gebhart/patrepeval huggingface dataset:
Lipid metabolic reprogramming in cancer cells (2016)

Many human diseases, including metabolic, immune and central nervous system disorders, as well as cancer, are the consequence of an alteration in lipid metabolic enzymes and their pathways. This illustrates the fundamental role played by lipids in maintaining membrane homeostasis and normal function in healthy cells. We reviewed the major lipid dysfunctions occurring during tumor development, as determined using systems biology approaches. In it, we provide detailed insight into the essential roles exerted by specific lipids in mediating intracellular oncogenic signaling, endoplasmic reticulum stress and bidirectional crosstalk between cells of the tumor microenvironment and cancer cells. Finally, we summarize the advances in ongoing research aimed at exploiting the dependency of cancer cells on lipids to abolish tumor progression.
T1/St2-Deficient Mice Demonstrate the Importance of T1/St2 in Developing Primary T Helper Cell Type 2 Responses (2000)

We have generated mice with a deficiency in T1/ST2 expression to clarify the roles of T1/ST2 in T helper cell type 2 (Th2) responses. Using immunological challenges normally characterized by a Th2-like response, we have compared the responses of T1/ST2-deficient mice with those generated by wild-type mice. Using a primary pulmonary granuloma model, induced with Schistosoma mansoni eggs, we demonstrate that granuloma formation, characterized by eosinophil infiltration, is abrogated in T1/ST2-deficient mice. Furthermore, we clearly demonstrate that in the absence of T1/ST2 expression, the levels of Th2 cytokine production are severely impaired after immunization. Thus, in a secondary pulmonary granuloma model, draining lymph node cells from the T1/ST2-deficient animals produced significantly reduced levels of IL-4 and IL-5, despite developing granulomas of a magnitude similar to those of wild-type mice and comparable antigen-specific immunoglobulin isotype production. These data clearly demonstrate that T1/ST2 expression plays a role in the development of Th2-like cytokine responses and indicate that effector functions are inhibited in its absence.
CCR4 is a glucose-regulated transcription factor whose leucine-rich repeat binds several proteins important for placing CCR4 in its proper promoter context. (1994)

The yeast CCR4 protein is required for the expression of a number of genes involved in nonfermentative growth, including glucose-repressible ADH2, and is the only known suppressor of mutations in the SPT6 and SPT10 genes, two genes which are believed to be involved in chromatin maintenance. We show here that although CCR4 did not bind DNA under the conditions tested, it was able to activate transcription when fused to a heterologous DNA-binding domain. The transcriptional activation ability of CCR4, in contrast to that of many other activators, was glucose regulated. Two activation domains one of which was glucose responsive and encompassed a glutamine-proline-rich region similar to that found in other eukaryotic transcriptional factors were identified. The two transactivation regions, when separated from the leucine-rich repeat and the C terminus of CCR4, were unable to complement a defective ccr4 allele, suggesting that the leucine-rich repeat and the C terminus make contacts that link the activation regions to the proper gene context. Native immunoprecipitation of CCR4 revealed that CCR4 was complexed with at least four other proteins. The leucine-rich repeat of CCR4 was both necessary and sufficient for interaction with at least two of these factors. We propose that the leucine-rich repeat links CCR4 through its associated factors to its promoter context at ADH2 and other loci where it is required for proper transcriptional regulation.
A Practical Synthesis of Nelfinavir, an HIV-Protease Inhibitor, Using a Novel Chiral C4 Building Block:  (5R,6S)-2,2-Dimethyl-5-hydroxy-1,3-dioxepan-6-ylammonium Acetate (1998)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Practical Synthesis of Nelfinavir, an HIV-Protease Inhibitor, Using a Novel Chiral C4 Building Block: (5R,6S)-2,2-Dimethyl-5-hydroxy-1,3-dioxepan-6-ylammonium AcetateTakashi Inaba, Angela G. Birchler, Yasuki Yamada, Shoichi Sagawa, Katsuyuki Yokota, Koji Ando, and Itsuo UchidaView Author Information Central Pharmaceutical Research Institute, Japan Tobacco, Inc., 1-1, Murasaki-cho Takatsuki Osaka, 569-1125, Japan, and Agouron Pharmaceuticals, Inc., 3565 General Atomics Court, San Diego, California 92121 Cite this: J. Org. Chem. 1998, 63, 22, 7582–7583Publication Date (Web):October 10, 1998Publication History Received28 July 1998Published online10 October 1998Published inissue 1 October 1998https://doi.org/10.1021/jo981472nCopyright © 1998 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1126Altmetric-Citations33LEARN 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 InReddit Read OnlinePDF (35 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Alcohols,Ethers,Hydroxyls,Ring opening reactions,Solvents Get e-Alerts
Internal Derivatization of Oligonucleotides with Selenium for X-ray Crystallography Using MAD (2001)

We have developed a route for the synthesis of 2'-selenium uridine analogues and oligonucleotides containing selenium labels, and have demonstrated for the first time a new strategy to covalently derivatize nucleotides with selenium for phase and structure determination in X-ray crystallography.
The dihydrofolate reductase amplicons in different methotrexate-resistant Chinese hamster cell lines share at least a 273-kilobase core sequence, but the amplicons in some cell lines are much larger and are remarkably uniform in structure. (1988)

We have previously cloned and characterized two different dihydrofolate reductase amplicon types from a methotrexate-resistant Chinese hamster ovary cell line (CHOC 400). The largest of these (the type I amplicon) is 273 kilobases (kb) in length. In the present study, we utilized clones from the type I amplicon as probes to analyze the size and variability of the amplified DNA sequences in five other independently isolated methotrexate-resistant Chinese hamster cell lines. Our data indicated that the predominant amplicon types in all but one of these cell lines are larger than the 273-kb type I sequence. In-gel renaturation experiments as well as hybridization analysis of large SfiI fragments separated by pulse-field gradient gel electrophoresis showed that two highly resistant cell lines (A3 and MK42) have amplified very homogeneous core sequences that are estimated to be at least 583 and 653 kb in length, respectively. Thus, the sizes of the major amplicon types can be different in different drug-resistant Chinese hamster cell lines. However, there appears to be less heterogeneity in size and sequence arrangement within a given methotrexate-resistant Chinese hamster cell line than has been reported for several other examples of DNA sequence amplification in mammalian systems.
Prenatal Stress Induces Schizophrenia-Like Alterations of Serotonin 2A and Metabotropic Glutamate 2 Receptors in the Adult Offspring: Role of Maternal Immune System (2013)

It has been suggested that severe adverse life events during pregnancy increase the risk of schizophrenia in the offspring. The serotonin 5-HT(2A) and the metabotropic glutamate 2 (mGlu2) receptors both have been the target of considerable attention regarding schizophrenia and antipsychotic drug development. We tested the effects of maternal variable stress during pregnancy on expression and behavioral function of these two receptors in mice. Prenatal stress increased 5-HT(2A) and decreased mGlu2 expression in frontal cortex, a brain region involved in perception, cognition, and mood. This pattern of expression of 5-HT(2A) and mGlu2 receptors was consistent with behavioral alterations, including increased head-twitch response to the hallucinogenic 5-HT(2A) agonist DOI [1-(2,5-dimethoxy-4-iodophenyl)-2-aminopropane] and decreased mGlu2-dependent antipsychotic-like effect of the mGlu2/3 agonist LY379268 (1R,4R,5S,6R-2-oxa-4-aminobicyclo[3.1.0]hexane-4,6-dicarboxylate) in adult, but not prepubertal, mice born to stressed mothers during pregnancy. Cross-fostering studies determined that these alterations were not attributable to effects of prenatal stress on maternal care. Additionally, a similar pattern of biochemical and behavioral changes were observed in mice born to mothers injected with polyinosinic:polycytidylic acid [poly(I:C)] during pregnancy as a model of prenatal immune activation. These data strengthen pathophysiological hypotheses that propose an early neurodevelopmental origin for schizophrenia and other psychiatric disorders.
Mid-infrared materials and devices on a Si platform for optical sensing (2014)

In this article, we review our recent work on mid-infrared (mid-IR) photonic materials and devices fabricated on silicon for on-chip sensing applications. Pedestal waveguides based on silicon are demonstrated as broadband mid-IR sensors. Our low-loss mid-IR directional couplers demonstrated in SiN <sub><i>x</i></sub> waveguides are useful in differential sensing applications. Photonic crystal cavities and microdisk resonators based on chalcogenide glasses for high sensitivity are also demonstrated as effective mid-IR sensors. Polymer-based functionalization layers, to enhance the sensitivity and selectivity of our sensor devices, are also presented. We discuss the design of mid-IR chalcogenide waveguides integrated with polycrystalline PbTe detectors on a monolithic silicon platform for optical sensing, wherein the use of a low-index spacer layer enables the evanescent coupling of mid-IR light from the waveguides to the detector. Finally, we show the successful fabrication processing of our first prototype mid-IR waveguide-integrated detectors.
Histamine and the antihistaminic drugs. (1950)

The tissues affected by histamine and anaphylactic reactions are identical. Epinephrine antagonizes the action of histamine by acting on effector cells in a direction opposite to that of histamine. The so-called antihistaminic drugs block rather than antagonize the action of histamine. The injection into the human body of epinephrine or certain antihistaminic substances provokes the release of histamine and thereby produces a rise in the histamine blood level. There is a remarkable conformity of potency of antihistaminics as determined by Dale experiments and by histamine intoxication experiments in the intact guinea pig. Neoantergan, Pyribenzamine and Histadyl are usually superior to other compounds when potency is assayed by these methods. All antihistaminics provide similar protection again animal anaphylaxis. Larger doses are necessary to protect against anaphylaxis than against histamine intoxication. The differences in potency as determined by Dale experiments and histamine experiments in animals are not found in clinical use. One compound is not generally superior to all others in the treatment of any one or several allergic disorders. The antihistaminic drugs are beneficial in the symptomatic treatment of allergic rhinitis, acute urticaria and angioneurotic edema, and mild non-infective bronchial asthma. Their effectiveness in the management of moderately severe and severe non-infective bronchial bronchial asthma; infective bronchial asthma; migraine; atopic dermatitis (disseminated neurodermatitis), and pruritus of skin disorders other than acute urticaria and angioneurotic edema, is not worthy of particular commendation. The size of the dose of any antihistaminic substance influences the incidence of but not the type of side-effect that may accompany its usage. The quality of side effects varies according to the drug, although there is an individuality of response for each patient which must be reckoned with. In selecting an antihistaminic compound it is necessary to consider the percentage of cases in which side effects occur, as well as the percentage of good results. Optimal results are obtained by employing combinations of compounds and changing from one to the other as the case demands.
Cloning and sequencing of RNA of hepatitis delta virus isolated from human serum (1990)

The RNA of hepatitis delta virus (HDV) 1682 nucleotides long, has been cloned from a human serum isolate. Comparison with the three complete published sequences shows that a region of the HDV genome, between positions 620 and 1350, which contains sequences involved in replication and possibly pathogenicity, is highly conserved.
Viruslike Particle Vaccine Induces Protection Against Respiratory Syncytial Virus Infection in Mice (2011)

This study demonstrates that VLP vaccination provides effective protection against RSV infection. VLPs containing RSV-F and/or RSV-G are potential vaccine candidates against RSV.
Pressure ulcer prevalence and prevention practices in care of the older person in the Republic of Ireland (2011)

Pressure ulcers are common, costly and impact negatively on individuals. Current practices in prevention show several areas for improvement, namely, risk assessment, care planning and documentation.
Cardiac arrhythmias on 24-h ambulatory electrocardiography in older women and men: The cardiovascular health study (1994)

Arrhythmias are common in the elderly, and their association with cardiovascular disease differs by gender. Although risk related to arrhythmias can only be determined by prospective study, such studies should have adequate power to examine potential gender differences in associations.
Liquid-Phase Synthesis of Combinatorial Libraries Based on 7-Trifluoromethyl-Substituted Pyrazolo[1,5-a]Pyrimidine Scaffold (2005)

The parallel solution-phase synthesis of more than 2200 7-trifluoromethyl-substituted pyrazolo[1,5-a]pyrimidine and 4,5,6,7-tetrahydropyrazolo[1,5-a]pyrimidine carboxamides on a 50-100-mg scale has been accomplished. Key reactions include assembly of the pyrazolo[1,5-a]pyrimidine ring by condensation of 5-aminopyrazole derivatives with the corresponding trifluoromethyl-beta-diketones. The libraries from libraries were then obtained in good yields and purities using solution-phase acylation and reduction methodologies. Simple manual techniques for parallel reactions using special CombiSyn synthesizers were coupled with easy purification procedures (crystallization from the reaction mixtures) to give high-purity final products. The scope and limitations of the developed approach are discussed.
A Potential New Pathway for Staphylococcus aureus Dissemination: The Silent Survival of S. aureus Phagocytosed by Human Monocyte-Derived Macrophages (2008)

Although considered to be an extracellular pathogen, Staphylococcus aureus is able to invade a variety of mammalian, non-professional phagocytes and can also survive engulfment by professional phagocytes such as neutrophils and monocytes. In both of these cell types S. aureus promptly escapes from the endosomes/phagosomes and proliferates within the cytoplasm, which quickly leads to host cell death. In this report we show that S. aureus interacted with human monocyte-derived macrophages in a very different way to those of other mammalian cells. Upon phagocytosis by macrophages, S. aureus persisted intracellularly in vacuoles for 3-4 days before escaping into the cytoplasm and causing host cell lysis. Until the point of host cell lysis the infected macrophages showed no signs of apoptosis or necrosis and were functional. They were able to eliminate intracellular staphylococci if prestimulated with interferon-gamma at concentrations equivalent to human therapeutic doses. S. aureus survival was dependent on the alternative sigma factor B as well as the global regulator agr, but not SarA. Furthermore, isogenic mutants deficient in alpha-toxin, the metalloprotease aureolysin, protein A, and sortase A were efficiently killed by macrophages upon phagocytosis, although with different kinetics. In particular alpha-toxin was a key effector molecule that was essential for S. aureus intracellular survival in macrophages. Together, our data indicate that the ability of S. aureus to survive phagocytosis by macrophages is determined by multiple virulence factors in a way that differs considerably from its interactions with other cell types. S. aureus persists inside macrophages for several days without affecting the viability of these mobile cells which may serve as vehicles for the dissemination of infection.
Direct expression of hepatitis B surface antigen gene inE coli (1983)

A 809 bp Sau 3A - Hpa I fragment containing a complete HBsAg gene and fragments 744 bp Hinc II - Hpa I and 712 bp Xba I - Hpa I containing a truncated HBsAg gene lacking the sequence encoding the NH2-terminal hydrophobic domain were prepared from a composite plasmid pHBV933 containing the 3.2 kb Eco RI DNA fragment of the entire HBV/adw genome and inserted into an expression vector pTRP801 to give plasmids pTRP SS-6, pTRP SS-39, and pTRP SS-50, respectively. The growth of a recombinant having pTRP SS-6 was greatly inhibited and the transformant expressed a low level of HBsAg, which is reactive to human anti-HBsAg antibody. Interestingly, the growth of transformants harbouring pTRP SS-39 and pTRP SS-50 was not inhibited and these transformants expressed a considerable level of the HBsAg. Minicells harbouring pTRP SS-6, pTRP SS-39, and pTRP SS-50 formed specific polypeptides of about 24 K, 23 K, and 22 K daltons, respectively.
A Combinatorial Library of Unsaturated Lipidoids for Efficient Intracellular Gene Delivery (2012)

A combinatorial library of unsaturated lipidoids was synthesized through the Michael addition of amines to oleyl acrylamide. Their capability in facilitating in vitro gene delivery was evaluated by transfecting HeLa cells with EGFP-encoding plasmid DNA and mRNA. The preliminary screening results indicated that lipidoids with unsaturated oleyl tails are superior transfection agents compared to saturated lipidoids with n-octadecyl tails under the same conditions. The different transfection abilities of the unsaturated and saturated lipidioids were ascribed to the large, tightly packed lipoplexes of saturated lipidoids. The potential applications of the library of lipidoids were further expanded by looking at their ability to transfect fibroblasts as well as different cancerous cell lines.
Topography Printing to Locally Control Wettability (2006)

This paper reports a new patterning method, which utilizes NaOH to facilitate the irreversible binding between the PDMS stamp and substrates and subsequent cohesive mechanical failure to transfer the PDMS patterns. Our method shows high substrate tolerance and can be used to "print" various PDMS geometries on a wide range of surfaces, including Si100, glass, gold, polymers, and patterned SU8 photoresist. Using this technique, we are able to locally change the wettability of substrate surfaces by printing well-defined PDMS architectures on the patterned SU8 photoresist. It is possible to generate differential wetting and dewetting properties in microchannels and in the PDMS printed area, respectively.
Clustered Transcription Factor Genes Regulate Nicotine Biosynthesis in Tobacco (2010)

Tobacco (Nicotiana tabacum) synthesizes nicotine and related pyridine alkaloids in the root, and their synthesis increases upon herbivory on the leaf via a jasmonate-mediated signaling cascade. Regulatory NIC loci that positively regulate nicotine biosynthesis have been genetically identified, and their mutant alleles have been used to breed low-nicotine tobacco varieties. Here, we report that the NIC2 locus, originally called locus B, comprises clustered transcription factor genes of an ethylene response factor (ERF) subfamily; in the nic2 mutant, at least seven ERF genes are deleted altogether. Overexpression, suppression, and dominant repression experiments using transgenic tobacco roots showed both functional redundancy and divergence among the NIC2-locus ERF genes. These transcription factors recognized a GCC-box element in the promoter of a nicotine pathway gene and specifically activated all known structural genes in the pathway. The NIC2-locus ERF genes are expressed in the root and upregulated by jasmonate with kinetics that are distinct among the members. Thus, gene duplication events generated a cluster of highly homologous transcription factor genes with transcriptional and functional diversity. The NIC2-locus ERFs are close homologs of ORCA3, a jasmonate-responsive transcriptional activator of indole alkaloid biosynthesis in Catharanthus roseus, indicating that the NIC2/ORCA3 ERF subfamily was recruited independently to regulate jasmonate-inducible secondary metabolism in distinct plant lineages.
Fusion of multi-sensory saliency maps for automated perception and control (2009)

In many real-world situations and applications that involve humans or machines (e.g., situation awareness, scene understanding, driver distraction, workload reduction, assembly, robotics, etc.) multiple sensory modalities (e.g., vision, auditory, touch, etc.) are used. The incoming sensory information can overwhelm processing capabilities of both humans and machines. An approach for estimating what is most important in our sensory environment (bottom-up or goal-driven) and using that as a basis for workload reduction or taking an action could be of great benefit in applications involving humans, machines or human-machine interactions. In this paper, we describe a novel approach for determining high saliency stimuli in multi-modal sensory environments, e.g., vision, sound, touch, etc. In such environments, the high saliency stimuli could be a visual object, a sound source, a touch event, etc. The high saliency stimuli are important and should be attended to from perception, cognition or/and action perspective. The system accomplishes this by the fusion of saliency maps from multiple sensory modalities (e.g., visual and auditory) into a single, fused multimodal saliency map that is represented in a common, higher-level coordinate system. This paper describes the computational model and method for generating multi-modal or fused saliency map. The fused saliency map can be used to determine primary and secondary foci of attention as well as for active control of a hardware/device. Such a computational model of fused saliency map would be immensely useful for a machine-based or robot-based application in a multi-sensory environment. We describe the approach, system and present preliminary results on a real-robotic platform.