gebhart/patrepeval huggingface dataset:
Dysregulation of the Hedgehog pathway in human hepatocarcinogenesis (2005)

Hedgehog (Hh) pathway activation promotes tumors in several endodermally derived tissues, but its role in the pathogenesis of hepatocellular carcinoma (HCC) is unknown. Although normal hepatocytes lack Hh signaling, activation of the Hh pathway in endodermal progenitors is required for liver development. Thus, we hypothesized that hepatocarcinogenesis may involve regulation of Hh signaling. This pathway is activated when Hh ligand binds to its receptor, Patched (PTC). In an unoccupied state, PTC normally functions as a tumor suppressor that inhibits Smoothened (SMO), a proto-oncoprotein, from activating downstream components and transcription of target genes. Here we show that in HCCs, overexpression of the Smo proto-oncogene, as well as an increase in the stoichiometric ratio of Smo to Ptc mRNA levels, correlated with tumor size, a prognostic indicator in HCC biology. In one tumor we identified a novel Smo mutation in an evolutionarily conserved residue. We also demonstrated that HCC cell lines (HepG2 and Hep3B) expressed Hh pathway components and activated Hh transcriptional targets. In Hep3B cells, cyclopamine, an inhibitor of wild-type SMO, had no effect, but KAAD-cyclopamine, a blocker of oncogenic SMO, inhibited Hh signaling activity by 50%, decreased expression of the hepatocarcinogenic oncogene, c-myc, by 8-fold, and inhibited the growth rate of Hep3B cells by 94%. These data support our hypothesis that Hh signaling is dysregulated in human hepatocarcinogenesis. We demonstrate that overexpression and/or tumorigenic activation of the Smo proto-oncogene mediates c-myc overexpression which plays a critical role in hepatocarcinogenesis and suggests that Smo is a prognostic factor in HCC tumorigenesis.
CT-guided Transthoracic Needle Aspiration Biopsy of Pulmonary Nodules: Needle Size and Pneumothorax Rate (2003)

Use of a smaller coaxial stabilizing needle produces a substantially decreased risk of pneumothorax with comparable diagnostic accuracy, sensitivity, and specificity for histopathologic diagnosis of pulmonary nodules.
Risk taking: a supervisory imperative. (1997)

Beset with job uncertainty and shifting responsibilities, today's health care supervisors are faced with frequent decisions that impact their careers and professional status. To stand pat and avoid change usually involve greater risk than taking chances and may result in job loss. To make bad decisions can also be detrimental. The goal of this article is to encourage one to accept accountability, to avoid the "victim complex," and to make decisions more effectively.
Handbook of Corrosion Data (1995)

Now in its second printing (first was Aug. DEGREES89), this book provides a starting point from which more detailed analysis of the literature may be initiated to fully evaluate the performance of metals in corrosive environments. It is an aid in eliminating alloys that are obviously inappropriate.
Advances in biomedical imaging using THz technology with applications to burn-wound assessment (2012)

Terahertz (THz) hydration sensing and image has been a topic of increased interest recently due largely to improvements in source and detector technology and the identification of applications where current hydration sensing techniques are insufficient. THz medical imaging is an expanding field of research and tissue hydration plays a key role in the contrast observed in THz tissue reflectance and absorbance maps. This paper outlines the most recent results in burn and corneal imaging where hydration maps were used to assess tissue status. A 3 day study was carried out in rat models where a THz imaging system was used to assess the severity and extent of burn throughout the first day of injury and at the 24, 48, and 72 hour time points. Marked difference in tissue reflectance were observed between the partial and full thickness burns and image features were identified that may be used as diagnostic markers for burn severity. Companion histological analysis performed on tissue excised on Day 3 confirms hypothesized burn severity. The results of these preliminary animal trials suggest that THz imaging may be useful in burn wound assessment where current clinical modalities have resolution and/or sensitivity insufficient for accurate diagnostics.
Ribonucleic acid isolated by cesium chloride centrifugation (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRibonucleic acid isolated by cesium chloride centrifugationVladimir Glisin, Radomir Crkvenjakov, and Craig ByusCite this: Biochemistry 1974, 13, 12, 2633–2637Publication Date (Print):June 1, 1974Publication History Published online1 May 2002Published inissue 1 June 1974https://pubs.acs.org/doi/10.1021/bi00709a025https://doi.org/10.1021/bi00709a025research-articleACS PublicationsRequest reuse permissionsArticle Views1338Altmetric-Citations1494LEARN 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
P111 BIOLOGICAL THERAPY FOR PAEDIATRIC IBD IN SCOTLAND 1/00 12/08: A NATIONWIDE ‘REAL LIFE’ EXPERIENCE (2009)

had not increased after the approval; 37 (2006), 37 (2007) and 28 (2008).AZA or 6-MP had been stopped in 36 patients (30 due to the recommendations and 6 due to intolerance).The withdrawal did not affect the disease activity in 25 patients whereas in 9 the activity had increased moderately, in 2 significantly.Only one of 36 patients had restarted AZA while 7 patients had been started on methotrexate. Conclusion:The recommendations to withdraw AZA and 6-MP had very little negative effect on the disease activity.The guidelines for the usage of IFX in paediatric patients were implemented to a high degree.
Comparison of HIV-1 and avian myeloblastosis virus reverse transcriptase fidelity on RNA and DNA templates. (1992)

A comparison of the fidelity of reverse transcriptases (RT) from human immunodeficiency virus (HIV-1) and avian myeloblastosis virus (AMV) is made using RNA and DNA primer-template molecules in vitro. Selected template target sites containing either uracil or thymine are used to measure nucleotide insertion fidelities and to compare the efficiency of extending mismatched nucleotides at primer 3'-termini. HIV-1 reverse transcriptase is observed to incorporate as many as three consecutive mismatches and to continue efficient elongation from mismatched primer 3'-termini without discernible pausing. Nucleotide misinsertion and mispair extension efficiencies are similar for both enzymes on RNA and DNA templates having identical surrounding sequence. HIV-1 and AMV reverse transcriptases form G.T and G.U mismatches most efficiently, between 1.6 x 10(-4) and 7 x 10(-4), and both enzymes extend G.U with exceptionally high efficiencies, 2.7 x 10(-2) for HIV-1 RT and 4.5 x 10(-2) for AMV RT. Extension of the G.T mismatch is similar for AMV RT (5.8 x 10(-2) but 20-fold less efficient for HIV-1 RT. C.U and C.T mismatches are formed by both enzymes in a frequency range of 4.4 x 10(-5)-2.4 x 10(-4). HIV-1 RT extends these mismatches with slightly higher efficiencies (5.5 x 10(-3)-5.9 x 10(-3)) than AMV RT (5.6 x 10(-4)-2.1 x 10(-3)). Insertion of dTMP opposite U and T occur at about 1 x 10(-4)-2 x 10(-4) for HIV-1 RT. For AMV RT, formation of T.U mispairs occurs with an 8-fold lower efficiency, whereas insertion of dTMP opposite T is not detected. This particular DNA template sequence generates a pause site for AMV RT but not HIV-1 RT. HIV-1 RT dissociation rate constants are about 8-fold larger from a DNA primer bound to a DNA template (0.5 s-1), as compared with an RNA template (0.06 s-1) at one site, and are at most 2-fold larger at another site. The equilibrium binding constant for HIV-1 RT bound to DNA primed RNA and DNA templates appears to be similar, KD approximately 2.5 nM. Values of kpol from 0.3 to 1.5 nucleotides/s are obtained for HIV-1 RT at the RNA and DNA template sites used to measure insertion and extension fidelity. The relatively high efficiency of mispair extension catalyzed by reverse transcriptases with both RNA and DNA templates suggests that a significant component of retroviral genetic variability may be related to the ability of reverse transcriptases to continue efficient synthesis of DNA containing mismatches on both RNA and DNA templates.
TTF-1 Phosphorylation Is Required for Peripheral Lung Morphogenesis, Perinatal Survival, and Tissue-specific Gene Expression (2003)

Thyroid transcription factor-1 (TTF-1) is a 43-kDa, phosphorylated member of the Nkx2 family of homeodomain-containing proteins expressed selectively in lung, thyroid, and the central nervous system. To assess the role of TTF-1 and its phosphorylation during lung morphogenesis, mice bearing a mutant allele, in which seven serine phosphorylation sites were mutated, Titf1PM/PM, were generated by homologous recombination. Although heterozygous Titf1PM/+ mice were unaffected, homozygous Titf1PM/PM mice died immediately following birth. In contrast to Titf1 null mutant mice, which lack peripheral lung tissues, bronchiolar and peripheral acinar components of the lung were present in the Titf1PM/PM mice. Although lobulation and early branching morphogenesis were maintained in the mutant mice, abnormalities in acinar tubules and pulmonary hypoplasia indicated defects in lung morphogenesis later in development. Although TTF-1PM protein was readily detected within the nuclei of pulmonary epithelial cells at sites and abundance consistent with that of endogenous TTF-1, expression of a number of known TTF-1 target genes, including surfactant proteins and secretoglobulin 1A, was variably decreased in the mutant mice. Vascular endothelial growth factor mRNA was decreased in association with decreased formation of peripheral pulmonary blood vessels. Genes mediating surfactant homeostasis, vasculogenesis, host defense, fluid homeostasis, and inflammation were highly represented among those regulated by TTF-1. Thus, in contrast to the null Titf1 mutation, the Titf1PM/PM mutant substantially restored lung morphogenesis. Direct and indirect transcriptional targets of TTF-1 were identified that are likely to play important roles in lung formation and function.
Transvenous Closure of Secundum Atrial Septal Defects (1997)

Background Our purpose was to evaluate a new prosthesis for percutaneous closure of secundum atrial septal defects (ASDs). Methods and Results Percutaneous closure of surgically created fossa ovalis ASD was attempted in 15 minipigs. The mean balloon-stretched ASD diameter was 12.3±2.3 mm (range, 10 to 16 mm). The self-expanding prosthesis was braided from 0.005-in Nitinol wires in the shape of two flat buttons with a short connecting waist with a diameter corresponding to that of the defect to be closed. Polyester filling was added to enhance thrombogenicity. Pulmonary arteriography with levo-phase was obtained before placement; immediately after placement; and at 1-week, 1-month, and 3-month follow-ups. Four animals were killed at 1 week, 1 month, and 3 months for histopathological correlation. Three deaths resulted from ventricular fibrillation (one during anesthesia and two during the placement procedure). Successful placement of the prosthesis was achieved in the remaining 12 animals. Overall immediate ASD closure on angiography occurred in 7 of 12 animals (all polyester-filled prostheses). Absent or trace shunt by angiography was present in 11 of 12 devices at 1 week, with the remaining one demonstrating a small shunt. All septal defects were completely closed at 1 month with the exception of one case in which delayed partial dislodgment of an undersized prosthesis into the right atrium had developed. Closure rate at 3 months was 100%. Neoendothelialization and fibrous incorporation of the prosthesis were completed within 1 to 3 months. Conclusions Effective and permanent occlusion of secundum ASDs is feasible with a device that offers the advantages of easy placement, self-centering, and repositionability.
The Effect of Thrombin Activation of Platelet-Rich Plasma on Demineralized Bone Matrix Osteoinductivity (2009)

Platelet-rich plasma significantly increased in vivo demineralized bone matrix osteoinductivity only when used without thrombin activation.
Development of new methodology for the synthesis of functionalized α-fluorophosphonates and its practical application to the preparation of phosphopeptide mimetics (2000)

New methodology for the synthesis of functionalized α-fluorophosphonates which utilizes organocopper-mediated reduction has been developed and applied to the preparation of a monofluoromethyl-substituted phosphoserine mimetic-containing peptide.
SOURCE MODELS FOR NATURAL LANGUAGE (1988)

A model of natural language is a collection of information that approximates the statistics and structure of the language being modeled. The purpose of the model may be to give insight into rules which govern how text is generated, or to predict properties of future samples of the language. This paper studies models of natural language from three different, but related, viewpoints. First, we examine the statistical regularities that are found empirically, based on the natural units of words and letters. Second, we study theoretical models of language, including simple random generative models of letters and words whose output, like genuine natural language, obeys Zipf's law. Innovation in text is also considered by modeling the appearance of previously unseen words as a Poisson process. Finally, we review experiments that estimate the information content inherent in natural text.
Human natural killer cell committed thymocytes and their relation to the T cell lineage. (1993)

Recent studies have demonstrated that mature natural killer (NK) cells can be grown from human triple negative (TN; CD3-, CD4-, CD8-) thymocytes, suggesting that a common NK/T cell precursor exists within the thymus that can give rise to both NK cells and T cells under appropriate conditions. In the present study, we have investigated human fetal and postnatal thymus to determine whether NK cells and their precursors exist within this tissue and whether NK cells can be distinguished from T cell progenitors. Based on the surface expression of CD56 (an NK cell-associated antigen) and CD5 (a T cell-associated antigen), three phenotypically distinctive populations of TN thymocytes were identified. CD56+, CD5-; CD56-, CD5-, and CD56-, CD5+. The CD56+, CD5- population of TN thymocytes, although displaying a low cytolytic function against NK sensitive tumor cell targets, were similar in antigenic phenotype to fetal liver NK cells, gave rise to NK cell clones, and were unable to generate T cells in mouse fetal thymic organ cultures (mFTOC). This population of thymocytes represents a relatively mature population of lineage-committed NK cells. The CD56-, CD5- population of TN thymocytes were similar to thymic NK cells in antigenic phenotype and NK cell clonogenic potential. Clones derived from this population of TN thymocytes acquired CD56 surface expression and NK cell cytolytic function. CD56-, CD5- TN thymocytes thus contain a novel population of NK cell-committed precursors. The CD56-, CD5- population of TN thymocytes also contains a small percentage of CD34+ cells, which demonstrate no in vitro clonogenic potential, but possess T cell reconstituting capabilities in mFTOC. The majority of TN thymocytes do not express CD56, but coexpress CD34 and CD5. These CD56-, CD5+, CD34+ cells demonstrate no NK or T cell clonogenic potential, but are extremely efficient in repopulating mFTOC and differentiating into CD3+, CD4+, CD8+ T cells. The results of this investigation have identified NK cells and NK cell precursors in the human thymus and have shown that these cell types are unable to differentiate along the T cell lineage pathway. Thus, while a common NK/T cell progenitor likely exists, once committed to the NK cell lineage these cells no longer have the capacity to develop along the T cell developmental pathway.
Passive mode converter with a periodically tilted InP/GaInAsP rib waveguide (1992)

TE to TM converters with constant 45 degrees operation are a key component in OEICs for coherent optical system applications. A passive TE/TM-mode converter with a laterally tilted rib waveguide fabricated on a stepped substrate is proposed and investigated. The conversion effect has been simulated using scalar and vectorial two-dimensional finite difference methods. The device fabricated on
Jump starting the future health care work force. (2002)

One of the busiest and most important departments in health care organizations today is human resources. As the fear of staffing shortages is becoming less of a future threat and more of a reality for many, hospitals must become creative in their approaches to recruiting and retaining health care professionals. Over the next four issues, Michigan Health & Hospitals magazine will feature four programs that are particularly innovative and are getting results.
An approximation for the distribution of the scan statistic (1987)

The scan statistic evaluates whether an apparent cluster of disease in time is due to chance. The statistic employs a 'moving window' of length w and finds the maximum number of cases revealed through the window as it scans or slides over the entire time period T. Computation of the probability of observing a certain size cluster, under the hypothesis of a uniform distribution, is infeasible when N, the total number of events, is large, and w is of moderate or small size relative to T. We give an approximation that is an asymptotic upper bound, easy to compute, and, for the purposes of hypothesis testing, more accurate than other approximations presented in the literature. The approximation applies both when N is fixed, and when N has a Poisson distribution. We illustrate the procedure on a data set of trisomic spontaneous abortions observed in a two year period in New York City.
Efficient Reagents for the Synthesis of 5-, 7-, and 5,7-Substituted Indoles Starting from Aromatic Amines:  Scope and Limitations (1996)

Upon reaction with IPy2BF4, 4-substituted anilines give regioselectively the corresponding o-iodoanilines in nearly quantitative yield, in a process that can be carried out on a multigram scale. Palladium-catalyzed coupling of the resulting 2-iodoanilines with (trimethylsilyl)acetylene (TMSA), followed by efficient CuI-mediated nitrogen cyclization onto alkynes with concurrent elimination of the TMS substituent, allows a straightforward elaboration of 5-mono- and 5,7-disubstituted indoles from aromatic amines. This new approach to the aforementioned indoles does not requires protective groups on nitrogen at any step and can be adapted for preparing related 7-monosubstituted indoles. Moreover, examples iterating the process are given, allowing bisannulation and sequential double annulation and resulting in synthesis of benzodipyrroles. Additionally, suitable conditions for iodination of some of the target indoles with IPy2BF4 are discussed.
Automatically labeling hierarchical clusters (2006)

Government agencies must often quickly organize and analyze large amounts of textual information, for example comments received as part of notice and comment rulemaking. Hierarchical organization is popular because it represents information at different levels of detail and is convenient for interactive browsing. Good hierarchical clustering algorithms are available, but there are few good solutions for automatically labeling the nodes in a cluster hierarchy.This paper presents a simple algorithm that automatically assigns labels to hierarchical clusters. The algorithm evaluates candidate labels using information from the cluster, the parent cluster, and corpus statistics. A trainable threshold enables the algorithm to assign just a few high-quality labels to each cluster. Experiments with Open Directory Project (ODP) hierarchies indicate that the algorithm creates cluster labels that are similar to labels created by ODP editors.
Carbodiimides. VI. The Reaction of Dicyclohexylcarbodiimide with Yeast Adenylic Acid. A New Method for the Preparation of Monoesters of Ribonucleoside 2'- and 3'-Phosphates (1954)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCarbodiimides. VI. The Reaction of Dicyclohexylcarbodiimide with Yeast Adenylic Acid. A New Method for the Preparation of Monoesters of Ribonucleoside 2'- and 3'-PhosphatesCharles A. Dekker and H. G. KhoranaCite this: J. Am. Chem. Soc. 1954, 76, 13, 3522–3527Publication Date (Print):July 1, 1954Publication History Published online1 May 2002Published inissue 1 July 1954https://pubs.acs.org/doi/10.1021/ja01642a049https://doi.org/10.1021/ja01642a049research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations48LEARN 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
AMP-Activated Protein Kinase Signaling Stimulates VEGF Expression and Angiogenesis in Skeletal Muscle (2005)

AMP-activated protein kinase (AMPK) is regulated by various cellular stresses. Vascular endothelial growth factor (VEGF), a key regulator of angiogenesis, is also upregulated by several stress-inducible factors such as hypoxia and stimulation by cytokines and growth factors. Here, we investigated whether AMPK signaling in muscle has a role in regulating VEGF-mediated angiogenic processes. AICAR stimulated VEGF mRNA and protein levels in C2C12 myotube cultures. Transduction with dominant-negative AMPK abolished AICAR-induced VEGF expression at both steady state mRNA and protein levels. AICAR increased VEGF mRNA stability without affecting VEGF promoter activity. AICAR also stimulated p38 mitogen-activated protein kinase (p38 MAPK) phosphorylation. Activation of p38 MAPK was suppressed by transduction with dominant-negative AMPK, suggesting that AMPK is upstream of p38 MAPK. The p38 MAPK inhibitor SB203580 blocked AICAR-induced increase in VEGF mRNA and protein levels, indicating that AICAR-mediated VEGF induction is dependent on p38 MAPK signaling. AICAR treatment increased VEGF expression and accelerated angiogenic repair of ischemic hindlimbs in mice in an AMPK-dependent manner. These data indicate that AMPK-p38 MAPK signaling cascade can increase VEGF production in muscle and promote angiogenesis in response to ischemic injury.