gebhart/patrepeval huggingface dataset:
Flavonoids as aryl hydrocarbon receptor agonists/antagonists: effects of structure and cell context. (2003)

Chemoprotective phytochemicals exhibit multiple activities and interact with several cellular receptors, including the aryl hydrocarbon (Ah) receptor (AhR). In this study we investigated the AhR agonist/antagonist activities of the following flavonoids: chrysin, phloretin, kaempferol, galangin, naringenin, genistein, quercetin, myricetin, luteolin, baicalein, daidzein, apigenin, and diosmin. We also investigated the AhR-dependent activities of cantharidin and emodin (in herbal extracts) in Ah-responsive MCF-7 human breast cells, HepG2 human liver cancer cells, and mouse Hepa-1 cells transiently or stably transfected with plasmids expressing a luciferase reporter gene linked to multiple copies of a consensus dioxin-responsive element. The AhR agonist activities of the compounds (1 and 10 micro M) were as high as 25% of the maximal response induced by 5 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and their potencies were dependent on cell context. Galangin, genistein, daidzein, and diosmin were active only in Hepa-1 cells, and cantharidin induced activity only in human HepG2 and MCF-7 cells. Western blot analysis confirmed that baicalein and emodin also induced CYP1A1 protein in the human cancer cell lines. The AhR antagonist activities of four compounds inactive as agonists in MCF-7 and HepG2 cells (kaempferol, quercetin, myricetin, and luteolin) were also investigated. Luteolin was an AhR antagonist in both cell lines, and the inhibitory effects of the other compound were dependent on cell context. These data suggest that dietary phytochemicals exhibit substantial cell context-dependent AhR agonist as well as antagonist activities. Moreover, because phytochemicals and other AhR-active compounds in food are present in the diet at relatively high concentrations, risk assessment of dietary toxic equivalents of TCDD and related compounds should also take into account AhR agonist/antagonist activities of phytochemicals.
Novel chimeric immunomodulatory compounds containing short CpG oligodeoxyribonucleotides have differential activities in human cells (2003)

Immunostimulatory DNA sequences (ISS) containing CpG motifs induce interferon-alpha (IFN-alpha) and interferon-gamma (IFN-gamma) from human peripheral blood mononuclear cells and stimulate human B cells to proliferate and produce IL-6. We studied the motif and structural requirements for both types of activity using novel chimeric immunomodulatory compounds (CICs), which contain multiple heptameric ISS connected by non-nucleoside spacers in both linear and branched configurations. We found that the optimal motifs and structure for IFN-alpha production versus B cell activation differed. IFN-alpha production was optimal for CICs containing the sequences 5'-TCGXCGX and 5'-TCGXTCG, where X is any nucleotide. The presentation of multiple copies of these heptameric ISS with free 5'-ends via long, hydrophilic spacers, such as hexaethylene glycol, significantly enhanced the induction of IFN-alpha. Conversely, human B cell activity was predominantly dependent on ISS motif, with 5'-TCGTXXX and 5'-AACGTTC being the most active sequences. Thus, we found CICs could be 'programmed' for IFN-alpha production or B cell activation as independent variables. Additionally, CICs with separate human- and mouse-specific motifs were synthesized and these were used to confirm in vivo activity in mice. CICs may offer unique advantages over conventional ISS because identification of the optimal motifs, spacers and structures for different biological properties allows for the assembly of CICs exhibiting a defined set of activities tailored for specific clinical applications.
Mechanism of transcriptional antirepression by GAL4-VP16. (1992)

Promoter- and enhancer-binding factors appear to function by facilitating the transcription reaction as well as by counteracting chromatin-mediated repression (antirepression). We have examined the mechanism by which a hybrid activator, GAL4-VP16, is able to counteract histone H1-mediated repression by using both H1-DNA complexes and reconstituted H1-containing chromatin templates. The GAL4 DNA binding domain alone was sufficient to disrupt local H1-DNA interactions, but a transcriptional region was additionally necessary for antirepression. GAL4-VP16-mediated antirepression required an auxiliary factor, denoted as a co-antirepressor, which was partially purified from Drosophila embryos. We have found that the co-antirepressor activity was sensitive to digestion with RNase A. Moreover, total RNA from Drosophila embryos could partially substitute for the co-antirepressor fraction, which indicated that the co-antirepressor may function as a histone acceptor ("histone sink"). These findings suggest a model for gene activation in which sequence-specific transcription factors disrupt H1-DNA interactions at the promoter to facilitate transfer of H1 to a histone acceptor, which then allows access of the basal transcription factors to the DNA template.
Molecular Structure and Some Physicochemical Properties of High‐Amylose Barley Starches (2000)

ABSTRACT The molecular structure and some physicochemical properties of starches from two high‐amylose cultivars of barley, high‐amylose Glacier A (HAG‐A) and N (HAG‐N), were examined and compared with those of a normal cultivar, Normal Glacier (NG). The true amylose contents of HAG‐A, HAG‐N, and NG were 41.0, 33.4, and 23.0%, respectively. Iodine affinities before and after defatting of starch, and thermograms of differential scanning calorimetry, indicated that HAG‐A and HAG‐N starches had a higher proportion of amylose‐lipid complex than did NG starch. The amylopectins from HAG‐A and HAG‐N were similar to NG amylopectin in average chain length (18–19), β‐amylolysis limit (β‐AL 56–57%), number‐average degrees of polymerization (DP n 6,000–7,500) and chain length distribution. Very long chains (1–2%) were found in amylopectins from all cultivars. HAG‐A amylopectin had a larger amount of phosphorus (214 ppm) than the others. The amyloses from HAG‐A and HAG‐N resembled NG amylose in DP n (950–1,080) and β‐AL (70–74%). However, HAG‐A and HAG‐N had a larger number of chains per molecule (NC 2.4–2.7) than NG amylose (1.8) and contained the branched amylose with a higher NC (9.5–10.6) than that of NG amylose (5.8), although molar fractions of the branched amylose (15–20%) were similar.
Domain-Specific Knowledge Systems in the Brain: The Animate-Inanimate Distinction (1998)

We claim that the animate and inanimate conceptual categories represent evolutionarily adapted domain-specific knowledge systems that are subserved by distinct neural mechanisms, thereby allowing for their selective impairment in conditions of brain damage. On this view, (some of) the category-specific deficits that have recently been reported in the cognitive neuropsychological literature—for example, the selective damage or sparing of knowledge about animals—are truly categorical effects. Here, we articulate and defend this thesis against the dominant, reductionist theory of category-specific deficits, which holds that the categorical nature of the deficits is the result of selective damage to noncategorically organized visual or functional semantic subsystems. On the latter view, the sensory/functional dimension provides the fundamental organizing principle of the semantic system. Since, according to the latter theory, sensory and functional properties are differentially important in determining the meaning of the members of different semantic categories, selective damage to the visual or the functional semantic subsystem will result in a category-like deficit. A review of the literature and the results of a new case of category-specific deficit will show that the domain-specific knowledge framework provides a better account of category-specific deficits than the sensory/functional dichotomy theory.
Transmembrane topology and sites of N-glycosylation of inositol 1,4,5-trisphosphate receptor. (1994)

To define the transmembrane topology of the inositol 1,4,5-trisphosphate receptor (InsP3R), we determined the subcellular location of the hydrophilic segment (residues 2463-2529 of mouse type 1 InsP3R) believed to be located at the luminal side of the endoplasmic reticulum (ER) in the six-transmembrane model but at the cytoplasmic side in the eight-transmembrane model. This hydrophilic segment includes two consensus sites for N-glycosylation (Asn-2475 and Asn-2503). We prepared an anti-peptide antibody against residues 2504-2523. Electron microscope immunocytochemical studies of mouse cerebellar Purkinje cells showed that binding of this antibody frequently occurs in the intracisternal space of the ER. We constructed three mutant receptors by site-directed mutagenesis of Asn to Gln (N2475Q, N2503Q, and N2475Q/N2503Q). By concanavalin A column chromatography of these receptors, we found that both Asn-2475 and Asn-2503 are glycosylated. These results indicate that residues 2504-2523, Asn-2475, and Asn-2503 are exposed to the ER lumen. We therefore propose that InsP3R has six membrane-spanning segments. Based on the transmembrane topology and subunit organization, we suggest that InsP3R is a member of the superfamily that includes the voltage- and second messenger-gated ion channels on the plasma membrane.
Durable Modification of Silica Aerogel Monoliths with Fluorescent 2,7-Diazapyrenium Moieties. Sensing Oxygen near the Speed of Open-Air Diffusion (1999)

Silica sol−gels were covalently modified with N-(3-trimethoxysilylpropyl)-2,7-diazapyrenium bromide (DAP). Luminescent aerogels are created in which none of the fluorophore leaches from the gels during either the washing or supercritical drying necessary to prepare DAP-modified aerogels. The bulk density (0.17 g/cm3), N2-adsorption surface area (870 m2/g), and thermogravimetric and scanning electron micrographic characteristics of the dye-modified aerogels remain identical to those of the unmodified silica aerogels. The bulk concentration of the dye in the aerogels was ≤6.6 mM; at these loadings the aerogels demonstrate bulk photoluminescence. As based on the mesoporous surface area, the surface coverage of the dye is 7−8% of a monolayer. The absorption, emission, and O2-quenching characteristics of the diazapyrenium dye in the aerogels parallel those obtained in alcoholic (rather than aqueous) solution, which further indicates that the dopant molecules are isolated from each other and that they see an environment with a ∼OH polarity. Time-resolved emission studies indicate that all DAP moieties reside in a single type of microenvironment. Emission quenching of ∼1-cm-diameter monoliths of DAP−silica aerogel is complete in <15 s, which compares very favorably with the best response times for pyrene guests in micrometer-thick xerogel films. The apparent diffusion coefficient of O2 or Ar in the DAP−aerogel monoliths was estimated at ≥0.01−0.02 cm2/s, which is only 10× less than the unimpeded diffusion coefficient of Ar in air.
Nramp1 Is Not a Major Determinant in the Control ofBrucella melitensisInfection in Mice (2003)

Brucella, the causative agent of brucellosis in animals and humans, can survive and proliferate within macrophages. Macrophages mediate mouse resistance to various pathogens through the expression of the Nramp1 gene. The role of this gene in the control of Brucella infection was investigated. When BALB/c mice (Nramp1(s)) and C.CB congenic mice (Nramp1(r)) were infected with Brucella melitensis, the number of Brucella organisms per spleen was significantly larger in the C.CB mice than in the BALB/c mice during the first week postinfection (p.i.). This Nramp1-linked susceptibility to Brucella was temporary, since similar numbers of Brucella were recovered from the two strains of mice 2 weeks p.i. The effect of Nramp1 expression occurred within splenocytes intracellularly infected by BRUCELLA: However, there was no difference between in vitro replication rates of Brucella in macrophages isolated from the two strains of mice infected in vivo or in Nramp1 RAW264 transfectants. In mice, infection with Brucella induced an inflammatory response, resulting in splenomegaly and recruitment of phagocytes in the spleen, which was amplified in C.CB mice. Reverse transcription-PCR (RT-PCR), performed 5 days p.i., showed that inducible nitric oxide synthase, tumor necrosis factor alpha (TNF-alpha), interleukin-12 p40 (IL-12p40), gamma interferon (IFN-gamma), and IL-10 mRNAs were similarly induced in spleens of the two strains. In contrast, the mRNA of KC, a C-X-C chemokine, was induced only in infected C.CB mice at this time. This pattern of mRNA expression was maintained at 14 days p.i., with IFN-gamma and IL-12p40 mRNAs being more intensively induced in the infected C.CB mice, but TNF-alpha mRNA was no longer induced. The higher recruitment of neutrophils observed in the spleens of infected C.CB mice could explain the temporary susceptibility of C.CB mice to B. melitensis infection. In contrast to infections with Salmonella, Leishmania, and Mycobacterium, the expression of the Nramp1 gene appears to be of limited importance for the natural resistance of mice to Brucella.
An Iron-Regulated Ferric Reductase Associated with the Absorption of Dietary Iron (2001)

The ability of intestinal mucosa to absorb dietary ferric iron is attributed to the presence of a brush-border membrane reductase activity that displays adaptive responses to iron status. We have isolated a complementary DNA, Dcytb (for duodenal cytochrome b), which encoded a putative plasma membrane di-heme protein in mouse duodenal mucosa. Dcytb shared between 45 and 50% similarity to the cytochrome b561 family of plasma membrane reductases, was highly expressed in the brush-border membrane of duodenal enterocytes, and induced ferric reductase activity when expressed in Xenopus oocytes and cultured cells. Duodenal expression levels of Dcytb messenger RNA and protein were regulated by changes in physiological modulators of iron absorption. Thus, Dcytb provides an important element in the iron absorption pathway.
Oral dehydroepiandrosterone (DHEA) replacement therapy in women with Addison's disease (2000)

A daily replacement dose of 50 mg of DHEA results in near physiological levels of DHEA, DHEA(S) androstenedione and testosterone in women with Addison's disease, without severe side-effects.
Many-access channels: The Gaussian case with random user activities (2014)

Classical multiuser information theory studies the fundamental limits of models with a fixed (often small) number of users as the coding blocklength goes to infinity. This work proposes a new paradigm, referred to as many-user information theory, where the number of users is allowed to grow with the blocklength. This paradigm is motivated by emerging systems with a massive number of users in an area, such as machine-to-machine communication systems and sensor networks. The focus of the current paper is the many-access channel model, which consists of a single receiver and many transmitters, whose number increases unboundedly with the blocklength. Moreover, an unknown subset of transmitters may transmit in a given block and need to be identified. A new notion of capacity is introduced and characterized for the Gaussian many-access channel with random user activities. The capacity can be achieved by first detecting the set of active users and then decoding their messages.
Intracellular methicillin selection of Listeria monocytogenes mutants unable to replicate in a macrophage cell line. (1989)

To dissect the determinants of Listeria monocytogenes that are required for pathogenicity, we designed an intracellular selection protocol based on penicillin selection to isolate mutants defective for intracellular growth. Eight independent mutants obtained by insertion of Tn916 were isolated that were resistant to methicillin treatment following internalization by the J774 macrophage-like cell line. Seven mutants were absolutely defective for intracellular growth, whereas one showed abortive intracellular growth. The majority of the mutants were nonhemolytic and lacked a secreted 58-kDa polypeptide thought to be the L. monocytogenes hemolysin, listeriolysin O. Southern blot analysis indicated that one mutant contained a Tn916 insertion in hlyA, the listeriolysin O structural gene, which resulted in a truncated listeriolysin O polypeptide, whereas another mutant contained an insertion immediately upstream of hlyA, which resulted in reduced expression of listeriolysin O. The other mutants contained Tn916 insertions in genes other than hlyA, although all but one were nonhemolytic. Revertants isolated by their ability to grow within tissue culture cells regained hemolytic activity. These data show that intracellular methicillin selection facilitates isolation of mutations in genes required for intracellular growth and strengthens the premise that listeriolysin O is essential for intracellular growth.
Cryptococcus neoformans induces alterations in the cytoskeleton of human brain microvascular endothelial cells (2003)

The fungal pathogen Cryptococcus neoformans has a predilection for the central nervous system (CNS), resulting in devastating meningoencephalitis. At present, it is unclear how C. neoformans traverses the blood-brain barrier (BBB) and causes CNS infection. The present study has examined and characterized the interaction of C. neoformans with human brain microvascular endothelial cells (HBMEC), which constitute the BBB. Adhesion of and transcytosis of HBMEC by C. neoformans was inoculum- and time-dependent and occurred with both encapsulated and acapsulated strains. C. neoformans induced marked morphological changes in HBMEC, for example membrane ruffling, irregular nuclear morphology and swelling of the mitochondria and the ER. These findings suggest that C. neoformans induced actin cytoskeletal reorganization of the host cells. In addition, it was observed that the dephosphorylated form of cofilin was increased during cryptococcal adherence to HBMEC, concomitant with the actin rearrangement. Cryptococcal binding to HBMEC was increased in the presence of Y27632, a Rho kinase (ROCK)-specific inhibitor. Since ROCK activates LIM kinase (LIMK), which phosphorylates cofilin (inactive form), this suggests the involvement of the ROCK-->LIMK-->cofilin pathway. In contrast, the phosphatase inhibitor sodium orthovanadate decreased adherence of Cryptococcus to HBMEC, concomitant with the increase of phosphorylation of cofilin. Furthermore, the tight junction marker protein occludin became Triton-extractable, indicating alteration of tight junctions in brain endothelial cells. This is the first demonstration that C. neoformans is able to adhere to and transcytose across the HBMEC monolayer and alter the cytoskeleton morphology in HBMEC. Further characterization of the interactions between C. neoformans and HBMEC should help the development of novel strategies to prevent cryptococcal meningitis and its associated morbidity.
Computer-generated orthoses. A review. (1993)

It is obvious with the various casting techniques used in the study that the ease with which individuals adjust to the fashionette orthotic makes it a desirable device. It is tolerated well with higher-heeled shoes and shoes that are used more for fashion purposes. Future studies need to assess the degree of control compared with the type of deformity and the type of symptoms the patient has. These types of devices may be sufficient to minimize stress on a given deformity, such as a neuroma, but may not be sufficient enough to eliminate the need for the removal of the neuroma. Recurrence of the neuroma after it has been resected and the patient prescribed a fashionette orthosis also needs to be assessed. A neuroma is one example of a type of deformity that needs to be controlled and evaluated with regard to cause and response to orthotic therapy. Abnormal tylomas and pressure lesions need to be assessed on a symptomatic basis for their control with the different types of devices and the pathomechanic causing the pressure. This study indicates that milled orthoses are tolerated better than pressed orthoses. Milled orthoses require less adjustment and the adjustment is tolerated better, regardless of the casting position. The degree of position control had some variations. When comparing the pressed and the milled functional orthoses, there is a more rapid adjustment with the milled type of orthoses. This suggests that possibly the milled orthoses have less alteration in shape and loss of contour from the direct milling and the digitizing process compared with the pressing techniques. The long-term effect of pressing compared with milled orthotics was not assessed during this study with regard to fluid distortion of the polypropylene over time. The fluid nature has a tendency to suffer a loss of contour and progressive loss of function. The milled process theoretically has less change in the contour with the passage of time, although this needs to be assessed in further studies. Possibly, the fluid nature of the orthosis can be assessed by determining how soon the symptoms return between adjustments. Posting surfaces tend to wear over a period of time and distort with the fluid nature. The posting can break down from the type of material from which it is made. A model of assessment for future studies may be to check the duration of when heel spur types of symptoms or postural complex types of symptoms, such as knee pain or lower back pain, recur.(ABSTRACT TRUNCATED AT 400 WORDS)
Human epidermal growth factor precursor: cDNA sequence, expressionin vitroand gene organization (1986)

Complementary DNA clones encoding the human kidney epidermal growth factor (EGF) precursor have been isolated and sequenced. They predict the sequence of a 1,207 amino acid protein which contains EGF flanked by polypeptide segments of 970 and 184 residues at its NH2- and COOH-termini, respectively. The structural organization of the human EGF precursor is similar to that previously described for the mouse protein and there is 66% identity between the two sequences. Transfection of COS-7 cells with the human EGF precursor cDNA linked to the SV40 early promoter indicate that it can be synthesized as a membrane protein with its NH2-terminus external to the cell surface. The human EGF precursor gene is approximately 110 kilobase pairs and has 24 exons. Its exon-intron organization revealed that various domains of the EGF precursor are encoded by individual exons. Moreover, 15 of the 24 exons encode protein segments that are homologous to sequences in other proteins. Exon duplication and shuffling appear to have played an important role in determining the present structure of this protein.
Diffraction from Highly Conducting Wire Gratings of Arbitrary Cross-section (1993)

Abstract A theory describing the diffraction properties of highly conducting wire gratings with arbitrary cross-sections is presented. The method incorporates the surface impedance boundary condition on the field along metallic interfaces and relies on the solution of a coupled system of ordinary differential equations for finding the field between wires. The theory is exemplified numerically for different wire profiles. The numerical results for gold gratings in the resonance region are compared with those obtained from a theory valid for perfectly conducting wires. Comparisons to measurements validate the effectiveness of the developed algorithm and show that it is particularly suited for dealing with metallic gratings in the infrared region.