gebhart/patrepeval huggingface dataset:
Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms (2002)

Massively parallel signature sequencing (MPSS) is one of the newest tools available for conducting in-depth expression profiling. MPSS is an open-ended platform that analyses the level of expression of virtually all genes in a sample by counting the number of individual mRNA molecules produced from each gene. There is no requirement that genes be identified and characterised prior to conducting an experiment. MPSS has a routine sensitivity at a level of a few molecules of mRNA per cell, and the datasets are in a digital format that simplifies the management and analysis of the data. Therefore, of the various microarray and non-microarray technologies currently available, MPSS provides many advantages for generating the type of complete datasets that will help to facilitate hypothesis-driven experiments in the era of digital biology.
Elevated troponin T and C-reactive protein predict impaired outcome for 4 years in patients with refractory unstable angina, and troponin T predicts benefit of treatment with abciximab in combination with PTCA (2003)

Troponin T as a marker of thrombosis and CRP as a marker of inflammation are independent predictors of impaired outcome at 4 years follow-up. The initial benefit from abciximab with regard to death and myocardial infarction was preserved at 4 years. No specific benefit with abciximab was observed for patients with elevated CRP, suggesting that a chronic inflammatory process is not affected by abciximab. In contrast the benefit of treatment in patients with elevated troponin T implies that the acute thrombotic process in refractory unstable angina is treated effectively.
Purification and partial characterization of a bacterial phospholipid: cholesterol acyltransferase. (1982)

A glycerophospholipid:cholesterol acyltransferase has been purified to near homogeneity from cell-free culture supernatants of Aeromonas salmonicida. The characteristics of the enzyme distinguish it from bacterial phospholipases; however, it shares several properties with the lecithin:cholesterol acyltransferase of mammalian plasma. Thus, the enzyme inhibits 2-positional specificity as an acyltransferase and it will act as a phospholipase A2 in the absence of cholesterol. Furthermore, it has no divalent cation requirement and it is stimulated both by albumin and by human apolipoprotein A-I. Unlike the mammalian acyltransferase, however, the bacterial enzyme is not specific for phosphatidylcholine and in addition it can use human erythrocyte membranes as substrates. Similar to Naja naja phospholipase A2, it acts asymmetrically on intact erythrocytes.
Prostratin: activation of latent HIV-1 expression suggests a potential inductive adjuvant therapy for HAART (2001)

Prostratin is a unique phorbol ester that stimulates protein kinase C activity but is nontumor promoting. Remarkably, prostratin is also able to inhibit de novo human immunodeficiency virus type 1 (HIV-1) infection yet up-regulate viral expression from latent proviruses. Prostratin's lack of tumor promotion, coupled with its ability to block viral spread yet induce latent proviral expression, prompted studies to determine whether this compound could serve as an inductive adjuvant therapy for patients treated with highly active antiretroviral therapy (HAART). The current experiments indicate that prostratin is a potent mitogen for mononuclear phagocytes possessing many of the activities of phorbol myristate acetate (PMA) with notable functional differences. Prostratin, like PMA, accelerates differentiation of the myeloid cell-lines, HL-60 and THP-1, as well as mononuclear phagocytes from bone marrow and peripheral blood. Enzyme-linked immunosorbent assay and gene array analyses indicate significant changes in the expression of proteins and messenger RNA after treatment of cells with prostratin, consistent with phagocyte activation and differentiation. Prostratin blocks HIV-1 infection relating to down-regulation of CD4 receptor expression. The array analysis indicates a similar down-regulation of the HIV-1 coreceptors, CXCR4 and CCR5, and this may also reduce viral infectivity of treated host cells. Finally, prostratin is capable of up-regulating HIV-1 expression from CD8+ T lymphocyte-depleted peripheral blood mononuclear cells of patients undergoing HAART. This novel observation suggests the agent may be an excellent candidate to augment HAART by inducing expression of latent HIV-1 with the ultimate goal of eliminating persistent viral reservoirs in certain individuals infected with HIV-1.
Effects of Glycemic Control on Diabetes Complications and on the Prevention of Diabetes (2004)

IN BRIEF Randomized, controlled clinical trials (RCTs), completed during the past several years or currently underway, are defining the scientific basis of contemporary diabetes care. In terms of glycemic control, landmark RCTs have demonstrated that meticulous glycemic control reduces risk of microvascular and neurological complications of diabetes. Studies in pre-diabetes have shown that early intervention slows progression to diabetes. Ongoing studies are examining the effects of glycemic interventions on macrovascular complications of diabetes, the impact of early treatment on the course of diabetes, and whether there are differences depending on the nature of the intervention used.
Phase retrieval algorithms: a comparison (1982)

Iterative algorithms for phase retrieval from intensity data are compared to gradient search methods. Both the problem of phase retrieval from two intensity measurements (in electron microscopy or wave front sensing) and the problem of phase retrieval from a single intensity measurement plus a non-negativity constraint (in astronomy) are considered, with emphasis on the latter. It is shown that both the error-reduction algorithm for the problem of a single intensity measurement and the Gerchberg-Saxton algorithm for the problem of two intensity measurements converge. The error-reduction algorithm is also shown to be closely related to the steepest-descent method. Other algorithms, including the input-output algorithm and the conjugate-gradient method, are shown to converge in practice much faster than the error-reduction algorithm. Examples are shown.
An analysis of fetal hemoglobin variation in sickle cell disease: the relative contributions of the X-linked factor, beta-globin haplotypes, alpha-globin gene number, gender, and age (1995)

Five factors have been shown to influence the 20-fold variation of fetal hemoglobin (Hb F) levels in sickle cell anemia (SS): age, sex, the alpha-globin gene number, beta-globin haplotypes, and an X-linked locus that regulates the production of Hb F-containing erythrocytes (F cells), ie, the F-cell production (FCP) locus. To determine the relative importance of these factors, we studied 257 Jamaican SS subjects from a Cohort group identified by newborn screening and from a Sib Pair study. Linear regression analyses showed that each variable, when analyzed alone, had a significant association with Hb F levels (P < .05). Multiple regression analysis, including all variables, showed that the FCP locus is the strongest predictor, accounting for 40% of Hb F variation. beta-Globin haplotypes, alpha-globin genes, and age accounted for less than 10% of the variation. The association between the beta-globin haplotypes and Hb F levels becomes apparent if the influence of the FCP locus is removed by analyzing only individuals with the same FCP phenotype. Thus, the FCP locus is the most important factor identified to date in determining Hb F levels. The variation within each FCP phenotype is modulated by factors associated with the three common beta-globin haplotypes and other as yet unidentified factor(s).
Synthesis and insecticidal activity of benzoheterocyclic analogues of N′‐benzoyl‐N‐(tert‐butyl)benzohydrazide: Part 3. Modification of N‐tert‐butylhydrazine moiety (2002)

Nineteen analogues were synthesized by modifying the tert-butylhydrazine moieties of N'-tert-butyl-N'-(3,5-dimethylbenzoyl)-5-methyl-2,3-dihydro-1,4-benzodioxine-6-carbohydrazide and N'-tert-butyl-N'-(3,5-dimethylbenzoyl)-5-methylchromane-6-carbohydrazide (chromafenozide), and the synthesized analogues were evaluated for their insecticidal activity against Spodoptera litura F. While all of the synthesized analogues had insecticidal activity inferior to those of the lead compounds, several of the analogues nonetheless showed high insecticidal activity. Chromafenozide has shown very high selectivity toward lepidopteran species.
Metabolic origins and clinical significance of LDL heterogeneity (2002)

LDLs in humans comprise multiple distinct subspecies that differ in their metabolic behavior and pathologic roles. Metabolic turnover studies suggest that this heterogeneity results from multiple pathways, including catabolism of different VLDL and IDL precursors, metabolic remodeling, and direct production. A common lipoprotein profile designated atherogenic lipoprotein phenotype is characterized by a predominance of small dense LDL particles. Multiple features of this phenotype, including increased levels of triglyceride rich lipoprotein remnants and IDLs, reduced levels of HDL and an association with insulin resistance, contribute to increased risk for coronary heart disease compared with individuals with a predominance of larger LDL. Increased atherogenic potential of small dense LDL is suggested by greater propensity for transport into the subendothelial space, increased binding to arterial proteoglycans, and susceptibility to oxidative modification. Large LDL particles also can be associated with increased coronary disease risk, particularly in the setting of normal or low triglyceride levels. Like small LDL, large LDL exhibits reduced LDL receptor affinity compared with intermediate sized LDL. Future delineation of the determinants of heterogeneity of LDL and other apoB-containing lipoproteins may contribute to improved identification and management of patients at high risk for atherosclerotic disease.
Phylogeny of Erysiphe, Microsphaera, Uncinula (Erysipheae) and Cystotheca, Podosphaera, Sphaerotheca (Cystotheceae) inferred from rDNA ITS sequences: some taxonomic consequences (2000)

Braun, U. &amp; Takamatsu, S. 2000: Phylogeny of Erysiphe, Microsphaera, Uncinula (Erysipheae) and Cystotheca, Podosphaera, and Sphaerotheca (Cystotheceae) inferred from rDNA ITS sequences – some taxonomic consequences. Schlechtendalia 4: 1-33. Die enge Verwandtschaft zwischen den Gattungen Erysiphe s.str. (= Erysiphe Sektion Erysiphe), Microsphaera und Uncinula, die durch zahlreiche morphologisch untermediäre Taxa verbunden sind, wird stark durch licht- und elektronenmikroskopische Merkmale unterstützt und durch neue Untersuchungen der Nukleotidsequenzen der rDNA-ITS-Region bestätigt, da diese Gattungen nicht zu verschiedenen monophyletischen Linien gehören. Erysiphe s.str. und Microsphaera bilden jedoch verschiedene kleine, gemischte Gruppen. Es hat sich herausgestellt, daß die Bildung verzweigter Fruchtkörperanhängsel keinen taxonomischen Wert auf Gattungsebene hat. Deshalb wird vorgeschlagen, Microsphaera als Synonym von Erysiphe zu betrachten. Die notwendigen Neukombinationen werden eingeführt. Uncinula-Arten bilden ein “Subclade” an der Basis des “Erysiphe s.str./Microsphaera (Pseudoidium)-Clades”. Da auch einige Erysiphe s.str.-Arten in dieses “Subclade” gehören, ist es notwendig, diese beiden Gattungen zu vereinigen. Erysiphe Sektion Erysiphe, E. Sektion Microsphaera und E. Sektion. Uncinula. Untersuchungen von Nukleotidsequenzen ribosomaler DNA (ITS) zahlreicher Taxa der Cystotheceae zeigten, daß Podosphaera und Sphaerotheca keine getrennten “Clades” bilden. Taxa von Sphaerotheca Sektion Sphaerotheca und Sektion Magnicellulatae bilden zusammen mit zwei verschiedenen Gruppen von Podosphaera-Arten getrennte “Subclades”. Auf Grundlage dieser Befunde und da Podosphaera- und Sphaerotheca-Arten morphologisch nur durch verzweigte und einfache Fruchtkörperanhängsel unterschieden sind, wird vorgeschlagen, beide Gattungen zu vereinigen. Neukombinationen von Sphaerotheca-Arten unter Podosphaera werden eingeführt. Podosphaera wird formal in folgende morphologisch, aber nicht phylogenetisch begründete Sektionen und Subsektionen gegliedert: Podosphaera Sektion Podosphaera, P. Sektion Sphaerotheca Subsektion Sphaerotheca, und Subsektion Magnicellulatae. Weiterhin werden einige Änderungen der Klassifizierung der Erysiphaceae vorgeschlagen. Folgende Kombinationen werden eingeführt: Erysiphaceae Tribus Cystotheceae Subtribus Sawadaeinae, Erysiphaceae Tribus Golovinomyceteae, Erysiphaceae Tribus Golovinomyceteae Subtribus Arthrocladiellinae und Subtribus Neoerysiphinae.
Labelling polymers and micellar nanoparticles via initiation, propagation and termination with ROMP (2013)

In this paper we compare and contrast three approaches for labelling polymers with functional groups via ring-opening metathesis polymerization (ROMP). We explored the incorporation of functionality via initiation, termination and propagation employing an array of novel initiators, termination agents and monomers. The goal was to allow the generation of selectively labelled and well-defined polymers that would in turn lead to the formation of labelled nanomaterials. Norbornene analogues, prepared as functionalized monomers for ROMP, included fluorescent dyes (rhodamine, fluorescein, EDANS, and coumarin), quenchers (DABCYL), conjugatable moieties (NHS esters, pentafluorophenyl esters), and protected amines. In addition, a set of symmetrical olefins for terminally labelling polymers, and for the generation of initiators <i>in situ</i> is described.
Epstein-Barr Virus Nuclear Antigen 3C and Prothymosin Alpha Interact with the p300 Transcriptional Coactivator at the CH1 and CH3/HAT Domains and Cooperate in Regulation of Transcription and Histone Acetylation (2002)

The Epstein-Barr virus nuclear antigen 3C (EBNA3C), encoded by Epstein-Barr virus (EBV), is essential for mediating transformation of human B lymphocytes. Previous studies demonstrated that EBNA3C interacts with a small, nonhistone, highly acidic, high-mobility group-like nuclear protein prothymosin alpha (ProT(alpha)) and the transcriptional coactivator p300 in complexes from EBV-infected cells. These complexes were shown to be associated with histone acetyltransferase (HAT) activity in that they were able to acetylate crude histones in vitro. In this report we show that ProT(alpha) interacts with p300 similarly to p53 and other known oncoproteins at the CH1 amino-terminal domain as well as at a second domain downstream of the bromodomain which includes the CH3 region and HAT domain. Similarly, EBNA3C also interacts with p300 at regions which include the CH1 and CH3/HAT domains, suggesting that ProT(alpha) and EBNAC3C may interact in a complex with p300. We also show that ProT(alpha) activates transcription when targeted to promoters by fusion to the GAL4 DNA binding domain and that this activation is enhanced by the addition of an exogenous source of p300 under the control of a heterologous promoter. This overall activity is down-modulated in the presence of EBNA3C. These results further establish the interaction of cellular coactivator p300 with ProT(alpha) and demonstrate that the associated activities resulting from this interaction, which plays a role in acetylation of histones and coactivation, can be regulated by EBNA3C. Furthermore, this study establishes for the first time a transcriptional role for ProT(alpha) in recruitment or stabilization of coactivator p300, as well as other basal transcription factors, at the nucleosomes for regulation of transcription.
A performance engineering tool and method for distributing applications (1997)

Recent advances in distributed object and Internet technologies have made it attractive for organizations to distribute application functions. Typical projects include: the re-hosting of legacy applications that move application functionality to or from mainframe/server environments, the creation of new target independent interfaces for legacy systems, and the development of new applications altogether. Design concerns for such systems include security, reliability, and performance. The performance of these systems often defy intuition and must be taken into account during their design. In this paper we present a performance engineering tool for developing predictive models for such systems. The tool automates model construction by developing the structure of the model and measuring parameters that are difficult to estimate or capture manually. Designers can then focus on the performance impact of system configuration alternatives. We show how these results have been integrated into a prototype of IBM's Distributed Application Development Toolkit (DADT). A case study is presented that considers the hosting of sample application across three architectural models: Client/Server using DCE, Web Server/Server using HTML/HTTP/CGI, and a JAVA/CORBA-ORB/ Server model.
Validation of the 12-Gene Colon Cancer Recurrence Score in NSABP C-07 As a Predictor of Recurrence in Patients With Stage II and III Colon Cancer Treated With Fluorouracil and Leucovorin (FU/LV) and FU/LV Plus Oxaliplatin (2013)

The 12-gene Recurrence Score predicts recurrence risk in stage II and stage III colon cancer and provides additional information beyond conventional clinical and pathologic factors. Incorporating Recurrence Score into the clinical context may better inform adjuvant therapy decisions in stage III as well as stage II colon cancer.
CCLVII.—Syntheses in the epinephrine series. Part II. The formation and properties of some 2 : 5- and 2 : 6-substituted pyrazines and their conversion into amino-ketones and imino-diketones (1910)

F. Tutin, J. Chem. Soc., Trans., 1910, 97, 2495 DOI: 10.1039/CT9109702495
Identification of prostaglandin E receptor ‘EP2’ cloned from mastocytoma cells as EP4 subtype (1995)

We previously cloned a cDNA for a mouse PGE receptor positively coupled to adenylate cyclase from mouse mastocytoma cells, and reported it as EP2 subtype of PGE receptor [Honda, A., Sugimoto, Y., Namba, T., Watabe, A., Irie, A., Negishi, M., Narumiya, S. and Ichikawa, A. (1993) J. Biol. Chem. 268, 7759-7762]. However, it is not sensitive to one of the EP2 agonists, butaprost. Recently another subtype of PGE receptor coupled to adenylate cyclase has been identified pharmacologically and named EP4. These findings have led us to examine whether the cloned receptor is the EP4 subtype. AH23848B, a selective EP4 antagonist, not only displaced the [3H]PGE2 binding to the cloned receptor but antagonized the PGE2-stimulated cAMP formation in the receptor. In contrast, EP2 specific agonist, butaprost and 19(R)OH-PGE2 neither bound to the receptor nor stimulated the cAMP formation. These results suggest that this receptor previously reported as 'EP2' subtype is identical to the pharmacologically defined EP4 subtype and not of EP2 subtype.
Antisense oligonucleotide therapy in cancer. (2003)

The sequencing of the human genome has highlighted some of the genes that are of importance in disease states. This has provided opportunities for the development of new therapeutics to target a wide range of human diseases. These new drugs are intended to be highly specific; antisense oligonucleotides (ONs) are one such class of new drugs. ONs are short pieces of DNA which hybridize to a specific target mRNA blocking its translation to protein, thereby inhibiting the action of the gene. Several genes known to be of importance in the regulation of apoptosis, cell growth, metastasis and angiogenesis provide a tantalizing prospect for the development of anticancer agents. The phosphorothioate antisense ONs are the current choice for antisense therapy. This article reviews the current strategies for antisense targets in cancer therapy.
Cell separation based on size and deformability using microfluidic funnel ratchets (2012)

The separation of biological cells by filtration through microstructured constrictions is limited by unpredictable variations of the filter hydrodynamic resistance as cells accumulate in the microstructure. Applying a reverse flow to unclog the filter will undo the separation and reduce filter selectivity because of the reversibility of low-Reynolds number flow. We introduce a microfluidic structural ratchet mechanism to separate cells using oscillatory flow. Using model cells and microparticles, we confirmed the ability of this mechanism to sort and separate cells and particles based on size and deformability. We further demonstrate that the spatial distribution of cells after sorting is repeatable and that the separation process is irreversible. This mechanism can be applied generally to separate cells that differ based on size and deformability.
Molecular Approaches To Detecting Herpes Simplex Virus and Enteroviruses in the Central Nervous System (2002)

The initial presentation of symptoms and clinical manifestations of viral central nervous system (CNS) infectious diseases often makes a specific diagnosis difficult and uncertain. For example, the clinical features of CNS disease due to nonpolio enteroviruses (EV) can overlap those caused by herpes simplex virus (HSV), which sometimes occur in young infants and adults in the absence of cutaneous lesions (4, 12, 39). The etiological agent and type of infection can determine potential prognoses as well as optimal treatment modality for the patient. Enterovirus infections often do not require antiviral intervention, but at least two new antivirals are undergoing trials, the more prominent of which is pleconaril (16, 22). Also, if a mean time of 24 h to diagnosis was assumed, 1.2 to 2.8 days of hospitalization per patient could be saved over current averages (1, 13, 18, 26). Mortality from HSV, however, before the use of acyclovir was 60 to 70% and has been reported to drop to 19 to 38% with therapy (27, 38). Early diagnosis and treatment of viral CNS infections, therefore, will decrease morbidity and mortality rates.
Stochastic language models for style-directed layout analysis of document images (2003)

Image segmentation is an important component of any document image analysis system. While many segmentation algorithms exist in the literature, very few i) allow users to specify the physical style, and ii) incorporate user-specified style information into the algorithm's objective function that is to be minimized. We describe a segmentation algorithm that models a document's physical structure as a hierarchical structure where each node describes a region of the document using a stochastic regular grammar. The exact form of the hierarchy and the stochastic language is specified by the user, while the probabilities associated with the transitions are estimated from groundtruth data. We demonstrate the segmentation algorithm on images of bilingual dictionaries.
Gene Expression During Normal and Malignant Differentiation (1985)

This book contains 18 selections. Some of the titles are: Exploring Carcinogenesis with Retroviral and Cellular Oncogenes; Retroviruses, Oncogenes and Evolution; HTLV and Human Neoplasi; Modes of Activation of cMyc Oncogene in B and T Lymphoid Tumors; The Structure and Function of the Epidermal Growth Factor Receptor: Its Relationship to the Protein Product of the V-ERB-B Oncogene; and Expression of Human Retrovirus Genes in Normal and Neoplastic Epithelial Cells.
美国“无过失离婚”的后果 (1992)

单纯一种离婚准则的改变,怎么会产生如此深远的影响?为什么一种旨在创造更加平等的财产分割的法律改革,却会以使得离婚妇女及其子女陷于穷困而告终? 当我刚刚开始这项研究时,我曾经以改革者的乐观主义态度假定,加利福尼亚的无过失离婚试验只能产生积极的结果。它不会仅排除那令人感到羞耻的证言,还法庭以尊严,而且还会促进公正、平等地解决离婚夫妻的经济纠纷。我相信,新法律所寻求的相互敌意和刻毒的消除,还会促进当事者双方在离婚后共同抚养子女方面的合作能力。此外,新法律要求实现男女在法律上平等,从而消除那种认为妇女应当处于服从地位的时代错误,承认妇女在婚姻关系中的完全平等地位。