gebhart/patrepeval huggingface dataset:
Synergism between Multiple Virus-induced Factor-binding Elements Involved in the Differential Expression of Interferon A Genes (1997)

Comparative transfection analysis of murine interferon A4 and interferon A11 promoter constructs transiently transfected in mouse L929 and human HeLa S3 cells infected with Newcastle disease virus showed that the second positive regulatory domain I-like domain (D motif), located between nucleotides -57 and -46 upstream of the transcription start site, contributes to the activation of virus-induced transcription of the interferon (IFN)-A4 gene promoter by cooperating with the positive regulatory domain I-like and TG-like domains previously described. Electrophoretic mobility shift assay performed with the virus-inducible fragments containing these motifs indicated that the binding activity that we have denoted as virus-induced factor (Génin, P., Bragança, J., Darracq, N., Doly, J., and Civas, A. (1995) Nucleic Acids Res. 23, 5055-5063) is different from interferon-stimulated gene factor 3. It binds to the D motif but not to the virus-unresponsive form of the D motif disrupted by a G-57 --> C substitution. We show that the low levels of IFN-A11 gene expression are caused essentially by the lack of two inducible enhancer domains disrupted by the A-78 --> G and the G-57 --> C substitutions. These data suggest a model taking account of the differential regulation of IFN-A gene family members. They also suggest that virus-induced factor may correspond to the primary transcription factor directly activated by virus that is involved in the initiation of IFN-A gene transcription.
A Bioavailability Score (2005)

Responding to a demonstrated need for scientists to forecast the permeability and bioavailability (F) properties of compounds before their purchase, synthesis, or advanced testing, we have developed a score that assigns the probability that a compound will have F > 10% in the rat. Neither the rule-of-five, log P, log D, nor the combination of the number of rotatable bonds and polar surface area successfully categorized compounds. Instead, different properties govern the bioavailability of compounds depending on their predominant charge at biological pH. The fraction of anions with >10% F falls from 85% if the polar surface area (PSA) is < or = 75 A(2), to 56% if 75 < PSA < 150 A(2), to 11% if PSA is > or = 150 A(2). On the other hand, whereas 55% of the neutral, zwitterionic, or cationic compounds that pass the rule-of-five have >10% F, only 17% of those that fail have > 10% F. This same categorization distinguishes compounds that are poorly permeable from those that are permeable in Caco-2 cells. Further validation is provided with human bioavailability values from the literature.
MAVIS 2: a new approach to content and concept based navigation (1999)

One of the most active areas of multimedia research is into content based retrieval (CBR) of multimedia information. Using tools from the disparate disciplines of image processing, audio processing, video processing and others, approaches to CBR for the different media are being produced and integrated into multimedia systems, quite frequently in an ad hoc way. Also, traditional hypertext systems allow textual information to be arbitrarily linked so that users can navigate between related parts of the information in a system. Many of these systems can use multimedia information such as images, sounds and video clips that can also be linked. In such hypermedia systems the links are usually created using specific locations in particular documents. Some systems, such as Microcosm, also allow links to be created by specifying the text that forms one anchor of the link. These links are created once and can be followed from any location where the text occurs. To achieve this, the system has to examine documents currently being viewed by the user and look for matches between text in the documents and text that forms anchors of links within the system. Where matches occur the system can highlight the text as a source anchor for a link. This is a form of content based navigation(CBN). Navigational links are dynamically created by matching the content of currently viewed documents with the content of previously created link anchors. For textual documents this is relatively easy to implement since comparing text strings is often straightforward. Content based navigation for multimedia documents also involves comparing and matching selections of images, video and sound with each other. Our MAVIS 1 project addressed the problem of integrated content based retrieval and navigation from non-text media but there are many limitations associated with such systems. This paper will describe some of the reasons for these limitations and present an overview of MAVIS 2, a new architecture for multimedia content based retrieval and navigation. The architecture not only presents a consistent cross media approach to CBR and CBN but also includes the integration of a multimedia thesaurus which can substantially improve the flexibility and versatility of the multimedia information system, enhancing the capabilities of both content based retrieval and content based navigation. MAVIS stands for Multimedia Architecture for Video, Image and Sound and the MAVIS 2 architecture also includes integration of intelligent agents which support navigation by utilising both the media content and semantic concepts in the multimedia thesaurus to develop rapid paths from media based features to semantic concepts or to generate pseudo thesaurus groupings by feature clustering when no semantic relations are available. MAVIS 2 is currently being implemented and the paper will not only present details of the architecture but also show examples of retrieval and navigation with the prototype system.
A Novel Index Supporting High Volume Data Warehouse Insertion (1999)

While the desire to support fast, ad hoc query processing for large data warehouses has motivated the recent introduction of many new indexing structures, with a few notable exceptions (namely, the LSM-Tree [4] and the Stepped Merge Method [1]) little attention has been given to developing new indexing schemes that allow fast insertions. Since additions to a large warehouse may number in the millions per day, indices that require a disk seek (or even a significant fraction of a seek) per insertion are not acceptable. In this paper, we offer an alternative to the B+-tree called the Y-tree for indexing huge warehouses having frequent insertions. The Y-tree is a new indexing structure supporting both point and range queries over a single attribute, with retrieval performance comparable to the B+-tree. For processing insertions, however, the Y-tree may exhibit a speedup of 100 times over batched insertions into a B+-tree.
Gene expression profiles of CD34+ cells in myelodysplastic syndromes: involvement of interferon-stimulated genes and correlation to FAB subtype and karyotype (2006)

To gain insight into the poorly understood pathophysiology of the myelodysplastic syndromes (MDSs), we have determined the gene expression profiles of the CD34+ cells of 55 patients with MDS by using a comprehensive array platform. These profiles showed many similarities to reported interferon-gamma-induced gene expression in normal CD34+ cells; indeed the 2 most up-regulated genes, IFIT1 and IFITM1, are interferon-stimulated genes (ISGs). Alterations in the expression of ISGs may play a role in the hematologic features of MDS, such as peripheral blood cytopenias. Up-regulation of IFIT1 is a potential diagnostic marker for MDS. We determined whether distinct gene expression profiles were associated with specific FAB and cytogenetic groups. CD34+ cells from patients with refractory anemia with ringed sideroblasts (RARS) showed a particular gene expression profile characterized by up-regulation of mitochondrial-related genes and, in particular, of those of heme synthesis (eg, ALAS2). CD34+ cells from patients with the del(5q) had a distinct gene expression profile, characterized by down-regulation of genes assigned to 5q, and up-regulation of the histone HIST1 gene cluster at chromosome 6p21 and of genes related to the actin cytoskeleton. This study provides important and new insights into the pathophysiology of MDS.
3D-printing technologies for electrochemical applications (2016)

Since its conception during the 80s, 3D-printing, also known as additive manufacturing, has been receiving unprecedented levels of attention and interest from industry and research laboratories. This is in addition to end users, who have benefited from the pervasiveness of desktop-size and relatively cheap printing machines available. 3D-printing enables almost infinite possibilities for rapid prototyping. Therefore, it has been considered for applications in numerous research fields, ranging from mechanical engineering, medicine, and materials science to chemistry. Electrochemistry is another branch of science that can certainly benefit from 3D-printing technologies, paving the way for the design and fabrication of cheaper, higher performing, and ubiquitously available electrochemical devices. Here, we aim to provide a general overview of the most commonly available 3D-printing methods along with a review of recent electrochemistry related studies adopting 3D-printing as a possible rapid prototyping fabrication tool.
Isolation, characterization, and function of 6-mycolyl-6'-acetyltrehalose in the H37Ra strain of Mycobacterium tuberculosis (1976)

The major mycolic acid containing extractable lipid of the H37Ra strain of Mycobacterium tuberculosis was established to be 6-mycolyl-6'-acetyltrehalose (MAT). This new glycolipid was extracted from harvested cells with chloroform-methanol (2:1, v/v) and initially precipitated out in acetone. A series of column (DEAE-cellulose, silicic acid, and Sephadex LH-20) and preparative thin-layer chromatography steps yielded a homogeneous preparation. A single sugar was released by saponification and it was identified to be trehalose by paper chromatography and gas-liquid chromatography of the trimethylsilyl derivative. The lipid moiety was determined to be exclusively mycolic acids. The major mycolic acid component of this glycolipid was isolated, purified as the methyl ester, and characterized to be methyl alpha-mycolate by nuclear magnetic resonance spectroscopy and mass spectrometry. The molar ratio of trehalose to mycolic acids was determined to be 1:1. The other acyl group in MAT was established to be acetate by gas-liquid chromatography. Methylation analysis showed the mycolate and acetate ester linkages to the 6 and 6' positions of trehalose. The time course of incorporation of 14C-labeled acetate into the mycolates of both MAT and total cellular fatty acids was followed. These results showed that the synthesis of MAT is rapid and linear for the initial 20 min of incubation whereas the curve for the total cellular mycolates minus MAT (an estimate of the cell wall mycolates) had a 25-30-min lag period. When the label in the lipids was chased out with an excess of unlabeled acetate, relatively rapid decline in the labeled MAT resulted with a corresponding rise in the level of radioactivity in the mycolates of the nonextractable cellular fraction (assumed to be the cell wall fraction). Thus mycolic acids are rapidly transferred from MAT to the cell wall of M. tuberculosis.
A role for thrombin in liver fibrosis (2004)

These data provide evidence that thrombin antagonism can reduce liver fibrogenesis. The early effect of SSR182289 on ASMA and TIMP-1 expression suggests that it is beneficial in reducing fibrogenic cell activation.
Thermostable NADP + -Dependent Medium-Chain Alcohol Dehydrogenase from Acinetobacter sp. Strain M-1: Purification and Characterization and Gene Expression in Escherichia coli (2000)

NADPH-dependent alkylaldehyde reducing enzyme, which was greatly induced by n-hexadecane, from Acinetobacter sp. strain M-1 was purified and characterized. The purified enzyme had molecular masses of 40 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 160 kDa as determined by gel filtration chromatography. The enzyme, which was shown to be highly thermostable, was most active toward n-heptanal and could use n-alkylaldehydes ranging from C(2) to C(14) and several substituted benzaldehydes, including the industrially important compounds cinnamyl aldehyde and anisaldehyde, as substrates. The alrA gene coding for this enzyme was cloned, and its nucleotide sequence was determined. The deduced amino acid sequence encoded by the alrA gene exhibited homology to the amino acid sequences of zinc-containing alcohol dehydrogenases from various sources. The gene could be highly expressed in Escherichia coli, and the product was purified to homogeneity by simpler procedures from the recombinant than from the original host. Our results show that this enzyme can be used for industrial bioconversion of useful alcohols and aldehydes.
IFI16 is an innate immune sensor for intracellular DNA (2010)

The detection of intracellular microbial DNA is critical to appropriate innate immune responses; however, knowledge of how such DNA is sensed is limited. Here we identify IFI16, a PYHIN protein, as an intracellular DNA sensor that mediates the induction of interferon-β (IFN-β). IFI16 directly associated with IFN-β-inducing viral DNA motifs. STING, a critical mediator of IFN-β responses to DNA, was recruited to IFI16 after DNA stimulation. Lowering the expression of IFI16 or its mouse ortholog p204 by RNA-mediated interference inhibited gene induction and activation of the transcription factors IRF3 and NF-κB induced by DNA and herpes simplex virus type 1 (HSV-1). IFI16 (p204) is the first PYHIN protein to our knowledge shown to be involved in IFN-β induction. Thus, the PYHIN proteins IFI16 and AIM2 form a new family of innate DNA sensors we call 'AIM2-like receptors' (ALRs).
CBSA: content-based soft annotation for multimodal image retrieval using bayes point machines (2003)

We propose a content-based soft annotation (CBSA) procedure for providing images with semantical labels. The annotation procedure starts with labeling a small set of training images, each with one single semantical label (e.g., forest, animal, or sky). An ensemble of binary classifiers is then trained for predicting label membership for images. The trained ensemble is applied to each individual image to give the image multiple soft labels, and each label is associated with a label membership factor. To select a base binary-classifier for CBSA, we experiment with two learning methods, support vector machines (SVMs) and Bayes point machines (BPMs), and compare their class-prediction accuracy. Our empirical study on a 116-category 25K-image set shows that the BPM-based ensemble provides better annotation quality than the SVM-based ensemble for supporting multimodal image retrievals.
Proline Accumulation in Maize (Zea maysL.) Primary Roots at Low Water Potentials. II. Metabolic Source of Increased Proline Deposition in the Elongation Zone1 (1999)

The proline (Pro) concentration increases greatly in the growing region of maize (Zea mays L.) primary roots at low water potentials (psiw), largely as a result of an increased net rate of Pro deposition. Labeled glutamate (Glu), ornithine (Orn), or Pro was supplied specifically to the root tip of intact seedlings in solution culture at high and low psiw to assess the relative importance of Pro synthesis, catabolism, utilization, and transport in root-tip Pro deposition. Labeling with [3H]Glu indicated that Pro synthesis from Glu did not increase substantially at low psiw and accounted for only a small fraction of the Pro deposition. Labeling with [14C]Orn showed that Pro synthesis from Orn also could not be a substantial contributor to Pro deposition. Labeling with [3H]Pro indicated that neither Pro catabolism nor utilization in the root tip was decreased at low psiw. Pro catabolism occurred at least as rapidly as Pro synthesis from Glu. There was, however, an increase in Pro uptake at low psiw, which suggests increased Pro transport. Taken together, the data indicate that increased transport of Pro to the root tip serves as the source of low-psiw-induced Pro accumulation. The possible significance of Pro catabolism in sustaining root growth at low psiw is also discussed.
Priming of Memory But Not Effector CD8 T Cells by a Killed Bacterial Vaccine (2001)

Killed or inactivated vaccines targeting intracellular bacterial and protozoal pathogens are notoriously ineffective at generating protective immunity. For example, vaccination with heat-killed Listeria monocytogenes (HKLM) is not protective, although infection with live L. monocytogenes induces long-lived, CD8 T cell-mediated immunity. We demonstrate that HKLM immunization primes memory CD8 T lymphocyte populations that, although substantial in size, are ineffective at providing protection from subsequent L. monocytogenes infection. In contrast to live infection, which elicits large numbers of effector CD8 T cells, HKLM immunization primes T lymphocytes that do not acquire effector functions. Our studies show that it is possible to dissociate T cell-dependent protective immunity from memory T cell expansion, and that generation of effector T cells may be necessary for long-term protective immunity.
Discovery of Conformationally Constrained Tetracyclic Compounds as Potent Hepatitis C Virus NS5B RNA Polymerase Inhibitors (2006)

We report a new series of hepatitis C virus NS5B RNA polymerase inhibitors containing a conformationally constrained tetracyclic scaffold. SAR studies led to the identification of 6,7-dihydro-5H-benzo[5,6][1,4]diazepino[7,1-a]indoles (19 and 20) bearing a basic pendent group with high biochemical and cellular potencies. These compounds displayed a very small shift in cellular potency when the replicon assay was performed in the presence of human serum albumin.
High-pressure optical study of HfW2O8 (2002)

A high-pressure optical absorption study and Raman and infrared spectroscopy are carried out on hafnium tungstate (HfW2O8) at room temperature. The band gap decreases rapidly with pressure until similar to9 GPa is reached, increases between 9 and 16 GPa, and slowly decreases with pressure from 16 to 47 GPa. The changes under pressure of the vibrational modes have been studied, and an estimate of the thermal expansion coefficient has been calculated,and found to be in reasonable agreement with the measured value. The alpha-gamma phase transition can be observed via Raman and infrared spectroscopy. Around 2 GPa, HfW2O8 undergoes an irreversible transition from the gamma-phase to an amorphous structure.
Silicon chip separation: Meeting demands of chip embedding packaging technology - eWLB (2010)

The objective of this paper is to present the key challenges in Silicon chip separation by mechanical dicing and changes needed in the saw street design to meet the additional demands in quality requirement put-forth by chip embedding packaging technology like the embedded Wafer Level Ball Grid array [eWLB]. When standard mechanical dicing process and saw street design meant for traditional packaging like wire bond or flip chip is used in assembly of chips in eWLB format, severe yield loss is observed at final test majority of them attributed to electrical short. Failure analysis of electrical shorts revealed metal burrs are in contact with redistribution layer [RDL] of the eWLB package. To overcome this issue, new saw street design has to be implemented in wafer fabrication and Silicon chip separation has to be optimized like blade selection and process parameters. After implementing these changes, Silicon chip separation process and eWLB assembly yield are monitored and final test yield shows elimination of electrical short failures. To date millions of eWLB packages housing highly integrated System on Chip Baseband processor, RF Transceiver, Power Management Unit and FM Radio manufactured in 65nm technology node with new saw street design and Silicon chip separation process are shipped to our customers eventually ending up in hands of the consumers in the form of hand phone.
Potentially chemotherapeutic purine analogues. Part V. Some hydrazone derivatives of pyrazole-4,5-diones and their cyclisation to pyrazolo-[3,4-e][1,2,4]triazines (1970)

4-Thiosemicarbazones of pyrazole-4,5-diones are prepared by the reaction of thiosemicarbazide with the diones themselves or with 4-p-diethylaminophenylimino-, 4-hydroxyimino-, or 4,4-dibromo-pyrazol-5-one. Cyclisation of 4-thiosemicarbazonopyrazol-5-ones under alkaline conditions leads to pyrazolo [3,4-e][1,2,4]triazine-3-thiols. The latter and their derivatives are of interest as potentially chemotherapeutic purine analogues.
Actions of adenosine and isoproterenol on isolated mammalian ventricular myocytes. (1983)

We investigated the effects of adenosine and isoproterenol on enzymatically dispersed ventricular myocytes from bovine and guinea pig hearts. Intracellular stimulation of relaxed myocytes with regular striation patterns and normal resting potential resulted in action potentials with full plateaus accompanied by contractions. Adenosine in concentrations up to 0.2 mM had no significant effect on any of the action potential parameters or on the basal contractility. In contrast, in the same cells, adenosine effectively antagonized the stimulatory effect of isoproterenol. Isoproterenol (1-10 nM) prolonged the action potentials by 34-41%, displaced the plateau to more positive potentials, and caused a 3-fold increase in the extent of myocyte sarcomere shortening. In the presence of adenosine (5-50 microM), isoproterenol increased the action potential duration by only 8-9%, the shift of the plateau was nearly abolished, and the increase in the extent of myocyte sarcomere shortening was less than 10%. In some of the myocytes, isoproterenol (1-10 nM) induced depolarizing afterpotentials accompanied by aftercontractions. The afterdepolarizations occasionally reached threshold resulting in triggered sustained rhythmic activity. Adenosine (20-50 microM) not only reduced the amplitude of the afterdepolarizations and aftercontractions, but also abolished the sustained rhythmic activity. We conclude, first, that isolated ventricular myocytes respond to isoproterenol and adenosine; second, that adenosine has no direct effect, but effectively antagonizes the stimulatory actions of isoproterenol; third, that findings are consistent with the ones reported for multicellular ventricular preparations; fourth, that adenosine concentrations required to attenuate the actions of isoproterenol are in the range of adenosine concentrations released by cardiac cells when oxygen availability is limited and/or demand is increased; and fifth, that endogenously released adenosine may modulate the electrophysiological and contractile effects of catecholamines.
How to design a medium-radius horizontal well (1989)

Medium-radius horizontal drilling is an outgrowth of the latest technical advances in directional drilling systems. The author discusses how proper planning of the overall operation is important to ensure the ultimate success of both directional and horizontal drilling projects. This article focuses on horizontal prospects, in which the planning stage is more critical because of the rapid vertical-to-horizontal transition rates and the minimal time available to make necessary course corrections. Build rates, sidetrack methods, and motor configurations are areas of major consideration in the horizontal planning process. The interaction of the individual system components also must be evaluated and coordinated.