gebhart/patrepeval huggingface dataset:
Topical Application of a Bioadhesive Black Raspberry Gel Modulates Gene Expression and Reduces Cyclooxygenase 2 Protein in Human Premalignant Oral Lesions (2008)

Reduced expression of proapoptotic and terminal differentiation genes in conjunction with increased levels of the proinflammatory and angiogenesis-inducing enzymes, cyclooxygenase 2 (COX-2) and inducible nitric oxide synthase (iNOS), correlate with malignant transformation of oral intraepithelial neoplasia (IEN). Accordingly, this study investigated the effects of a 10% (w/w) freeze-dried black raspberry gel on oral IEN histopathology, gene expression profiles, intraepithelial COX-2 and iNOS proteins, and microvascular densities. Our laboratories have shown that freeze-dried black raspberries possess antioxidant properties and also induce keratinocyte apoptosis and terminal differentiation. Oral IEN tissues were hemisected to provide samples for pretreatment diagnoses and establish baseline biochemical and molecular variables. Treatment of the remaining lesional tissue (0.5 g gel applied four times daily for 6 weeks) began 1 week after the initial biopsy. RNA was isolated from snap-frozen IEN lesions for microarray analyses, followed by quantitative reverse transcription-PCR validation. Additional epithelial gene-specific quantitative reverse transcription-PCR analyses facilitated the assessment of target tissue treatment effects. Surface epithelial COX-2 and iNOS protein levels and microvascular densities were determined by image analysis quantified immunohistochemistry. Topical berry gel application uniformly suppressed genes associated with RNA processing, growth factor recycling, and inhibition of apoptosis. Although the majority of participants showed posttreatment decreases in epithelial iNOS and COX-2 proteins, only COX-2 reductions were statistically significant. These data show that berry gel application modulated oral IEN gene expression profiles, ultimately reducing epithelial COX-2 protein. In a patient subset, berry gel application also reduced vascular densities in the superficial connective tissues and induced genes associated with keratinocyte terminal differentiation.
Editorial Renal denervation after the symplicity HTN-3 trial (2014)

AMA Warchoł-Celińska E, Januszewicz A, Prejbisz A, Kądziela J. EditorialRenal denervation after the symplicity HTN-3 trial. Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej. 2014;10(2):75-77. doi:10.5114/pwki.2014.43509. APA Warchoł-Celińska, E., Januszewicz, A., Prejbisz, A., & Kądziela, J. (2014). EditorialRenal denervation after the symplicity HTN-3 trial. Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej, 10(2), 75-77. https://doi.org/10.5114/pwki.2014.43509 Chicago Warchoł-Celińska, Ewa, Andrzej Januszewicz, Aleksander Prejbisz, and Jacek Kądziela. 2014. "EditorialRenal denervation after the symplicity HTN-3 trial". Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej 10 (2): 75-77. doi:10.5114/pwki.2014.43509. Harvard Warchoł-Celińska, E., Januszewicz, A., Prejbisz, A., and Kądziela, J. (2014). EditorialRenal denervation after the symplicity HTN-3 trial. Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej, 10(2), pp.75-77. https://doi.org/10.5114/pwki.2014.43509 MLA Warchoł-Celińska, Ewa et al. "EditorialRenal denervation after the symplicity HTN-3 trial." Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej, vol. 10, no. 2, 2014, pp. 75-77. doi:10.5114/pwki.2014.43509. Vancouver Warchoł-Celińska E, Januszewicz A, Prejbisz A, Kądziela J. EditorialRenal denervation after the symplicity HTN-3 trial. Advances in Interventional Cardiology/Postępy w Kardiologii Interwencyjnej. 2014;10(2):75-77. doi:10.5114/pwki.2014.43509.
Silicon-based optoelectronics (1993)

The decade of the 1990's is an opportune time for scientists and engineers to create cost-effective silicon "superchips" that merge silicon photonics with advanced silicon electronics on a silicon substrate. We can expect significant electrooptical devices from Column IV materials (Si, Ge, C and Sn) for a host of applications. The best devices will use strained-layer epitaxy, doped heterostructures, and bandgap engineering of quantum-confined structures. This paper reviews Si-based photonic components and optoelectronic integration techniques, both hybrid and monolithic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Prevention of Acute Lung Allograft Rejection in Rat by CTLA4Ig (2002)

CTLA4 immunoglobulin (CTLA4Ig), which binds with a high affinity to B7-1 and B7-2, interrupts T-cell activation by inhibiting costimulatory signal. CTLA4Ig has been used in hopes of achieving antigen-specific tolerance induction in several solid organ transplants. In lung allograft rejection, however, its use has been controversial in terms of its effect on prevention of rejection. In the present study, the effect of murine CTLA4Ig on rat-lung allograft rejection was investigated. Rat left-lung transplantation was performed in an RT1 incompatible donor (Brown Norway; BN)-recipient (F344) combination. All allografts (n = 12) without any treatment were rejected within 7 days after transplantation. A single injection of murine form CTLA41g at a dose of 100 microg intraperitoneally (ip) or intravenously (iv) on day 1 post-transplantation achieved long-term graft survival (>90days) in 2/5 (40%) and 3/8 (38%), respectively. Moreover, 6/7 (86%) allografts in rats that received iv injection of 500 microg CTLA4Ig survived more than 90days. Allograft survival in the CTLA4Ig 500 microg iv recipient group was significantly longer than that in the no-treatment control or control immunoglobulin group (p <0.01). Four out of seven recipients bearing functional allografts for more than 90 days with the CTLA4Ig treatment accepted donor-specific skin grafts, whereas all third-party skin grafts (n=3) were rejected. Prevention of rat-lung allograft rejection could be achieved by intravenous administration of CTLA4Ig, resulting in long-term allograft survival with acceptance of donor-specific skin grafts.
Targeted Disruption of theGRA2Locus inToxoplasma gondiiDecreases Acute Virulence in Mice (1998)

Following invasion into the host cell, the protozoan Toxoplasma gondii secretes a variety of proteins that modify the parasitophorous vacuole. Within the vacuole, the 28-kDa dense granule protein known as GRA2 is specifically targeted to the tubulovesicular network which forms connections with the vacuolar membrane. To investigate the importance of GRA2, we derived from strain RH a mutant T. gondii line in which GRA2 was disrupted by replacement with the marker Ble (selecting for phleomycin resistance). The Deltagra2 mutant invaded and grew normally in both fibroblasts and macrophages in vitro; however, it was less virulent during acute infection in mice. The survival rate of mice inoculated with Deltagra2 was significantly higher; some infected mice survived the acute infection, whereas all mice infected with the wild-type strain RH succumbed to early death. Chronic infection by Deltagra2 was detected by positive serology, immunohistochemical detection of parasites and cysts in the brain, and reisolation of parasites by bioassay at 6 weeks postinfection. Thus, absence of GRA2 partially attenuates the virulence of T. gondii during the acute phase of infection and allows for establishment of chronic infection by the otherwise highly virulent RH strain. These results establish that GRA2 plays an important role during in vivo infection and provide a potential model for examining acute pathogenesis by T. gondii.
Analysis ofB1field profiles and SAR values for multi-strut transverse electromagnetic RF coils in high field MRI applications (2001)

In this work, the B1 field homogeneity and specific absorption rate (SAR) values were evaluated for three high-frequency (340 MHz) radio frequency coils designed for use in human magnetic resonance imaging at 8 tesla. Eight-, 16-, and 24-strut transverse electromagnetic (TEM) resonators were examined both experimentally and with the finite difference time domain numerical method. It was observed that increasing the number of TEM elements acted to lower the maximal achievable frequency of the coil and to increase the experimental complexities associated with tuning and matching. In addition, it is demonstrated from experiment and numerical analysis that the circularly polarized component of the B1 (B1+) field homogeneity in the head improved most from 8- to 16-strut coils. Numerical analysis revealed little difference in terms of SAR distribution between these coils; however, stronger tissue/coil coupling and consequently higher SAR peak values were obtained for the 8-strut case.
Vaccination with poly-L-arginine as immunostimulant for peptide vaccines: induction of potent and long-lasting T-cell responses against cancer antigens. (2002)

Vaccines that induce high numbers of sustained T cell responses are urgently needed for the treatment of numerous diseases including cancer. Antigen-presenting cells (APCs), the most important of which are dendritic cells, orchestrate antigen-dependent T cell responses in that they present antigens to T cells in an appropriate environment. Here we present evidence that after vaccination with a simple mixture of the cationic poly-amino acid poly-L-arginine and tumor antigen-derived peptide antigens, large numbers of antigen-specific T cells are induced and APCs mediate the generation of T lymphocytes. We observe that after s.c. injection, MHC class II(+) cells infiltrate injection sites and are loaded with large amounts of antigen in vivo under the influence of poly-L-arginine. Consequently, numerous antigen-charged APCs can be detected in draining lymph nodes of vaccinated animals. Antigen-specific T cell responses induced are systemic and were readily detected more than 4 months after the last vaccination, the latest time point we measured. By contrast, even after repeat injections, we were consistently unable to detect antibody responses against poly-L-arginine, allowing this compound to be used for numerous booster injections. Clinical trials in cancer patients using poly-L-arginine as immunostimulant will be carried out in the near future.
SCAN methodology optimization based on correlation (2003)

This paper presents a new scheme for lossless image coding with SCAN image data scanning (Maniccam et al. (2001)). A methodology for creation of a convenient space-filling curve based on correlation is introduced.
Dopaminergic neuronal loss and motor deficits inCaenorhabditis elegansoverexpressing human α‐synuclein (2003)

Overexpression of human alpha-synuclein in model systems, including cultured neurons, drosophila and mice, leads to biochemical and pathological changes that mimic synucleopathies including Parkinson's disease. We have overexpressed both wild-type (WT) and mutant alanine53-->threonine (A53T) human alpha-synuclein by transgenic injection into Caenorhabditis elegans. Motor deficits were observed when either WT or A53T alpha-synuclein was overexpressed with a pan-neuronal or motor neuron promoter. Neuronal and dendritic loss were accelerated in all three sets of C. elegans dopaminergic neurons when human alpha-synuclein was overexpressed under the control of a dopaminergic neuron or pan-neuronal promoter, but not with a motor neuron promoter. There were no significant differences in neuronal loss between overexpressed WT and A53T forms or between worms of different ages (4 days, 10 days or 2 weeks). These results demonstrate neuronal and behavioral perturbations elicited by human alpha-synuclein in C. elegans that are dependent upon expression in specific neuron subtypes. This transgenic model in C. elegans, an invertebrate organism with excellent experimental resources for further genetic manipulation, may help facilitate dissection of pathophysiologic mechanisms of various synucleopathies.
A new type of nano-sized silicon/carbon composite electrode for reversible lithium insertion (2005)

A new type of nano-sized silicon/carbon composite was developed. It shows superior electrochemical cycling properties as negative electrode material for possible use in lithium-ion batteries with respect to high reversible and low irreversible capacity, and low fading.
Mutation of Neuraminidase Cysteine Residues Yields Temperature-Sensitive Influenza Viruses (1999)

The influenza virus neuraminidase (NA) is a tetrameric, virus surface glycoprotein possessing receptor-destroying activity. This enzyme facilitates viral release and is a target of anti-influenza virus drugs. The NA structure has been extensively studied, and the locations of disulfide bonds within the NA monomers have been identified. Because mutation of cysteine residues in other systems has resulted in temperature-sensitive (ts) proteins, we asked whether mutation of cysteine residues in the influenza virus NA would yield ts mutants. The ability to rationally design tight and stable ts mutations could facilitate the creation of efficient helper viruses for influenza virus reverse genetics experiments. We generated a series of cysteine-to-glycine mutants in the influenza A/WSN/33 virus NA. These were assayed for neuraminidase activity in a transient expression system, and active mutants were rescued into infectious virus by using established reverse genetics techniques. Mutation of two cysteines not involved in intrasubunit disulfide bonds, C49 and C146, had modest effects on enzymatic activity and on viral replication. Mutation of two cysteines, C303 and C320, which participate in a single disulfide bond located in the beta5L0,1 loop, produced ts enzymes. Additionally, the C303G and C320G transfectant viruses were found to be attenuated and ts. Because both the C303G and C320G viruses exhibited stable ts phenotypes, they were tested as helper viruses in reverse genetics experiments. Efficiently rescued were an N1 neuraminidase from an avian H5N1 virus, an N2 neuraminidase from a human H3N2 virus, and an N7 neuraminidase from an H7N7 equine virus. Thus, these cysteine-to-glycine NA mutants allow the rescue of a variety of wild-type and mutant NAs into influenza virus.
Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery (2014)

The elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the family D archaeal polymerases.
Measurement of Circulating Cell-Free DNA Levels by a New Simple Fluorescent Test in Patients With Primary Colorectal Cancer (2011)

Elevated circulating cell-free DNA (CFD) levels were found in patients with cancer. The standard CFD assays are work-intensive and expensive. The aim was to evaluate in patients with cancer a new simple CFD assay. In mice inoculated with cancer cells, CFD levels correlated with tumor size. Compared with healthy subjects, 38 patients with colorectal cancer (CRC) had higher preoperative CFD levels (798 ± 409 vs 308 ± 256 ng/mL; P < .0001). Compared with patients free of disease at 1 year, CFD levels were elevated in patients who remained with disease or died (DD). CFD correlated with DD (P = .033), and a combined index of carcinoembryonic antigen × CFD exhibited a better correlation to DD than did pathologic staging (P = .0027 vs P = .0065). For patients with CRC, CFD levels were prognostic of death and disease. A large prospective study will need to be performed to truly evaluate the efficacy of this method for early detection, follow-up, and evaluation of patient response to treatment.
Failure analysis for full-scan circuits (2002)

We present a complete system for failure analysis of full-scan circuits. A novel scheme has been proposed to handle multiple faults up to a certain extent by ranking the faults according to the likelihood of being present in the defective part. The user can interactively recompute the suspect fault list by changing some parameters. If the suspect fault list is large, we generate new test patterns to distinguish the faults in the suspect list. User can iterate over a defective part several times until the suspect fault list is reasonably small. Then each suspect site is probed using E-beam. This tool is integrated into design environment of LSI Logic Corporation and produced good results when applied on a few industry circuits.
There are NO fundamental limits to optical nanolithography (2004)

This work demonstrates that optical techniques, particularly coherent interference effects, can not only reach nanoscale dimensions but also offer the many advantages of optical lithography including parallel writing of large numbers of nanostructures over large areas, alignment to underlying patterns, and cost-effectiveness.
Vision meets robotics: The KITTI dataset (2013)

We present a novel dataset captured from a VW station wagon for use in mobile robotics and autonomous driving research. In total, we recorded 6 hours of traffic scenarios at 10–100 Hz using a variety of sensor modalities such as high-resolution color and grayscale stereo cameras, a Velodyne 3D laser scanner and a high-precision GPS/IMU inertial navigation system. The scenarios are diverse, capturing real-world traffic situations, and range from freeways over rural areas to inner-city scenes with many static and dynamic objects. Our data is calibrated, synchronized and timestamped, and we provide the rectified and raw image sequences. Our dataset also contains object labels in the form of 3D tracklets, and we provide online benchmarks for stereo, optical flow, object detection and other tasks. This paper describes our recording platform, the data format and the utilities that we provide.
Models for the binding site in bromoperoxidase: mononuclear vanadium(V) phenolate complexes of the hydridotris(3,5-dimethylpyrazolyl)borate ligand (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTModels for the binding site in bromoperoxidase: mononuclear vanadium(V) phenolate complexes of the hydridotris(3,5-dimethylpyrazolyl)borate ligandStephen Holmes and Carl J. CarranoCite this: Inorg. Chem. 1991, 30, 6, 1231–1235Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/ic00006a014https://doi.org/10.1021/ic00006a014research-articleACS PublicationsRequest reuse permissionsArticle Views123Altmetric-Citations45LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Trace-Driven Cache Attacks on AES. (2006)

Cache based side-channel attacks have recently been attracted significant attention due to the new developments in the field. In this paper, we present efficient trace-driven cache attacks on a widely used implementation of the AES cryptosystem. We also evaluate the cost of the proposed attacks in detail under the assumption of a noiseless environment. We develop an accurate mathematical model that we use in the cost analysis of our attacks. We use two different metrics, specifically, the expected number of necessary traces and the cost of the analysis phase, for the cost evaluation purposes. Each of these metrics represents the cost of a different phase of the attack.
Recent advances in the understanding of skeletal muscle fatigue (2002)

Prolonged or repeated contractions of skeletal muscles lead to impaired muscle function, fatigue develops. Fatigue may be caused by factors within the muscle cells (peripheral fatigue) and diminished activation from the central nervous system (central fatigue). The relative importance of peripheral central fatigue depends on the type of physical activity. Central fatigue may be more prominent in elderly subjects. Increased concentration of inorganic phosphate seems to be of major importance for acute peripheral fatigue. There is frequently a long-lasting depression of force production after fatiguing muscle activity, especially at low stimulation frequencies. This low-frequency fatigue seems to be due to "structural" changes in proteins involved in intracellular Ca handling. Contractions in which the muscle is stretched (eccentric contractions) cause muscle weakness and damage. The initial defect induced by eccentric contractions is overstretched sarcomeres, but these appear to cause localized membrane tears that subsequently contribute to muscle weakness and damage.