gebhart/patrepeval huggingface dataset:
Detection of Salmonella enteritidis in incubated pools of egg contents by fluorescence polarization and lateral flow immunodiffusion (2003)

Efficient detection of Salmonella enteritidis inside eggs is critical for confirming that individual commercial laying flocks present a risk to public health. In most standard bacteriological culturing protocols, an initial incubation step is necessary to allow the typically very small population of S. enteritidis cells in pools of egg contents to multiply to more easily detectable levels. In the present study, two rapid methods were evaluated as alternatives to plating on selective media for detecting S. enteritidis in incubated egg pools. By using either fluorescence polarization or lateral flow immunodiffusion assays, S. enteritidis could be consistently detected in egg pools at 10(8) cfu/mL (and in most pools at 10(7) cfu/mL). Although the rapid assays were significantly less sensitive than culturing, they both were consistently able to detect contamination when pools of 10 eggs were inoculated with approximately 10 cfu of S. enteritidis and incubated for 72 h at 25 degrees C.
Disoriented Pen-Gestures for Identifying Users around the Tabletop without Cameras and Motion Sensors (2006)

We present an effective corollary from our works in pen gesture technologies, originally intended for conventional digital screen environments, that gives significant influence when expanded into the domain of tabletop displays. By virtue of incorporating angular and velocity type "trace features" for pen gesture cognition into current classical linear classifiers, we are able to place a greater emphasis not on the similarity of the "visual representation" of the gestures, but rather, on determining exactly from which corners of the table the gestures were conceived. In other words, we can find out which one of the four users around the table is interfacing with the tabletop display at any particular time, and do this without the need for additional sensing paraphernalia. We illustrate this inception by discussing our treatment of "disoriented" pen gestures with our version of a 'manual' Monopoly board game for the tabletop.
Negative selection of thymocytes. A novel polymerase chain reaction-based molecular analysis detects requirements for macromolecular synthesis (1992)

Self-tolerance is mainly established through clonal deletion of autoreactive T cells during thymic differentiation. The mechanisms by which deletion is achieved are poorly understood. Here we use a specific polymerase chain reaction-based system to characterize DNA fragmentation and show that after in vivo treatment of neonatal mice with staphylococcus enterotoxin B, selective apoptosis of V beta 8+ thymocytes occurs. This process precedes detectable deletion of V beta 8+ cells as determined by phenotypic analysis. Moreover, in vivo administration of cycloheximide and, to a lesser extent, actinomycin D, inhibits apoptosis of staphylococcus enterotoxin B specific thymocytes. Thus, macromolecular synthesis is a requirement for negative selection.
Contribution to the mechanism of the acid-catalyzed hydrolysis of purine nucleosides (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTContribution to the mechanism of the acid-catalyzed hydrolysis of purine nucleosidesL. Hevesi, E. Wolfson-Davidson, J. B. Nagy, O. B. Nagy, and A. BruylantsCite this: J. Am. Chem. Soc. 1972, 94, 13, 4715–4720Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/ja00768a046https://doi.org/10.1021/ja00768a046research-articleACS PublicationsRequest reuse permissionsArticle Views231Altmetric-Citations64LEARN 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
Specific Suppression of Human Tumor Necrosis Factor-α Synthesis by Antisense Oligodeoxynucleotides (1996)

Recent clinical studies using neutralizing antibodies point to a key role for tumor necrosis factor-alpha (TNF-alpha) in chronic inflammatory diseases. Antisense technique is a recent approach aiming at inhibition of single proteins. Previously, we described nonspecific induction of TNF by phosphorothioate oligonucleotides. In this study, we established an in vitro model that allows specific inhibition of TNF synthesis, bypassing TNF induction. Freshly isolated human monocytes were incubated with oligonucleotides and the cationic lipid lipofectin in different ratios. TNF synthesis was stimulated with lipopolysaccharide and quantified by a specific radioimmunoassay (RIA). Among all sequences tested, one of the antisense oligonucleotides complementary to the translation initiation region of TNF mRNA (5'-CAT GCT TTC AGT CAT-3') revealed highest efficacy. At 2 microM, the antisense oligonucleotide inhibited TNF synthesis by up to 79%. A concentration as low as 250 nM of the antisense oligonucleotide was effective. Scrambled controls and controls with different, defined degrees of mismatches confirmed a sequence-specific action. Examination with confocal fluorescence microscopy showed a marked difference comparing lipofectin-mediated vs. spontaneous uptake. This study defines criteria that from the prerequisite necessary for design and application of antisense oligonucleotides against TNF in vivo.
Introduction (2010)

This book presents a synthesis of the Prehistory of Asia Minor between about 20,000 and 2000 BC. It discusses the transformations of human societies in Asia Minor from small-scale groups engaged in hunting and gathering to complex, hierarchically organised communities with an economy based on agriculture and industry.
Nerve stimulation for chronic pelvic pain and bladder pain syndrome: a systematic review (2013)

Chronic pelvic pain (CPP) and bladder pain syndrome (BPS) can have a negative impact on quality of life. Neuromodulation has been suggested as a possible treatment for refractory pain. To assess the effectiveness of tibial and sacral nerve stimulation in the treatment of BPS and CPP. We searched until July 2012: the Cochrane Library, EMBASE (1980-2012), Medline (1950-2012), Web of knowledge (1900-2012), LILACS (1982-2012) and SIGLE (1990-2012) with no language restrictions. We manually searched through bibliographies and conference proceedings of the International Continence Society. Randomized and prospective quasi-randomized controlled studies vs. sham nerve stimulation treatment or usual care of patients with CPP and BPS who underwent sacral or tibial nerve stimulation were included. Any studies involving transcutaneous stimulation were excluded. The outcome was a cure or improvement in symptoms. Three studies with 169 patients treated with tibial nerve stimulation were included; two for CPP and one for BPS. There were improvements in pain, urinary and quality of life scores. There were no reported data for sacral nerve stimulation. There is scanty literature reporting variable success of posterior tibial nerve stimulation in improving pain, urinary symptoms and quality of life in CPP and BPS. In view of the dearth of quality literature, a large multi-centered clinical trial investigating the effectiveness of electrical nerve stimulation to treat BPS and CPP along with the cost-analysis of this treatment is recommended.
Quantum Computing Using Dissipation to Remain in a Decoherence-Free Subspace (2000)

We propose a new approach to the implementation of quantum gates in which decoherence during the gate operations is strongly reduced. This is achieved by making use of an environment induced quantum Zeno effect that confines the dynamics effectively to a decoherence-free subspace.
Anti‐inflammatory drugs (1974)

In the ideal sequence of events in developing a drug, one would first select a particular disease and then proceed to learn sufficient relevant facts about it (the first difficulty); then, one would know how to predict which particular chemical structure would have the required therapeutic effects without toxicity (the second difficulty); one would then synthesize the drug (perhaps difficult but probably possible); then, one would have valid and reliable testing models of the disease in animals (not presently known for any skin disease); after proof of efficacy and safety, finally the drug would be tested in the clinic (possible). Such a sequence has never been accomplished. The etiology of inflammatory diseases, particularly, is known to a limited extent only, and the dermal manifestations of them are understood still less. The pharmacologist therefore has many good opportunities here for rewarding work.
Three Cell Wall Mannoproteins Facilitate the Uptake of Iron in Saccharomyces cerevisiae (2001)

Analysis of iron-regulated gene expression in Saccharomyces cerevisiae using cDNA microarrays has identified three putative cell wall proteins that are directly regulated by Aft1p, the major iron-dependent transcription factor in yeast. FIT1, FIT2, and FIT3 (for facilitator of iron transport) were more highly expressed in strains grown in low concentrations of iron and in strains in which AFT1-1(up), a constitutively active allele of AFT1, was expressed. Northern blot analysis confirmed that FIT1, FIT2, and FIT3 mRNA transcript levels were increased 60-230-fold in response to iron deprivation in an Aft1p-dependent manner. Fit1p was localized exclusively to the cell wall by indirect immunofluorescence. Deletion of the FIT genes, individually or in combination, resulted in diminished uptake of iron bound to the siderophores ferrioxamine B and ferrichrome, without diminishing the uptake of ferric iron salts, or the siderophores triacetylfusarinine C and enterobactin. FIT-deletion strains exhibited increased expression of Aft1p target genes as measured by a FET3-lacZ reporter gene or by Arn1p Western blotting, indicating that cells respond to the absence of FIT genes by up-regulating systems of iron uptake. Aft1p activation in FIT-deleted strains occurred when either ferrichrome or ferric salts were used as sources of iron during growth, suggesting that the FIT genes enhance uptake of iron from both sources. Enzymatic digestion of the cell wall resulted in the release of significant amounts of iron from cells, and the relative quantity of iron released was reduced in FIT-deletion strains. Fit1p, Fit2p, and Fit3p may function by increasing the amount of iron associated with the cell wall and periplasmic space.
A novel minigene scaffold for therapeutic cancer vaccines (2014)

Genetic vaccines are emerging as a powerful modality to induce T-cell responses to target tumor associated antigens (TAA). Viral or plasmid DNA or RNA vectors harbor an expression cassette encoding the antigen of choice delivered in vivo by vaccination. In this context, immunizations with minigenes containing selected, highly antigenic, T-cell epitopes of TAAs may have several advantages relative to full-length proteins. The objective of this study was to identify an optimal scaffold for minigene construction. We generated a number of minigenes containing epitopes from the carcinoembryonic antigen (CEA) model TAA and utilized muscle DNA electro-gene-transfer (DNA-EGT) to vaccinate HLA-A*0201 (HHD) and CEA/HHD double transgenic mice. The components utilized to construct the minigenes included CD8<sup>+</sup> T cell epitopes and (or) anchor modified analogs that were selected on the basis of their predicted binding to HLA-*A0201, their uniqueness in the human proteome, and the likelihood of cancer cell natural processing and presentation via MHC-I. Other candidate components comparatively tested included: helper CD4<sup>+</sup> T-cell epitopes, flanking regions for optimal epitope processing (including both proteasome-dependent and furin-dependent polypeptide processing mechanisms), and immunoenhancing moieties. Through a series of comparative studies and iterations we have identified an optimal minigene scaffold comprising the following elements: human tissue plasminogen activator (TPA) signal peptide, T-cell epitopes connected by furin sensitive linkers, and the <i>E. Coli</i> enterotoxin B subunit. The selected epitope modified minigenes (EMM) delivered by DNA-EGT were able to break immune tolerance in CEA/HHD mice and induce a strong immune response against all epitopes tested, independently of their relative positions within the scaffold. Furthermore, the optimized EMMs delivered via DNA-EGT were more immunogenic and exerted more powerful antitumor effects in a B16-CEA/HHD metastatic melanoma model than a DNA vector encoding the full-length protein or a mixture of the same peptides injected subcutaneously. Our data may shed light on the optimal design of a universal vehicle for epitope-targeted, genetic cancer vaccines.
Interferences of Ultrashort Free Electron Wave Packets (2002)

Interferences of free electron wave packets generated by a pair of identical, time-delayed, femtosecond laser pulses which ionize excited atomic potassium have been observed. Two different schemes are investigated: threshold electrons produced by one-photon ionization with parallel laser polarization and above threshold ionization electrons produced by a two-photon transition with crossed laser polarization. Our results show that the temporal coherence of light pulses is transferred to free electron wave packets, thus opening the door to a whole variety of exciting experiments.
ChemInform Abstract: Mn—Zn Soft Magnetic Ferrite Nanoparticles Synthesized from Spent Alkaline Zn—Mn Batteries. (2011)

Abstract Mn 0.5 Zn 0.5 Fe 2 O 4 nanoparticles are prepared using spent alkaline batteries as raw materials by a multi‐step process including acid leaching, chemical treatment of iron shells, and citrate—nitrate precursor auto‐combustion.
Regression trees for analysis of mutational spectra in nucleotide sequences. (1999)

The REGRT program is available upon request from V.Berikov.
Retinoid X Receptors in the Kidney: Their Protein Expression and Functional Significance (1997)

Retinoid X receptors (RXRs) heterodimerize with 1,25-dihydroxyvitamin D3 (VD) receptor (VDR), and play important roles in VD-regulated transactivation. VD acts on many tissues including kidney for the regulation of calcium homeostasis. In the kidney, the expression of VDR in the tubular cells has been well studied. In contrast, little is known about the localization and the functional significance of RXRs there. In order to elucidate these questions, we first performed immunohistochemical analyses of rat kidney using isoform-specific antimouse RXR antibodies we have previously reported. Interestingly, all RXR isoforms, predominantly RXR alpha, mainly localized to the proximal and the distal tubules, but not to the glomeruli. The serial section staining using anti-VDR antibody showed the colocalization of RXR alpha and VDR in those tubular cells. In order to elucidate the functional significance of endogenous receptors in the tubular cells, we next performed transient transfection studies using the tubular-cell derived Madin-Darby bovine kidney cells, which express both endogenous VDR and RXR. We transfected a reporter plasmid containing direct repeat 3 (DR3) sequence, to which only RXR/VDR heterodimer can bind, and found that VD and 9-cis retinoic acid, as well as VD and RXR selective agonist LG100153, had an additive effect for the DR3 transactivation. Taken together, we speculate that endogenous RXRs co-localize with VDR, and coregulate VD-dependent genes in the tubular cells of the kidney as RXR/VDR heterodimer.
Comparison of Heating of Nonliving Soft Tissue produced by 45 kHz and 1 MHz Frequency Ultrasound Machines (1996)

Ultrasound of 1 MHz frequency is used routinely for patient treatment because it can penetrate to and heat deeply located tissue. Benefits are claimed for newly introduced 45 kHz ultrasound machines, yet little evidence is available to confirm these benefits. This paper compares claims supporting the therapeutic use of 45 kHz ultrasound with those supporting the traditional MHz frequencies. The results of an empirical study comparing the heating effects are also presented. Thermocouples placed at different tissue depths in nonliving pig tissue measured temperature variations over a 40-minute period. Direct heating produced by the 45 kHz ultrasound machine was very superficial. By contrast, the 1 MHz ultrasound machine produced direct heating at all tissue depths. The results confirmed that although 45 kHz ultrasound machines may be useful for heating superficial tissues, they have limited or no use in heating deeper tissues. For treatment of deeply located tissue, 1 MHz ultrasound should continue to be used.
Pythagoras (1999)

Wer war Pythagoras? Was hat er geleistet? Warum hat er es geleistet? Diese Fragen sind nicht leicht zu beantworten, obwohl der Name noch heute allgemein bekannt ist.
Stress hormone epinephrine promoting the growth of human hepatocellular carcinoma cells via β2-AR-mediated activation of ERK1/2 (2010)

Objective To investigate the effect of the stress hormone epinephrine (EPI) on the growth of human Hepatocellular carcinoma (HCC) cells.Methods The effects of EPI on the growth of human HCC HepG2 and MHCC97H cells were investigated by using proliferation assay in correlation with α1-/β2-adrenergic receptors (α1-/β2-ARs),proliferative activity and signaling pathways of adenyl cyclase/protein kinase A (AC/PKA),mitogen-activated protein kinase/extracellular signal-regulated kinase 1/2 (MAPK/ERK1/2) and phosphatidylinositol-3-kinase/protein kinase B ( PI3 K/AKT/PKB).Results EPI significantly promoted the growth of HCC cells rather than human normal hepatic cells (L-02) in a dose-dependent and time-dependent manner (P ＜ 0.05 ).The maximal growth rate was presented at concentration of 10 μmol/L and 24-48 h [HepG2/(215 ±4)% and MHCC97H/(207 ± 10)%].In HepG2 and MHCC97H cells,α1-AR was reduced to 30% and 34%,and β2-AR was elevated to 331% and 309% of that in L-02,respectively.The selective β2-AR antagonist ICI 118551 efficiently attenuated the growth-promoting effect of EPI,and the β-AR agonist isoproterenol (ISO) exhibited a similar growth-promoting effect on HCC cells.The effect of ISO was efficiently attenuated either by ICI 118551 or the MAPK/ERK kinase 1/2 (MEK1/2) inhibitor U0126,but partially inhibited either by the PKA inhibitor H-89 or PI3K inhibitor LY294002.The phospho-ERK1/2 was transiently elevated by 3.49/3.02 folds in HepG2 and 3.15/2.73 folds in MHCC97H cells,which could be down-regulated either by the treatment of ICI 118551 or U0126.Conclusion β2-AR was over-expressed in both HepG2 and MHCC97H cells.EPI promoted the growth of HepG2 and MHCC97H cells mainly through the β2-AR-mediated activation of ERK1/2.

Key words: 
Carcinoma,hepatocellular; Stress; Adrenergic receptor; Extracellular signalregulated kinase 1/2
A Concise Synthesis of the Antifungal Agent (+)-Preussin (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA Concise Synthesis of the Antifungal Agent (+)-PreussinMark Overhand and Sidney M. HechtCite this: J. Org. Chem. 1994, 59, 17, 4721–4722Publication Date (Print):August 1, 1994Publication History Published online1 May 2002Published inissue 1 August 1994https://pubs.acs.org/doi/10.1021/jo00096a007https://doi.org/10.1021/jo00096a007research-articleACS PublicationsRequest reuse permissionsArticle Views1055Altmetric-Citations60LEARN 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
RNA-Seq analysis of glioma tumors to reveal targetable gene fusions. (2017)

2019 Background: Fusions involving oncogenes have been reported in gliomas and may serve as novel therapeutic targets. We aim to use RNA-sequencing to interrogate a large cohort of gliomas for targetable genetic fusions. Methods: Gliomas were profiled using the ArcherDx FusionPlex Assay at a CLIA-certified lab (Caris Life Sciences) and 52 gene targets were analyzed. Fusions with preserved kinase domains were investigated. Results: Among 404 gliomas tested, 39 (9.7%) presented potentially targetable fusions, of which 24/226 (11%) of glioblastoma (GBM), 5/42 (12%) of anaplastic astrocytoma (AA), 2/25 (8%) of grade II astrocytoma and 3 of 7 (43%) of pilocytic astrocytoma (PA) harbored targetable fusions. In GBMs, 1 of 15 (6.7%) IDH-mutated tumors had a fusion while 22 of 175 (12.6%) IDH-wild type tumors had fusions. 46 oligodendroglial tumors were profiled and no fusions were seen, which was lower than frequency of fusions in astrocytic tumors (34/300, p = 0.0236). The most frequent fusions seen involved FGFR3 (N = 12), including 10 FGFR3-TACC3 (1 AA, 6 GBM and 3 glioma NOS); 1 FGFR3-NBR1 (AA) and 1 FGFR3-BRAP (GBM). 11 fusions involving MET were seen, 10 in GBM and 1 in AA. The most common MET fusion was PTPRZ1-MET (1 in AA and 4 in GBM), followed by ST7-MET (N = 3, GBM), CAPZA2-Met (N = 2, GBM) and TPR-MET (N = 1, GBM). 8 NTRK fusions were seen; 1 involving NTRK1 (BCAN-NTRK1, PA), 6 NTRK2 (1 NOS1AP-NTRK2 in AA; GKAP1-NTRK2, KCTD8-NTRK2, TBC1D2-NTRK2 and SOSTM1-NTRK2, 1 each in GBM and 1 VCAN-NTRK2 in grade II astrocytoma) and 1 NTRK3 (EML4-NTRK3 in GBM). EGFR fusions (2 EGFR-SEPT14 and 1 EGFR-VWC2) were seen in 3 GBMs, BRAF in 3 (1 KIAA1549-BRAF, 1 LOC100093631-BRAF in PA and 1 ZSCAN23-BRAF in glioma NOS) and PDGFRA (RAB3IP-PDGFRA, in GBM) in 1. C11orf95-RELA fusions were seen in 2 of 3 grade III ependymomas but not in the 2 grade II ependymomas. Conclusions: We report targetable fusion genes involving NTRK, MET, EGFR, FGFR3, BRAF and PDGFRA including novel fusions that haven’t been previously described in gliomas (e.g., EGFR-VWC2; FGFR3-NBR1). Fusions were seen in over 10% of astrocytic tumors, while none was seen oligodendrogliomas. Identification of such kinase-associated fusion transcripts may allow us to exploit therapeutic opportunities with targeted therapies in gliomas.