gebhart/patrepeval huggingface dataset:
West Nile Virus Detection in American Crows (2003)

A dipstick immunochromatographic assay used for West Nile virus (WNV) detection in mosquitoes was investigated for application to testing of fecal, saliva, and tissue samples from dead American Crows (Corvus brachyrhynchos). Results suggest that VecTest may be an efficient method for WNV detection in field-collected, dead American Crows, although confirmation of results and further investigation are warranted.
Effects of strong electric fields on resonant structures in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msup><mml:mrow><mml:mi mathvariant="normal">H</mml:mi></mml:mrow><mml:mrow><mml:mo>−</mml:mo></mml:mrow></mml:msup></mml:mrow></mml:math>photodetachment (1983)

Relativistic kinematics with an 800-MeV ${\mathrm{H}}^{\ensuremath{-}}$ beam at the Clinton P. Anderson Meson Physics Facility (LAMPF) at Los Alamos allows the observation, with very little background, of resonant structures in the photodetachment spectrum of ${\mathrm{H}}^{\ensuremath{-}}$ in intense electric fields. We report studies of the $^{1}P$ resonances near $n=2$ in ${\mathrm{H}}^{\ensuremath{-}}$ in electric fields as high as 1.3 MV/cm. The splitting of the $^{1}P$ Feshbach resonance can be explained by Stark mixing with a nearly degenerate $^{1}S$ resonance. For field values above those required to quench the Feshbach resonances a $^{1}D$ state is observed, apparently induced by Stark mixing with the $^{1}P$ shape resonance. The systematics of the behavior of these resonances are compared with the results of a simple perturbation model.
Metformin and the Risk of Cancer (2012)

Although observational studies are important to better understand the effects of drugs, their proper design and analysis is essential to avoid major time-related biases. With respect to metformin, the scientific evidence of its potential beneficial effects on cancer would need to be reassessed critically before embarking on further long and expensive trials.
DEEPFOCAL: A method for direct focal length estimation (2015)

Estimating the focal length of an image is an important preprocessing step for many applications. Despite this, existing methods for single-view focal length estimation are limited in that they require particular geometric calibration objects, such as orthogonal vanishing points, co-planar circles, or a calibration grid, to occur in the field of view. In this work, we explore the application of a deep convolutional neural network, trained on natural images obtained from Internet photo collections, to directly estimate the focal length using only raw pixel intensities as input features. We present quantitative results that demonstrate the ability of our technique to estimate the focal length with comparisons against several baseline methods, including an automatic method which uses orthogonal vanishing points.
Cell-Delivered Entry Inhibitors for HIV-1: <i>CCR5</i> Downregulation and Blocking Virus/Membrane Fusion in Defending the Host Cell Population (2016)

HIV-1 infection requires the presence of the CD4 receptor on the target cell surface and a coreceptor, predominantly CC-chemokine receptor 5 (CCR5). It has been shown that individuals who are homozygous for a defective CCR5 gene are protected from HIV-1 infection. A novel self-inactivating lentiviral vector LVsh5/C46 (Cal-1) has been engineered to block HIV-1 infection with two viral entry inhibitors, conferring resistance to HIV-1 infection from both CCR5 and CXCR4 tropic strains. Cal-1 encodes a short hairpin RNA (sh5) to downregulate CCR5 and C46, an HIV-1 fusion inhibitor. Gene therapy by Cal-1 is aimed at transducing CD4<sup>+</sup> T cells and CD34<sup>+</sup> hematopoietic stem/progenitor cells in an autologous transplant setting. Pre-clinical safety and efficacy studies in vitro and in vivo (humanized mouse model and nonhuman primates) have shown that Cal-1 is safe with no indication of any toxicity risk and acts to decrease viral load and increase CD4 counts. Two clinical trials are underway using Cal-1: a phase I/II study to assess safety and feasibility in an adult HIV-1-positive population not on antiretroviral therapy (ART); and a second Fred Hutchinson Investigator Initiated phase I study to assess safety and feasibility in adults with HIV-1-associated non-Hodgkin or Hodgkin lymphoma.
Spoofing prevention method (2005)

A new approach for filtering spoofed IP packets, called spoofing prevention method (SPM), is proposed. The method enables routers closer to the destination of a packet to verify the authenticity of the source address of the packet. This stands in contrast to standard ingress filtering which is effective mostly at routers next to the source and is ineffective otherwise. In the proposed method a unique temporal key is associated with each ordered pair of source destination networks (AS's, autonomous systems). Each packet leaving a source network S is tagged with the key K(S, D), associated with (S, D), where D is the destination network. Upon arrival at the destination network the key is verified and removed. Thus the method verifies the authenticity of packets carrying the address s which belongs to network S. An efficient implementation of the method, ensuring not to overload the routers, is presented. The major benefits of the method are the strong incentive it provides to network operators to implement it, and the fact that the method lends itself to stepwise deployment, since it benefits networks deploying the method even if it is implemented only on parts of the Internet. These two properties, not shared by alternative approaches, make it an attractive and viable solution to the packet spoofing problem.
Effect of Diluents on the Swelling Force of the Tablet (2011)

The swelling force, especially the swelling force development rate, is a very important parameter in studying the effect of a disintegrant in a tablet. However, a tablet also contains diluents in most cases and the effect of diluents on the swelling force has not been studied. In this study two commonly used diluents, microcrystalline cellulose and calcium phosphate dihydrate, were investigated for their effect on the swelling force with or without a superdisintegrant, Polyplasdone XL. It was found that microcrystalline cellulose alone can develop swelling force depending on the compression force of the tablet. When combined with Polyplasdone XL, it can significantly change the swelling force of Polyplasdone XL. The effect of diluents on the swelling force is not consistent with the disintegration and dissolution studies of the tablet.
Cross-presenting CD103+ dendritic cells are protected from influenza virus infection (2012)

CD8+ cytotoxic T cells are critical for viral clearance from the lungs upon influenza virus infection. The contribution of antigen cross-presentation by DCs to the induction of anti-viral cytotoxic T cells remains controversial. Here, we used a recombinant influenza virus expressing a nonstructural 1-GFP (NS1-GFP) reporter gene to visualize the route of antigen presentation by lung DCs upon viral infection in mice. We found that lung CD103+ DCs were the only subset of cells that carried intact GFP protein to the draining LNs. Strikingly, lung migratory CD103+ DCs were not productively infected by influenza virus and thus were able to induce virus-specific CD8+ T cells through the cross-presentation of antigens from virally infected cells. We also observed that CD103+ DC resistance to infection correlates with an increased anti-viral state in these cells that is dependent on the expression of type I IFN receptor. These results show that efficient cross-priming by migratory lung DCs is coupled to the acquisition of an anti-viral status, which is dependent on the type I IFN signaling pathway.
A Survey of Cloud Detection Techniques For Satellite Images (2015)

The detection of clouds in satellite imagery has a number of important applications in weather and climate studies. Satellite images plays a major role for monitoring earth changes in land covers such as forest, cities, agriculture, coastal area etc. but presence of clouds is a challenging issue in most of the satellite imaging based applications. Accurate detection and removal of cloud region is very important for satellite images. In this paper a review of several cloud detection technique is presented. The major challenge of cloud detection approaches is high misclassification rate of cloud pixels due to lower contrast of cloud edges against the land or sea background. A posteriori probability-Markov random field (MAP-MRF) approach shows improved classification rate of cloud pixels than other cloud detection techniques, which solve high misclassification rate of cloud pixels. To improve the classification rate, two different functional forms are used. The first one is an effective and efficient implementation of the probability hypothesis density (PHD) filter, which is based on Gaussian mixtures (GMs). The second one is a region matching procedure based on a maximum cross-correlation (MCC).
Transseptal Guidewire Stabilization Facilitates Stent-Graft Deployment for Persistent Proximal Ascending Aortic Dissection (2000)

A transseptal approach enables the guidewire to follow the curvature of the aortic arch, providing precise control of the stent-graft delivery system. This case illustrates the applicability of endovascular techniques to repair ascending aortic pathologies using readily available techniques, equipment, and drugs.
Enzymatic Preparation of a<scp>d</scp>-Amino Acid from a Racemic Amino Acid or Keto Acid (2008)

The d-amino acid (R)-2-amino-3-(7-methyl-1 H-indazol-5-yl)propanoic acid (3) is a key intermediate needed for synthesis of a drug candidate compound. Enzymatic routes to 3 were explored. d-Amino acid 3 was prepared in 68% isolated yield with >99% ee from racemic amino acid 1 using l-amino acid deaminase from Proteus mirabilis expressed in Escherichia coli in combination with a commercially available d-transaminase using d-alanine as amino donor. The d-enantiomer was also prepared in 79% isolated yield with >99% ee from the corresponding keto acid 2 using the d-transaminase with racemic alanine as the amino donor. The rate and yield of this reaction could be accelerated by addition of lactate dehydrogenase (with NAD, formate and formate dehydrogenase to regenerate NADH) to remove the inhibitory pyruvate produced during the reaction. A d-transaminase was purified from a soil organism identified as Bacillus thuringiensis and cloned and expressed in E. coli. The d-transaminase was very effective for the preparation of 3 and gave a nearly complete conversion of 2 to 3 without the need for additional enzymes for pyruvate removal.
Inducible and tissue-specific expression of rat <i>alpha</i> -1-acid glycoprotein in transgenic mice. (1990)

alpha-1-Acid glycoprotein (AGP), which is produced in the mammalian liver and secreted into the blood-stream, is regulated by steroid hormones and by mediators of the acute phase response. In vitro transfection studies have shown that the response to glucocorticoids requires a cis-acting regulatory element, termed the glucocorticoid response element, that is located within 120 bp of the transcriptional start-site of the gene; induction by the acute phase mediators requires a different element, termed the distal regulatory element (DRE), that is located about 5 kb upstream of the start-site. To determine if these elements function in vivo, we have produced and characterized transgenic mice containing rat AGP gene constructs with and without the DRE. Five transgenic lines were produced from a 9.5-kb genomic AGP containing 4.7 kb of the 5' flanking region; this construct lacks the DRE. Another transgenic line was derived from a 10.7-kb clone that contains 5.3 kb of 5' flanking sequences including the DRE. All transgenic mice produced high levels of immunologically detectable rat AGP in the circulation, comparable to or in excess of that found in normal rats. There were correspondingly high concentrations of rat AGP transcripts in the liver. Transgene expression in all lines was induced in response to dexamethasone and during acute inflammation resulting from LPS treatment. The DRE-containing transgene underwent a greater induction in response to LPS than to dexamethasone; the transgene lacking the DRE responded similarly to both treatments. In cultured primary hepatocytes, the DRE-containing transgene was induced by the acute phase cytokines IL-1 and IL-6, and by dexamethasone, administered individually or in combination; the transgene lacking the DRE responded only to dexamethasone, and was not affected by the peptide hormones. Together, these results provide in vivo evidence supporting the notion that a minimum of two upstream sequences are responsible for the inflammatory induction of rat AGP. One element, which is located within the smaller 9.7-kb restriction fragment, is responsive to glucocorticoids and is likely to be the glucocorticoid response element located close to the transcriptional start site. The other element, the DRE, is located much further upstream and is responsible for imparting responsiveness to the acute phase cytokines.
The Effect of Methylphenidate and Clonidine on Response Inhibition and State Regulation in Children with ADHD (1999)

The goal of this study was to evaluate the effect of methylphenidate (MPH) and clonidine in comparison with placebo on response inhibition and state regulation in children with Attention Deficit Hyperactivity Disorder (ADHD). The study utilised a double-blind cross-over design in which children were randomly assigned without replacement to placebo, MPH, and clonidine following baseline assessment. The primary dependent measures were derived from children's performance (reaction time and errors) on a GO-NO GO task under three conditions that altered the inter-stimulus interval (ISI) for presented GO-NO GO stimuli: ISI of 1 sec (fast condition), 4 sec (medium condition), and 8 sec (slow condition). Findings indicated no difference in task performance between groups treated for 7 weeks with placebo, MPH, and clonidine. We concluded that the state regulation problem in ADHD is resistant to MPH and clonidine.
Collecting Data From the Criminal Courts (2008)

Because court policies and programs must be evaluated, the relationship between researchers and the staff members overseeing court data is an essential part of the process. Past research indicates that researchers commonly believe that their efforts are hampered by court staff members, who, accordingly, often have suspicions about the agendas of researchers. The present study examines an alternative viewpoint—the perspectives of court staff members who oversee the data requests of researchers. Specifically, 30 county-level and 30 state-level court staff members were interviewed about their relations with researchers in the data collection process, and the strategies they believe researchers can use to make the process more efficient. The authors find that staff members do not view their relations with researchers to be as problematic as the researchers perceive. The authors also discovered that there are several approaches that both sides can use to establish a better data collection process.
Monolayer-thick GaAs-GaSbAs strained layer quantum-well lasers (1991)

Strained layer GaSbAs-GaAs quantum wells have the potential for longer emission wavelengths than InGaAs-GaAs quantum wells even though Eg(GaSb)>Eg(InAs) and the lattice mismatch is worse. Longer wavelength (lower energy) emission is possible because of the large valence band discontinuity. In this work we report the growth and operation of strained layer GaSbAs-GaAs quantum-well lasers.
Optical coherence tomography (OCT) in hereditary retinal degenerations: Layer-by-layer analyses in normal and diseased retinas (1999)

OCT is a new technique for non-invasive, non-contact, cross-sectional imaging of biological tissues with micrometer longitudinal resolution. As it applies to the field of ophthalmology, OCT can delineate retinal sublayers based on their backscattering characteristics, and permit quantitative measurement of the structure of retina in vivo. This dissertation intended to clarify the basis of the OCT signals and whether this procedure has potential for diagnosis and monitoring of human retinal degenerative diseases. Key to this goal are quantitation of OCT signal features and accurate, layer-by-layer correlation of these features with underlying retinal microanatomy. In normal and degenerate avian and swine retinas, OCT signal features were quantified using custom computer programs, and were correlated with cryosections of unfixed retinas obtained at the same retinal location. The results suggested a definable and quantifiable relationship between OCT signal components and retinal microanatomy. The correlation in the outer retina indicated that the OCT posterior highly reflective band, or the outer-retina-choroid complex (ORCC), is attributable to the photoreceptor layer, RPE, and anterior choroid. Further evidence of OCT signal origin was provided by the rd chicken and the rhodopsin P347L mutant transgenic swine. In these animals where photoreceptors had degenerated, OCT abnormalities were observed at the level of and vitreal to the ORCC, consistent with the hypothesis that photoreceptors contribute to the ORCC. Studies of quantitative OCT analysis in man were also performed. In selected hereditary retinal degenerative diseases in which there was regional difference in retinal function, frequently observed OCT abnormalities that were associated with visual dysfunction were reduced OCT thickness, reduced ORCC thickness, increased reflectivity posterior to ORCC, and abnormal OCT signal lamination. These preliminary results suggested that OCT abnormalities at the level of and posterior to the ORCC are prominent features in these retinal degenerations. This dissertation represents the first report of quantitative OCT results in hereditary retinal degenerations in experimental animals and humans. Considering that OCT is being used increasingly to investigate, diagnose, and monitor human retinal diseases, insight gained in these studies may direct further studies in mammalian and human retinas and advance this technology to its full potential in ophthalmology.
Atmospheric Pressure Ionization in a Miniature Mass Spectrometer (2005)

A miniature cylindrical ion trap mass spectrometer featuring an atmospheric pressure interface allowing atmospheric pressure chemical ionization and electrospray ionization is described together with its analytical performance characteristics. The vacuum system, ion optics, mass analyzer, control electronics system, and detection system have all been designed and built in-house. The design is based upon a three-stage, differentially pumped vacuum system with the instrument capable of being interfaced to many types of atmospheric pressure ionization sources. Ions are transferred through home-built ion optics, and instrument control is achieved through custom-designed electronics and LabView control software. Corona discharge ionization and electrospray ionization sources are implemented and used to allow the analysis of both gaseous- and solution-phase samples during the characterization of the instrument. An upper mass/charge limit of approximately 450 Th with unit resolution was achieved using a 2.5-mm-internal radius cylindrical ion trap as the mass analyzer. The specificity of the instrument can be increased by employing the MS/MS capabilities of the ion trap and has been demonstrated for nitrobenzene. Limits of detection for the trace analysis in air of the chemical warfare agent simulant methyl salicylate (1.24 ppb) and for nitrobenzene (629 pptr) are achieved. The dynamic range of the instrument is currently limited to approximately 2 orders of magnitude by saturation of the detection electronics. Isolation and collision-induced dissociation efficiencies in MS/MS experiments both greater than 50% are reported. Electrospray/nanospray data are presented on solutions including 100 microM (D,L)-arginine, 10 microM (-)-ephedrine, and 10 microM lomefloxacin.
The surface-tension-driven Benard conventions and unique sub-grain cellular microstructures in 316L steel selective laser melting (2018)

The unique sub-grain patterns have been found in some particular alloys (316L, Al-Si, Co-Cr-Mo) selective laser melting (SLM), the submicron-scale cellular, elongated cellular or even band structures are always coexisting inside one single macro-solidified grain. Furthermore, the cellular structures are symmetrical with hexagonal, pentagonal and square cellular patterns where the cellular size is only around 1μm. Single-layer and bulk 316L SLM experiments are presented that reveals the forming mechanism of these sub-grain cellular microstructures. Complex cellular sub-micron patterns were formed by the local convection and Bénard Instabilities in front of the solid/liquid (S/L) interface (so-called mushy zones) affected by intricate temperature and surface tension gradients. In other words, this nonlinear self-organization phenomenon (Bénard Instability) occurring at the S/L interface is superimposed on the macro-grain solidification process to form the sub-grain patterns/structures and elemental microsegregations. This simple and unified explanation can be expanded to other eutectic alloys formed by SLM, like the Al-Si system.
Zebrafish androgen receptor is required for spermatogenesis and maintenance of ovarian function (2018)

The androgen receptor (AR) is a nuclear receptor protein family member and inducible transcription factor that modulates androgen target gene expression. Studies using a mouse model confirmed the need for <i>ar</i> in reproductive development, particularly spermatogenesis. Here, we investigated the role of <i>ar</i> in zebrafish using CRISPR/Cas9 gene targeting technology. Targeted disruption of <i>ar</i> in zebrafish increases the number of female offspring and increases offspring weight. In addition, <i>ar</i>-null male zebrafish have female secondary sex characteristics. More importantly, targeted disruption of <i>ar</i> in zebrafish causes male infertility via defective spermatogenesis and female premature ovarian failure during growth. Mechanistic assays suggest that these effects are caused by fewer proliferated cells and more apoptotic cells in <i>ar</i>-null testes. Moreover, genes involved in reproductive development, estradiol induction and hormone synthesis were dys-regulated in testes and ovaries and the reproductive-endocrine axis was disordered. Our data thus suggest that the zebrafish <i>ar</i> is required for spermatogenesis and maintenance of ovarian function, which confirms evolutionarily conserved functions of <i>ar</i> in vertebrates, as well as indicates that <i>ar</i>-null zebrafish are a suitable model for studying pathologic mechanisms related to androgen disorders.
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity (2014)

SSpro, SSpro8, ACCpro and ACCpro20 programs, data and web servers are available through the SCRATCH suite of protein structure predictors at http://scratch.proteomics.ics.uci.edu.