gebhart/patrepeval huggingface dataset:
Molecular characterization and phylogenetic distribution of the streptococcal superantigen gene (ssa) from Streptococcus pyogenes (1994)

A striking increase in the frequency and severity of invasive infections caused by Streptococcus pyogenes has occurred in recent years. Among these diseases is streptococcal toxic-shock-like syndrome (TSLS), a condition characterized by fulminant soft-tissue destruction and multiorgan failure. Streptococcal superantigen (SSA), a superantigen isolated from a TSLS-inducing, serotype M3 S. pyogenes strain, has recently been identified. We here describe the cloning, sequencing, and phylogenetic distribution of the SSA structural gene. The 783-bp open reading frame encodes a predicted 260-amino-acid protein that is similar in size to several other bacterial superantigens. The deduced sequence of the mature protein is 60.2% identical to that of staphylococcal enterotoxin B but only 49% identical to that of streptococcal pyrogenic exotoxin A. Southern blot and PCR analysis of 138 group A streptococcal strains representing 65 M protein serotypes and 15 nontypeable isolates identified ssa in 68 strains from 10 distinct clonal lineages. All ssa-positive clones expressed SSA. Of the two clones associated with TSLS, the ET 2-M3 lineage, but not the ET 1-M1 lineage, carried the SSA gene. Further analysis of the ET 2-M3 lineage found evidence for temporal variation in ssa association. Contemporary ET 2-M3 disease isolates had ssa, but two older isolates of this clone recovered in 1910 and 1920 lacked the gene. The clonal and temporal distribution patterns of ssa suggest a relatively recent acquisition of this superantigen-encoding gene by the ET 2-M3 lineage, perhaps by horizontal transfer and recombination.
Cover Picture: Angew. Chem. Int. Ed. 4/2003 (2003)

Flexible and dynamic channels created by an interdigitated framework of microporous coordination polymers are shown on the cover picture. The compound undergoes reversible crystal‐to‐crystal transformation from a nonporous (closed‐form) to a microporous (open‐form) structure, which is triggered by adsorption of supercritical gases. A hysteretic isotherm, shown bottom left, displays abrupt adsorption at a gate‐opening pressure and equally sharp desorption at a gate‐closing pressure. More about this coordination polymer is reported in the Communication by S. Kitagawa et al. on page 428 ff.
GENETIC CONTROL OF THE ANTIBODY RESPONSE TO TYPE III PNEUMOCOCCAL POLYSACCHARIDE IN MICE (1972)

The IgM antibody response to Type III pneumococcal polysaccharide (SSS-III) was assessed in F(1), F(2), and backcross progeny derived from high (BALB/cAnN) and extremely low (CBA/HN) responding parental strains of inbred mice. The results of these studies indicated that a major component involved in the antibody response is X-linked, i.e., carried on the X chromosome; this component determines responsiveness to SSS-III in an almost quantal or "all-or-none" manner. Other factors, presumably autosomal genes, regulate the magnitude of the antibody response produced by mice possessing the X-linked gene; these appear to influence independently the number of antibody-producing cells found after immunization and the amount of antibody made by such cells. Strains of inbred mice varied widely in their ability to respond to SSS-III. Responsiveness was not associated with H-2 histocompatibility type. The implications of these findings with respect to the genetic control of the antibody response to SSS-III are discussed.
MiyakoDori: A Memory Reusing Mechanism for Dynamic VM Consolidation (2012)

In Infrastructure-as-a-Service datacenters, the placement of Virtual Machines (VMs) on physical hosts are dynamically optimized in response to resource utilization of the hosts. However, existing live migration techniques, used to move VMs between hosts, need to involve large data transfer and prevents dynamic consolidation systems from optimizing VM placements efficiently. In this paper, we propose a technique called “memory reusing” that reduces the amount of transferred memory of live migration. When a VM migrates to another host, the memory image of the VM is kept in the source host. When the VM migrates back to the original host later, the kept memory image will be “reused”, i.e. memory pages which are identical to the kept pages will not be transferred. We implemented a system named MiyakoDori that uses memory reusing in live migrations. Evaluations show that MiyakoDori significantly reduced the amount of transferred memory of live migrations and reduced 87% of unnecessary energy consumption when integrated with our dynamic VM consolidation system.
Development of an adenoviral vector system with adenovirus serotype 35 tropism; efficient transient gene transfer into primary malignant hematopoietic cells (2004)

Our study will facilitate the generation of fiber-retargeted adenoviral vectors and enable transient genetic manipulation of primary malignant hematopoietic cells.
Antiandrogenic steroidal sulfonylpyrazoles (1990)

The steroidal sulfonylpyrazole 1 bound to the rat ventral prostate androgen receptor in vitro; it inhibited testosterone propionate induced increases in ventral prostate weight in vivo in the castrated, immature male rat with an ED50 of 15 mg/kg po. Compound 1 lacked androgenic activity in vivo in contrast to the parent steroidal pyrazole 5, which was both androgenic and antiandrogenic. The 2'- and 5'-methylsulfonyl isomers 6 and 6a did not bind to the androgen receptor. Introduction of an alkylsulfonyl at the N-1'-position has served, therefore, to isolate the intrinsic antiandrogenic properties of the steroidal heterocycle free of apparent hormone agonist properties. Structure-activity relationship studies revealed that a methylsulfonyl group at N-1' together with a C-17 alpha-substituent were the optimal combination for in vitro androgen receptor binding, in vivo antiandrogenic potency, and a lack of androgenic activity.
Repetitive transcranial magnetic stimulation has a beneficial effect on bradykinesia in Parkinsonʼs disease (1999)

The effect of focal 5 Hz repetitive transcranial magnetic stimulation (rTMS) of the motor hand area (M1) on bradykinesia was studied in 12 unmedicated patients with Parkinson's disease (PD). On 2 separate days, a real-rTMS was applied to M1 contralaterally to the more severely affected limb or a frontal sham-rTMS was applied 3 cm anteriorly to Fz in a random order. Stimulus intensity was 10% below resting motor threshold. Before and 20 min after rTMS, patients performed 15 consecutive pointing movements with the index finger contralaterally to the stimulated M1. Compared with sham-rTMS, real-rTMS over the contralateral M1 caused a significant decrease in total movement time without affecting end-point accuracy. Our data provide evidence that 5 Hz rTMS over M1 can improve bradykinesia in PD patients beyond the time of magnetic stimulation.
3-Hydroxyisoxazole-5-hydroxamic acid (1977)

&lt;p&gt;In the present study, effects of hydrogen induction on combustion characteristics of a compression ignition diesel engine were investigated and a comprehensive model for identifying knocking combustion was developed. This was done by defining number of critical local regions within the CFD (computational fluid dynamics) computational domain for a hydrogen assisted compression ignition engine. Regional parameters such as local pressure rise rate, local heat release rate and local concentration change of specific chemical species were used for knock identification. Comprehensive chemical kinetics mechanisms of diesel and hydrogen fuels were used enabling detailed chemistry predictions. After validation of the model for extensive diesel operating conditions; 1%, 3%, 5% and 7% hydrogen induction in volume in intake air was considered for a single case to investigate knocking combustion. Using the developed knock prediction model, results showed knocking combustion for hydrogen-air premixed charges richer than 5% by volume. This was well captured by the regional pressure rise rate and heat release rate diagrams. Moreover, regional data showed that knock occurred in central parts of the piston bowl and above the piston crown, whereas location near to cylinder wall did not show the same trend. In former locations, very high rate of production and consumption for HO&lt;sub&gt;2&lt;/sub&gt; as a free radical was resulted. This was coincided with higher hydrogen consumption and temperature rise.&lt;/p&gt;
Tumor-infiltrating myeloid cells induce tumor cell resistance to cytotoxic T cells in mice (2011)

Cancer immunotherapeutic approaches induce tumor-specific immune responses, in particular CTL responses, in many patients treated. However, such approaches are clinically beneficial to only a few patients. We set out to investigate one possible explanation for the failure of CTLs to eliminate tumors, specifically, the concept that this failure is not dependent on inhibition of T cell function. In a previous study, we found that in mice, myeloid-derived suppressor cells (MDSCs) are a source of the free radical peroxynitrite (PNT). Here, we show that pre-treatment of mouse and human tumor cells with PNT or with MDSCs inhibits binding of processed peptides to tumor cell-associated MHC, and as a result, tumor cells become resistant to antigen-specific CTLs. This effect was abrogated in MDSCs treated with a PNT inhibitor. In a mouse model of tumor-associated inflammation in which the antitumor effects of antigen-specific CTLs are eradicated by expression of IL-1β in the tumor cells, we determined that therapeutic failure was not caused by more profound suppression of CTLs by IL-1β-expressing tumors than tumors not expressing this proinflammatory cytokine. Rather, therapeutic failure was a result of the presence of PNT. Clinical relevance for these data was suggested by the observation that myeloid cells were the predominant source of PNT in human lung, pancreatic, and breast cancer samples. Our data therefore suggest what we believe to be a novel mechanism of MDSC-mediated tumor cell resistance to CTLs.
Experimental vaccination withCandida albicansribosomes in cyclophosphamide-treated animals (1981)

A study was carried out to determine whether protection against experimental systemic candidiasis can be induced by vaccination with Candida albicans ribosomes in animals compromised by cyclophosphamide (CY) treatment. ICR mice treated with CY showed a reduction in the number of leukocytes and a decrease in spleen and body weights. CY-treated mice were more susceptible to intraperitoneal (IP) or intravenous (IV) challenge with live C. albicans than the untreated animals. Vaccination of CY-treated mice with C. albicans ribosomes, with or without addition of incomplete Freund's adjuvant, led to a partial protection against a lethal IP or IV challenge with live yeasts. These results indicate the possible effectiveness of ribosomal vaccination in protecting the compromised host against experimental candidiasis.
Generation of Dendritic Cells In Vitro From Peripheral Blood Mononuclear Cells With Granulocyte-Macrophage-Colony-Stimulating Factor, Interleukin-4, and Tumor Necrosis Factor-α for Use in Cancer Immunotherapy (1997)

Generation of mature DC in the authors' serum-free clinically applicable conditions is similar to serum-containing conditions and requires CD14+ precursors, differentiation through a CD14-CD83- immature stage under the influence of GM-CSF and IL-4, and maturation into a CD83+ DC under the influence of TNF-alpha.
Thyroid hormone regulation of a transcriptional coactivator in Xenopus laevis: Implication for a role in postembryonic tissue remodeling (2002)

Thyroid hormone (TH) affects biological processes by regulating gene transcription through TH receptors (TRs). In the presence of TH, TR activates target gene transcription by recruiting one or more transcription coactivators belonging to diverse groups. Here, we demonstrate that during TH-dependent anuran metamorphosis, one such coactivator gene, the Xenopus laevis homolog of human Trip7, is up-regulated by TH. Kinetic studies suggest that Xenopus Trip7 is most likely induced indirectly by TH in a tissue-dependent manner. In the intestine, which undergoes extensive remodeling as the animal changes from being herbivorous to carnivorous, Trip7 is expressed at high levels during but not before or after metamorphosis. It is also up-regulated in other growing or remodeling tissues such as the brain and limb but not in degenerating tadpole tail skin. By using frog oocyte as a model, we show that Trip7 influences basal transcription in a chromatin structure-dependent manner but enhances the function of liganded TR regardless of the chromatin structure of the target promoter. In vitro studies indicate that Trip7 interacts directly with TR. These results suggest that during Xenopus metamorphosis, TH up-regulates, albeit indirectly, Trip7 to enhance TR function during larval-to-adult tissue transformation.
Josephson Traveling-Wave Parametric Amplifier with Three-Wave Mixing (2016)

Josephson parametric amplifiers (JPAs) are important tools in quantum information technology, and traveling-wave JPAs with extended bandwidth are especially desired for frequency multiplexing, $e.g.$ in qubit readout. So far these devices have required the four-wave mixing condition to operate. The author shows, however, that there is a way to realize $t\phantom{\rule{0}{0ex}}h\phantom{\rule{0}{0ex}}r\phantom{\rule{0}{0ex}}e\phantom{\rule{0}{0ex}}e-w\phantom{\rule{0}{0ex}}a\phantom{\rule{0}{0ex}}v\phantom{\rule{0}{0ex}}e$ mixing, with negligible phase mismatch. This simple traveling-wave amplifier would offer large gain, wide bandwidth, and ultimately quantum-limited characteristics, outperforming its state-of-the-art four-wave counterparts.
A convenient method for the reduction of ozonides to alcohols with borane-dimethyl sulfide complex (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convenient method for the reduction of ozonides to alcohols with borane-dimethyl sulfide complexLee A. Flippin, David W. Gallagher, and Keyvan Jalali-AraghiCite this: J. Org. Chem. 1989, 54, 6, 1430–1432Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/jo00267a035https://doi.org/10.1021/jo00267a035research-articleACS PublicationsRequest reuse permissionsArticle Views1075Altmetric-Citations121LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Functions of Heat Shock Proteins in Pathways of the Innate and Adaptive Immune System (2014)

For more than 50 years, heat shock proteins (HSPs) have been studied for their role in protecting cells from elevated temperature and other forms of stress. More recently, several roles have been ascribed to HSPs in the immune system. These include intracellular roles in Ag presentation and expression of innate receptors, as well as extracellular roles in tumor immunosurveillance and autoimmunity. Exogenously administered HSPs can elicit a variety of immune responses that have been used in immunotherapy of cancer, infectious diseases, and autoimmune disease.
Fluorogenic peptide substrates for carboxydipeptidase activity of cathepsin B. (2004)

Cathepsin B is a lysosomal cysteine protease exhibiting mainly dipeptidyl carboxypeptidase activity, which decreases dramatically above pH 5.5, when the enzyme starts acting as an endopeptidase. Since the common cathepsin B assays are performed at pH 6 and do not distinguish between these activities, we synthesized a series of peptide substrates specifically designed for the carboxydipeptidase activity of cathepsin B. The amino-acid sequences of the P(5)-P(1) part of these substrates were based on the binding fragments of cystatin C and cystatin SA, the natural reversible inhibitors of papain-like cysteine protease. The sequences of the P'(1)-P'(2) dipeptide fragments of the substrates were chosen on the basis of the specificity of the S'(1)-S'(2) sites of the cathepsin B catalytic cleft. The rates of hydrolysis by cathepsin B and papain, the archetypal cysteine protease, were monitored by a continuous fluorescence assay based on internal resonance energy transfer from an Edans to a Dabcyl group. The fluorescence energy donor and acceptor were attached to the C- and the N-terminal amino-acid residues, respectively. The kinetics of hydrolysis followed the Michaelis-Menten model. Out of all the examined peptides Dabcyl-R-L-V-G-F- E(Edans) turned out to be a very good substrate for both papain and cathepsin B at both pH 6 and pH 5. The replacement of Glu by Asp turned this peptide into an exclusive substrate for cathepsin B not hydrolyzed by papain. The substitution of Phe by Nal in the original substrate caused an increase of the specificity constant for cathepsin B at pH 5, and a significant decrease at pH 6. The results of kinetic studies also suggest that Arg in position P(4) is not important for the exopeptidase activity of cathepsin B, and that introducing Glu in place of Val in position P(2) causes an increase of the substrate preference towards this activity.
Enhanced expression of ASB6 and IFIT2 in oral squamous cell carcinoma (2006)

910 Oral squamous cell carcinoma (OSCC) is the most common cancer of the head and neck region and accounts for over 300,000 new cancer cases worldwide every year. In Taiwan, OSCC accounts for the sixth leading cause of cancer mortality and the fourth most common cancer in males, while the occurrence of 80% OSCC is associated with areca chewing. To identify tumor biomarkers, we have recently identified that the expression of ankyrin repeat and SOCS box-containing 6 (ASB6) and interferon-induced protein with tetratricopeptide repeats 2 (IFIT2) were significantly enhanced in OSCC tissue samples. Using RT-PCR analysis, 60% and 95% of OSCC tissues were shown with enhanced ASB6 and IFIT2 expression, respectively, as compared to non-cancerous matched tissues. ASB6 is a member of suppressor of cytokine signaling family, while IFIT2 belongs to interferon-induced protein without a known function. Since most OSCC patients in Taiwan are areca chewers, we therefore treated OEC-M1 cells, an OSCC cell line, with various concentrations (0 to 80 μg/ml) of areca nut extracts (ANE) for 48 to 72 h. Our results demonstrated that ANE treatment remarkably elevated the expression of both ASB6 and IFIT2 genes. These results imply a possible association of elevated expression of these two genes with areca chewing. In addition, we also found that the protein levels of IFIT2 were enhanced in OEC-M1 cells following TGF-β1 treatment. Whether ASB6 and IFIT2 can serve as tumor markers for OSCC patients warrants our further investigation.
Ensembl 2018 (2017)

The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser.
TRP Vanilloid 2 Knock-Out Mice Are Susceptible to Perinatal Lethality But Display Normal Thermal and Mechanical Nociception (2011)

TRP vanilloid 2 (TRPV2) is a nonselective cation channel expressed prominently in medium- to large-diameter sensory neurons that can be activated by extreme heat (>52°C). These features suggest that TRPV2 might be a transducer of noxious heat in vivo. TRPV2 can also be activated by hypoosmolarity or cell stretch, suggesting potential roles in mechanotransduction. To address the physiological functions of TRPV2 in somatosensation, we generated TRPV2 knock-out mice and examined their behavioral and electrophysiological responses to heat and mechanical stimuli. TRPV2 knock-out mice showed reduced embryonic weight and perinatal viability. As adults, surviving knock-out mice also exhibited a slightly reduced body weight. TRPV2 knock-out mice showed normal behavioral responses to noxious heat over a broad range of temperatures and normal responses to punctate mechanical stimuli, both in the basal state and under hyperalgesic conditions such as peripheral inflammation and L5 spinal nerve ligation. Moreover, behavioral assays of TRPV1/TRPV2 double knock-out mice or of TRPV2 knock-out mice treated with resiniferatoxin to desensitize TRPV1-expressing afferents revealed no thermosensory consequences of TRPV2 absence. In line with behavioral findings, electrophysiological recordings from skin afferents showed that C-fiber responses to heat and C- and Aδ-fiber responses to noxious mechanical stimuli were unimpaired in the absence of TRPV2. The prevalence of thermosensitive Aδ-fibers was too low to permit comparison between genotypes. Thus, TRPV2 is important for perinatal viability but is not essential for heat or mechanical nociception or hypersensitivity in the adult mouse.
Neural Network Deinterlacing Using Multiple Fields and Field-MSEs (2007)

Generally, deinterlacing algorithms can be either classified as intra methods or inter methods. Intra methods interpolate missing lines by using surrounding pixels in the current field. Inter methods interpolate missing lines by using pixels and the motion information of multiple fields. Neural network deinterlacing that uses multiple fields has been proposed. It provides improved performance compared to existing neural network deinterlacing algorithms that use a single field. However, when adjacent fields are very different, neural network deinterlacing that uses multiple fields may not provide good performance. To address this problem, we propose using field-MSE values as additional inputs. These MSE values can provide helpful information so that the networks can consider field differences in using multiple fields. Experimental results show that the use of the proposed algorithm results in improved performance.