gebhart/patrepeval huggingface dataset:
Improving SNP discovery by base alignment quality (2011)

hengli@broadinstitute.org.
Histamine induces leukocyte rolling in post-capillary venules. A P-selectin-mediated event. (1994)

The objective of this study was to systematically assess the molecular mechanisms and kinetics of histamine-induced leukocyte rolling in rat mesenteric venules using intravital microscopy. A complicating factor in these studies is surgical preparation-induced leukocyte rolling (spontaneous rolling), which leads to a lack of effect of histamine on this parameter. Therefore, we identified the source of the surgery-induced leukocyte rolling (partial mast cell degranulation) and established that pretreatment of animals with sodium cromoglycate (connective tissue mast cell stabilizer) inhibited spontaneous leukocyte rolling. Superfusion of the mast cell-stabilized rat mesentery with histamine caused a profound increase in leukocyte rolling which persisted for the entire hour of experimentation. Diphenhydramine (H1-receptor antagonist) but not cimetidine (H2-receptor antagonist) prevented the rise in histamine-induced leukocyte rolling. An anti-P-selectin Ab but not an anti-CD18 Ab reversed the histamine-induced leukocyte rolling in a dose-dependent fashion. In this model of low base line rolling, exposure of the mesentery to the chemotactic agent platelet-activating factor did not induce leukocyte rolling or adhesion. However, co-administration of histamine with platelet-activating factor did indeed promote leukocyte adhesion suggesting that the presence of at least one effector of P-selectin is a minimal requirement for chemotactically-stimulated leukocytes to adhere to postcapillary venules. This study demonstrates for the first time that histamine induces leukocyte rolling via a P-selectin-dependent mechanism in vivo. This is a prolonged, H1 receptor-mediated event that may contribute significantly to the early phase of inflammation.
An Experimental and Computational Fluid Dynamic Study of Axis-Symmetric Coanda Configuration for VTOL MAV Applications (2014)

This project is designed to find out a proper shape for the Coanda effect and use them for helping a vertical takeoff vehicle to create additional lift. Experiment and numerical calculations were conducted. The model was set up by placing a propeller at 10 cm above the surface. Shape, height and model with a hold at the center were investigated by ANSYS Fluent. Propeller was simulated by applying actuator disk. First shape is a semi sphere with 50 cm diameter. Second, surface in invert parabolic shape with 50 cm diameter with varying height 15, 25 and 35 cm are considered. The last shape is similar to the second case with 15 and 35 cm height, but it is made hollow by varying the hold's diameter as 7, 11 and 15 cm. The total number of the entire cases is 10. The result shows that the best shape for the Coanda effect is a semi sphere shape but total lift of all models without a hole in the middle, in the first and the second cases, are negative and tend to decline when the height of the shape increases. For the third case, the shape with a height of 35 cm and 15 cm hold diameter has the least negative lift.
Formation of a deposit by electrophoresis (1940)

H. C. Hamaker, Trans. Faraday Soc., 1940, 35, 279 DOI: 10.1039/TF9403500279
Ability of iron(III)‐loaded carboxylated polyacrylamide‐grafted sawdust to remove phosphate ions from aqueous solution and fertilizer industry wastewater: Adsorption kinetics and isotherm studies (2002)

Iron(III)-loaded carboxylated polyacrylamide-grafted sawdust was investigated as an adsorbent for the removal of phosphate from water and wastewater. The carboxylated polyacrylamide-grafted sawdust was prepared by graft copolymerization of acrylamide and N,N′-methylenebisacrylamide onto sawdust in the presence of an initiator, potassium peroxydisulfate. Iron(III) was strongly attached to the carboxylic acid moiety of the adsorbent. The adsorbent material exhibits a very high adsorption potential for phosphate ions. The coordinated unsaturated sites of the iron(III) complex of polymerized sawdust were considered to be the adsorption sites for phosphate ions, the predominating species being H2PO ions. Maximum removal of 97.6 and 90.3% with 2 g L−1 of the adsorbent was observed at pH 2.5 for an initial phosphate concentration of 100 and 250 μmol L−1, respectively. The adsorption process follows second-order kinetics. Adsorption rate constants as a function of concentration and temperature and kinetic parameters, such as ΔG±, ΔH±, and ΔS±, were calculated to predict the nature of adsorption. The L-type adsorption isotherm obtained in the sorbent indicated a favorable process and fitted the Langmuir equation model well. The adsorption capacity calculated by the Langmuir adsorption isotherm gave 3.03 × 10−4 mol g−1 of phosphate removal at 30°C and pH 2.5. The isosteric heat of adsorption was also determined at various surface loadings of the adsorbent. The adsorption efficiency toward phosphate removal was tested using industrial wastewater. Different reagents were tested for extracting phosphate ions from the spent adsorbent. About 98.2% of phosphate can be recovered from the adsorbent using 0.1M NaOH. Alkali regeneration was tried for several cycles with a view to recover the adsorbed phosphate and also to restore the adsorbent to its original state. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 84: 2541–2553, 2002
On Smoothing and Inference for Topic Models (2012)

Latent Dirichlet analysis, or topic modeling, is a flexible latent variable framework for modeling high-dimensional sparse count data. Various learning algorithms have been developed in recent years, including collapsed Gibbs sampling, variational inference, and maximum a posteriori estimation, and this variety motivates the need for careful empirical comparisons. In this paper, we highlight the close connections between these approaches. We find that the main differences are attributable to the amount of smoothing applied to the counts. When the hyperparameters are optimized, the differences in performance among the algorithms diminish significantly. The ability of these algorithms to achieve solutions of comparable accuracy gives us the freedom to select computationally efficient approaches. Using the insights gained from this comparative study, we show how accurate topic models can be learned in several seconds on text corpora with thousands of documents.
Blending parametric objects by implicit techniques (1993)

A blending surface is a transition surface between two intersecting or non-intersecting surfaces which smoothes out peaks, valleys, kinks, creases and so forth.A typical geomernc model of a mechanical part consists of two kinds of surfaces -primaryand secondary.The overall functionality of the model is decided by primary surfaces whereas secondary surfaces are used to smoothly connect primary surfaces.Blending surfaces can be classified as secondary surfaces. MOTIVATIONBlend surfaces can, in general, be classified into implicit and parametric surfaces.The problem of implicit blending is addressed by Bossignac & Requicha '84], [Rockwood & Owen '87] and [Hoffinsn & Hopcroft '87].With the growing trend of incorporatingfree form surfaces into solid modeling systems and due to the fact that these free form surfaces me represented by some kind of parametric surfaces the problem of blending these parametric surfaces becomes important.Various approaches have been taken to find a blend between parametric surfaces; see [Filip '89], [Choi & Ju '89] etc.Many of these approaches involve defining "rail curves" on the base surfaces and a set of "profiie curves" between them and finding an interpolating or approximating blend surface between them.Many of these methods suffer from the disadvantage rhatif the base surfaces am somewhat "uneven" the resulting blend may gouge them.This is due the fact that these methods do not take underlying geometry of the base surfaces into account when calculating blend surface.For more discussion on disadvantages of some of the previous parametric blending approaches see [Korparkar '91] and [Bien andCheng'91 ].
Melatonin Promotes Osteoblast Differentiation and Bone Formation (1999)

Prior studies have demonstrated that the pineal hormone, melatonin, can stimulate chloramphenicol acetyltransferase activity in Drosophila SL-3 cells transfected with a chloramphenicol acetyltransferase reporter construct containing the response element of rat bone sialoprotein (BSP). Based on these findings, studies were performed to determine whether melatonin could similarly modulate the expression of BSP in two cell lines, the MC3T3-E1(MC3T3) pre-osteoblast and rat osteoblast-like osteosarcoma 17/2.8 cell. Initial studies demonstrated that MC3T3 cells grown in the presence of 50 nM melatonin underwent cell differentiation and mineralization by day 12 instead of the 21-day period normally required for cells grown in untreated media. Melatonin increased gene expression of BSP and the other bone marker proteins, including alkaline phosphatase (ALP); osteopontin; secreted protein, acidic and rich in cysteine; and osteocalcin in MC3T3 cells in a concentration-dependent manner. Levels of melatonin as low as 10 nM were capable of stimulating transcription of these genes when cells were grown in the presence of beta-glycerophosphate and ascorbic acid. Under these conditions, melatonin induced gene expression of the bone marker proteins; however, this does not occur until the 5th day after seeding the culture dishes. Thereafter, MC3T3 cells responded to melatonin within 2 h of treatment. The fully differentiated rat osteoblast-like osteosarcoma 17/2.8 cells responded rapidly to melatonin and displayed an increase in the expression of BSP, ALP, and osteocalcin genes within 1 h of exposure to the hormone. To determine whether melatonin-induced osteoblast differentiation and bone formation are mediated via the transmembrane receptor, MC3T3 cells were treated in the presence and absence of melatonin with either luzindole, a competitive inhibitor of the binding of melatonin to the transmembrane receptors, or pertussis toxin, an uncoupler of G(i) from adenylate cyclase. Both luzindole and pertussis toxin were shown to reduce melatonin-induced expression of BSP and ALP. These results demonstrate, for the first time, that the pineal hormone, melatonin, is capable of promoting osteoblast differentiation and mineralization of matrix in culture and suggest that this hormone may play an essential role in regulating bone growth.
Atrioventricular Nodal Conduction During Atrial Fibrillation (1999)

Posteroseptal ablation does not eliminate the slow pathway. Ventricular rate slowing can be obtained if the ablation procedure results in a posteroanterior intra-atrial block leading to a reduction of the rate of AV nodal bombardment.
Testing cognitive function in elderly populations: the PROSPER study (2002)

Normative data are provided that can be used for one time neuropsychological testing as well as for assessing individual and group change. Methods for analysing cognitive change are proposed.
Interim analysis of a phase 2 study of lenvatinib (LEN) monotherapy as second-line treatment in unresectable biliary tract cancer (BTC). (2017)

310 Background: LEN inhibits the activity of vascular endothelial growth factor receptor, fibroblast growth factor receptor, and platelet-derived growth factor receptor–α. These targets have been shown to be expressed in patients (pts) with BTC. The objective of this study is to evaluate LEN as a potential treatment option for these pts. Methods: This is an open-label, phase 2 study conducted in Japan. Pts aged ≥ 20 years with confirmed diagnosis of unresectable BTC, measureable disease per Response Evaluation Criteria in Solid Tumors v1.1, and 1 prior gemcitabine-based doublet chemotherapy, will receive LEN 24 mg/d. The primary endpoint is objective response rate. Secondary objectives include disease control rate (DCR), safety, and pharmacokinetics. Enrollment of 25 pts is planned. The study includes an interim evaluation for futility. If there is no objective response and disease control is achieved in &lt; 5 pts of 15‒17 pts, the study will end. Results: An interim evaluation was performed with 17 pts enrolled (data cutoff: 25 July 2016). Ten (59%) pts were aged &lt; 65 years, 10 (59%) were male, 2 (12%) had prior surgery, and 13 (76%) received prior gemcitabine + cisplatin therapy. Efficacy results appear in the table. One pt had a partial response (PR) and 13 had stable disease (SD). The DCR was 82%. All pts experienced treatment-emergent adverse events (TEAEs). Grade ≥ 3 TEAEs occurred in 11 (65%) and serious AEs (SAEs) occurred in 7 (41%) pts. There were no fatal SAEs. TEAEs leading to LEN discontinuation, dose reduction, and dose interruption occurred in 1 (6%), 12 (71%), and 9 (53%) pts, respectively. Analysis of trough plasma concentration in 13 pts from this study showed no difference versus that observed in a previous phase 3 study of LEN in differentiated thyroid cancer. Conclusions: Because results of this interim evaluation did not meet futility criteria, the study was continued, with findings suggesting possible activity of LEN in pts with unresectable BTC who failed gemcitabine-based doublet chemotherapy. Toxicities were generally manageable with dose modifications as only 1 pt required discontinuation from LEN. Clinical trial information: NCT02579616. [Table: see text]
Molecular cloning and characterization of WNT14B, a novel member of the WNT gene family (2001)

WNT14B was cloned and characterized in this study. WNT14B encoded 357-amino acid WNT family protein with the signal peptide and an N-linked glycosylation site. WNT14B was most homologous to WNT14 (61.4% total amino acid identity). WNT15 cDNA fragment previously isolated by another group corresponds to a part of ORF of the WNT14B cDNA (codon 216-335). Exon-intron boundaries were conserved between WNT14B and WNT14 genes. WNT14B and WNT3 genes were clustered in the human chromosome 17q21 region in head to head manner. Intergenic region between WNT14B and WNT3 genes was about 33 kb in size. The 6.6-kb WNT14B mRNA was moderately expressed in fetal kidney and adult kidney. Although WNT14B mRNA was not detected in fetal brain and adult brain by northern blot analyses, WNT14B mRNA was detected in brain, especially in occipital lobe, by RNA dot blot analysis. Among 48 human cancer cell lines derived from various tissues, WNT14B was expressed in a teratocarcinoma cell line NT2 with the potential to differentiate into neuronal cells. WNT14B mRNA was significantly up-regulated by all-trans retinoic acid in NT2 cells. These results strongly suggest that WNT14B might be implicated in the early process of neuronal differentiation of NT2 cells induced by retinoic acid.
Changes that Challenge the Soul (1994)

It is hard to dispute many of the descriptive elements of David Bartlett's vision of future electronic journalism. Modern communications technologies, which are abundant rather than scarce, are, indeed, undermining old communications industries and forcing revision of the laws and policies that have traditionally governed them. Communications and computing continue to converge and, in the process, old industry structures distinguishing among print, broadcasting, cable television, and data processing become less relevant. The work of journalists and the role they play in society are changing dramatically. Journalists are less able to function as authoritative gatekeepers. News consumers can already circumvent gates, obtain more raw information unprocessed by journalists, and demand information content and packaging custom-tailored to their tastes and perceived information needs. These changes, already present but likely to accelerate, can empower information consumers, profoundly transforming the world of the journalist and the information consumer alike.
Synthesis of Pyrrolo[2,3-d]pyrimidines. The Aglycone of Toyocamycin1,2 (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of Pyrrolo[2,3-d]pyrimidines. The Aglycone of Toyocamycin1,2Edward C. Taylor and Raymond W. HendessCite this: J. Am. Chem. Soc. 1965, 87, 9, 1995–2003Publication Date (Print):May 1, 1965Publication History Published online1 May 2002Published inissue 1 May 1965https://pubs.acs.org/doi/10.1021/ja01087a025https://doi.org/10.1021/ja01087a025research-articleACS PublicationsRequest reuse permissionsArticle Views520Altmetric-Citations50LEARN 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
Normal embryo fibroblasts release transforming growth factors in a latent form (1984)

Abstract Normal chicken, mouse, and human embryo fibroblasts release into their culture media transforming growth factors (TGFs) in a latent form. Their soft agar colony‐forming activity on two widely used target cells, rat NRK‐49F and mouse AKR‐2B, is essentially revealed only after prior acidification of cell‐conditioned media. These TGFs are EGF‐dependent when assayed on NRK‐49F cells and EGF‐independent on AKR‐2B cells. The TGF activity from the chicken source is released in three (apparent) molecular weight forms of 500 kd, 125 kd, and 20 kd.
Achievements in Understanding and Treatment of Myelodysplastic Syndromes (2000)

The myelodysplastic syndromes (MDS) constitute a challenge for the biologist as well as for the treating physician. In Section I, Dr. Willman reviews the current classifications and disease mechanisms involved in this heterogeneous clonal hematopoietic stem cell disorder. A stepwise genetic progression model is proposed in which inherited or acquired genetic lesions promote the acquisition of “secondary” genetic events mainly characterized by gains and losses of specific chromosome regions. The genetic risk to develop MDS is likely multifactorial and dependent on various constellations of risk-producing and -protecting alleles. In Section II Dr. Barrett with Dr. Saunthararajah addresses the immunologic factors that may act as important secondary events in the development of severe pancytopenia. T cells from patients with MDS may suppress autologous erythroid and granulocytic growth in vitro, and T cell suppression by antithymocyte globulin or cyclosporine may significantly improve cytopenia, especially in refractory anemia. Recent studies have also demonstrated an increased vessel density in MDS bone marrow, and a phase II trial of thalidomide showed responses in a subgroup of MDS patients especially in those with low blast counts. In Section III Dr. Hellström-Lindberg presents results of allogeneic and autologous stem cell transplantation (SCT), intensive and low-dose chemotherapy. The results of allogeneic SCT in MDS are slowly improving but are still poor for patients with unfavorable cytogenetics and/or a high score according to the International Prognostic Scoring System. A recently published study of patients between 55-65 years old showed a disease-free survival (DFS) at 3 years of 39%. Consolidation treatment with autologous SCT after intensive chemotherapy may result in long-term DFS in a proportion of patients with high-risk MDS. Low-dose treatment with 5-azacytidine has been shown to significantly prolong the time to leukemic transformation or death in patients with high-risk MSA. Erythropoietin and granulocyte colony-stimulating factor may synergistically improve hemoglobin levels, particularly in sideroblastic anemia. Recent therapeutic advances have made it clear that new biological information may lead to new treatment modalities and, in combination with statistically developed predictive models, help select patients for different therapeutic options.
Effect of single dose administration of diuretics on the blood sugar of alloxan‐diabetic mice or mice made hyperglycaemic by the acute administration of diazoxide (1973)

1. Frusemide produced hyperglycaemia in mice when administered together with diazoxide. The interaction between the drugs in elevating the blood sugar was shown to be additive.2. The diuretic, natriuretic and kaliuretic effects of frusemide were very markedly attenuated by diazoxide.3. Neither ethacrynic acid nor hydrochlorothiazide exerted any effect upon blood sugar when administered together with diazoxide.4. Bilateral nephrectomy completely prevented the hyperglycaemic effect of frusemide in normal mice and in mice treated with diazoxide. Diazoxide itself still produced hyperglycaemia in nephrectomized mice.5. Frusemide, ethacrynic acid and diazoxide, but not hydrochlorothiazide, each produced hyperglycaemia in alloxan-diabetic mice, this being prevented by bilateral nephrectomy.
Thermal Rearrangements of Monoterpenes and Monoterpenoids (2009)

Abstract The thermal conversions of monoterpenes and monoterpenoids are an interesting field of research with respect to mechanistic, kinetic, and theoretical issues. Since the beginning of the 20th century, these reactions have attracted the interest of many research groups, and even today there are sufficient problems and questions to deal with. This review covers the thermal isomerization chemistry of pinanes, pinenes, carenes, and thujenes over the past 70 years. Categorization of these compounds into groups, each of them being represented by a small parent molecule (cyclobutane, vinylcyclobutane, vinylcyclopropane), allows systematization of multitude of publications.
Detailed deletion mapping on chromosome arm 12q in human pancreatic adenocarcinoma: Identification of a 1-cM region of common allelic loss (1996)

As a first step toward understanding molecular mechanisms in human pancreatic carcinogenesis, we searched for the location of tumor suppressor genes by examining loss of heterozygosity (LOH) in 44 pancreatic cancer specimens. We used 46 microsatellite markers that spanned all of the autosomes. Frequent LOH was observed in six chromosomal regions: in chromosome arms lp (32%), 6q (37%), 9p (50%), 12q (30%), 17p (59%), and 18q (35%). Because chromosome arm 12q is a reported target for allelic loss in some other cancers, we focused on this region with 66 primary specimens and identified the minimal common region of allelic loss within a I-cM interval in 12q22-q23.l. Microsatellite instability (MI) was also examined in this study, and the incidence of MI(+) cases, in which MI of two or more microsatellite loci was detected, was 61% (27 of 44 informative cases). In pancreatic tumors with MI(+), mutations of the transforming growth factor beta receptor II (RII) gene were not detected.