gebhart/patrepeval huggingface dataset:
Scanning slit aperture confocal microscopy for three‐dimensional imaging (1990)

Abstract A scanning confocal microscope using stationary slit apertures of variable width is described. Scanning is achieved by employing an oscillating mirror galvanometer capable of scanning images at 160 frames/s. The microscope depth‐of‐focus is characterized for several slit widths and shown to approach diffraction‐limited performance as width decreases. Reduction of flare in images taken with narrow slit widths is demonstrated. In addition, the optical sectioning capability of the system is demonstrated using polymer casts of the vasculature of rat kidney.
Prostate-specific membrane antigen association with filamin A modulates its internalization and NAALADase activity. (2003)

Prostate-specific membrane antigen (PMSA) is an integral membrane protein highly expressed by prostate cancer cells. We reported previously that PSMA undergoes internalization via clathrin-coated pits (Liu et al., Cancer Res., 58: 4055-4060, 1998). In this study we demonstrate that filamin A, an actin cross-linking protein, associates with the cytoplasmic tail of PSMA and that this association of PSMA with filamin is involved in its localization to the recycling endosomal compartment. By ectopically expressing PSMA in filamin-negative and -positive cell lines, we additionally show that filamin binding to PSMA reduces the internalization rate of PSMA and its N-acelylated-alpha linked-acidic dipeptidase activity. These results suggest that filamin might be an important regulator of PSMA function.
Depth Image Super Resolution Based on Edge-Guided Method (2018)

Depth image super-resolution (SR) is a technique which can reconstruct a high-resolution (HR) depth image from a low-resolution (LR) depth image. Its purpose is to obtain HR details to meet the needs of various applications in computer vision. In general, conventional depth image SR methods often cause edges in the final HR image to be blurred or ragged. To solve this problem, an edge-guided method for depth image SR is presented in this paper. To get high-quality edge information, a pair of sparse dictionaries was applied to reconstruct edges of depth image. Then, with the guidance of these high-quality edges, a depth image was interpolated by using a modified joint bilateral filter. Edge-guided method can preserve the sharpness of edges and effectively avoid generating blurry and ragged edges when SR is performed. Experiments showed that the proposed method can get better results on both subjective and objective evaluation, and the reconstructed performance was superior to conventional depth image SR methods.
A global network of coexisting microbes from environmental and whole-genome sequence data (2010)

Microbes are the most abundant and diverse organisms on Earth. In contrast to macroscopic organisms, their environmental preferences and ecological interdependencies remain difficult to assess, requiring laborious molecular surveys at diverse sampling sites. Here, we present a global meta-analysis of previously sampled microbial lineages in the environment. We grouped publicly available 16S ribosomal RNA sequences into operational taxonomic units at various levels of resolution and systematically searched these for co-occurrence across environments. Naturally occurring microbes, indeed, exhibited numerous, significant interlineage associations. These ranged from relatively specific groupings encompassing only a few lineages, to larger assemblages of microbes with shared habitat preferences. Many of the coexisting lineages were phylogenetically closely related, but a significant number of distant associations were observed as well. The increased availability of completely sequenced genomes allowed us, for the first time, to search for genomic correlates of such ecological associations. Genomes from coexisting microbes tended to be more similar than expected by chance, both with respect to pathway content and genome size, and outliers from these trends are discussed. We hypothesize that groupings of lineages are often ancient, and that they may have significantly impacted on genome evolution.
Chronic Resuscitation After Trauma-Hemorrhage and Acute Fluid Replacement Improves Hepatocellular Function and Cardiac Output (1998)

Because chronic resuscitation with 5 mL/kg/hr RL after trauma-hemorrhage and acute fluid replacement restored hepatocellular function and hepatic microvascular blood flow and decreased plasma levels of IL-6, we propose that chronic fluid resuscitation in addition to acute fluid replacement should be routinely used in experimental studies of trauma-hemorrhage.
Race/Ethnicity, Poverty Status, and Renal Transplant Outcomes (2005)

African-Americans and Hispanics had higher rates of graft failure compared to whites after adjustment for poverty and other covariates whereas poverty, but not race/ethnicity, was related to functional status following renal transplantation. National datasets should include individual-level measures of socioeconomic status in order to improve evaluation of social and environmental causes of disparities in renal transplant outcomes.
Influence of Anti-Inflammatory Flavonoids on Degranulation and Arachidonic Acid Release in Rat Neutrophils (1994)

We assessed the effects of 24 flavonoid derivatives, reported as anti-inflammatory, on lysosomal enzyme secretion and arachidonic acid release in rat neutrophils. Amentoflavone, quercetagetin-7-O-glucoside, apigenin, fisetin, kaempferol, luteolin and quercetin were the most potent inhibitors of beta-glucuronidase and lysozyme release. The first compound was also able to inhibit basal release. These flavonoids besides chrysin and to a reduced extent, naringenin, significantly inhibited arachidonic acid release from membranes. A correlation between degranulation and arachidonic acid release was found for this series of compounds. Structure-activity relationships and implications for the anti-inflammatory effects of these flavonoids were discussed.
Mass Spectrometry of Nucleic Acids (1999)

We read with interest the review by Kricka (1) on nucleic acid detection technologies, in which he mentioned that nucleic acids do not have any intrinsic properties for direct detection. In response to this, we would like to point out the determination of intrinsic molecular weights of nucleic acids using mass spectrometry (MS) has been widely accepted as one of the most accurate methods to …
Improvement in Aqueous Solubility in Small Molecule Drug Discovery Programs by Disruption of Molecular Planarity and Symmetry (2011)

ADVERTISEMENT RETURN TO ISSUEPerspectiveNEXTImprovement in Aqueous Solubility in Small Molecule Drug Discovery Programs by Disruption of Molecular Planarity and SymmetryMinoru Ishikawa* and Yuichi HashimotoView Author Information Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan*Phone: +81.3.5841.7849. Fax: +81.3.5841.8495. E-mail: [email protected]Cite this: J. Med. Chem. 2011, 54, 6, 1539–1554Publication Date (Web):February 23, 2011Publication History Received19 October 2010Published online23 February 2011Published inissue 24 March 2011https://pubs.acs.org/doi/10.1021/jm101356phttps://doi.org/10.1021/jm101356preview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views24218Altmetric-Citations449LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Agonists,Hydrophobicity,Partition coefficient,Solubility,Transition temperature Get e-Alerts
Effects of Methotrexate on Transfected DNA Stability in Mammalian Cells (1990)

The chromosomal locations, amounts, and level of expression of transfected, amplified c-myc and dihydrofolate reductase sequences were measured in cells cultured in the presence and absence of methotrexate. These studies show that the location and amount of transfected sequences, as well as the level of expression, were more variable when the cells were cultured in methotrexate.
The Arabidopsis ATHB-8 HD-Zip Protein Acts as a Differentiation-Promoting Transcription Factor of the Vascular Meristems (2001)

ATHB-8, -9, -14, -15, and IFL1/REV are members of a small homeodomain-leucine zipper family whose genes are characterized by expression in the vascular tissue. ATHB-8, a gene positively regulated by auxin (Baima et al., 1995), is considered an early marker of the procambial cells and of the cambium during vascular regeneration after wounding. Here, we demonstrate that although the formation of the vascular system is not affected in athb8 mutants, ectopic expression of ATHB-8 in Arabidopsis plants increased the production of xylem tissue. In particular, a careful anatomical analysis of the transgenic plants indicated that the overexpression of ATHB-8 promotes vascular cell differentiation. First, the procambial cells differentiated precociously into primary xylem. In addition, interfascicular cells also differentiated precociously into fibers. Finally, the transition to secondary growth, mainly producing xylem, was anticipated in transgenic inflorescence stems compared with controls. The stimulation of primary and secondary vascular cell differentiation resulted in complex modifications of the growth and development of the ATHB-8 transgenic plants. Taken together, these results are consistent with the hypothesis that ATHB-8 is a positive regulator of proliferation and differentiation, and participates in a positive feedback loop in which auxin signaling induces the expression of ATHB-8, which in turn positively modulates the activity of procambial and cambial cells to differentiate.
Effect of Black Tea on Lipid Peroxidation in Carbon Tetrachloride Treated Male Rats (2000)

This study examined the effects of black tea (Camellia sinensis L.) on lipid peroxidation and glutathione levels in carbon tetrachloride (CCl4)-treated male Wistar rats. Three groups of rats formed two control groups and one treatment group. The control groups were fed with a standard diet, while the black tea group were fed the standard diet plus 6% by weight dried black tea leaves. After two months, the rats in the black tea group and in one control group were administered a single dose of CCl4 (1 ml/kg, i.p.) and sacrificed two hours later. Rats in the other control group were administered olive oil in a similar fashion. Lipid peroxide levels in liver and plasma, glutathione (GSH) levels in liver and alanine transaminase (ALT) and aspartate transaminase (AST) activities in plasma were measured. Rats in the black tea group were found to have significantly decreased liver lipid peroxide levels, and ALT and AST activities compared with the rats in the CCl4-treated control group. In addition, liver glutathione levels were decreased in the black tea group. These data suggest that black tea attenuates CCl4-induced hepatic injury.
<title>Internet traffic load balancing using dynamic hashing with flow volume</title> (2002)

Sending IP packets over multiple parallel links is in extensive use in today's Internet and its use is growing due to its scalability, reliability and cost-effectiveness. To maximize the efficiency of parallel links, load balancing is necessary among the links, but it may cause the problem of packet reordering. Since packet reordering impairs TCP performance, it is important to reduce the amount of reordering. Hashing offers a simple solution to keep the packet order by sending a flow over a unique link, but static hashing does not guarantee an even distribution of the traffic amount among the links, which could lead to packet loss under heavy load. Dynamic hashing offers some degree of load balancing but suffers from load fluctuations and excessive packet reordering. To overcome these shortcomings, we have enhanced the dynamic hashing algorithm to utilize the flow volume information in order to reassign only the appropriate flows. This new method, called dynamic hashing with flow volume (DHFV), eliminates unnecessary flow reassignments of small flows and achieves load balancing very quickly without load fluctuation by accurately predicting the amount of transferred load between the links. In this paper we provide the general framework of DHFV and address the challenges in implementing DHFV. We then introduce two algorithms of DHFV with different flow selection strategies and show their performances through simulation.
Engineering RNA sequence specificity of Pumilio repeats (2006)

Puf proteins bind RNA sequence specifically and regulate translation and stability of target mRNAs. A "code" for RNA recognition has been deduced from crystal structures of the Puf protein, human Pumilio1, where each of eight repeats binds an RNA base via a combination of three side chains at conserved positions. Here, we report the creation of seven soluble mutant proteins with predictably altered sequence specificity, including one that binds tightly to adenosine-uracil-rich element RNA. These data show that Pumilio1 can be used as a scaffold to engineer RNA-binding proteins with designed sequence specificity.
A novel function for apolipoprotein B: lipoprotein synthesis in the yolk sac is critical for maternal-fetal lipid transport in mice (1996)

Apolipoprotein (apo) B, the principal structural component necessary for the synthesis and secretion of triglyceride-rich lipoproteins by the intestine and liver, is highly expressed in the yolk sac visceral endoderm of mammals, although its function in this tissue has been hitherto unclear. Disruption of the apoB gene in mice results in embryonic lethality (approximately 9.5 - 10.5 d). Here we demonstrate that apoB is normally expressed at early time points in embryonic development in yolk sac visceral endodermal cells, and that this expression is associated with the synthesis and secretion of apoB-containing lipoproteins. The lack of apoB in the visceral endoderm resulted in an accumulation of intracellular lipid droplets, an absence of lipoproteins from the secretory pathway, and reduced concentrations of cholesterol and alpha-tocopherol in tissues of apoB-/- embryos. Visceral endoderm of apoB+/- embryos exhibited an intermediate phenotype. Our results suggest that apoB plays an essential role in the transport of lipid nutrients to the developing mouse embryo via the yolk sac-mediated synthesis and secretion of apoB-containing lipoproteins.
Molecular mechanisms in prostate cancer. A review. (2004)

Genetic studies have provided remarkable clues to the causes of prostate cancer (PCa). For example, in addition to the expected role of androgens in facilitating the development of PCa, the possibility that infections might lead to prostate cancer has been raised with the identification of RNASEL and MSR1 as familial prostate cancer genes; that insight will profoundly affect future studies and may ultimately lead to new approaches to the prevention of prostate cancer. The identification of key molecular alterations in prostate cancer cells implicates carcinogen defenses, including GSTP1, growth factor signaling pathways (such as NKX3.1, PTEN and p27) and androgens as critical determinants of the phenotype of PCa cells and defines specific targets for detection, diagnosis and treatment of PCa.
Channel assignment schemes for cellular mobile telecommunication systems: a comprehensive survey (1996)

This article provides a detailed discussion of wireless resource and channel allocation schemes. The authors provide a survey of a large number of published papers in the area of fixed, dynamic, and hybrid allocation schemes and compare their trade-offs in terms of complexity and performance. We also investigate these channel allocation schemes based on other factors such as distributed/centralized control and adaptability to traffic conditions. Moreover, we provide a detailed discussion on reuse partitioning schemes, the effect of handoffs, and prioritization schemes. Finally, we discuss other important issues in resource allocation such as overlay cells, frequency planning, and power control.
Interleukin-10 Production by Th1 Cells Requires Interleukin-12-Induced STAT4 Transcription Factor and ERK MAP Kinase Activation by High Antigen Dose (2009)

CD4(+) T cells producing interleukin-10 (IL-10) and interferon-gamma (IFN-gamma) are reported in chronic infections. However, the signals that direct the development of IL-10-producing T helper 1 (Th1) cells are undefined. We showed that development of IL-10-producing Th1 cells required high T cell receptor (TCR) ligation, sustained ERK1 and ERK2 MAP kinases phosphorylation, and IL-12-induced STAT4 transcription factor activation. Repeated TCR triggering led to enhanced IL-10 production by Th1 cells, and continued IL-12 action and high-dose TCR signaling were required for the development and maintenance of IL-10-producing Th1 cells. Although Th1, Th2, and Th17 cells require the activation of distinct STATs for their differentiation, activation of ERK1 and ERK2 was a common requirement for production of IL-10 by all Th cell subsets. IL-10 expression also correlated with c-maf expression. Despite having distinct functions in protection against pathogens, all Th cells share the important task of controlling overexuberant immune responses by means of IL-10 production.
Nonuniform temperature distribution in electronic devices cooled by flow in parallel microchannels (2001)

We fabricated a novel thermal microsystem (simulating a computer chip) consisting of a heater, microchannels, inlet and outlet plena and we studied the effect of the geometry on the flow and heat transfer. The vapor-water two-phase flow patterns were observed in the parallel microchannels through a microscope and high-speed video camera. It was observed that hydraulic instabilities occur. Existence of a periodic annular flow was also observed, which consists of a symmetrically distributed liquid ring surrounding the vapor core. Along the microchannel axis, the periodic dry zone appears and develops. The thermal visualization and temperature measurements of the heated device were carried out using infrared thermography. As long as the flow was single phase liquid, the forced convection heat transfer resulted in a moderate irregularity on the heated chip. These temperature differences do not cause damage to a real electronic device. The steady-state heat transfer for different types of microchannels has been studied also at the range of heat flux where phase change of the working fluid from liquid to vapor took place. Under conditions of flow boiling in microchannels, a significant enhancement of heat transfer was established. In the case of uniform heat flux the hydraulic instabilities lead to irregularity of temperature distribution on the heated chip. In the case of nonuniform heat flux the irregularity increased drastically.
Two novel point mutations correlate with an altered developmental expression of blood coagulation factor IX (hemophilia B Leyden phenotype) (1989)

Hemophilia B Leyden is characterized by low levels of factor IX antigen and activity before the age of 15 years, whereas after puberty factor IX levels rise at a rate of about 5% per year. Two distinct point mutations (deletion of A, A----G) were identified at position +13 of the factor IX gene of a Greek and an American patient with hemophilia B Leyden. The nucleotide changes have occurred 32 basepairs downstream of a previously reported point mutation in a Dutch kindred with the same hemophilic phenotype. The results point to the importance of sequences surrounding the putative start site for the constitutive expression of the factor IX gene and to the possible significance of an imperfect direct repeat of DNA.
Organization of amyloid‐β protein precursor intracellular domain‐associated protein‐1 in the rat brain (2010)

Sustained activity-dependent synaptic modifications require protein synthesis. Although proteins can be synthesized locally in dendrites, long-term changes also require nuclear signaling. Amyloid-beta protein precursor intracellular domain-associated protein-1 (AIDA-1), an abundant component of the biochemical postsynaptic density fraction, contains a nuclear localization sequence, making it a plausible candidate for synapse-to-nucleus signaling. We used immunohistochemistry to study the regional, cellular, and subcellular distribution of AIDA-1. Immunostaining was prominent in the hippocampus, cerebral cortex, and neostriatum. Along with diffuse staining of neuropil, fluorescence microscopy revealed immunostaining of excitatory synapses throughout the forebrain, and immunoreactive puncta within and directly outside the nucleus. Presynaptic staining was conspicuous in hippocampal mossy fibers. Electron microscopic analysis of material processed for postembedding immunogold revealed AIDA-1 label within postsynaptic densities in both hippocampus and cortex. Together with previous work, these data suggest that AIDA-1 serves as a direct signaling link between synapses and the nucleus in adult rat brain.
Dendritic cell-based immunotherapy for malignant gliomas (2005)

Despite dramatic advances in surgical techniques, imaging and adjuvant radiotherapy or chemotherapy, the prognosis for patients with malignant glial tumors remains dismal. Based on the current knowledge regarding immune responses in the healthy CNS and glioma-bearing hosts, this review discusses dendritic cell-based immunotherapeutic approaches for malignant gliomas and the relevance of recent clinical trials and their outcomes. It is now recognized that the CNS is not an immunologically tolerated site and clearance of arising glioma cells is a routine physiologic function of the normal, noncompromised immune system. To escape from immune surveillance, however, clinically apparent gliomas develop complex mechanisms that suppress tumoricidal immune responses. Although the use of dendritic cells for the treatment of glioma patients may be the most appropriate approach, an effective treatment paradigm for these tumors may eventually require the use of several types of treatment. Additionally, given the heterogeneity of this disease process and an immune-refractory tumor cell population, the series use of rational multiple modalities that target disparate tumor characteristics may be the most effective therapeutic strategy to treat malignant gliomas.