gebhart/patrepeval huggingface dataset:
Development of an indirect immunofluorescence assay for PCV3 antibody detection based on capsid protein (2021)

Abstract Porcine circovirus type 3 (PCV3) is a novel porcine circovirus associated with porcine dermatitis and nephritis syndrome (PDNS), reproductive failure, and multisystemic inflammation. Capsid protein (Cap) encoded by PCV3 ORF2 gene has been identified as an immunogenic protein. Currently, there is no immunofluorescence assay (IFA) available for serological diagnosis. Here, the N-terminal 33 amino acids of Cap protein were predicted to serve as a PCV3 nuclear localization signal (NLS). Two types of recombinant plasmids were constructed for recombinant protein expression in Sf9 cells by using a baculovirus expression system: plasmid rvBac-Pc for full-length Cap protein expression and rvBac-Sc for Cap protein expression with a honeybee melittin signal peptide in place of the predicted NLS sequence. Expression of the nuclear localization sequences was further analyzed by IFA. Strong and specific fluorescence signals were observed in the nucleus of rvBac-Pc-transfected cells and in the cytoplasm of rvBac-Sc-transfected cells. No cross-reactivity was observed with porcine circovirus type 2, porcine pseudorabies virus, classical swine fever virus, or porcine reproductive and respiratory syndrome virus. In summary, we developed two fluorescence detection modes for Cap protein that can be used to detect PCV3 antibodies. This method is suitable for the diagnosis and epidemiological investigation of PCV3. This study provides a reliable detection method for monitoring PCV3 antibody level in pigs in the future.
Increase of bulk optical damage threshold fluences of KDP crystals by laser irradiation and heat treatment (1982)

The bulk optical damage threshold fluence of potassium dihydrogen phosphate (KDP) crystals is increased by irradiating the crystals with laser pulses of duration 1 to 20 nanoseconds of increasing fluence, below the optical damage threshold fluence for untreated crystals, or by baking the crystals for times of the order of 24 hours at temperatures of 110 to 165/sup 0/C, or by a combination of laser irradiation and baking.
Alternative Fuels for Transportation: PowerPoint Presentation (2003)

Introduction Near term alternatives Alcohol as Fuel Biodiesel Hybrid Cars Long term alternatives Hydrogen Electricity generation Tidal Power Solar Power Conclusion
Notice of Removal: Assessment of left bundle branch related strain dyssynchrony: A comparison with tagged MRI (2017)

Removed.
Autogenous Regulation of Gene Expression (1974)

A new term, autogenous regulation, is used to describe a phenomenon that is not a new discovery but rather is newly appreciated as a mechanism common to a number of systems in both prokaryotic and eukaryotic organisms. In this mechanism the product of a structural gene regulates expression of the operon in which that structural gene resides. In many (perhaps all) cases, the regulatory gene product has several functions, since it may act not only as a regulatory protein but also as an enzyme, structural protein, or antibody, for example. In a few cases, this protein is the multimeric allosteric enzyme that catalyzes the first step of a metabolic pathway, gearing together the two most important mechanisms for controlling the biosynthesis of metabolites in bacterial cells-feedback inhibition and repression. Autogenous regulation may provide a mechanism for amplification of gene expression (84); for severe and prolonged inactivation of gene expression (85); for buffering the response of structural genes to changes in the environment (45, 52); and for maintaining a constant intracellular concentration of a protein, independent of cell size or growth rate (86). Thus, autogenous regulation provides the cell with means for accomplishing a number of different regulatory tasks, each suited to better satisfying the needs of the organism for its survival.
Structure of a conjugative element in Streptococcus pneumoniae (1986)

We have cloned and mapped a 69-kilobase (kb) region of the chromosome of Streptococcus pneumoniae DP1322, which carries the conjugative omega (cat-tet) insertion from S. pneumoniae BM6001. This element proved to be 65.5 kb in size. Location of the junctions was facilitated by cloning a preferred target region from the wild-type strain Rx1 recipient genome. This target site was preferred by both the BM6001 element and the cat-erm-tet element from Streptococcus agalactiae B109. Within the BM6001 element cat and tet were separated by 30 kb, and cat was flanked by two copies of a sequence that was also present in the recipient strain Rx1 DNA. Another sequence at least 2.4 kb in size was found inside the BM6001 element and at two places in the Rx1 genome. Its role is unknown. The ends of the BM6001 element appear to be the same as those of the B109 element, both as seen after transfer to S. pneumoniae and as mapped by others in pDP5 after transposition in Streptococcus faecalis. We see no homology between the ends of the BM6001 element and find no evidence suggesting that it ever circularizes.
A large impact crater beneath Hiawatha Glacier in northwest Greenland (2019)

The discovery of a 31-kilometer-wide impact crater in northwest Greenland, beneath up to a kilometer of ice, implies an instantly vaporizing rock that sent shock waves across the Arctic. Its impact must have had a powerful effect on global climate; a thousand-year global cooling event.
A photonic analog-to-digital converter using phase modulation and self-coherent detection with spatial oversampling (2014)

We propose a new type of photonic analog-to-digital converter (ADC), designed for high-resolution (>7 bit) and high sampling rates (scalable to tens of GS/s). It is based on encoding the input analog voltage signal onto the phase of an optical pulse stream originating from a mode-locked laser, and uses spatial oversampling as a means to improve the conversion resolution. This paper describes the concept of spatial oversampling and draws its similarities to the commonly used temporal oversampling. The design and fabrication of a LiNbO(3)/silica hybrid photonic integrated circuit for implementing the spatial oversampling is shown, and its abilities are demonstrated experimentally by digitizing gigahertz signals (frequencies up to 18GHz) at an undersampled rate of 2.56GS/s with a conversion resolution of up to 7.6 effective bits. Oversampling factors of 1-4 are demonstrated.
Frequent loss of heterozygosity and altered expression of the candidate tumor suppressor gene 'FAT' in human astrocytic tumors (2009)

These results point to a role of the FAT in astrocytic tumorigenesis and demonstrate the use of RAPD analysis in identifying specific alterations in astrocytic tumors.
The Luminosity Function of z>4 Quasars from the Second Palomar Sky Survey (1995)

This paper is the second in a series of papers describing the search for z &gt; 4 quasars using the digitized Second Palomar Sky Survey. This is a photographic multicolor search in three bands, JFN, calibrated to Gunn- Thuan gri, over the range 16.5^m^ &lt; r &lt; 19.6^m^. In the first paper, the search techniques were described and the discovery of our first six quasars (five previously unknown) was reported. Here we report the discovery of four additional new quasars, and present coordinates, finding charts, and spectra for these objects. In addition, we describe our adopted candidate selection procedures developed in light of our initial discoveries. The selection criteria have been applied objectively to our data sets, allowing us to estimate our survey completeness through Monte Carlo simulations, and calculate quasar space densities at high redshift. So far, we have covered 27 plate fields, for an effective area of 681 deg^2^. Follow-up spectroscopy is complete for large portions of the color-color space. At our median redshift of z = 4.35, we find that quasar space densities are down by a factor of 7 from z 2.0, and we see no evidence for luminosity dependent density evolution from z = 2 to z =4. We discuss how these findings compare to other surveys for quasars at high redshift.
The DNA replication protein PriA and the recombination protein RecG bind D-loops (1997)

The PriA protein of Escherichia coli provides a vital link between recombination and DNA replication. To establish the molecular basis for this link, we investigated the ability of PriA to target DNA substrates modelled on D-loops, the intermediates formed during the early stages of RecA-mediated recombination. We show that PriA binds D-loops and unwinds the DNA in reactions that rely on its ability to function as a helicase. The minimal structure that binds PriA is a duplex DNA molecule with unpaired single strands at one end, an arrangement likely to occur at a D-loop. It resembles features of the stem-loop formed by primosome assembly site (PAS) sequences in the DNA of bacteriophage phiX174 and plasmid ColE1, and which enable PriA to assemble active primosomes for the initiation of lagging strand synthesis. We suggest that PAS sequences may have evolved to mimic the natural D-loop target for PriA formed in the chromosome of E. coli during recombination and DNA repair. Genetic studies have revealed an interaction between PriA and RecG, a DNA helicase that drives branch migration of recombination intermediates. We therefore compared PriA and RecG for their ability to bind and unwind DNA. RecG, like PriA, binds D-loops and unwinds the DNA. However, it prefers branched structures with at least two duplex components. The possibility that it competes with PriA for binding recombination intermediates is discussed.
Multiclass Weighted Loss for Instance Segmentation of Cluttered Cells (2018)

We propose a new multiclass weighted loss function for instance segmentation of cluttered cells. We are primarily motivated by the need of developmental biologists to quantify and model the behavior of blood T -cells which might help us in understanding their regulation mechanisms and ultimately help researchers in their quest for developing an effective immunotherapy cancer treatment. Segmenting individual touching cells in cluttered regions is challenging as the feature distribution on shared borders and cell foreground are similar thus difficulting discriminating pixels into proper classes. We present two novel weight maps applied to the weighted cross entropy loss function which take into account both class imbalance and cell geometry. Binary ground truth training data is augmented so the learning model can handle not only foreground and background but also a third touching class. This framework allows training using U - N et. Experiments with our formulations have shown superior results when compared to other similar schemes, outperforming binary class models with significant improvement of boundary adequacy and instance detection. We validate our results on manually annotated microscope images of T-cells.
Crystallization of a large single crystal of a B-DNA decamer for a neutron diffraction experiment by the phase-diagram technique (2001)

Crystallization of a large single crystal of a B-DNA decamer, d(CCATTAATGG), for a neutron-diffraction experiment has been accomplished by an analysis of its solubility phase diagram and a large single crystal was successfully crystallized at around the minimum solubility point of the oligonucleotide: 30%(v/v) MPD, 100 mM MgCl(2) pD 6.6 using 0.4 ml D(2)O solutions of the DNA (sample concentration 1.5 mM). It is confirmed that the resulting crystal (dimensions: 1.7 x 1.3 x 0.6 mm) diffracts sufficiently well for neutron data collection.
Maintaining a focus on user requirements throughout the development of clinical workstation software (1997)

Article Free Access Share on Maintaining a focus on user requirements throughout the development of clinical workstation software Authors: Janette M. Coble Washington Univ. School of Medicine, Box 8005, 660 S. Euclid, St. Louis, MO Washington Univ. School of Medicine, Box 8005, 660 S. Euclid, St. Louis, MOView Profile , John Karat IBM T. J. Watson Research, 30 Saw Mill River Road, Hawthorne, NY IBM T. J. Watson Research, 30 Saw Mill River Road, Hawthorne, NYView Profile , Michael G. Kahn Washington Univ. School of Medicine, Box 8005, 660 S. Euclid, St. Louis, MO Washington Univ. School of Medicine, Box 8005, 660 S. Euclid, St. Louis, MOView Profile Authors Info & Claims CHI '97: Proceedings of the ACM SIGCHI Conference on Human factors in computing systemsMarch 1997 Pages 170–177https://doi.org/10.1145/258549.258698Published:27 March 1997Publication History 27citation1,256DownloadsMetricsTotal Citations27Total Downloads1,256Last 12 Months44Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
A 2.4GHz 0.18μm CMOS self-biased cascode power amplifier with 23dBm output power (2005)

A two-stage self-biased cascode power amplifier in 0.18 /spl mu/m CMOS process for Class 1 Bluetooth application provides 23 dBm output power with 31 dB gain and 42% PAE at 2.4 GHz. The power amplifier die occupies 0.46 mm/sup 2/.
Kidney‐in‐a‐lymph node: A novel organogenesis assay to model human renal development and test nephron progenitor cell fates (2019)

Stem cell-derived organoids are emerging as sophisticated models for studying development and disease and as potential sources for developing organ substitutes. Unfortunately, although organoids containing renal structures have been generated from mouse and human pluripotent stem cells, there are still critical unanswered questions that are difficult to attain via in vitro systems, including whether these nonvascularized organoids have a stable and physiologically relevant phenotype or whether a suitable transplantation site for long-term in vivo studies can be identified. Even orthotopic engraftment of organoid cultures in the adult does not provide an environment conducive to vascularization and functional differentiation. Previously, we showed that the lymph node offers an alternative transplantation site where mouse metanephroi can differentiate into mature renal structures with excretory, homeostatic, and endocrine functions. Here, we show that the lymph node lends itself well as a niche to also grow human primary kidney rudiments and can additionally be viewed as a platform to interrogate emerging renal organoid cultures. Our study has a wide-ranging impact for tissue engineering approaches to rebuild functional tissues in vivo including-but not limited to-the kidney.
Single base mutation in the type III procollagen gene that converts the codon for glycine 883 to aspartate in a mild variant of Ehlers-Danlos syndrome IV (1989)

Experiments were carried out to test the hypothesis that a 19-year-old proband with a mild variant of Ehlers-Danlos syndrome type IV had a mutation in the gene for type III procollagen. cDNA and genomic DNA were analyzed by using the polymerase chain reaction and cloning of the products into M13 filamentous phage. A mutation was found that converted the codon for glycine 883 of the triple-helical domain in one allele for type III procollagen to a codon for aspartate. The polymerase chain reaction introduced a few artifactual single base substitutions. Also, it was difficult to distinguish copies from the two alleles in many of the M13 clones. Therefore, several different strategies and analyses of about 50,000 nucleotide sequences in a series of clones were used to demonstrate that the mutation in the codon for glycine 883 was the only mutation in coding sequences for the triple-helical domain of type III procollagen that could have contributed to the phenotype. The same mutation in the codon for glycine 883 in one allele for type III procollagen was found in the proband's 52-year-old father who also had a mild variant of Ehlers-Danlos syndrome type IV. The type III procollagen synthesized by the proband's fibroblasts was analyzed by polyacrylamide gel electrophoresis. Less type III procollagen was secreted by the proband's fibroblasts than by control fibroblasts. Also, the thermal stability of the type III procollagen synthesized by the proband's fibroblasts was lower than the thermal stability of normal type III procollagen as assayed by brief protease digestion. The results, therefore, demonstrated that the single base mutation that converted the codon of glycine 883 to a codon for aspartate destabilized the entire triple helix of type III procollagen and probably accounted for the mild phenotype of Ehlers-Danlos syndrome type IV seen in the proband and her father.
ZONAL CENTRIFUGATION OF SOLUBLE IMMUNE COMPLEXES (1971)

In an attempt to determine the distribution of soluble complexes formed when 131 I‐labelled HSA reacts with fluorescein labelled anti‐HSA we have used zonal centrifugation in A sucrose gradient combined with a subsequent analysis of the cuts by radioactivity, fluorescence and polarization of fluorescence measurements. The method is both reproducible and sensitive, and has a potential advantage over other methods for separating soluble complexes in that the sedimentation coefficients as well as antibody ratio of the complexes can be determined on microgram quantities of sample. Using this method, we have been able to follow the dissociation of antigen‐antibody complexes with time, and to demonstrate the building up of large numbers of complexes at the equivalence zone. Full technical details of the method are given, together with suggestions for further improvements.
Random walk in the three-body problem and applications (2008)

The process of random walk is described, in general, and how it can be applied in the three-body problem in a systematic manner. Several applications are considered. The main one which is a focus of this paper is on the evolution of horseshoe orbits and their transition to breakout motion in the restricted three-body problem. This connection is related to their use for an Earth-impactor in a theory on the formation of the Moon. We briefly discuss another application on the instability of asteroid orbits.
Dynamic Fingerprinting Combination for Improved Mobile Localization (2011)

This paper proposes a dynamic fingerprinting combination (DFC) algorithm that improves mobile localization by dynamically weighting the spatial correlation from multiple location fingerprinting systems. This DFC algorithm first extracts the complementary advantages of fingerprinting functions to construct a fusion profile, and then dynamically combines individual outputs based on the fusion profile surrounding the test sample. The proposed algorithm generates more accurate location estimates and reduces the risk of selecting a poorly-performing fingerprinting approach. This study applies DFC to an actual GSM network with realistic measurements. Experimental results show that DFC improves the positioning accuracy of base fingerprinting algorithms, including the Bayesian approach and a neural network model.
Broadband optical absorbance spectroscopy using a whispering gallery mode microsphere resonator (2008)

We demonstrate the ability to excite and monitor many whispering gallery modes (WGMs) of a microsphere resonator simultaneously in order to make broadband optical absorbance measurements. The 340 microm diameter microsphere is placed in a microfluidic channel. A hemispherical prism is used for coupling the WGMs into and out of the microsphere. The flat surface of the prism seals the microfluidic channel. The slight nonsphericity in the microsphere results in coupling to precessed modes whose emission is spatially separated from the reflected excitation light. The evanescent fields of the light trapped in WGMs interact with the surrounding environment. The change in transmission observed in the precessed modes is used to determine the absorbance of the surrounding environment. In contrast to our broadband optical absorbance measurements, previous WGM sensors have used only a single narrow mode to measure properties such as refractive index. With the microfluidic cell, we have measured the absorbance of solutions of dyes (lissamine green B, sunset yellow, orange G, and methylene blue), aromatic molecules (benzylamine and benzoic acid), and biological molecules (tryptophan, phenylalanine, tyrosine, and o-phospho-L-tyrosine) at visible and ultraviolet wavelengths. The microsphere surface was reacted with organosilane molecules to attach octadecyl groups, amino groups, and fluorogroups to the surface. Both electrostatic and hydrophobic interactions were observed between the analytes and the microsphere surface, as indicated by changes in the measured effective pathlength with different organosilanes. For a given analyte and coated microsphere, the pathlength measurement was repeatable within a few percent. Methylene blue dye had a very strong interaction with the surface and pathlengths of several centimeters were measured. Choosing an appropriate surface coating to interact with a specific analyte should result in the highest sensitivity detection.
The Effects Of Trivalent Arsenicals And Thioredoxin Reductase Inhibitors On Selenium Metabolism In Lung Cell Culture Models (2007)

Arsenic exposure, through various routes, is associated with the development of cancer of the skin, lung, liver, kidney, and bladder. Treatment of cells in culture with trivalent arsenicals has been shown to increase reactive oxygen species (ROS). In particular, monomethylarsonous acid (MMAIII), a trivalent metabolite of arsenite, is highly cytotoxic and possibly carcinogenic. Three trivalent arsenicals; arsenite, arsenic trioxide (ATO), and MMAIII, are also known inhibitors of the selenoprotein thioredoxin reductase (TrxR). Selenium, an essential micronutrient in mammals, is needed in the form of selenocysteine for activity of this enzyme and other selenoproteins. TrxR is part of a key component of the cell's ability to defend against ROS. It has been speculated that TrxR is also involved directly in selenium metabolism, but this has yet to be demonstrated in vivo. The promoter region of the gene encoding the cytosolic TrxR (TrxR1) also contains an antioxidant responsive element (ARE). The ARE is activated by the transcription factor, Nrf2, which is governed by the Nrf2/Keap1 response, and can be triggered by certain oxidants. ATO and arsenite both inhibited incorporation of selenium into selenoproteins. Auranofin, a gold chemotherapeutic inhibitor of TrxR1, also inhibited selenoprotein synthesis. These results seem to support the hypothesis that TrxR1 is needed for selenoprotein synthesis. However, siRNA mediated reduction of TrxR1 did not block incorporation of selenium into selenoproteins. It is likely that ATO and auranofin are forming As-Se and Au-Se complexes, respectively. We also found that exposure of primary lung fibroblasts (WI-38) to MMAIII led to increased synthesis of TrxR1. This increase was dependent on the activation of transcription of the TrxR1 gene, specifically mediated through the ARE element. These results indicate exposure to MMAIII induces the Nrf2 response. The results obtained in these studies aid in both our understanding of the carcinogenic potential of arsenic as well as give new insight into the mechanism of action of emerging cancer drugs.