gebhart/patrepeval huggingface dataset:
Structural and Regulatory Characterization of the Placental Epigenome at Its Maternal Interface (2011)

Epigenetics can be loosely defined as the study of cellular "traits" that influence biological phenotype in a fashion that is not dependent on the underlying primary DNA sequence. One setting in which epigenetics is likely to have a profound influence on biological phenotype is during intrauterine development. In this context there is a defined and critical window during which balanced homeostasis is essential for normal fetal growth and development. We have carried out a detailed structural and functional analysis of the placental epigenome at its maternal interface. Specifically, we performed genome wide analysis of DNA methylation in samples of chorionic villus (CVS) and maternal blood cells (MBC) using both commercially available and custom designed microarrays. We then compared these data with genome wide transcription data for the same tissues. In addition to the discovery that CVS genomes are significantly more hypomethylated than their MBC counterparts, we identified numerous tissue-specific differentially methylated regions (T-DMRs). We further discovered that these T-DMRs are clustered spatially along the genome and are enriched for genes with tissue-specific biological functions. We identified unique patterns of DNA methylation associated with distinct genomic structures such as gene bodies, promoters and CpG islands and identified both direct and inverse relationships between DNA methylation levels and gene expression levels in gene bodies and promoters respectively. Furthermore, we found that these relationships were significantly associated with CpG content. We conclude that the early gestational placental DNA methylome is highly organized and is significantly and globally associated with transcription. These data provide a unique insight into the structural and regulatory characteristics of the placental epigenome at its maternal interface and will drive future analyses of the role of placental dysfunction in gestational disease.
Steel factor and c-kit regulate cell-matrix adhesion (1994)

Steel (SI) and white spotting (W) loci encode steel factor (c-kit ligand) and the c-kit tyrosine kinase receptor, respectively. Mutations at these loci affect migration and differentiation of primordial germ cells, neural crest-derived melanoblasts, and hematopoietic cells. In these processes, cell adhesion molecules are hypothesized to be crucial. We have examined the role of steel factor and c-kit in cell- extracellular matrix adhesion using bone marrow-derived mast cells as a model system. Steel factor stimulates mast cells to bind to fibronectin and, to a lesser extent, to vitronectin, whereas interleukin-3 and interleukin-4, which are also mast cell growth factors, do not. Activation of adhesiveness is transient, occurs at concentrations of steel factor 100-fold lower than required for growth stimulation, and requires the integrin VLA-5. Mast cells from c-kit mutant mice adhere to fibronectin on stimulation with phorbol 12-myristate 13-acetate (PMA), but not on stimulation with steel factor, indicating that stimulation of integrin adhesiveness requires activation of the c-kit protein tyrosine kinase. By contrast, c-kit mutant and wild-type mast cells adhere equally well to COS cells expressing membrane-anchored steel factor, showing that the kinase activity of c-kit is not required for adhesion directly mediated by c-kit. Our findings suggest that regulation of adhesion is an important biologic function of steel factor.
Dynamic model based algorithms for screening and genotyping over 100K SNPs on oligonucleotide microarrays (2005)

The DM algorithm is available in Affymetrix's Genotyping Tools software package and in Affymetrix's GDAS software package. See http://www.affymetrix.com for further information. 10 K and 100 K mapping array data are available on the Affymetrix website.
Inhibitory Effect of Natural Carotenoids on Epstein-Barr Virus Activation Activity of a Tumor Promoter in Raji Cells. A Screening Study for Anti-tumor Promoters. (1995)

As a screening study for anti-tumor promoters, 51 carotenoids with diverse structures were examined for their inhibitory effects on the Epstein-Barr virus activation activity of 12-O-tetradecanoylphorbol-13-acetate (TPA) in Raji cells. The results showed that most of the carotenoids exhibited inhibitory activity, and in general, no cytotoxicity on Raji cells was observed in the assay. Among the carotenoids, beta-cryptoxanthin, lutein, and lactucaxanthin showed the strongest inhibitory activity, superior to the well known anti-tumor promoter, beta-carotene. Heteroxanthin, peridinin, and halocynthiaxanthin showed cytotoxicity at the high concentration (1000 molar ratio per TPA), but indicated a strong inhibitory effect at the lower concentrations, which were only weakly toxic (500 and 100 molar ratios). Based on these results, the essential moiety for the activity of carotenoids was considered to be the 3-hydroxy-epsilon-end group.
ChemInform Abstract: A Facile Method for Synthesis of Calix[4]crowns Containing Nitrogen and Sulfur Atoms. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New Hypoglycemic Constituents in "Gymnemic Acid" from Gymnema sylvestre. (1996)

Investigation of hypoglycemic activity of major saponin constituents from "gymnemic acid", a crude saponin fraction of G. sylvestre, exposed not only two new saponins, gymnemosides a (1) and b (2), but also gymnemoside b and gymnemic acid V (7) as active principles. Furthermore, an acetyl group linked 16- or 22-hydroxy group in 1 and 2 was found to migrate easily to primary 28-hydroxyl group, while acyl migration from 28-hydroxy group in 3 was little observed.
Low-power polygon renderer for computer graphics (2002)

Polygon rasterization is the most computational and memory intense stage in rendering synthesized computer images. The authors present a low-power, real-time hardware implementation for this task. Rasterization of two-dimensional Gouraud-shaded polygons at 90,000 polygons/sec is achievable with computational power consumption of about 12 mW at 1.5 V operation, using an array configuration of 16 render engines for a 512 /spl times/ 512-pixel frame. A transmission format for wireless implementations is proposed with a typical bandwidth of 4 MHz. This screen and format configurable design has potential applications in portable devices, wireless communication and head-mounted display for virtual reality systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Defined Nongrowth Media for Stage II Development of Competence in Haemophilus influenzae (1970)

The composition of a defined nongrowth medium used in stage II development of competence of Haemophilus influenzae affects the course of this development. The development of competence in two nongrowth media, M-IV and M-V, is rapid, logarithmic, and independent of the cell concentration. This last property indicates that there is probably no transfer of a competence factor from competent to noncompetent cells, in contrast to results reported for other organisms. Levels of competence reached in these completely defined media are such that 1 to 5% of the cells are transformed in the presence of an excess of marked deoxyribonucleic acid. The method of evaluating competence, which depends on the frequency of multiple independent transformations, has been reexamined. This and other methods are compared on samples taken from a culture during development of competence.
Targeted Disruption of Migration Inhibitory Factor Gene Reveals Its Critical Role in Sepsis (1999)

To study the biologic role of migration inhibitory factor (MIF), a pleiotropic cytokine, we generated a mouse strain lacking MIF by gene targeting in embryonic stem cells. Analysis of the role of MIF during sepsis showed that MIF-/- mice were resistant to the lethal effects of high dose bacterial lipopolysaccharide (LPS), or Staphylococcus aureus enterotoxin B (SEB) with D-galactosamine and had lower plasma levels of tumor necrosis factor alpha (TNF-alpha) than did wild-type mice, but normal levels of interleukin (IL)-6 and IL-10. When stimulated with LPS and interferon gamma, macrophages from MIF-/- mice showed diminished production of TNF-alpha, normal IL-6 and IL-12, and increased production of nitric oxide. MIF-/- animals cleared gram-negative bacteria Pseudomonas aeruginosa instilled into the trachea better than did wild-type mice and had diminished neutrophil accumulation in their bronchoalveolar fluid compared to the wild-type mice. Thioglycollate elicited peritoneal exudates in uninfected MIF-/- mice, but showed normal neutrophil accumulation. Finally, the findings of enhanced resistance to P. aeruginosa and resistance to endotoxin-induced lethal shock suggest that the counteraction or neutralization of MIF may serve as an adjunct therapy in sepsis.
Both the basal and inducible transcription of the tyrosine hydroxylase gene are dependent upon a cAMP response element (1993)

The cAMP response element (CRE) mediates cAMP responsiveness in many eukaryotic genes (Roesler, W. J., Vandenbark, G. R., and Hansen, R. W. (1988) J. Biol. Chem. 263, 9063-9066). The tyrosine hydroxylase gene (TH) contains a single copy of a consensus CRE at -45 to -38 base pair (bp) upstream of the transcription initiation site. Deletional and mutational analyses of the upstream 2400-base pair region of the rat TH gene using transient transfection assay demonstrated that the CRE was essential for both cAMP-mediated induction and basal transcription of the TH gene. Another domain between -365 and -151 bp, containing the AP1 site, contributed to transcription to a smaller degree. Thus, the CRE appears to play an important dual role as a basal promoter element and an inducible enhancer for TH transcription. Interactions between the DNA binding factors in nuclear extract and CRE-containing oligonucleotides were investigated by gel retardation and competition assays. Oligonucleotides corresponding to the CRE regions of the TH or somatostatin gene gave rise to a pair of distinct protein-DNA complexes with identical mobilities in the gel retardation assay, suggesting that similar nuclear factor(s) might bind to the CREs of the TH and somatostatin genes. This study emphasizes a fundamental role of the CRE in transcriptional activation of the TH gene in catecholaminergic cells.
Hitting bacteria at the heart of the central dogma: sequence-specific inhibition (2007)

An important objective in developing new drugs is the achievement of high specificity to maximize curing effect and minimize side-effects, and high specificity is an integral part of the antisense approach. The antisense techniques have been extensively developed from the application of simple long, regular antisense RNA (asRNA) molecules to highly modified versions conferring resistance to nucleases, stability of hybrid formation and other beneficial characteristics, though still preserving the specificity of the original nucleic acids. These new and improved second- and third-generation antisense molecules have shown promising results. The first antisense drug has been approved and more are in clinical trials. However, these antisense drugs are mainly designed for the treatment of different human cancers and other human diseases. Applying antisense gene silencing and exploiting RNA interference (RNAi) are highly developed approaches in many eukaryotic systems. But in bacteria RNAi is absent, and gene silencing by antisense compounds is not nearly as well developed, despite its great potential and the intriguing possibility of applying antisense molecules in the fight against multiresistant bacteria. Recent breakthrough and current status on the development of antisense gene silencing in bacteria including especially phosphorothioate oligonucleotides (PS-ODNs), peptide nucleic acids (PNAs) and phosphorodiamidate morpholino oligomers (PMOs) will be presented in this review.
The P2Y12 Antagonists, 2MeSAMP and Cangrelor, Inhibit Platelet Activation through P2Y12/Gi-Dependent Mechanism (2012)

These data together demonstrate that 2MeSAMP and Cangrelor inhibit platelet function through the P2Y(12)-dependent mechanism both in vitro and in vivo.
Visible Light-Promoted Metal-Free C–H Activation: Diarylketone-Catalyzed Selective Benzylic Mono- and Difluorination (2013)

We report herein an operationally simple method for the direct conversion of benzylic C-H groups to C-F. We show that visible light can activate diarylketones to abstract a benzylic hydrogen atom selectively. Adding a fluorine radical donor yields the benzylic fluoride and regenerates the catalyst. The selective formation of mono- and difluorination products can be achieved by catalyst control. 9-Fluorenone catalyzes benzylic C-H monofluorination, while xanthone catalyzes benzylic C-H difluorination. The scope and efficiency of this new C-H fluorination method are significantly better than those of the existing methods. This is also the first report of selective C-H gem-difluorination.
Human cytomegalovirus virion protein complex required for epithelial and endothelial cell tropism (2005)

Human cytomegalovirus replicates in many different cell types, including epithelial cells, endothelial cells, and fibroblasts. However, laboratory strains of the virus, many of which were developed as attenuated vaccine candidates by serial passage in fibroblasts, have lost the ability to infect epithelial and endothelial cells. Their growth is restricted primarily to fibroblasts, due to mutations in the UL131-UL128 locus. We now demonstrate that two products of this locus, pUL130 and pUL128, form a complex with gH and gL, but not gO. The AD169 laboratory strain, which lacks a functional UL131 protein, produces virions containing only the gH-gL-gO complex. An epithelial and endothelial cell tropic AD169 variant in which the UL131 ORF has been repaired, termed BADrUL131, produces virions that carry both gH-gL-gO and gH-gL-pUL128-pUL130 complexes. Antibodies against pUL130 and pUL128 block infection of epithelial and endothelial cells by BADrUL131 and the fusion-inducing factor X clinical human cytomegalovirus isolate but do not affect the efficiency with which fibroblasts are infected.
Development of Real-Time Reverse Transcriptase PCR Assays To Detect and Serotype Dengue Viruses (2006)

Serotyping dengue virus (DENV) from suspect human specimens is crucial for developing sound epidemiological control measurements early in the transmission season and for effective patient management. We modified DENV consensus D1 (mD1) and serotype-specific TS2 (mTS2) and redesigned serotype-specific TS1 (rTS1) and TS4 (rTS4) as described previously in the conventional capsid and premembrane gene (C-prM) protocol (R. S. Lanciotti, C. H. Calisher, D. J. Gubler, G.-J. Chang, A. V. Vorndam, J. Clin. Microbiol. 30:545-551, 1992). In addition, we designed two new sets of amplimers and probes, located at nonstructural protein 5 (NS5) and the 3' noncoding region (3'NC) of DENV. The NS5 protocol utilizes two flaviviral consensus outer amplimers (mFU1 and CFD2) and four dengue virus serotype-specific TaqMan fluorogenic probes. The 3'NC protocol uses two DENV consensus amplimers, DC10418 and CDC10564. The conventional gel-based, heminested detection method was adapted for the C-prM protocol for detecting and serotyping dengue viruses. In addition, we developed the real-time SYBR green I and postamplification melting temperature curve analysis for the mD1/TS and 3'NC protocols using identical amplification conditions. The NS5 amplimer/probe set was formulated as a one-tube, multiplex, real-time reverse transcriptase PCR for serotype identification. Three sets of amplimers and probes were verified for their specificity in tests with yellow fever, Japanese encephalitis, St. Louis encephalitis, and West Nile viruses; optimized against 109 DENV strains; and validated for detection of the virus in sera from two different panels of acute-phase human dengue serum specimens and one panel of virus isolates from dengue patients' serum specimens. Clinical evaluation by two separate laboratories indicated that the C-prM was more sensitive (100%) than the NS5 (91%) or the 3'NC (91%) protocol.
The impact of psoriasis on quality of life: results of a 1998 National Psoriasis Foundation patient-membership survey. (2001)

The unprecedented response to the survey provides compelling evidence that individuals with psoriasis believe that the disease has a profound emotional and social as well as physical impact on their quality of life. Many patients with psoriasis, particularly those with severe disease, are frustrated with the management of their disease and by the perceived ineffectiveness of their therapies. Physicians may need to improve communication with their patients and should reevaluate their management of psoriasis.
Efficient Elimination of Fluorescence Background from Raman Spectra Collected in a Liquid Core Optical Fiber (2000)

Liquid core optical fiber (LCOF) waveguides have been used to enhance the Raman sensitivity of liquid sample measurements by more than two orders of magnitude. These waveguides can also enhance photobleaching of fluorescence in transparent liquids. We report the reduction of fluorescence intensity by more than two orders of magnitude by rapid photobleaching of solutions illuminated in an LCOF. The same solutions showed no detectable photobleaching when illuminated in a cuvette. The observed rates of photobleaching are in good quantitative agreement with theory.
Autoclave performance and practitioner knowledge of autoclave use: a survey of selected UK practices. (1998)

Further education of practitioners may be necessary to enhance their awareness of the need for routine checking of autoclave effectiveness.
A New Synthesis of 2-Aryl-2H-Pyrazino[2,1-B]quinazolin-3,6[1H,4H)-diones (1991)

Abstract A new synthesis of 2-aryl-2H-pyrazino [2,1-b] quinazolin-3,6(1H, 4H)-diones starting from 2-chloromethylquinazolin-4(3H)-one is described.
Electron Spin Resonance of Doped Glow‐Discharge Amorphous Silicon (1981)

Abstract The influence of doping on the ESR spectra of glow‐discharge a‐Si:H is systematically investigated in the X‐ and Q‐band for phosphorus‐ and boron‐doped samples up to a high doping level. Whereas for undoped and moderately doped material the well‐known line with g = 2.0055 is observed, for highly boron‐doped samples the broader line at g = 2.01 predominates as does the g = 2.0043 line in the case of high phosphorus doping. The linewidth of the resonance at g = 2.01, due to holes in localized valence band tail states, is mainly determined by a g ‐value spectrum. With increasing boron doping the width of this spectrum decreases and its centre of gravity shifts to smaller g ‐values. The narrower line with g = 2.0043, due to electrons in localized conduction band tail states, however, broadens with increasing phosphorus doping due to hyperfine interaction with the phosphorus nuclei. From these features it is concluded that the wave function of holes in valence band tail states is much more localized than that of electrons in the conduction band tail. At the same high doping level the spin density for the hole resonance at g = 2.01 is a factor of about 10 2 larger than for the electron line with g = 2.0043. This difference is explained by a different correlation energy U . Besides these lines a relatively weak resonance at g = 2.0026 is found for boron‐doped samples and for phosphorus‐doped material as well. Measurements on compensated samples indicate that by doping dangling bonds are created.
Self-Trapping of Electrons at Surfaces (1998)

Electrons in solid materials can deform the surrounding atomic lattice in a way that can trap the electron. These excitations are called polarons and are important in the physical properties of conducting polymers and superconductors. In his commentary, Hi?½fer discusses results reported in the same issue by
 Ge
 et al . in which ultrafast lasers were used to probe the behavior of these polarons in a layer of alkane on top of a metal substrate. The experiments have revealed the dynamics of electrons at surfaces with unprecedented detail, and the technique may have applications in fields such as photosynthesis research.
Cytokinin Regulation of Flower and Pod Set in Soybeans (Glycine max(L.) Merr.) (2001)

Exogenous application of cytokinin to raceme tissues of soybean ( Glycine max (L.) Merr.) has been shown to stimulate flower production and to prevent flower abortion. The effects of these hormone applications have been ascertained for treated tissues, but the effects of cytokinins on total seed yields in treated plants have not been evaluated. Our objectives were to examine the effects of systemic cytokinin applications on soybean yields using an experimental line of soybeans, SD-87001, that has been shown to be highly sensitive to exogenous cytokinin application. Soybeans were grown hydroponically or in pots in the greenhouse, and 6-benzylaminopurine (BA) was introduced into the xylem stream through a cotton wick for 2 weeks during anthesis. After the plants had matured, the number of pods, seeds per pod, and the total seed weight per plant were measured. In the greenhouse, application of 3.4 × 10 −7 moles of BA resulted in a 79% increase in seed yield compared with controls. Results of field trials showed much greater variability within treatments, with consistent, but non-significant increases in seed number and total yields of about 3%. Data suggest that cytokinin levels play a significant role in determining total yield in soybeans, and that increasing cytokinin concentrations in certain environments may result in increased total seed production. Copyright 2001 Annals of Botany Company
Expression of the Candida albicans Gene ALS1 in Saccharomyces cerevisiae Induces Adherence to Endothelial and Epithelial Cells (1998)

To identify genes encoding adhesins that mediate the binding of Candida albicans to endothelial cells, a genomic library from this organism was constructed and used to transform Saccharomyces cerevisiae. These transformed organisms were screened for adherence to endothelial cells, and a highly adherent clone was identified. The adherence of this clone to endothelial cells was over 100-fold greater than that of control S. cerevisiae transformed with the empty plasmid. This clone also exhibited enhanced adherence to epithelial cells. The C. albicans gene contained within this clone was found to be ALS1. These results indicate that ALS1 may encode a candidal adhesin.
Wide Field Of View Varifocal Near-Eye Display Using See-Through Deformable Membrane Mirrors (2017)

Accommodative depth cues, a wide field of view, and ever-higher resolutions all present major hardware design challenges for near-eye displays. Optimizing a design to overcome one of these challenges typically leads to a trade-off in the others. We tackle this problem by introducing an all-in-one solution - a new wide field of view, gaze-tracked near-eye display for augmented reality applications. The key component of our solution is the use of a single see-through, varifocal deformable membrane mirror for each eye reflecting a display. They are controlled by airtight cavities and change the effective focal power to present a virtual image at a target depth plane which is determined by the gaze tracker. The benefits of using the membranes include wide field of view (100° diagonal) and fast depth switching (from 20 cm to infinity within 300 ms). Our subjective experiment verifies the prototype and demonstrates its potential benefits for near-eye see-through displays.