gebhart/patrepeval huggingface dataset:
Improved Detection of Microsatellite Instability in Early Colorectal Lesions (2015)

Microsatellite instability (MSI) occurs in over 90% of Lynch syndrome cancers and is considered a hallmark of the disease. MSI is an early event in colon tumor development, but screening polyps for MSI remains controversial because of reduced sensitivity compared to more advanced neoplasms. To increase sensitivity, we investigated the use of a novel type of marker consisting of long mononucleotide repeat (LMR) tracts. Adenomas from 160 patients, ranging in age from 29-55 years old, were screened for MSI using the new markers and compared with current marker panels and immunohistochemistry standards. Overall, 15 tumors were scored as MSI-High using the LMRs compared to 9 for the NCI panel and 8 for the MSI Analysis System (Promega). This difference represents at least a 1.7-fold increase in detection of MSI-High lesions over currently available markers. Moreover, the number of MSI-positive markers per sample and the size of allelic changes were significantly greater with the LMRs (p = 0.001), which increased confidence in MSI classification. The overall sensitivity and specificity of the LMR panel for detection of mismatch repair deficient lesions were 100% and 96%, respectively. In comparison, the sensitivity and specificity of the MSI Analysis System were 67% and 100%; and for the NCI panel, 75% and 97%. The difference in sensitivity between the LMR panel and the other panels was statistically significant (p<0.001). The increased sensitivity for detection of MSI-High phenotype in early colorectal lesions with the new LMR markers indicates that MSI screening for the early detection of Lynch syndrome might be feasible.
Modern Petroleum: A Basic Primer of the Industry (1978)

Adopted at more than 23 universities as a basic petroleum text, this text uses layman's language to provide an overview of every aspect of the petroleum industry.
Platelets in inflammation and atherogenesis (2005)

Platelets represent an important linkage between inflammation, thrombosis, and atherogenesis. Inflammation is characterized by interactions among platelets, leukocytes, and ECs. These interactions trigger autocrine and paracrine activation processes that lead to leukocyte recruitment into the vascular wall. Platelet-induced chronic inflammatory processes at the vascular wall result in development of atherosclerotic lesions and atherothrombosis. This Review highlights the molecular machinery and inflammatory pathways used by platelets to initiate and accelerate atherothrombosis.
How Do We Advise the Pest Control Industry in the Post-Organochlorine Era? (1991)

Abstract: Given the banning of organochlorines for use as termiticides in North America, and with the possibility of such bans occurring in future in Australia and elsewhere, how do we as entomologists advise the pest control industry in termite control? A brief historical review of pesticide bans and the relevance of these bans to the present situation are discussed. Suggestions are offered for entomologists to pursue an integrated pest management approach to termite control based on sound ecological parameters and social priorities. Before attempting to offer suggestions as how best to advise the pest control industry in the post-organochlorine era, I think it is as fruitful to understand the social and political context in which bans on pesticide use have been imposed historically, as to offer resolutions that may
Urinary 3-(3-Hydroxyphenyl)-3-hydroxypropionic Acid, 3-Hydroxyphenylacetic Acid, and 3-Hydroxyhippuric Acid Are Elevated in Children with Autism Spectrum Disorders (2016)

Autism spectrum disorders (ASDs) are a group of mental illnesses highly correlated with gut microbiota. Recent studies have shown that some abnormal aromatic metabolites in autism patients are presumably derived from overgrown Clostridium species in gut, which may be used for diagnostic purposes. In this paper, a GC/MS based metabolomic approach was utilized to seek similar biomarkers by analyzing the urinary information in 62 ASDs patients compared with 62 non-ASDs controls in China, aged 1.5-7. Three compounds identified as 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), 3-hydroxyphenylacetic acid (3HPA), and 3-hydroxyhippuric acid (3HHA) were found in higher concentrations in autistic children than in the controls (p < 0.001). After oral vancomycin treatment, urinary excretion of HPHPA (p < 0.001), 3HPA (p < 0.005), and 3HHA (p < 0.001) decreased markedly, which indicated that these compounds may also be from gut Clostridium species. The sensitivity and specificity of HPHPA, 3HPA, and 3HHA were evaluated by receiver-operating characteristic (ROC) analysis. The specificity of each compound for ASDs was very high (>96%). After two-regression analysis, the optimal area under the curve (AUC, 0.962), sensitivity (90.3%), and specificity (98.4%) were obtained by ROC curve of Prediction probability based on the three metabolites. These findings demonstrate that the measurements of the three compounds are strong predictors of ASDs and support the potential clinical utility for identifying a subgroup of ASDs subjects.
Signaling properties of mouse and human corticotropin-releasing factor (CRF) receptors: decreased coupling efficiency of human type II CRF receptor. (1995)

CRF is the primary neuroregulator of the function of the hypothalamic-pituitary-adrenal axis. We have recently cloned a mouse CRF receptor (mCRF-R) complementary DNA (cDNA) from an AtT-20 cell cDNA library by polymerase chain reaction. To compare the functions of mCRF-R to those of the human type I and type II CRF receptors (hCRF-RI and hCRF-RII), cDNAs were cloned into the expression vector pcDNA1 and transfected into COS-7 cells. CRF binding and CRF-stimulated cAMP accumulation as well as phosphoinositide hydrolysis were measured. Scatchard analysis of the binding of 125I-labeled [Tyr0]r/hCRF ([125I]CRF) to COS-7 cells expressing mCRF-R and hCRF-RI cDNAs revealed the same apparent Kd (9 nM). In contrast, the apparent binding Kd for hCRF-RII was 20 nM CRF. Maximal stimulatory concentrations (1 microM) of rat/human CRF-(1-41) (r/hCRF) increased cAMP accumulation in COS-7 cells transfected with mCRF-R, hCRF-RI, and hCRF-RII cDNA plasmid (10 micrograms each) from basal values of 8-19 pmol/10(5) cells.15 min to 84 +/- 10, 87 +/- 16, and 45 +/- 16 pmol/10(5) cells.15 min, respectively. The EC50 values of r/hCRF-stimulated cAMP accumulation in COS-7 cells expressing mCRF-R and hCRF-RI cDNAs were similar at 0.4 +/- 0.2 and 0.7 +/- 0.2 nM, respectively. Conversely, the EC50 of r/hCRF-stimulated cAMP accumulation in hCRF-RII-transfected COS-7 cells was 47.5 +/- 18.9 nM. As the level of expression of hCRF-RII was lower than that of hCRF-RI, we compared r/hCRF-stimulated cAMP accumulation in COS-7 cells expressing low and high levels of hCRF-RI. The EC50 for r/hCRF-stimulated cAMP accumulation in COS-7 cells transfected with hCRF-RI did not change when receptor expression was varied by a factor of 1- to 8.4-fold. In contrast, the EC50 for r/hCRF-stimulated cAMP accumulation mediated by hCRF-RII was at least 100-fold higher than that mediated by the hCRF-RI in COS-7 cells, which suggests poor coupling between hCRF-RII and adenylate cyclase. Inositol phosphate (IP) levels were also determined in mCRF-R, hCRF-RI, and hCRF-RII cDNA-transfected COS-7 cells stimulated with increasing concentrations of r/hCRF. r/hCRF-stimulated IPs accumulation was dose dependent in COS-7 cells expressing mCRF-R and hCRF-RI using 100 and 1000 nM r/hCRF. Concentrations of 10 (or less) nM r/hCRF had no effect on IP generation. hCRF-RII did not mediate stimulation of IP even at 1000 nM r/hCRF.(ABSTRACT TRUNCATED AT 400 WORDS)
Strong sub-band-gap infrared absorption in silicon supersaturated with sulfur (2006)

Silicon supersaturated with up to 0.6at.% sulfur in solid solution was fabricated by ion implantation and pulsed-laser-melting-induced rapid solidification. The optical absorption coefficient over the range of 1200–2500nm is uniformly high at ∼2.5×104∕cm, which is at least an order of magnitude greater than the maximum value attributable to free carriers. High crystal quality was confirmed by transmission electron microscopy and ion channeling. The absorption coefficient decreases markedly with subsequent furnace annealing over the range of 200–600°C. We propose that the high absorptivity is due to a broad distribution of sulfur-related localized states within the band gap.
Postoperative Infections Traced to Contamination of an Intravenous Anesthetic, Propofol (1995)

With the increasing use of lipid-based medications, which support rapid bacterial growth at room temperature, strict aseptic techniques are essential during the handling of these agents to prevent extrinsic contamination and dangerous infectious complications.
Interstitial cells in the human prostate: A new therapeutic target? (2003)

There is evidence for interstitial cells in the human prostate. Taken together their topography and immunohistochemical characterization, the discovery of slow wave potentials in guinea pig prostate and the knowledge of interstitial cells in other organs, interstitial cells are likely to be involved in normal prostate physiology.
Modelo cultural de formação docente (2010)

Neste artigo, foi analisada a Revista de Educação publicada pelos professores da antiga Escola Normal de Piracicaba (SP) entre 1921 e 1923, com o objetivo de compreender, por meio da análise do ciclo de vida, da materialidade e do conteúdo do periódico, como os professores estavam sendo formados nesse período. Esta pesquisa foi realizada sob a perspectiva da História Cultural, baseada em Roger Chartier. Esse referencial toma o impresso em sua materialidade de objeto cultural, preocupando-se com as práticas que o produzem e os usos que são feitos dele. Como considerações finais, verifico que a Revista de Educação funciona como estratégia editorial, como suporte material das práticas escolares e como dispositivo de normatização pedagógica, que tinha por objetivo formar o professor primário com a divulgação das ideias educacionais propostas pela Reforma Sampaio Dória, e que as temáticas e o conjunto de saberes abordados pelos artigos formavam um modelo cultural de formação docente.
Evaluation of α1‐adrenoceptors in the rabbit iris: pharmacological characterization and expression of mRNA (1999)

Subtypes of alpha1-adrenoceptor in rabbit iris have been examined in functional, binding and molecular biological experiments. In functional studies, exogenous and endogenous noradrenaline produced contractions of the iris dilator muscle. The contractile responses to noradrenaline were competitively antagonized by a range of alpha1-adrenoceptor antagonists (pA2 values): prazosin (8.1), WB4101 (8.2), BMY7378 (5.9), YM617 (9.5), JTH-601 (8.8), HV723 (7.8) and KMD-3213 (9.8). The same order of inhibitory potency was seen in the adrenergic responses to electrical stimulation. This affinity profile corresponds well to that of the putative alpha1L-adrenoceptor, which has been proposed in lower urinary tract tissues. In binding studies on rabbit iris membrane however, prazosin, KMD-3213 and WB4101 displayed high affinity (pKd or pKi: 9.6, 10.3, 9.6, respectively), and BMY7378 displayed low affinity (pKi: 6.9). These results show that the binding sites typically correspond to alpha1A-adrenoceptor subtype in character, and we could not detect the significant amount of alpha1L-adrenoceptor subtype. The expression of the three distinct mRNAs that encode proteins of alpha1a-, alpha1b- and alpha1d-adrenoceptors was studied using reverse transcription-polymerase chain reaction (RT-PCR). RT-PCR demonstrated the strongest expression of the alpha1a-adrenoceptor, weak expression of the alpha1b-adrenoceptor and undetectable expression of the alpha1d-adrenoceptor. The present study suggests that alpha1A-adrenoceptor is a major subtype detectable in binding and RT-PCR studies in rabbit iris, but that the adrenergic contractions of iris dilator muscle are mediated via activation of alpha1-adrenoceptor subtype having low affinity for prazosin and WB4101.
ChemInform Abstract: Polymeric Nanoparticles with Biomedical Applications (2011)

Abstract Review: 68 refs.
FILAMENTOUS FLOWER, a meristem and organ identity gene of Arabidopsis, encodes a protein with a zinc finger and HMG-related domains (1999)

Distinctive from that of the animal system, the basic plan of the plant body is the continuous formation of a structural unit, composed of a stem with a meristem at the top and lateral organs continuously forming at the meristem. Therefore, mechanisms controlling the formation, maintenance, and development of a meristem will be a key to understanding the body plan of higher plants. Genetic analyses of filamentous flower (fil) mutants have indicated that FIL is required for the maintenance and growth of inflorescence and floral meristems, and of floral organs of Arabidopsis thaliana. FIL encodes a protein carrying a zinc finger and a HMG box-like domain, which is known to work as a transcription regulator. As expected, the FIL protein was shown to have a nuclear location. In situ hybridization clearly demonstrated that FIL is expressed only at the abaxial side of primordia of leaves and floral organs. Transgenic plants, ectopically expressing FIL, formed filament-like leaves with randomly arranged cells at the leaf margin. Our results indicate that cells at the abaxial side of the lateral organs are responsible for the normal development of the organs as well as for maintaining the activity of meristems.
Cellular senescence mediates fibrotic pulmonary disease (2017)

Idiopathic pulmonary fibrosis (IPF) is a fatal disease characterized by interstitial remodelling, leading to compromised lung function. Cellular senescence markers are detectable within IPF lung tissue and senescent cell deletion rejuvenates pulmonary health in aged mice. Whether and how senescent cells regulate IPF or if their removal may be an efficacious intervention strategy is unknown. Here we demonstrate elevated abundance of senescence biomarkers in IPF lung, with p16 expression increasing with disease severity. We show that the secretome of senescent fibroblasts, which are selectively killed by a senolytic cocktail, dasatinib plus quercetin (DQ), is fibrogenic. Leveraging the bleomycin-injury IPF model, we demonstrate that early-intervention suicide-gene-mediated senescent cell ablation improves pulmonary function and physical health, although lung fibrosis is visibly unaltered. DQ treatment replicates benefits of transgenic clearance. Thus, our findings establish that fibrotic lung disease is mediated, in part, by senescent cells, which can be targeted to improve health and function.
Cloning of Genomic and Complementary DNA from Shaker , a Putative Potassium Channel Gene from Drosophila (1987)

On the basis of electrophysiological analysis of Shaker mutants, the Shaker locus of Drosophila melanogaster has been proposed to encode a structural component of a voltage-dependent potassium channel, the A channel. Unlike sodium channels, acetylcholine receptors, and calcium channels, K+ channels have not been purified biochemically. To facilitate biochemical studies of a K+ channel, genomic DNA from the Shaker locus has been cloned. Rearrangements in five Shaker mutants have been mapped to a 60-kilobase segment of the genome. Four complementary DNA clones have been analyzed. These clones indicate that the Shaker gene contains multiple exons distributed over at least 65 kilobases of genomic DNA in the region where the mutations mapped. Furthermore, the gene may produce several classes of alternatively spliced transcripts. Two of the complementary DNA clones have been sequenced and their sequences support the hypothesis that Shaker encodes a component of a K+ channel.
On the inner workings of Monte Carlo codes (2013)

We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as zeolites and metal-organic frameworks. Conventional MC is discussed and compared to advanced techniques such as reactive MC, configurational-bias Monte Carlo and continuous fractional MC. The latter technique overcomes the problem of low insertion probabilities in open systems. Other modern methods are (hyper-)parallel tempering, Wang-Landau sampling and nested sampling. Details on the techniques and acceptance rules as well as to what systems these techniques can be applied are provided. We highlight consistency tests to help validate and debug MC codes.
One‐Dimensional Assemblies of Nanoparticles: Preparation, Properties, and Promise (2005)

Abstract Nanoparticle (NP) assemblies are of considerable interest for both fundamental research and applications, since they provide direct bridges between nanometer‐scale objects and the macroscale world. Unlike two‐dimensional or three‐dimensional NP assemblies, which have been extensively studied and reviewed, reports on one‐dimensional (1D) NP assemblies are rather rare, even though these assemblies are likely to play critical roles in the improvement of the efficiencies of various electronic, optoelectronic, magnetic, and other devices based on single NPs or their composites. Additionally, 1D assemblies of NPs, i.e., chains, can significantly help in the understanding of a number of biological processes and fundamental quantum mechanics of nanometer‐scale systems. The difficulties are very evident when one wants to realize anisotropic 1D assemblies from presumably isotropic, zero‐dimensional NPs. In this context, the authors present a systemic review of current research on 1D NP assemblies. Their preparation methods are classified and novel characteristics of NP chains, such as collective properties and directional transfer of photons, electrons, spins, etc., are elucidated. Current problems underlying the fundamental research and practical applications of 1D NP assemblies are also addressed.
Expanding the Porphyrin π-System by Fusion with Anthracene (2008)

Synthesis of beta,meso,beta-anthracene triply fused and beta,meso-anthracene doubly fused porphyrins has been achieved via oxidative intramolecular ring closure of meso-(9-anthryl)porphyrins and meso-(1-anthryl)porphyrins, respectively. Fusion was only possible when the anthracene carried electron-donating alkoxy substituents. The fused porphyrins exhibit strongly red-shifted UV-vis absorption spectra and reduced electrochemical HOMO-LUMO gaps (relative to the unfused tetraaryl porphyrin precursor).
Characterization of the interaction between anthrax toxin and its cellular receptors (2006)

Mutations in capillary morphogenesis gene 2 (CMG2), one of the two closely related proteins that act as anthrax toxin receptors, cause two rare human autosomal recessive conditions, juvenile hyaline fibromatosis (JHF) and infantile systemic hyalinosis (ISH). Here we demonstrate that CMG2 proteins with certain JHF- and ISH-associated single amino acid substitutions in their von Willebrand factor A domain or transmembrane region do not function as anthrax toxin receptors. However, an ISH-associated CMG2 variant having a truncated cytosolic domain does still function as an anthrax receptor, and in fact makes cells hyper-sensitive to toxin, distinguishing the roles of CMG2 in physiology and anthrax pathology. Site-specific mutagenesis was used to characterize the role that domain 2 of the anthrax toxin protective antigen (PA) plays in interaction with CMG2, focusing on the interaction between the PA 2beta(3)-2beta(4) loop and a pocket (Glu-122 pocket) adjacent to the metal ion-dependent adhesion site in CMG2. Substitutions that disrupted the salt bridge between PA Arg-344 and CMG2 Glu-122 decreased the affinity of PA to CMG2 three- to fourfold. Furthermore, mutation of CMG2 Tyr-119 (within the Glu-122 pocket) to His lowered the pH threshold for PA prepore-to-pore conversion in the endocytic pathway.
Influence of von Willebrand factor on the reactivity of human factor VIII inhibitors with factor VIII (2001)

In order to determine the difference in reactivity of factor (F) VIII inhibitors against the FVIII/von Willebrand factor (vWF) complex and against vWF‐deficient FVIII, we investigated a panel of 10 antibodies to FVIII from multitransfused individuals with severe haemophilia A and other pathologies. Immunoblotting of purified FVIII and purified thrombin‐cleaved FVIII revealed that in all cases inhibitor epitopes could be localized in the heavy chain (A2 subunit) while in four cases they were also present in the light chain. One of the FVIII inhibitors remained unclassified. The effect on FVIII:C of purified IgG from inhibitor plasmas was tested against a high purity FVIII/vWF concentrate and a monoclonally purified FVIII concentrate with only trace contents of vWF, by two different functional assays. Our results suggest that for those inhibitors showing A2 plus light chain (LC) reactivity, the IgG concentration required to inhibit 50% of FVIII activity in vitro is higher for the FVIII/vWF complex than for the vWF‐deficient FVIII. We conclude that there might be a protective role of vWF (at least in vitro ) against FVIII inhibitors with A2 and LC subunit specificity.
High Glucose Induces Human Endothelial Cell Apoptosis Through a Phosphoinositide 3-Kinase–Regulated Cyclooxygenase-2 Pathway (2005)

These results suggest that HG, via PI3K/Akt signaling, induces NF-kappaB-related upregulation of COX-2, which in turn triggers the caspase-3 activity that facilitates HUVEC apoptosis. Also, HG may cause ROS generation in HUVECs through a PI3K/Akt-dependent pathway.
Interleukin-6 and interleukin-10 levels in chronic lymphocytic leukemia: correlation with phenotypic characteristics and outcome (2001)

The objective of this study was to examine the correlation between serum interleukin-6 (IL-6) and IL-10 levels and outcome in chronic lymphocytic leukemia (CLL). Serum IL-6 and IL-10 levels were measured by enzyme-linked immunoabsorbent assays from 159 and 151 CLL patients, respectively, and from healthy control subjects (n = 55 [IL-6]; n = 37 [IL-10]). Cytokine levels were correlated with clinical features and survival. Serum IL-6 levels were higher in CLL patients (median, 1.45 pg/mL; range, undetectable to 110 pg/mL) than in control subjects (median, undetectable; range, undetectable to 4. 30 pg/mL) (P <.0001). Serum IL-10 levels were higher in CLL patients (median, 5.04 pg/mL; range, undetectable to 74 pg/mL) than in normal volunteers (median, undetectable; range, undetectable to 13.68 pg/mL) (P <.00001). Assays measuring both Epstein-Barr virus-derived and human IL-10 yielded higher values than assays measuring primarily human IL-10 (P <.05). Patients with elevation of serum IL-6 or IL-10 levels, or both, had worse median and 3-year survival (log rank P <.001) and unfavorable characteristics (prior treatment, elevated beta(2)-microglobulin or lactate dehydrogenase, or Rai stage III or IV). Elevated IL-6 and IL-10 levels were independent prognostic factors for survival when analyzed individually or in combination (Cox regression analysis). However, if beta(2)-microglobulin was incorporated into the analysis, it was selected as an independent prognostic feature, and IL-6/IL-10 were no longer selected. In patients with CLL, serum IL-6 and IL-10 (viral and human) levels are elevated and correlate with adverse disease features and short survival. In multivariate analysis, however, beta(2)-microglobulin is the most important prognostic factor.