gebhart/patrepeval huggingface dataset:
Optimization of intradermal vaccination by DNA tattooing in human skin (2008)

The intradermal administration of DNA vaccines by tattooing is a promising delivery technique for genetic immunization, with proven high immunogenicity in mice and in nonhuman primates. However, the parameters that result in optimal expression of DNA vaccines that are applied by this strategy to human skin are currently unknown. To address this issue we set up an ex vivo human skin model in which DNA vaccine-induced expression of reporter proteins could be monitored longitudinally. Using this model we demonstrate the following: First, the vast majority of cells that express DNA vaccine-encoded antigen in human skin are formed by epidermal keratinocytes, with only a small fraction (about 1%) of antigen-positive epidermal Langerhans cells. Second, using full randomization of DNA tattoo variables we show that an increase in DNA concentration,needle depth, and tattoo time all significantly increase antigen expression ( p < 0.001), with DNA concentration forming the most critical variable influencing the level of antigen expression. Finally, in spite of the marked immunogenicity of this vaccination method in animal models, transfection efficiency of the technique is shown to be extremely low, estimated at approximately 2 to 2000 out of 1 x 10(10) copies of plasmid applied. This finding, coupled with the observed dependency of antigen expression on DNA concentration, suggests that the development of strategies that can enhance in vivo transfection efficacy would be highly valuable. Collectively, this study shows that an ex vivo human skin model can be used to determine the factors that control vaccine-induced antigen expression and define the optimal parameters for the evaluation of DNA tattoo or other dermal delivery techniques in phase 1 clinical trials.
Code Developments to Improve the Efficiency of Automated MS/MS Spectra Interpretation (2002)

We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a computational approach to narrow charge states of precursor ions from nominal resolution ion-trap tandem mass spectra. The preprocessing code, 2to3, determines the charge state of the precursor ion using its mass-to-charge ratio (m/z) and fragment ions contained in the tandem mass spectrum. For each possible charge state the program calculates the expected fragment ions that account for precursor ion m/z values. If any one of the numbers is less than an empirically determined threshold value then the spectrum corresponding to that charge state is removed. If both numbers are higher than the threshold value then +2 and +3 copies of the spectrum are kept. We present the comparison of results from protein identification experiments with and without using 2 to 3. It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results. The decrease reduces computer requirements and researcher efforts for analysis of the results.
Quartz Crystal Microbalance Study of DNA Immobilization and Hybridization for Nucleic Acid Sensor Development (1997)

The immobilization of two 30-mer oligonucleotides, one biotinylated (biotin-DNA) and the other having a mercaptohexyl group at the 5'-phosphate end (BS1-SH), onto modified gold surfaces has been examined using a quartz crystal microbalance (QCM). Both single-layer and multilayer DNA films were prepared. The single-layer films of biotin-DNA were constructed by binding to a precursor layer of avidin, which had been attached to the QCM either covalently using a water-soluble carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) or via electrostatic interaction with poly(allylamine hydrochloride) (PAH). Single-layer films of BS1-SH were also formed on PAH via the electrostatic attraction between the amine groups on PAH and the negatively charged phosphate backbone of DNA. Multilayer films of DNA were fabricated by the successive deposition of avidin and poly(styrenesulfonate) (PSS), up to a total of nine avidin/PSS layers, followed by DNA adsorption. DNA immobilization and hybridization of the immobilized DNAs was monitored in situ from QCM frequency changes. Hybridization was induced by exposure of the DNA-containing films to complementary DNA in solution. Equal frequency changes were observed for the DNA immobilization and hybridization steps for the single-layer films, indicating a DNA probe-to-hybridized DNA target ratio of 1:1. The multilayer DNA films also exhibited DNA hybridization, with a greater quantity of DNA hybridized compared with the single-layer films. The multilayer films provide a novel means for the fabrication of DNA-based thin films with increased capacity for nucleic acid detection.
Tumor Suppressor RARRES1 Regulates DLG2, PP2A, VCP, EB1, and Ankrd26 (2010)

Retinoic Acid Receptor Responder (RARRES1) initially identified as a novel retinoic acid receptor regulated gene in the skin is a putative tumor suppressor of unknown function. RARRES1 was knocked down in immortalized human prostatic epithelial cell line PWR-1E cells and differential protein expression was identified using differential in-gel electrophoresis (DIGE) followed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry and western Blot analysis excluding highly abundant proteins routinely identified in almost all proteomics projects. Knock-down of RARRES1: 1- down-regulates PP2A, an enzyme involved in the negative regulation of the growth hormone-stimulated signal transduction pathways; 2- down-regulates Valosin-containing protein causing impaired autophagy; 3- up-regulates the tumor suppressor disks large 2; 4- up-regulates Ankrd26 that belongs to the POTE family of genes that are highly expressed in cancer patients with poor outcome; and 5- down-regulates EB1, a protein that is involved in spindle dynamics and chromosome alignment during mitosis.
Subtyping Salmonella enterica Serovar Enteritidis Isolates from Different Sources by Using Sequence Typing Based on Virulence Genes and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) (2011)

Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.
The Impact of the Nonpeptide Corticotropin-Releasing Hormone Antagonist Antalarmin on Behavioral and Endocrine Responses to Stress (1999)

The nonpeptide CRH antagonist antalarmin has been shown to block both behavioral and endocrine responses to CRH. However, it's potential activity in blunting behavioral and endocrine sequelae of stressor exposure has not been assessed. Because antagonism of central CRH by α-helical CRH attenuates conditioned fear responses, we sought to test antalarmin in this regard. In addition, it remains unclear as to whether this is a result of receptor blockade during conditioning or during testing. Thus, we explored whether CRH mediates the induction or expression of conditioned fear (freezing in a context previously associated with 2 footshocks; 1.0 mA, 5 sec each). Furthermore, because rats previously exposed to inescapable shock (IS; 100 shocks, 1.6 mA, 5 sec each), demonstrate enhanced fear conditioning, we investigated whether this effect would be blocked by antalarmin. Antalarmin (20 mg/kg·2 ml ip) impaired both the induction and expression of conditioned fear. In addition, antalarmin blocked the enhancement of fear conditioning produced by prior exposure to IS. Despite the marked behavioral effects observed in antalarmin-treated rats, antalarmin had no effect on IS-induced rises in ACTH or corticosterone. However, antalarmin did block the ACTH response produced by exposure to 2 footshocks.
Improved Efficiency of a Salmonella -Based Vaccine against Human Papillomavirus Type 16 Virus-Like Particles Achieved by Using a Codon-Optimized Version of L1 (2004)

Cervical cancer results from cervical infection by human papillomaviruses (HPVs), especially HPV16. An effective vaccine against these HPVs is expected to have a dramatic impact on the incidence of this cancer and its precursor lesions. The leading candidate, a subunit prophylactic HPV virus-like particle (VLP) vaccine, can protect women from HPV infection. An alternative improved vaccine that avoids parenteral injection, that is efficient with a single dose, and that induces mucosal immunity might greatly facilitate vaccine implementation in different settings. In this study, we have constructed a new generation of recombinant Salmonella organisms that assemble HPV16 VLPs and induce high titers of neutralizing antibodies in mice after a single nasal or oral immunization with live bacteria. This was achieved through the expression of a HPV16 L1 capsid gene whose codon usage was optimized to fit with the most frequently used codons in Salmonella. Interestingly, the high immunogenicity of the new recombinant bacteria did not correlate with an increased expression of L1 VLPs but with a greater stability of the L1-expressing plasmid in vitro and in vivo in absence of antibiotic selection. Anti-HPV16 humoral and neutralizing responses were also observed with different Salmonella enterica serovar Typhimurium strains whose attenuating deletions have already been shown to be safe after oral vaccination of humans. Thus, our findings are a promising improvement toward a vaccine strain that could be tested in human volunteers.
β‐Mannosidosis: Prenatal biochemical and morphological characteristics (1983)

Caprine beta-mannosidosis, an autosomal recessive disorder of glycoprotein catabolism, as yet undetected in man, was expressed in a 96/150 day gestation goat fetus. Deficiency of plasma, kidney, brain, liver and skin fibroblast acidic beta-mannosidase activity was associated with the accumulation of tissue oligosaccharides. Characteristic lucent cytoplasmic lysosomal storage vacuoles were present in the brain, thyroid, kidney and other tissues. Axonal spheroids were present in the central nervous system. The biochemical and morphological prenatal expressions of beta-mannosidosis which were documented by this investigation may facilitate the identification of the disease in man.
Novel Five‐Membered Iminocyclitol Derivatives as Selective and Potent Glycosidase Inhibitors: New Structures for Antivirals and Osteoarthritis (2006)

A novel 5-membered iminocyclitol derivative was found to be a potent and selective inhibitor of the glycoprotein-processing alpha-glucosidase with a Ki value of 53 nM. This compound was further derivatized to antiviral agents against Japanese encephalitis virus, dengue virus serotype 2 (DEN-2), human SARS coronavirus, and human beta-hexosaminidase (Ki = 2.6 nM), a new target for the development of osteoarthritis therapeutics.
Agents That Target Androgen Synthesis in Castration-Resistant Prostate Cancer (2013)

In April 2011, abiraterone acetate (in combination with low-dose steroids) was approved by the US Food and Drug Administration for the treatment of men with metastatic, castration-resistant prostate cancer who have previously been treated with docetaxel-based chemotherapy. The development of abiraterone was the successful result of an improved understanding of the role of the androgen receptor signaling pathway in castration-resistant prostate cancer. Abiraterone is a rationally designed potent inhibitor of cytochrome P450, family 17, subfamily A, polypeptide 1, which is essential for synthesis of testosterone from nongonadal precursors. More recently, other drugs that act along the androgen0synthesis pathway, such as orteronel (TAK-700) and galeterone (TOK-001), have shown promise in early clinical trials. Here, we review the discovery and clinical development of abiraterone and other novel androgen-synthesis inhibitors for the management of advanced prostate cancer.
Stabilization and Acidic Dissolution Mechanism of Single-Crystalline ZnO(0001) Surfaces in Electrolytes Studied by In-Situ AFM Imaging and Ex-Situ LEED (2008)

A combined approach of pH-dependent in-situ AFM topography and ex-situ LEED studies of the stability and dissolution of single-crystalline ZnO(0001)-Zn surfaces in aqueous media is presented. Hydroxide-stabilized and single-crystalline ZnO(0001)-Zn surfaces turned out to be stable within a wide pH range between 11 and 4 around the point of zero charge of pH PZC = 8.7 +/- 0.2. Hydroxide stabilization turned out to be a very effective stabilization mechanism for polar oxide surfaces in electrolyte solutions. The dissolution of the oxide surface started at an acidic pH level of 5.5 and occurred selectively at the pre-existing step edges, which consist of nonpolar surfaces. In comparison, the oxide dissolution along the ZnO(0001) direction proved to be effectively inhibited above a pH value of 3.8. On the basis of these microscopic observations, the mechanistic understanding of the acidic dissolution process of ZnO could be supported. Moreover, both the in-situ AFM and the ex-situ LEED studies showed that the stabilization mechanism of the ZnO(0001) surfaces changes in acidic electrolytes. At pH values below 3.8, the hydroxide-stabilized surface is destabilized by dissolution of the well-ordered radical3. radical3. R30 hydroxide ad-layer as proven by LEED. Restabilization occurs and leads to the formation of triangular nanoterraces with a specific edge termination. However, below pH 4 the surface structure of the crystal itself is ill-defined on the macroscopic scale because preferable etching along crystal defects as dislocations into the bulk oxide results in very deep hexagonal etching pits.
Toward Na-ion Batteries—Synthesis and Characterization of a Novel High Capacity Na Ion Intercalation Material (2012)

The rapid growth of the worldwide demand of lithium for batteries (LIBs) can possibly lead to a shortage of its reserves. Sodium batteries represent a promising alternative because they enable much higher energy densities than other battery systems, with the exception of LIBs, and are not limited by sodium availability. Herein, we present a novel, Na+ ion intercalation material, Na0.45Ni0.22Co0.11Mn0.66O2 (space group P63/mmc) synthesized in air by a coprecipitation method followed by a thermal treatment and a water-rinsing step. This material performs a specific capacity of 135 mA h g–1 with a Coulombic efficiency exceeding 99.7%. Upon long-term cycling tests the material shows excellent capacity retention after more than 250 cycles. Such an overall performance, superior to that of presently known sodium-ion cathodes, represents a step further toward the realization of sustainable batteries for efficient stationary energy storage.
Sequence Homology and Morphologic Similarity of HTLV-III and Visna Virus, a Pathogenic Lentivirus (1985)

A study was conducted of the genetic relation between human T-cell lymphotropic retroviruses and visna virus. The human T-cell lymphotropic viruses include those associated with T-cell malignancies (HTLV-I and HTLV-II) as well as the etiologic agent of the acquired immune deficiency syndrome (HTLV-III). Visna virus, a slowly replicating and pathogenic but nononcogenic retrovirus of sheep, is a member of the subfamily Lentivirinae. Results obtained by molecular hybridization and heteroduplex analysis indicated that a greater extent of nucleotide sequence homology exists between HTLV-III and visna virus than between HTLV-III and any of the other viruses. The homology observed under conditions of low stringency spanned the entire genome, but was strongest in the gag/pol region. The morphogenesis and fine structure of HTLV-III and visna virus also demonstrated striking similarities. The data provide strong evidence for a close taxonomic and thus evolutionary relation between HTLV-III and the Lentivirinae subfamily.
Pathogenicity of West Nile Virus in Chickens (2000)

In the fall of 1999, West Nile virus (WNV) was isolated for the first time in the Western Hemisphere during an outbreak of neurologic disease in humans, horses, and wild and zoo birds in the northeastern United States. Chickens are a potential reservoir for WNV, and little is known about the pathogenicity of WNV in domestic chickens. Seven-week-old chickens derived from a specific-pathogen-free flock were inoculated subcutaneously with 1.8 x 10(3) 50% tissue culture infectious dose of a crow isolate of WNV in order to observe clinical signs and evaluate the viremic phase, gross and microscopic lesions, contact transmission, and immunologic response. There were no observable clinical signs in the WNV-inoculated chickens during the 21-day observation period. However, histopathologic examination of tissues revealed myocardial necrosis, nephritis, and pneumonitis at 5 and 10 days postinoculation (DPI); moderate to severe nonsuppurative encephalitis also was observed in brain tissue from one of four inoculated birds examined at 21 DPI. WNV was recovered from blood plasma for up to 8 DPI. Virus titers as high as 10(5)/ml in plasma were observed at 4 DPI. Fecal shedding of virus was detected in cloacal swabs on 4 and 5 DPI only. The WNV also was isolated from myocardium, spleen, kidney, lung, and intestine collected from chickens euthanatized at 3, 5, and 10 DPI. No virus was isolated from inoculated chickens after 10 DPI. Antibodies specific to WNV were detected in inoculated chickens as early as 5 DPI by the plaque reduction neutralization test and 7 DPI by the indirect fluorescent antibody test. Chickens placed in contact with inoculated chickens at 1 DPI lacked WNV-specific antibodies, and no WNV was isolated from their blood plasma or cloacal swabs throughout the 21 days of the experiment.
Hierarchically Porous Bioactive Glass Scaffolds Synthesized with a PUF and P123 Cotemplated Approach (2007)

Hierarchically porous bioactive glass (CaO−SiO2−P2O5) scaffolds have been prepared by using nonionic block copolymer EO20PO70EO20 (P123) and polyurethane (PUF) as cotemplates. It exhibits a hierarchical structure with interconnected macropores (about 200−400 or 500−700 μm), which provide the potential for tissue ingrowth and the neovascularization, and uniform mesopores (3.68 nm), which cause an increase in the specific surface area and enhanced bioactivity and release of ionic products. The ordered hierarchically porous scaffold has the advantages of both mesoporosity and macroporosity, which may find potential applications in tissue engineering and drug storage.
Quantitative measurement of proteins by western blotting with Cy5-coupled secondary antibodies. (1999)

The concentration of proteins in cells is an important parameter that determines how a protein will interact with other proteins or pharmacological agents. Recent developments in Western blotting techniques have now made this a method of choice to measure protein concentration in complex solutions such as total cell extracts. We show that detection of Cy5-coupled secondary antibodies by PhosphorImager analysis produces signals that approach linearity with respect to protein concentration over a 20-fold range. We used this technique to estimate cellular levels of zyxin, which is an important protein component of the actin cytoskeleton in mammalian cells. By producing specific protein standards based on sequences that are available from public databases, it is now possible to estimate the concentration of almost any protein by this technique.
Radioprotection of IDH1 -Mutated Cancer Cells by the IDH1-Mutant Inhibitor AGI-5198 (2015)

Isocitrate dehydrogenase 1 (IDH1) is mutated in various types of human cancer to IDH1(R132H), a structural alteration that leads to catalysis of α-ketoglutarate to the oncometabolite D-2-hydroxyglutarate. In this study, we present evidence that small-molecule inhibitors of IDH1(R132H) that are being developed for cancer therapy may pose risks with coadministration of radiotherapy. Cancer cells heterozygous for the IDH1(R132H) mutation exhibited less IDH-mediated production of NADPH, such that after exposure to ionizing radiation (IR), there were higher levels of reactive oxygen species, DNA double-strand breaks, and cell death compared with IDH1 wild-type cells. These effects were reversed by the IDH1(R132H) inhibitor AGI-5198. Exposure of IDH1 wild-type cells to D-2-hydroxyglutarate was sufficient to reduce IDH-mediated NADPH production and increase IR sensitivity. Mechanistic investigations revealed that the radiosensitivity of heterozygous cells was independent of the well-described DNA hypermethylation phenotype in IDH1-mutated cancers. Thus, our results argue that altered oxidative stress responses are a plausible mechanism to understand the radiosensitivity of IDH1-mutated cancer cells. Further, they offer an explanation for the relatively longer survival of patients with IDH1-mutated tumors, and they imply that administration of IDH1(R132H) inhibitors in these patients may limit irradiation efficacy in this setting.
Optical interconnects: out of the box forever? (2003)

Based on a variety of optimization criteria, recent research has suggested that optical interconnects are a viable alternative to electrical interconnects for board-to-board, chip-to-chip, and on-chip applications. However, the design of modern high-performance computing systems must account for a variety of performance scaling factors that are not included in these analyses. We will give an overview of the performance scaling that has driven current computer design, with a focus on architectural design and the effects of these designs on interconnect implementation. We then discuss the potential of optics at each of these interconnect levels, in the context of extant electrical technology.