection pressure. Among the open reading frames within the viral genome, ORF3, ORF5, and the nsp2-coding region of ORF1a accumulated the majority of nucleotide substitutions during persistence, with ORF3 and ORF5 having the highest intrahost evolutionary rates. The findings presented here provide a novel insight into the evolutionary mechanisms of EAV and identified critical regions of the viral genome likely associated with the establishment and maintenance of persistent infection in the stallion reproductive tract.<b>IMPORTANCE</b> EAV can persist in the reproductive tract of infected stallions, and consequently, long-term carrier stallions constitute its sole natural reservoir. Previous studies demonstrated that the ampullae of the vas deferens are the primary site of viral persistence in the stallion reproductive tract and the persistence is associated with a significant inflammatory response that is unable to clear the infection. This is the first study that describes EAV full-length genomic evolution during acute and long-term persistent infection in the stallion reproductive tract using next-generation sequencing and contemporary sequence analysis techniques. The data provide novel insight into the intrahost evolution of EAV during acute and persistent infection and demonstrate that persistent infection is characterized by extensive genome-wide purifying selection and a nonstochastic evolutionary pattern mediated by intrahost selective pressure, with important nucleotide substitutions occurring in ORF1a (region encoding nsp2), ORF3, and ORF5.
Electrochemical Tuning of Silver Nanoparticles Fabricated by Nanosphere Lithography (2005)

An electrochemical method is developed to quantitatively modify and spectroscopically monitor the size and shape of Ag nanotriangles fabricated by nanosphere lithography (NSL) on an indium tin oxide (ITO) electrode surface. AFM and SEM results demonstrate that the preferential order of electrochemical oxidation for a nanotriangle is, surprisingly, bottom edges first, then triangular tips, then out-of-plane height.
Modeling and Multi‐Objective Optimization of a Chromatographic System (2013)

Chromatography is a separation technique that plays a crucial role in the downstream of several pharmaceutical and fine-chemical industries. The annual turnover of such industries can be several billions of dollars, but they typically have low material output compared to the bulk chemical processes. The chromatographic units in these industries handle gram to kilogram scale of very high-value products per day and are sometimes employed to process different kinds of products over the year. So, unlike the processes of bulk chemicals, chromatographic processes in the pharmaceutical or fine-chemical industries may be required to be redesigned after a period of time, depending on the changes in the product lines or other requirements. Current industrial practice mostly relies on empirical methods to develop the operating conditions; but, given the high cost of the products, there is a huge incentive to apply model-based multi-objective optimization studies to improve the performance of such processes. While the utility of model-based studies is certainly appreciated in the industrial research labs, unavailability of appropriate tools and related knowhow limit their use. The main objective of the current chapter is to describe the development of a model-based optimization program and to demonstrate ways of conducting optimization studies with this model. The specific example chosen for this chapter is the separation of enantiomers in batch processes. There is a strong requirement in industry for quicker separation of enantiomers. In the pharmaceutical and allied industries, especially, a huge variety of intermediates and active pharmaceutical ingredients (APIs), at each stage of drug trial, need to be separated quickly for businesses to stay competitive. A quicker separation method, however, needs to sacrifice product recovery, as the sample mixture may not have enough time to separate entirely. As one must also ensure higher recovery along with speed, the situation leads to a perfect example of multi-objective optimization, having conflicting objectives. The chapter provides the basic understanding of developing a model to simulate such a system, formulate the objective functions, identify the constraints and the most useful decision variables, and finally, with the help of a genetic algorithm, determine the Pareto optimal solutions.
Laser interaction and related plasma phenomena (1998)

Report on the Thirteenth International Conference held at the Naval Postgraduate School, Monterey, California, United States of America, 13-18 April 1997.
Designing tailored free-form surfaces for general illumination (2003)

3-D tailoring is a constructive method for the design of free-form optical elements for illumination. The light of a point source is redirected in a controlled manner to cast a prescribed irradiation pattern on a target surface. Free parameters can be used to control the shape of the surface resulting from the tailoring process. Every change in the parameters may lead to an entirely different design. Hence the choice of parameters is crucial for the technical feasibility and the visual appearance of the luminaire. Examples of free parameters are the chosen caustics, trimming of the surface, the choice between mirror and lens optics, and the mutual orientation of source and optical elements.
Trade-off Between Computational Power and Common Knowledge in Anonymous Rings* (1995)

We give an exact characterization of the My of functions that can be computed distributively in an anonymous ring, diversifying the type of knowledge of the processors about the inpat configuration I, where I is the sequence of processor labels, |I| = n. We consider two kinds of knowledge, namely an upper-bound M on n model RM), and the exact number V of distinct labels in I (model RV). Moreover we prove that such fo11ctios can be computed on the asynchronous RM (RV) exchanging O(nM) (O(n min {log n, V})) messages. We show that the general protocol used to attain the above results cannot be improved with respect to the message complexity, since there are functions requiring Ω(nM) (Ω(n min (log n, V})) messages, respectively. Furthermore, we investigate the problem of electing a leader in RM and RV using randomization.
Novel fluorinated antifolates. Enzyme inhibition and cytotoxicity studies on 2'- and 3'-fluoroaminopterin (1983)

Two novel analogues of aminopterin with a single fluorine substitution in the 2' (compound 8) or in the 3' (compound 9) position of the p-aminobenzoyl group were synthesized and evaluated as inhibitors of dihydrofolate reductase from two bacterial species and from human HeLa cells. The 2'-fluoro compound was bound essentially the same as aminopterin itself, while the 3'-fluoro derivative bound two- to threefold more tightly in all cases. UV spectral shifts indicated normal binding of the pteridine. Cytotoxicity studies against mouse leukemia L1210 cells and the human stomach cancer line HuTu80 indicated equivalent toxicity of the parent drug with the 2'-fluoro analogue. 3'-Fluoroaminopterin was, however, twice as toxic as aminopterin to both cell lines.
Strategic Timing of Glial HMOX1 Expression Results in Either Schizophrenia-Like or Parkinsonian Behavior in Mice (2019)

<b><i>Aims:</i></b> In this original research communication, we assess the impact of shifting the window of glial <i>HMOX1</i> overexpression in mice from early-to-midlife to mid-to-late life, resulting in two disparate conditions modeling schizophrenia (SCZ) and Parkinson's disease (PD). Mesolimbic hyperdopaminergia is a widely accepted feature of SCZ, while nigrostriatal hypodopaminergia is the <i>sine qua non</i> of idiopathic PD. Although the advent of parkinsonian features in SCZ patients after treatment with antidopaminergic agents is intuitive, subtle features of parkinsonism commonly observed in young, drug-naïve schizophrenics are not. Similarly, emergent psychosis in PD subjects receiving levodopa replacement is not unusual, whereas spontaneous hallucinosis in nonmedicated persons with idiopathic PD is enigmatic. Investigations using GFAP.HMOX1 mice may shed light on these clinical paradoxes. <b><i>Results:</i></b> Astroglial heme oxygenase-1 (HO-1) overexpression in mice throughout embryogenesis until 6 or 12 months of age resulted in hyperdopaminergia, hyperkinesia/stereotypy ameliorated with clozapine, deficient prepulse inhibition of the acoustic startle response, reduced preference for social novelty, impaired nest building, and cognitive dysfunction reminiscent of SCZ. On the contrary, astroglial HO-1 overexpression between 8.5 and 19 months of age yielded a PD-like behavioral phenotype with hypodopaminergia, altered gait, locomotor incoordination, and reduced olfaction. <b><i>Innovation:</i></b> We conjecture that region-specific disparities in the susceptibility of dopaminergic and other circuitry to the trophic and degenerative influences of glial <i>HMOX1</i> induction may permit the concomitant expression of mixed SCZ and PD traits within affected individuals. <b><i>Conclusion:</i></b> Elucidation of these converging mechanisms may (i) help better understand disease pathogenesis and (ii) identify HO-1 as a potential therapeutic target in neurodevelopmental and neurodegenerative disorders.
Design of compact size excitation device for antenna pattern using fractal architectures (2005)

RF wireless systems are gaining in interest for many applications like communication, identification and localization. The objective of this communication is to address the design of a quite versatile antenna in terms of isotropy and size. The basic idea behind this work is the association of simple antenna elements and their integration into the same substrate. The studied antenna is composed of three /spl lambda//2 dipoles printed on a substrate. The spatial position of the dipoles and the excitation signals will influence strongly the radiation pattern. So, dipole positions and excitation signals are the two key elements to the design procedure.
Pan I Version 4.0: An Introduction For Users (1991)

Pan is a prototype and testbed for language-based editors and views. Its design addresses the needs of experienced users who manage complex objects such as large software systems. Al of Pan''s components are multilingual, incremental, description-driven, customizable, and extensible. Viewing is facilitated by semantics-based browsing and an object model that integrates text and structure. Pan is intended to share information with other tools, allowing integration into a larger language, program, and document development environment. This document, a users manual, describes the basic operational facilities of Pan I (version 4.0), the current implementation. It explains the concepts behind Pan''s editing environment, introduces editing commands, and discusses techniques for customization. Appendices list command bindings (to both keystrokes and menus), view options, and view flags.
Homing in on the rare virosphere reveals the native host of giant viruses (2023)

Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems<sup>1,2</sup>. They play major roles as evolutionary drivers of eukaryotic plankton<sup>3</sup> and regulators of global biogeochemical cycles<sup>4</sup>. Recent metagenomic studies have significantly expanded the known diversity of marine giant viruses<sup>1,5-7</sup>, but we still lack fundamental knowledge about their native hosts, thereby hindering our understanding of their lifecycle and ecological importance. Here, we aim to discover the native hosts of giant viruses using a novel, sensitive single-cell metatranscriptomic approach. By applying this approach to natural plankton communities, we unraveled an active viral infection of several giant viruses, from multiple lineages, and identified their native hosts. We identify a rare lineage of giant virus (Imitervirales-07) infecting a minute population of protists (class Katablepharidaceae) and revealed the prevalence of highly expressed viral-encoded cell-fate regulation genes in infected cells. Further examination of this host-virus dynamics in a temporal resolution suggested this giant virus controls its host population demise. Our results demonstrate how single-cell metatranscriptomics is a sensitive approach for pairing viruses with their authentic hosts and studying their ecological significance in a culture-independent manner in the marine environment.
Dysuria Following Stereotactic Body Radiation Therapy for Prostate Cancer (2015)

The rate and severity of dysuria following SBRT is comparable to patients treated with other radiation modalities.
Shear flow behavior of a dynamically symmetric polymeric bicontinuous microemulsion (2007)

We have investigated the shear flow behavior of a dynamically symmetric polymeric bicontinuous microemulsion using rheology and in situ small angle x-ray scattering. The microemulsion consists of a ternary blend of poly (ethylene-alt-propylene) (PEP), poly (butylene oxide) (PBO), and a PEP-PBO diblock copolymer. Steady shear experiments reveal an unusual shear thickening behavior at the onset of the non-Newtonian regime, which is consistent with the strain hardening and frequency thickening (at large strains) under oscillatory shear. Scattering experiments indicate development of anisotropy in the bicontinuous structure within the thickening regime. Subsequent shear thinning is observed at intermediate shear rates. Shear-induced bulk phase separation is detected at very high rates. This work complements previous studies on a dynamically extremely asymmetric bicontinuous microemulsion, and thereby establishes the universal rheological properties of polymeric microemulsions. Possible underlying molecular mechanisms for these rich rheological phenomena are discussed.
Fluidic Integration of Nanophotonic Devices Using Decomposable Polymers (2015)

Polynorbornene-based decomposable polymer which can be patterned with ultraviolet or electron-beam radiation is used to create micrometer-scale fluidic channels. Silicon nitride substrates are used to fabricate nanophotonic wavegide and resonators operating in the visible range of the spectrum. Fluidic channels generated by thermally decomposing the polymer through the oxide cladding is used to deliver ultra-small amounts of florescent samples to the optical sensors.
Luminescent concentrators enable highly efficient and broadband photodetection (2022)

With luminescent concentrators, the high quantum yield luminescence emitted by embedded chromophores, featuring a broad absorption spectrum, can be well-tuned to match the peak response of integrated photodetectors. This integration can substantially enhance the device photoresponse all the way from deep UV to near-IR.
Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia (2017)

Intra-tumoral genetic heterogeneity has been characterized across cancers by genome sequencing of bulk tumors, including chronic lymphocytic leukemia (CLL). In order to more accurately identify subclones, define phylogenetic relationships, and probe genotype-phenotype relationships, we developed methods for targeted mutation detection in DNA and RNA isolated from thousands of single cells from five CLL samples. By clearly resolving phylogenic relationships, we uncovered mutated <i>LCP1</i> and <i>WNK1</i> as novel CLL drivers, supported by functional evidence demonstrating their impact on CLL pathways. Integrative analysis of somatic mutations with transcriptional states prompts the idea that convergent evolution generates phenotypically similar cells in distinct genetic branches, thus creating a cohesive expression profile in each CLL sample despite the presence of genetic heterogeneity. Our study highlights the potential for single-cell RNA-based targeted analysis to sensitively determine transcriptional and mutational profiles of individual cancer cells, leading to increased understanding of driving events in malignancy.
2-D approach for reconstruction in electrical impedance tomography (2002)

A new reconstruction algorithm for Electrical Impedance Tomography (EIT) and the results of the reconstruction using 2D EIT system are presented. The analysis of the images of the physical and mathematical phantoms allowed conclusions to be made about spatial and contrast resolution in EIT. The successful imaging of the explanted canine heart makes an optimistic prognosis about utilization of this technology and proposed reconstruction algorithm in medicine.
Supplementary Figure 1 from Plasminogen Kringle 5 Induces Apoptosis of Brain Microvessel Endothelial Cells: Sensitization by Radiation and Requirement for GRP78 and LRP1 (2023)

Supplementary Figure 1 from Plasminogen Kringle 5 Induces Apoptosis of Brain Microvessel Endothelial Cells: Sensitization by Radiation and Requirement for GRP78 and LRP1
Novel Low-temperature Solid-carburizing Using C60 Fullerene for Austenitic Stainless Steel SUS316L (2012)

In this study, the full potential of C60 fullerene for use in the low-temperature solid-carburizing of SUS316L stainless steel is demonstrated. The carburizing of this austenitic stainless steel with C60 was conducted in a vacuum atmosphere without any surface activation treatment of the specimen surfaces. The uncarburized SUS316L had the lattice parameter of approx. 3.5963 ± 0.0001 Å and the Vickers hardness of 172 MPa measured by the Nanoindentation method. After carburizing at 475°C for 200 h, the lattice parameter of the specimen surface was approx. 3.6545 ± 0.0001 Å and the Vickers hardness was approx. 742 MPa. After carburizing at 500°C for 100 h, the lattice parameter of the specimen surface was approx. 3.6592 ± 0.0002 Å and the Vickers hardness was approx. 837 MPa. These results are comparable to those obtained by low-temperature gas- and plasma-carburizing reported in previous works.
The fabrication of particulate composite by in situ oxidation process. (1992)

A new technique for making particulate composites has been investigated. Unstable oxides such as CuO, SnO2 ZnO and Cr2O3 whose absolute value of standard free energy of formation is smaller than that of Al2O3 were added to moleton aluminum and Al-3.0%Mg alloy. Al2O3 particles are formed in Al-Cu matrix by adding CuO to moleton aluminum at 1273K. Furthermore, by adding CuO the moleton Al-3.0%Mg alloy, MgAl2O4 (spinel) particles are
Editorial: Energy and Environmental Optics Express—an expanded publication venue for Optics Express (2019)

Editor-in-Chief James Leger announces that the Energy Express section of Optics Express is being expanded to include environmental optics, and introduces its newest Deputy Editor Svetlana Boriskina.
Excited-state properties of dioxorhenium(V). Generation and reactivity of dioxorhenium(VI) (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExcited-state properties of dioxorhenium(V). Generation and reactivity of dioxorhenium(VI)H. Holden Thorp, J. Van Houten, and Harry B. GrayCite this: Inorg. Chem. 1989, 28, 5, 889–892Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/ic00304a017https://doi.org/10.1021/ic00304a017research-articleACS PublicationsRequest reuse permissionsArticle Views236Altmetric-Citations48LEARN 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
The Rps23rg gene family originated through retroposition of the ribosomal protein s23 mRNA and encodes proteins that decrease Alzheimer's -amyloid level and tau phosphorylation (2010)

Retroposition is an important mechanism for gene origination. However, studies to elucidate the functions of new genes originated through retroposition, especially the functions related to diseases, are limited. We recently identified a mouse gene, Rps23 retroposed gene 1 (Rps23rg1), that regulates beta-amyloid (Abeta) level and tau phosphorylation, two major pathological hallmarks of Alzheimer's disease (AD), and found that Rps23rg1 originated through retroposition of the mouse ribosomal protein S23 (Rps23) mRNA. Here we show that retroposition of Rps23 mRNA occurred multiple times in different species but only generated another functionally expressed Rps23rg1-homologous gene, Rps23rg2, in mice, whereas humans may not possess functional Rps23rg homologs. Both Rps23rg1 and Rps23rg2 are reversely transcribed relative to the parental Rps23 gene, expressed in various tissues and encode proteins that interact with adenylate cyclases. Similar to the RPS23RG1 protein, RPS23RG2 can upregulate protein kinase A activity to reduce the activity of glycogen synthase kinase-3, Abeta level and tau phosphorylation. However, the effects of RPS23RG2 are weaker than those of RPS23RG1 and such a difference could be attributed to the extra carboxyl-terminal region of RPS23RG2, which may have an inhibitory effect. In addition, we show that the transmembrane domain of RPS23RG1 is important for its function. Together, our results present a new gene family, whose products and associated signaling pathways might prevent mice from developing AD-like pathologies.
Design of a Class EF2 Power Oscillator for RF Communication Application (2013)

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