gebhart/patrepeval huggingface dataset:
Lysophosphatidylcholine upregulates the level of heparin-binding epidermal growth factor-like growth factor mRNA in human monocytes. (1994)

Lysophosphatidylcholine is increased in the plasma of hypercholesterolemic patients, is a component of oxidatively modified low-density lipoprotein, and, as such, may play an important role in atherosclerosis. Here we demonstrate that in human monocytes, lysophosphatidylcholine increases the level of mRNA encoding the heparin-binding epidermal growth factor-like growth factor (HB-EGF), a potent smooth muscle mitogen. Lysophosphatidylcholine treatment also enhances the release of heparin-binding mitogenic activity by these cells in culture. The anti-inflammatory glucocorticoid dexamethasone inhibits the upregulation of HB-EGF mRNA induced by either lysophosphatidylcholine or bacterial lipopolysaccharide in cultured monocytes. However, the responses induced by lysophosphatidylcholine and by lipopolysaccharide differ in their kinetics. In addition, the response to lysophosphatidylcholine is resistant to the action of cycloheximide, whereas the response to lipopolysaccharide is not, suggesting that the activation mechanisms induced by these two stimuli are different. Since a nuclear run-on assay showed no effect of lysophosphatidylcholine on the transcription of the HB-EGF gene, we speculate that lysophosphatidylcholine may increase the level of HB-EGF mRNA by altering the processing or degradation of primary or mature transcripts. Lysophosphatidylcholine enhancement of monocyte production of HB-EGF may represent an important result of the interactions among oxidized low-density lipoprotein and monocyte-derived macrophages and may play a role in initiation of smooth muscle proliferation in atherogenesis.
Modeling the performance of algorithms on flash memory devices (2008)

NAND flash memory is fast becoming popular as a component of large scale storage devices. For workloads requiring many random I/Os, flash devices can provide two orders of magnitude increased performance relative to magnetic disks. Flash memory has some unusual characteristics. In particular, general updates require a page write, while updates of 1 bits to 0 bits can be done in-place. In order to measure how well algorithms perform on such a device, we propose the "EWOM" model for analyzing algorithms on flash memory devices. We introduce flash-aware algorithms for counting, listmanagement, and B-trees, and analyze them using the EWOM model. This analysis shows that one can use the incremental 1-to-0 update properties of flash memory in interesting ways to reduce the required number of page-write operations.
Hydrolysis of a Phosphate Diester by Simultaneous Carboxylate and Carboxyl Group Participation in a Rigid System with Kinetically Unfavorable Rotamers Frozen Out (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHydrolysis of a Phosphate Diester by Simultaneous Carboxylate and Carboxyl Group Participation in a Rigid System with Kinetically Unfavorable Rotamers Frozen OutThomas C. Bruice, Andrei Blasko, Ramesh D. Arasasingham, Jang-Seob Kim, and Mark E. PetyakCite this: J. Am. Chem. Soc. 1995, 117, 12, 3639–3640Publication Date (Print):March 1, 1995Publication History Published online1 May 2002Published inissue 1 March 1995https://doi.org/10.1021/ja00117a044Request reuse permissionsArticle Views73Altmetric-Citations5LEARN 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 PDF (777 KB) Get e-Alertsclose Get e-Alerts
OLEX2: a complete structure solution, refinement and analysis program (2009)

New software, OLEX2 , has been developed for the determination, visualization and analysis of molecular crystal structures. The software has a portable mouse-driven workflow-oriented and fully comprehensive graphical user interface for structure solution, refinement and report generation, as well as novel tools for structure analysis. OLEX2 seamlessly links all aspects of the structure solution, refinement and publication process and presents them in a single workflow-driven package, with the ultimate goal of producing an application which will be useful to both chemists and crystallographers.
Characterizing quantum gates via randomized benchmarking (2012)

We describe and expand upon the scalable randomized benchmarking protocol proposed in Phys. Rev. Lett. 106, 180504 (2011) which provides a method for benchmarking quantum gates and estimating the gate dependence of the noise. The protocol allows the noise to have weak time and gate dependence, and we provide a sufficient condition for the applicability of the protocol in terms of the average variation of the noise. We discuss how state-preparation and measurement errors are taken into account and provide a complete proof of the scalability of the protocol. We establish a connection in special cases between the error rate provided by this protocol and the error strength measured using the diamond norm distance.
Association Between Development of Hypothyroidism and Improved Survival in Patients With Head and Neck Cancer (2006)

Development of hypothyroidism may be associated with improved survival and increased recurrence-free survival. Larger, prospective studies appear warranted to test the beneficial effect of hypothyroidism.
Multiple passive element enriched photoacoustic computed tomography (2011)

Recently, we presented a method using laser-induced ultrasound from an external absorber (passive element) to image the ultrasound transmission parameters of an object under photoacoustic tomographic investigation. The method suffers from long measurement times due to the requirement for a large number of views and consequently physical projections around the object. Here we propose and validate an approach that permits a multitude of views to be obtained within a limited projection scenario. The approach uses a plurality of spatially distributed external absorbers in the path of the light, that results in multiple laser-induced ultrasound sources to interrogate the object from a number of angles. This reduces the required number of rotation angles or physical projections around the object, permitting a considerable reduction in imaging time without significant degradation in image quality. The approach brings the concept of hybrid imaging of ultrasound transmission parameters together with photoacoustic imaging, into the realm of practical application.
ICARUS: An Interactive Integrated Circuit Layout Program (1978)

ICARUS (Integrated Circuit ARtwork Utility System) is a software system which allows the user to create and modify an integrated circuit layout directly on a refresh CRT screen. The system can generate check plots on the matrix type printers available from Versatec or on a raster-scan laser printer such as the 9700 Xerox has recently announced. The ICARUS files can be used to create standard pattern generation tapes from which integrated circuit masks can be made. All the software to accomplish these various steps runs on a small experimental minicomputer known as the Alto.
Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications (1992)

The synthesis, proof of structure, and the absorption and fluorescence properties of two new unsymmetrical cyanine dyes, thiazole orange dimer (TOTO; 1,1'-(4,4,7,7-tetramethyl-4,7- diazaundecamethylene)-bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiaz ole)-2- methylidene]-quinolinium tetraiodide) and oxazole yellow dimer (YOYO; an analogue of TOTO with a benzo-1,3-oxazole in place of the benzo-1,3-thiazole) are reported. TOTO and YOYO are virtually non-fluorescent in solution, but form highly fluorescent complexes with double-stranded DNA (dsDNA), up to a maximum dye to DNA bp ratio of 1:4, with greater than 1000-fold fluorescence enhancement. The dsDNA-TOTO (lambda max 513 nm; lambda maxF 532 nm) and dsDNA-YOYO (lambda max 489 nm; lambda maxF 509 nm) complexes are completely stable to electrophoresis on agarose and acrylamide gels. Mixtures of restriction fragments pre-labeled with ethidium dimer (EthD; lambda maxF 616 nm) and those pre-labeled with either TOTO or YOYO were separated by electrophoresis. Laser excitation at 488 nm and simultaneous confocal fluorescence detection at 620-750 nm (dsDNA-EthD emission) and 500-565 nm (dsDNA-TOTO or dsDNA-YOYO emission) allowed sensitive detection, quantitation, and accurate sizing of restriction fragments ranging from 600 to 24,000 bp. The limit of detection of dsDNA-TOTO and YOYO complexes with a laser-excited confocal fluorescence gel scanner for a band 5-mm wide on a 1-mm thick agarose gel was 4 picograms, about 500-fold lower than attainable by conventional staining with ethidium bromide.
Cloned Mice Derived from Embryonic Stem Cell Karyoplasts and Activated Cytoplasts Prepared by Induced Enucleation (2003)

Our objective was to induce enucleation (IE) of activated mouse oocytes to yield cytoplasts capable of supporting development following nuclear transfer. Fluorescence microscopy for microtubules, microfilaments, and DNA was used to evaluate meiotic resumption after ethanol activation and the effect of subsequent transient treatments with 0.4 micro g/ml of demecolcine. Using oocytes from B6D2F1 (C57BL/6 x DBA/2) donors, the success of IE of chromatin into polar bodies (PBs) was dependent on the duration of demecolcine treatment and the time that such treatment was initiated after activation. Similarly, variations in demecolcine treatment altered the proportions of oocytes exhibiting a reversible compartmentalization of chromatin into PBs. Treatment for 15 min begun immediately after activation yielded an optimized IE rate of 21% (n = 80) when oocytes were evaluated after overnight recovery in culture. With this protocol, 30-50% of oocytes were routinely scored as compartmentalized when assessed 90 min postactivation. No oocytes could be scored as such following overnight recovery, with 66% of treated oocytes cleaving to the 2-cell stage (n = 80). Activated cytoplasts were prepared by mechanical removal of PBs from oocytes whose chromatin had undergone IE or compartmentalization. These cytoplasts were compared with mechanically enucleated, metaphase (M) II cytoplasts whose activation was delayed in nuclear transfer experiments using HM-1 embryonic stem cells. Using oocytes from either B6D2F1 or B6CBAF1 (C57BL/6 x CBA) donors, the in vitro development of cloned embryos using activated cytoplasts was consistently inferior to that observed using MII cytoplasts. Live offspring were derived from both oocyte strains using the latter, whereas a single living mouse was cloned from activated B6CBAF1 cytoplasts.
Performance of N95 Respirators: Filtration Efficiency for Airborne Microbial and Inert Particles (1998)

In 1995 the National Institute for Occupational Safety and Health issued new regulations for nonpowered particulate respirators (42 CFR Part 84). A new filter certification system also was created. Among the new particulate respirators that have entered the market, the N95 respirator is the most commonly used in industrial and health care environments. The filtration efficiencies of unloaded N95 particulate respirators have been compared with those of dust/mist (DM) and dust/fume/mist (DFM) respirators certified under the former regulations (30 CFR Part 11). Through laboratory tests with NaCl certification aerosols and measurements with particle-size spectrometers, N95 respirators were found to have higher filtration efficiencies than DM and DFM respirators and noncertified surgical masks. N95 respirators made by different companies were found to have different filtration efficiencies for the most penetrating particle size (0.1 to 0.3 micron), but all were at least 95% efficient at that size for NaCl particles. Above the most penetrating particle size the filtration efficiency increases with size; it reaches approximately 99.5% or higher at about 0.75 micron. Tests with bacteria of size and shape similar to Mycobacterium tuberculosis also showed filtration efficiencies of 99.5% or higher. Experimental data were used to calculate the aerosol mass concentrations inside the respirator when worn in representative work environments. The penetrated mass fractions, in the absence of face leakage, ranged from 0.02% for large particle distributions to 1.8% for submicrometer-size welding fumes. Thus, N95 respirators provide excellent protection against airborne particles when there is a good face seal.
Internal Initiation of Translation Directed by the 5′-Untranslated Region of the mRNA for eIF4G, a Factor Involved in the Picornavirus-induced Switch from Cap-dependent to Internal Initiation (1996)

The eIF4 group initiation factors carry out recognition of the mRNA cap, unwinding of mRNA secondary structure, and binding of mRNA to the 43 S preinitiation complex. Infection by picornaviruses results in proteolytic cleavage of one of these factors, eIF4G, an event that severely restricts cap-dependent translation but permits cap-independent initiation to proceed from internal ribosome entry sequences in picornaviral RNAs. The 5'-untranslated region (5'-UTR) of eIF4G mRNA resembles such picornaviral sequences in being unusually long and containing multiple open reading frames and a polypyrimidine tract. When inserted upstream of a luciferase reporter gene, this 5'-UTR served as a translational enhancer in four different cell lines. Mutation of all four upstream ATG codons to AAG did not alter the translational enhancement. The presence of the eIF4G 5'-UTR between an RNA hairpin and the luciferase cistron stimulated expression 119-fold. Similarly, the presence of the 5'-UTR between the two cistrons of a bicistronic mRNA stimulated expression of the downstream cistron 42-fold. These results indicate that the eIF4G 5'-UTR directs internal initiation. The ability to continue synthesis of eIF4G when the cell is unable to carry out normal cap-dependent translation may represent an autoregulatory mechanism or be part of the cellular response to stresses that interrupt cap-dependent translation.
La nueva visión. El impacto estético de la iluminación en las ciudades (2010)

Two-dimensional statistics and Q-penalty performance under the combination of two major impairments induced by polarization-dependent loss, namely level imbalance and loss of orthogonality between polarization-multiplexed tributaries, for a polarization-division-multiplexing digital coherent transmission at over 100-Gb/s are presented for the first time to estimate the outage probability needed for designing the system.
Gonadal and extragonadal expression of inhibin alpha, beta A, and beta B subunits in various tissues predicts diverse functions. (1988)

The S1-nuclease analysis was used to investigate the pattern of inhibin expression in the rat. In a first series of experiments, expression of the alpha, beta A, and beta B subunits of inhibin were monitored in various tissues from male and female rats. Two observations emerge from these studies. First, expression of inhibin subunits was found in gonadal and extragonadal tissues. In addition to the ovary and testis, inhibin alpha, beta A, and beta B RNAs were detected in the placenta, pituitary, adrenal, bone marrow, kidney, spinal cord, and brain. Detection of inhibin RNAs in the brain and spinal cord suggested that these subunits may exert neuroregulatory functions in the central and peripheral nervous systems. Furthermore, the presence of inhibin alpha and beta subunits in the placenta and the pituitary gland, two cell types that have clearly been shown to be regulated by exogenous inhibin, may reflect existing paracrine and/or autocrine processes active in these tissues. The second observation is that expression of inhibin subunit RNAs may vary by severalfold in a tissue-specific fashion. for example, alpha-subunit RNA levels are abundant in the gonads, whereas beta A-subunit RNA is predominant in the placenta and bone marrow. Finally, it is noted that expression of testicular inhibin RNA subunits decreases during sexual maturation. We conclude that the dimers comprised of inhibin subunits possess diverse functions and may act as growth/differentiation factors as well as a hormone.
Impaired infiltration of tumor-specific cytolytic T cells in the absence of interferon-gamma despite their normal maturation in lymphoid organs during CD137 monoclonal antibody therapy. (2002)

Engagement of CD137 receptor by agonistic monoclonal antibodies (mAb) stimulates IFN-gamma production and eradicates established tumors in syngeneic mouse models. Using IFN-gamma-deficient mice or neutralizing mAb, we demonstrate that IFN-gamma is an absolute requirement for the antitumor effect of CD137 mAb. Despite progressive tumor growth in IFN-gamma-depleted mice, a fully competent CD8(+) cytolytic T cell (CTL) response developed in the lymph nodes. In addition, tumor cell sensitivity to IFN-gamma was not required because expression of a dominant-negative IFN-gamma receptor on the tumor did not affect the therapeutic effect of CD137 mAb. However, in the absence of IFN-gamma, the number of tumor-infiltrating CD8(+) CTLs was drastically decreased. Our results demonstrate that IFN-gamma is a critical factor regulating the infiltration of antigen-specific CTL into the tumor.
Distinct modes of human immunodeficiency virus type 1 proviral latency revealed by superinfection of nonproductively infected cell lines with recombinant luciferase-encoding viruses (1994)

To study the basis of cellular latency of human immunodeficiency virus (HIV), we have used a recombinant luciferase-encoding HIV (HXB-Luc) to superinfect nonproductively HIV-1-infected human leukemic cell lines. HXB-Luc contains the Photinus pyralis luciferase gene in place of the nef gene and provides a highly sensitive, simple assay for HIV infection and expression. To circumvent any superinfection block in latently infected cells, we also generated viruses pseudotyped with murine leukemia virus amphotropic envelope (HXB-Luc:ampho). The parental uninfected lines, U937 and A3.01, from which the latently infected cell lines U1 and ACH-2, respectively, were derived could be readily infected with pseudotyped or nonpseudotyped reporter viruses. However, superinfection of U1 cells with either HXB-Luc or HXB-Luc:ampho resulted in only low levels of luciferase activity. Like the endogenous provirus, HXB-Luc provirus could be efficiently activated by phorbol ester treatment of HXB-Luc:ampho-superinfected U1 cells. In contrast, superinfection of ACH-2 cells resulted in active expression of the secondarily introduced virus even in unstimulated cells and luciferase production higher than in the parental cell line A3.01. Thus, the proviral latency in U1 cells appears to result from a defect in the cellular environment (a trans effect), whereas the latency in ACH-2 is specific to the integrated provirus and is probably a cis effect due to the site of integration. These results demonstrate distinct modes of proviral latency in these two cell line models and may have implications in our understanding of the regulation and significance of cellular latency in HIV infection.
Biology and action of colony-stimulating factor-1 (1997)

Colony-stimulating factor-1 (CSF-1), also known as macrophage colony-stimulating factor, controls the survival, proliferation, and differentiation of mononuclear phagocytes and regulates cells of the females reproductive tract. It appears to play an autocrine and/or paracrine role in cancers of the ovary, endometrium, breast, and myeloid and lymphoid tissues. Through alternative mRNA splicing and differential post-translational proteolytic processing, CSF-1 can either be secreted into the circulation as a glycoprotein or chondroitin sulfate-containing proteoglycan or be expressed as a membrane-spanning glycoprotein on the surface of CSF-1-producing cells. Studies with the op/op mouse, which possesses an inactivating mutation in the CSF-1 gene, have established the central role of CSF-1 in directly regulating osteoclastogenesis and macrophage production. CSF-1 appears to preferentially regulate the development of macrophages found in tissues undergoing active morphogenesis and/or tissue remodeling. These CSF-1 dependent macrophages may, via putative trophic and/or scavenger functions, regulate characteristics such as dermal thickness, male fertility, and neural processing. Apart from its expression on mononuclear phagocytes and their precursors, CSF-1 receptor (CSF-1R) expression on certain nonmononuclear phagocytic cells in the female reproductive tract and studies in the op/op mouse indicate that CSF-1 plays important roles in female reproduction. Restoration of circulating CSF-1 to op/op mice has preliminarily defined target cell populations that are regulated either humorally or locally by the synthesis of cell-surface CSF-1 or by sequestration of the CSF-1 proteoglycan. The CSF-1R is a tyrosine kinase encoded by the c-fms proto-oncogene product. Studies by several groups have used cells expressing either the murine or human CSF-1R in fibroblasts to pinpoint the requirement of kinase activity and the importance of various receptor tyrosine phosphorylation sites for signaling pathways stimulated by CSF-1. To investigate post-CSF-1R signaling in the macrophage, proteins that are rapidly phosphorylated on tyrosine in response to CSF-1 have been identified, together with proteins associated with them. Studies on several of these proteins, including protein tyrosine phosphates 1C, the c-cbl proto-oncogene product, and protein tyrosine phosphatase-phi are discussed.
Entrainment of chaotic activities in brain and heart during MBSR mindfulness training (2016)

The activities of the brain and the heart are dynamic, chaotic, and possibly intrinsically coordinated. This study aims to investigate the effect of Mindfulness-Based Stress Reduction (MBSR) program on the chaoticity of electronic activities of the brain and the heart, and to explore their potential correlation. Electroencephalogram (EEG) and electrocardiogram (ECG) were recorded at the beginning of an 8-week standard MBSR training course and after the course. EEG spectrum analysis was carried out, wavelet entropies (WE) of EEG (together with reconstructed cortical sources) and heart rate were calculated, and their correlation was investigated. We found enhancement of EEG power of alpha and beta waves and lowering of delta waves power during MBSR training state as compared to normal resting state. Wavelet entropy analysis indicated that MBSR mindfulness meditation could reduce the chaotic activities of both EEG and heart rate as a change of state. However, longitudinal change of trait may need more long-term training. For the first time, our data demonstrated that the chaotic activities of the brain and the heart became more coordinated during MBSR training, suggesting that mindfulness training may increase the entrainment between mind and body. The 3D brain regions involved in the change in mental states were identified.