gebhart/patrepeval huggingface dataset:
Methodology of optical topography measurements for functional brain imaging and the development and implementation of functional optical signal analysis software. (2007)

September 2007I would like to dedicate this work to my father, Kim Huat, who would so much have liked to have seen its completion. Near-infrared spectroscopy (NIRS) has been used extensively in recent years as a noninvasive tool for investigating cerebral haemodynamics and oxygenation. The technique exploits the different optical absorption of oxy-haemoglobin and deoxy-haemoglobin in the near infrared region to measure changes in their concentrations in tissue. By making multiple NIRS measurement simultaneously, optical topography (OT) provides spatial maps of the changes in haemoglobin concentration levels from specific regions of the cerebral cortex. The thesis describes several key developments in optical topography studies of functional brain activation. These include the development of a novel data analysis software to process the experimental data and a new statistical methodology for examining the spatial and temporal variance of OT data.
Tetrahedrally-Oriented Four-Armed Star and Branched Aramids (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTetrahedrally-Oriented Four-Armed Star and Branched AramidsVeronica R. Reichert and Lon J. MathiasCite this: Macromolecules 1994, 27, 24, 7024–7029Publication Date (Print):November 1, 1994Publication History Published online1 May 2002Published inissue 1 November 1994https://pubs.acs.org/doi/10.1021/ma00102a003https://doi.org/10.1021/ma00102a003research-articleACS PublicationsRequest reuse permissionsArticle Views383Altmetric-Citations25LEARN 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 Get e-Alerts
A review of urban computing for mobile phone traces (2013)

In this work, we present three classes of methods to extract information from triangulated mobile phone signals, and describe applications with different goals in spatiotemporal analysis and urban modeling. Our first challenge is to relate extracted information from phone records (i.e., a set of time-stamped coordinates estimated from signal strengths) with destinations by each of the million anonymous users. By demonstrating a method that converts phone signals into small grid cell destinations, we present a framework that bridges triangulated mobile phone data with previously established findings obtained from data at more coarse-grained resolutions (such as at the cell tower or census tract levels). In particular, this method allows us to relate daily mobility networks, called motifs here, with trip chains extracted from travel diary surveys. Compared with existing travel demand models mainly relying on expensive and less-frequent travel survey data, this method represents an advantage for applying ubiquitous mobile phone data to urban and transportation modeling applications. Second, we present a method that takes advantage of the high spatial resolution of the triangulated phone data to infer trip purposes by examining semantic-enriched land uses surrounding destinations in individual's motifs. In the final section, we discuss a portable computational architecture that allows us to manage and analyze mobile phone data in geospatial databases, and to map mobile phone trips onto spatial networks such that further analysis about flows and network performances can be done. The combination of these three methods demonstrate the state-of-the-art algorithms that can be adapted to triangulated mobile phone data for the context of urban computing and modeling applications.
Generation of definitive hematopoietic stem cells from murine early yolk sac and paraaortic splanchnopleures by aorta-gonad-mesonephros region–derived stromal cells (2001)

There is controversy as to whether murine definitive hematopoiesis originates from yolk sac (YS) or the intraembryonic region. This study reports the generation of definitive hematopoietic stem cells (HSCs) from both early YS and intraembryonic paraaortic splanchnopleures (P-Sp) on AGM-S3 stromal cells derived from the aorta-gonad-mesonephros (AGM) region at 10.5 days post coitum (dpc). YS and P-Sp cells at 8.5 dpc generated no definitive hematopoiesis-derived colony-forming cells in cocultures with AGM-S3 cells, but spleen colony-forming cells and HSCs capable of reconstituting definitive hematopoiesis in adult mice simultaneously appeared on day 4 of coculture. Precursors for definitive HSCs were present in YS and P-Sp at 8.0 dpc, a time when YS and embryo were not connected by blood vessels. It is proposed that precursors with the potential to generate definitive HSCs appear independently in YS and intraembryonic P-Sp and that the P-Sp or AGM region affords the microenvironment that facilitates generation of definitive hematopoiesis from precursors.
Survival of Mature CD4 T Lymphocytes Is Dependent on Major Histocompatibility Complex Class II–expressing Dendritic Cells (1997)

Thymic T cell development is controlled by T cell receptor (TCR)-major histocompatibility complex (MHC) interactions, whereas a further dependence of peripheral mature T cells on TCR-MHC contact has not been described so far. To study this question, CD4 T cell survival was surveyed in mice lacking MHC class II expression and in mice expressing MHC class II exclusively on dendritic cells. Since neither of these mice positively select CD4 T cells in the thymus, they were grafted with MHC class II-positive embryonic thymic tissue, which had been depleted of bone marrow derived cells. Although the thymus grafts in both hosts were repopulated with host origin thymocytes of identical phenotype and numbers, an accumulation of CD4+ T cells in peripheral lymphoid organs could only be observed in mice expressing MHC class II on dendritic cells, but not in mice that were completely MHC class II deficient. As assessed by histology, the accumulating peripheral CD4 T cells were found to be in close contact with MHC class II+ dendritic cells, suggesting that CD4 T cells need peripheral MHC class II expression for survival and that class II+ dendritic cells might play an important role for the longevity of CD4 T cells.
Phosphorylation of Transcriptional Coactivator Peroxisome Proliferator-activated Receptor (PPAR)-binding Protein (PBP) (2002)

Peroxisome proliferator-activated receptor (PPAR)-binding protein (PBP) is an important coactivator for PPARgamma and other transcription factors. PBP is an integral component of a multiprotein thyroid hormone receptor-associated protein (TRAP)/vitamin D(3) receptor-interacting protein (DRIP)/activator-recruited cofactor (ARC) complex required for transcriptional activity. To study the regulation of PBP by cellular signaling pathways, we identified the phosphorylation sites of PBP. Using a combination of in vitro and in vivo approaches and mutagenesis of PBP phosphorylation sites, we identified six phosphorylation sites on PBP: one exclusive protein kinase A (PKA) phosphorylation site at serine 656, two protein kinase C (PKC) sites at serine 796 and serine 1345, a common PKA/PKC site at serine 756, and two extracellular signal-regulated kinase 2 sites of the mitogen-activated protein kinase (MAPK) family at threonine 1017 and threonine 1444. Binding of PBP to PPARgamma1 or retinoid-X-receptor for 9-cis-retinoic acid (RXR) is independent of their phosphorylation states, implying no changes in protein-protein interaction after modification by phosphorylation. Overexpression of RafBXB, an activated upstream kinase of the MAPK signal transduction pathway, exerts a significant additive inductive effect on PBP coactivator function. This effect is significantly diminished by overexpression of RafBXB301, a dominant negative mutant of RafBXB. These results identify phosphorylation as a regulatory modification event of PBP and demonstrate that PBP phosphorylation by Raf/MEK/MAPK cascade exerts a positive effect on PBP coactivator function. The functional role of PKA and PKC phosphorylation sites in PBP remains to be elucidated.
Regulation of metastasis‐suppressive gene Nm23‐H1 on glycosyl‐transferases involved in the synthesis of sialyl Lewis antigens (2005)

By using reverse transcriptase-polymerase chain reaction (RT-PCR), the mRNA expressions of three families of glycosyltransferases involved in the synthesis of sialyl Lewis antigens were determined in H7721 human hepatocarcinoma cell line before and after the transfection of metastasis-suppressive gene nm23-H1. These glycosyltransferases included alpha1,3fucosyltransferase (alpha1,3FucT)-III, -IV, -VI, -VII, and -IX, alpha2,3-sialyltransferase (ST3Gal)-I, -II, -III, and -IV as well as O-glycan core 2 beta1,6 N-acetylglucosaminyltransferase (C2GnT)-I and -II. In mock cells transfected with the vector, the expression-order of alpha1,3FucTs was IV>VI>III>VII>IX, that of ST3Gals was IV>I>II>III, and that of C2GnT was I>II. Nm23-H1 downregulated the mRNA expressions of all five subtypes of alpha1,3FucT and -I, -III, -IV subtypes of ST3Gal, but not ST3Gal-II and C2GnT-I, II. On the other hand, the expressions of cell surface sialyl Lewis X (SLe(x)) and alpha2,3 sialyl residues were decreased on nm23-H1 transfected cells as detected with monoclonal antibody of SLe(x) and enzyme-labeled lectins, respectively. Since SLe(x) was reported to be a metastasis-associated glycan structure, the reduced expressions of SLe(x) and some enzymes related to its synthesis may be one of the mechanisms to explain the metastasis-suppressive effect of nm23-H1.
Dihydro-7-benzofurancarboxylic Acid: An Intermediate in the Synthesis of the Enterokinetic Agent R108512 (2003)

A facile and scalable method for the synthesis of 4-amino-5-chloro-2,3-dihydro-7-benzofurancarboxylic acid, an intermediate in the synthesis of the enterokinetic agent R108512, has been developed. The key step in the synthesis is a zinc mediated ring closure of methyl 4-(acetylamino)-3-bromo-2-(2-bromoethoxy)-5-chlorobenzoate. The ring closure can be achieved without preliminary activation of the zinc on condition that the oxygen content in the reaction mixture is lower than 0.5%. The new process eliminates hazardous chemicals (ethyleneoxide) and low temperature reactions (-70°C, n-BuLi)
Characterization of Two Isoforms of the Skeletal Muscle LIM Protein 1, SLIM1 (1999)

We have cloned and characterized a novel isoform of the skeletal muscle LIM protein 1 (SLIM1), designated SLIMMER. SLIM1 contains an N-terminal single zinc finger followed by four LIM domains. SLIMMER is identical to SLIM1 over the first three LIM domains but contains a novel C-terminal 96 amino acids with three potential bipartite nuclear localization signals, a putative nuclear export sequence, and 27 amino acids identical to the RBP-J binding region of KyoT2, a murine isoform of SLIM1. SLIM1 localized to the cytosol of Sol8 myoblasts and myotubes. SLIMMER was detected in the nucleus of myoblasts and, following differentiation into myotubes, was exclusively cytosolic. Recombinant green fluorescent protein-SLIM1 localized to the cytoplasm and associated with focal adhesions and actin filaments in COS-7 cells, while green fluorescent protein-SLIMMER was predominantly nuclear. SLIMMER truncation mutants revealed that the first nuclear localization signal mediates nuclear localization. The addition of the proposed nuclear export sequence decreased the level of exclusively nuclear expression and increased cytosolic SLIMMER expression in COS-7 cells. The leucine-rich nuclear export signal was required for the export of SLIMMER from the nucleus of myoblasts to the cytoplasm of myotubes. Collectively, these results suggest distinct roles for SLIM1 and SLIMMER in focal adhesions and nuclear-cytoplasmic communication.
Repeated CT elements bound by zinc finger proteins control the absolute and relative activities of the two principal human c-myc promoters. (1993)

Transcription of the human proto-oncogene c-myc is governed by two tandem principal promoters, termed P1 and P2. In general, the downstream promoter, P2, is predominant, which is in contrast to the promoter occlusion phenomenon usually observed in genes containing tandem promoters. A shift in human c-myc promoter usage has been observed in some tumor cells and in certain physiological conditions. However, the mechanisms that regulate promoter usage are not well understood. The present studies identify regulators which are required to promote transcription from both human c-myc promoters, P1 and P2, and have a role in determining their relative activities in vivo. A novel regulatory region located 101 bp upstream of P1 was characterized and contains five tandem repeats of the consensus sequence CCCTCCCC (CT element). The integrity of the region containing all five elements is required to promote transcription from P1 and for maximal activity from P2 in vivo. A single copy of this same element, designated CT-I2, also appears in an inverted orientation 53 bp upstream of the P2 transcription start site. This element has an inhibitory effect on P1 transcription and is required for P2 transcription. The transcription factor Sp1 was identified as the factor that binds specifically to the tandem CT elements upstream of P1 and to the CT-I2 element upstream of P2. In addition, the recently cloned zinc finger protein ZF87, or MAZ, was also able to bind these same elements in vitro. The five tandem CT elements can be functionally replaced by a heterologous enhancer that only in the absence of CT-I2 reverses the promoter usage, similar to what is observed in the translocated c-myc allele of Burkitt's lymphoma cells.
Genetic modifiers of the insulin resistance phenotype in mice. (2000)

Insulin resistance can result from genetic interactions among susceptibility alleles. To identify genetic loci predisposing to insulin resistance, we used crosses between different strains of mice with a targeted null allele of the insulin receptor gene. On the genetic background of B6 mice, the insulin receptor gene mutation causes mild hyperinsulinemia. In contrast, on the genetic background of 129/Sv mice, the same mutation causes severe hyperinsulinemia, suggesting that the 129/Sv strain harbors alleles that interact with the insulin receptor mutation and predispose to insulin resistance. As a first step to identify these alleles, we generated an F2 intercross between insulin receptor heterozygous mutant mice on B6 and 129/Sv backgrounds (B6IR x 129IR) and performed a genome-wide scan with polymorphic markers at a 20-cM resolution. We report the identification of loci on chromosomes 2 (logarithm of odds [LOD] 5.58) and 10 (LOD 5.58) that show significant evidence for linkage to plasma insulin levels as a quantitative trait. These findings indicate that targeted mutations in knockout mice can be used to unravel the complex genetic interactions underlying insulin resistance.
The role of dendritic cells in immune regulation and allergic airway inflammation (2003)

Dendritic cells (DC) are potent antigen presenting cells that display an extraordinary capacity to present antigen to naïve T-cells and initiate primary immune responses. In the context of the lung and upper airway it is clear that DC play a key role in the regulation of adaptive immune responses to inhaled antigen. DC are particularly sensitive to signals derived from microbes, allergens and the airway tissue microenvironment. By the nature of the signals they provide at the time of antigen presentation, DC can polarize naïve T-cells into either T-helper type 1 (Th1) or Th2 effector cells, and are increasingly recognized as having a central role in the establishment of T-cell memory and peripheral immune tolerance. DC form a network within the upper airway and lung, and are rapidly recruited from the circulation in response to a variety of proinflammatory stimuli. Studies using animal models have highlighted the role of DC in both the initiation and maintenance of allergic airway inflammation. In early childhood, human DC are functionally immature, and this is thought to contribute to the development of allergic sensitization in those children who are genetically at risk for the development of atopy. Increased numbers of airway mucosal DC are found in both allergic rhinitis and asthma, while studies of blood-derived DC have emphasized important differences between the function of DC from atopic and normal individuals. This article reviews recent information on the involvement of DC in allergic airway disease, and the mechanisms by which DC could be exploited as targets for therapy in asthma and allergic rhinitis.
Surfaces for radiative cooling: Silicon monoxide films on aluminum (1980)

Efficient radiative cooling is feasible with surfaces which radiate predominantly in the 8–13-μm wavelength range, where the atmosphere emittance is low. The desired reflectance profile was approximated with 1.0 μm of SiO evaporated onto Al. It results from strong lattice absorption in SiO in conjunction with destructive interference. Refrigeration to 40 K below the ambient appears to be possible under suitable climatic conditions.
Potential Novel Therapies for Chronic Obstructive Pulmonary Disease (2000)

While considerable progress has been made in development of drugs for asthma, there have been few advances in the treatment of chronic obstructive pulmonary disease (COPD). New therapeutic approaches to prevent disease progression are urgently needed and these will arise out of better understanding of the disease process at a cell and molecular level. The inflammatory response in COPD differs markedly from that of asthma, with differences in inflammatory cells, mediators and response to therapy. The neutrophilic inflammation is orchestrated by chemotactic factors, such as interleukin (IL)-8, other CXC chemokines and leukotriene B4; receptor blockers (CXCR1, CXCR2, BLT antagonists) or synthesis inhibitors (5'-lipoxygenase inhibitors) might be effective. Tumour necrosis factor (TNF) alpha may be an important amplifying cytokine and there are several strategies for blocking it (antibodies, soluble receptors, TACE inhibitors). IL-10 is effective in blocking the synthesis of IL-8 and TNF alpha as well as proteases. Oxidative stress and peroxynitrite may be important in COPD; more effective antioxidants are now in development. The inflammatory response in COPD is essentially steroid-resistant so that alternative anti-inflammatory treatments are needed. Phosphodiesterase 4 inhibitors look promising in early clinical studies. Nuclear factor-kappa B inhibitors and p38 MAP kinase inhibitors may also be effective. Several protease inhibitors are in development including those for neutrophil elastase, selective matrix metalloproteinase and cathepsin.
The Arizona Sexual Experience Scale (ASEX): Reliability and Validity (2000)

Although sexual dysfunction is common in psychiatric patients, quantification of sexual dysfunction is limited by the paucity of validated, user-friendly scales. In order to address this problem, the authors have developed the Arizona Sexual Experiences Scale (ASEX), a five-item rating scale that quantifies sex drive, arousal, vaginal lubrication/penile erection, ability to reach orgasm, and satisfaction from orgasm. Possible total scores range from 5 to 30, with the higher scores indicating more sexual dysfunction. This study assesses the internal consistency, test-retest reliability, and convergent and discriminant validity of the ASEX.
Phenotypic and genotypic heterogeneity in familial Milroy lymphedema. (1998)

Familial Milroy lymphedema (ML) is classified as an autosomal dominant disorder characterized by peripheral edema of the lower extremities at birth or in early childhood. The variety of phenotypes are not well described, and the genomic location and functional expression of the gene or genes underlying this and related familial lymphedema syndromes remain largely unknown. In this collaborative study between the University of Arizona and the University of São Paulo, we collected clinical pedigrees on 6 ML families, carried out clinical examination of affected and unaffected individuals, and, in representative affected members of two of the families performed dynamic lymphangioscintigraphy (LAS) of the lower and upper limbs to delineate further the ML lymphangiodysplastic phenotype. To localize the gene for ML, we conducted a genome-wide search in 4 of the families using 387 polymorphic dinucleotide-repeat markers at approximate 10 cM spacing in 54 subjects (affected, unaffected bloodline relatives, and spouses). In all 6 families (86 subjects), we specifically examined the suggested linkage to the vascular endothelial growth factor (VEGF)-C receptor (Flt4) gene localized to the chromosome region 5q34-q35. The findings provide evidence for a spectrum of ML clinical and LAS phenotypes and also suggest ML locus heterogeneity.
Probing Solid-State Nanopores with Light for the Detection of Unlabeled Analytes (2014)

Nanopore sensing has enabled label-free single-molecule measurements on a wide variety of analytes, including DNA, RNA, and protein complexes. Much progress has been made toward biotechnological applications; however, electrically probing the ion current introduces nonideal noise components. Here we further develop a method to couple an ionic current to a photon-by-photon counting of fluorescent signal from Ca(2+)-sensitive dyes and demonstrate label-free optical detection of biopolymer translocation through solid-state nanopores using TIRF and confocal microscopy. We show that by fine adjustment of the CaCl2 gradient, EGTA concentration, and voltage, the optical signals can be localized to the immediate vicinity of the pore. Consequently, the noise spectral density distribution in the optical signal exhibits a nearly flat distribution throughout the entire frequency range. With the use of high-speed photon counting devices in confocal microscopy and higher photon count rates using stronger light sources, we can improve the signal-to-noise ratio of signal acquisition, while the use of wide-field imaging in TIRF can allow for simultaneous quantitative imaging of large arrays of nanopores.
Dynamic range improvement through multiple exposures (2003)

This paper presents an approach for improving the effective dynamic range of cameras by using multiple photographs of the same scene taken with different exposure times. Using this method enables the photographer to accurately capture scenes that contain a high dynamic range, i.e., scenes that have both very bright and very dark regions. The approach requires an initial calibration, where the camera response function is determined. Once the response function for a camera is known, high dynamic range images can be computed easily. The high dynamic range output image consists of a weighted average of the multiply-exposed input images, and thus contains information captured by each of the input images. From a computational standpoint, the proposed algorithm is very efficient, and requires little processing time to determine a solution.