gebhart/patrepeval huggingface dataset:
Controlling ground-state rotational dynamics of molecules by shaped femtosecond laser pulses (2004)

We report controlled excitation of ground-state rotational wave packet by pulse-shaping technique. The experiment is conducted in nitrogen $({\mathrm{N}}_{2})$ at room temperature and atmospheric pressure. A femtosecond laser pulse produces rotational coherences in the vibronic ground state of ${\mathrm{N}}_{2}$ through an impulsive Raman process. The laser pulse is tailored using a spatial light modulator producing spectral phase modulation. Periodic phase steps are applied in order to control the excitation of specific rotational Raman transitions. The outcome is the modification of the relative excitation between odd and even rotational states which allows the control of the symmetry and rephasing period of the wave packet.
IOP-Lowering Effect of ONO-9054, A Novel Dual Agonist of Prostanoid EP3 and FP Receptors, in Monkeys (2015)

A more profound and longer-lasting reduction in IOP in normotensive monkeys can be observed with ONO-9054, which simultaneously stimulates both EP3 and FP receptors, compared with prostaglandin analogs.
Endothelin Receptor Blockade in Patients with Diabetic Nephropathy (2011)

Diabetic nephropathy constitutes a major health care challenge. In the current review we summarize the rationale and preclinical data that suggest involvement of the endothelin (ET) system in the pathogenesis of this complication of diabetes. Early clinical studies suggest that blockade of the ET system indeed may have renoprotective effects, as reflected by a strong reduction in albumin excretion. A major challenge in the clinical development of ET receptor blockades for this indication will be to tease out the protective effects from potential off-target effects. Of particular concern is the edema formation during ET receptor blockade.
ChemInform Abstract: Heparin—Protein Interactions (2002)

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.
Dynamic taxonomies: a model for large information bases (2000)

A novel taxonomic model for structuring and accessing large heterogeneous information bases is presented. The model is designed to simplify both classification and access by computer-illiterate people. It defines simple and intuitive operations to access large information bases at the conceptual level and at different levels of abstraction, in a totally assisted way, through a simple, yet effective visual interface. The model can also be used to summarize result sets computed by other query methods, such as information retrieval, shape retrieval, etc., and to provide user maps for complex hypermedia networks. The experience gained by applying this model to commercial applications is reported.
Pathobiology of H5N2 Mexican Avian Influenza Virus Infections of Chickens (1997)

To determine the association between specific structural changes in the hemagglutinin gene and pathogenicity of avian influenza viruses (AIVs), groups of 4-week-old White Plymouth Rock chickens were inoculated intravenously or intranasally with AIVs of varying pathogenicities isolated from chickens in central Mexico during 1994-1995. Mildly pathogenic (MP) viruses had a common hemagglutinin-connecting peptide sequence of Pro-Gln-Arg-Glu-Thr-Arg decreases Gly and had restricted capability for replication and production of lesions in tissues. The principle targets for virus replication or lesion production were the lungs, lymphoid organs, and visceral organs containing epithelial cells, such as kidney and pancreas. Death was associated with respiratory and/or renal failure. By contrast, highly pathogenic (HP) AIVs had one substitution and the addition of two basic amino acids in the hemagglutinin connecting peptide, for a sequence of Pro-Gln-Arg-Lys-Arg-Lys-Thr-Arg decreases Gly. The HP AIVs were pantropic in virus replication and lesion production ability. However, the most severe histologic lesions were produced in the brain, heart, adrenal glands, and pancreas, and failure of multiple critical organs was responsible for disease pathogenesis and death. No differences in lesion distribution patterns or in sites of AIV replication were evident to explain the variation in mortality rates for different HP AIVs, but HP AIVs that produced the highest mortality rates had more severe necrosis in heart and pancreas. The ability of individual HP AIVs to produce low or high mortality rates could not be explained by changes in sequence of the hemagglutinin-connecting peptide alone, but probably required the addition of other undetermined genomic changes.
Ox-40 Ligand: A Potent Costimulatory Molecule for Sustaining Primary CD4 T Cell Responses (1998)

Ox-40 and Ox-40 ligand (Ox-40L) are thought to be involved in T cell-APC interactions. However, their exact role in T cell responses is undefined. Using fibroblast transfectants expressing Ox-40L and/or B7-1, and CD4 cells from TCR transgenic mice, we investigated the effect of Ox-40 signaling on primary responses to the Ag pigeon cytochrome c. Ox-40 expression on naive CD4 cells peaked 2 to 3 days after activation, and was lost by 4 to 5 days. APCs with Ox-40L promoted partial activation of naive T cells with some IL-2 secretion, but were unable to enhance proliferation, unlike those with B7-1. APCs coexpressing Ox-40L with B7-1 induced large quantities of IL-2 and promoted proliferative responses that persisted for several days. Effector cells taken 5 days after naive T cell activation reexpressed Ox-40 within 4 h and responded strongly to APCs expressing Ox-40L, whereas B7-1 had little effect. Synergy was also seen between Ox-40L and B7-1, with primarily IL-2 being elevated, although IL-4 and IL-5 were also up-regulated. The most striking action was on effector T cell proliferation, which continued at high levels for up to 4 days, with little proliferation evident at this time in the absence of Ox-40 signals. These data suggest that Ox-40/Ox-40L interactions act after initial activation events to prolong clonal expansion and enhance effector cytokine secretion, and may be involved in promoting long-lived primary CD4 responses.
Sixteen New Records of Ascomycetes from Crop Field Soil in Korea (2016)

The present study reports 16 species of Ascomycota that were previously unknown in Korea, namely Acremonium cellulolyticus (KNU14-25), Acremonium zonatum (KNU14-15), Chaetomium madrasense (KNU14-9), Cladosporium silenes (KNU 14-18-1), Humicolopsis cephalosporioides (KNU15-3), Leptosphaerulina chartarum (KNU14-16), Paecilomyces marquandii (KNU14- 8), Paecilomyces tenuis (KNU14-18-2), Paraphaeosphaeria sporulosa (KNU15-2), Penicillium rubidurum (KNU14-12), Pochonia suchlasporia (KNU15-6), Sporothrix inflata (KNU15-8), Thielavia hyrcaniae (KNU15-1), Thielavia terricola (KNU14-23-1), Xylogone sphaerospora (KNU15-7), and Zopfiella longicaudata (KNU15-5). These fungal species were isolated from soil samples collected from various regions of Korea and identified based on their morphological characteristics and rDNA internal transcribed spacer sequence data. Full descriptions and illustrations for each species are provided.
Mutational analysis of influenza virus promoter elements in vivo (1995)

RNA polymerase I transcription in vivo in transiently DNA-transfected cells has been used to express influenza virus vRNA molecules coding for chloramphenicol acetyltransferase (CAT) in an antisense orientation. Influenza virus superinfection provided viral RNA polymerase and other proteins required for transcriptional conversion of minus-strand vRNA into plus-strand viral mRNA molecules expressing CAT activity. This system has been used for analysis of the vRNA sequences which cooperatively constitute the vRNA promoter structure via nucleotide exchanges as well as deletions and insertions of both terminal segments. Several mutants caused greatly enhanced expression over wild-type levels, which was transmitted during serial passage of progeny virus. The data obtained for the mutations in various promoter elements support a model implicating double-stranded vRNA promoter structures in binding of viral polymerase, and in consecutive steps during initiation of RNA synthesis.
Review of the clinical experience with 5-azacytidine and 5-aza-2'-deoxycytidine in solid tumors. (2002)

In recent years the importance of epigenetic changes in carcinogenesis has been unfolding. It is now clear that the fifth base of the genome, methylcytosine, plays a critical role in the control of gene expression during normal development and carcinogenesis. Efforts to decrease methylation in neoplasias as a therapeutic strategy have been productive in hematologic malignancies but disappointing in solid tumors. The following is a review of the clinical experience with the agents 5-azacytidine and 5-aza-2'-deoxycytidine in solid malignancies and a discussion of the difficulties encountered.
Epoxomicin, a new antitumor agent of microbial origin. (1992)

An actinomycete strain No. Q996-17 produced a novel compound, epoxomicin, which exhibited in vivo antitumor activity against B16 melanoma. Structural studies indicated that it is a new member of the epoxy-beta-aminoketone group, and is closely related to eponemycin.
MycDB: an integrated mycobacterial database (1994)

As part of ongoing efforts to investigate the molecular biology of the human pathogens in the genus Mycobacterium, a customized database was developed specifically for these organisms and implemented in ACEDB database manager software. The data loaded include the IMMYC Antigen List, details of reagents available from the CDC/WHO Antibody Bank, more than 1 Mb of sequences of mycobacterial genes and proteins from public databases, the physical maps of Mycobacterium leprae and Mycobacterium tuberculosis developed at the Institut Pasteur, as well as a subset of the references found in MedLine. The ACEDB software allows both quick and intuitive access to the data and to connections between facts by a simple mouse-driven interface, as well as by more powerful query mechanisms.
Nucleotide sequence of the human N-myc gene. (1986)

Human neuroblastomas frequently display amplification and augmented expression of a gene known as N-myc because of its similarity to the protooncogene c-myc. It has therefore been proposed that N-myc is itself a protooncogene, and subsequent tests have shown that N-myc and c-myc have similar biological activities in cell culture. We have now detailed the kinship between N-myc and c-myc by determining the nucleotide sequence of human N-myc and deducing the amino acid sequence of the protein encoded by the gene. The topography of N-myc is strikingly similar to that of c-myc: both genes contain three exons of similar lengths; the coding elements of both genes are located in the second and third exons; and both genes have unusually long 5' untranslated regions in their mRNAs, with features that raise the possibility that expression of the genes may be subject to similar controls of translation. The resemblance between the proteins encoded by N-myc and c-myc sustains previous suspicions that the genes encode related functions.
Posttranscriptional Regulation of miRNAs Harboring Conserved Terminal Loops (2008)

We recently found that hnRNP A1, a protein implicated in many aspects of RNA processing, acts as an auxiliary factor for the Drosha-mediated processing of a microRNA precursor, pri-miR-18a. Here, we provide the mechanism by which hnRNP A1 regulates this event. We show that hnRNP A1 binds to the loop of pri-miR-18a and induces a relaxation at the stem, creating a more favorable cleavage site for Drosha. We found that approximately 14% of all pri-miRNAs have highly conserved loops, which we predict act as landing pads for trans-acting factors influencing miRNA processing. In agreement, we show that 2'O-methyl oligonucleotides targeting conserved loops (LooptomiRs) abolish miRNA processing in vitro. Furthermore, we present evidence to support an essential role of conserved loops for pri-miRNA processing. Altogether, these data suggest the existence of auxiliary factors for the processing of specific miRNAs, revealing an additional level of complexity for the regulation of miRNA biogenesis.
Enzymatic reaction with unnatural substrates: DNA photolyase ( Escherichia coli ) recognizes and reverses thymine [2+2] dimers in the DNA strand of a DNA/PNA hybrid duplex (1998)

Peptide nucleic acids (PNA) are mimics with normal bases connected to a pseudopeptide chain that obey Watson-Crick rules to form stable duplexes with itself and natural nucleic acids. This has focused attention on PNA as therapeutic or diagnostic reagents. Duplexes formed with PNA mirror some but not all properties of DNA. One fascinating aspect of PNA biochemistry is their reaction with enzymes. Here we show an enzyme reaction that operates effectively on a PNA/DNA hybrid duplex. A DNA oligonucleotide containing a cis, syn-thymine [2+2] dimer forms a stable duplex with PNA. The hybrid duplex is recognized by photolyase, and irradiation of the complex leads to the repair of the thymine dimer. This finding provides insight into the enzyme mechanism and provides a means for the selective repair of thymine photodimers.
Targeting specific HATs for neurodegenerative disease treatment: translating basic biology to therapeutic possibilities (2013)

Dynamic epigenetic regulation of neurons is emerging as a fundamental mechanism by which neurons adapt their transcriptional responses to specific developmental and environmental cues. While defects within the neural epigenome have traditionally been studied in the context of early developmental and heritable cognitive disorders, recent studies point to aberrant histone acetylation status as a key mechanism underlying acquired inappropriate alterations of genome structure and function in post-mitotic neurons during the aging process. Indeed, it is becoming increasingly evident that chromatin acetylation status can be impaired during the lifetime of neurons through mechanisms related to loss of function of histone acetyltransferase (HAT) activity. Several HATs have been shown to participate in vital neuronal functions such as regulation of neuronal plasticity and memory formation. As such, dysregulation of such HATs has been implicated in the pathogenesis associated with age-associated neurodegenerative diseases and cognitive decline. In order to counteract the loss of HAT function in neurodegenerative diseases, the current therapeutic strategies involve the use of small molecules called histone deacetylase (HDAC) inhibitors that antagonize HDAC activity and thus enhance acetylation levels. Although this strategy has displayed promising therapeutic effects, currently used HDAC inhibitors lack target specificity, raising concerns about their applicability. With rapidly evolving literature on HATs and their respective functions in mediating neuronal survival and higher order brain function such as learning and memory, modulating the function of specific HATs holds new promises as a therapeutic tool in neurodegenerative diseases. In this review, we focus on the recent progress in research regarding epigenetic histone acetylation mechanisms underlying neuronal activity and cognitive function. We discuss the current understanding of specific HDACs and HATs in neurodegenerative diseases and the future promising prospects of using specific HAT based therapeutic approaches.
Epidermal growth factor receptor expression in stage II-III colon carcinoma: A preliminary study (2004)

9718 Background: Epidermal growth factor receptor (EGFR) is a protoncogen that is found overexpressed in colorectal carcinomas (CRC) and it correlates with a worse prognosis. The aim was to describe EGFR overexpression patterns in non-metastatic CRC and to correlate these data with follow-up. Methods: We analyzed a series of 56 CRC. Inclusion criteria were: a) resected primary adenocarcinoma; b) curative surgery; c) pT3 N0–2 M0 without progression during the first 6 months post surgery; d) minimum follow-up over 3 years. EGFR overexpression was analyzed by immunohistochemistry (IHC) using the Dako PharmaDx kit (Glostrup, Denmark). As positive control the Dako slides and a bloc cell of A431-AAM cells were used. Presence of cytoplasmic and membrane patterns (intensity 1(+), 2(+) and 3(+)) were evaluated as well as the percentage of positive cells. Statistical analysis: association between qualitative variables was analyzed by Fisher's exact test. Disease-free and overall survival distributions were estimated by the Kaplan-Meier method and were analyzed with the log rank test. All P values are from two-sided statistical tests. Results: Characteristics of the patients (pts) were as follows: mean age: 68,4 years (range: 28–91); sex: 24 male and 32 female; location: 19 right colon and 37 left colon; follow-up: 44 pts alive without disease (78,5%), 9 died of disease (16,5%) and 3 died of other causes (5%). 10 pts had metastasis in the follow-up. IHC: Forty-two cases were positive (75%) and were classified as follows: 17 with >50% of positive cells (30%), 7 with 25–50% of positive cells (13%) and 18 cases with < 25% of positive cells. Patterns of staining were cytoplasmic predominance in 27 cases (48%) and 15 with membrane predominance (27%): 4 with intensity 1(+), 9 with 2(+) and 2 with 3(+). Only those patients with tumors harboring membrane positivity 2(+) and 3(+) had more probability to present metastasis (p= 0.067). Conclusions: EGFR overexpression evaluated as a membrane pattern with 2(+) and 3(+) intensity is related with metastatic development in colon carcinoma. Suported by a grant of C.I.R. Hospital de Sabadell. Consorci Sanitari Parc Taulí. Sabadell. Spain No significant financial relationships to disclose.
Insulating gate III-N heterostructure field-effect transistors for high-power microwave and switching applications (2003)

Describes the properties of novel III-N-based insulating gate heterostructure field-effect transistors (HFETs). For the gate isolation, these devices use either SiO/sub 2/ layer (in metal-oxide-semiconductor HFET (MOSHFET) structures) or Si/sub 3/N/sub 4/ layer (in metal-insulator-semiconductor HFET structures). These insulating gate HFETs have the gate-leakage currents 4-6 orders of magnitude lower than HFETs, even at elevated temperatures up to 300/spl deg/C. A double-heterostructure MOSHFET with SiO/sub 2/ gate isolation exhibits current collapse-free performance with extremely low gate-leakage current. Insulating gate devices, including large periphery multigate structures, demonstrate high-power stable operation and might find applications in high-performance power amplifiers and microwave and high-power switches with operating temperatures up to 300/spl deg/C or even higher.
Integrin-mediated cell adhesion activates mitogen-activated protein kinases. (1994)

Integrins can function as signal-transducing receptors capable of modulating cell growth and gene expression (Juliano, R. L., and Haskill, S. (1993) J. Cell Biol. 120, 577-585; Hynes, R. O. (1992) Cell 69, 11-25). An early event in integrin signaling in fibroblasts and other cells involves activation of pp125FAK, a cytoplasmic tyrosine kinase (Hanks, S. K., Calalb, M. B., Harper, M. C., and Patel, S. K. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 8487-8491; Schaller, M. D., Borgman, C. A., Cobb, B. S., Vines, R. R., Reynolds, A. B., and Parsons, J. T. (1992) Proc. Natl. Acad. Sci. U. S. A. 89, 5192-5196). Here we report a novel aspect of integrin-mediated signal transduction. We demonstrate that adhesion of cells to substrata coated with extracellular matrix proteins, or with a synthetic peptide containing the RGD sequence, can cause activation of mitogen-activated protein (MAP) kinases in 3T3 or REF52 fibroblasts. Activation of MAP kinases seems to depend on integrin engagement rather than simply on cell attachment. Thus, MAP kinases are activated when cells adhere to substrata coated with the integrin ligands fibronectin or laminin, but not when cells adhere to poly-D-lysine, a nonspecific adhesion-promoting polypeptide. Treatment of cells with cytochalasin D, an inhibitor of actin microfilament assembly, almost completely blocks adhesion-induced MAP kinase activation, indicating a critical role for the cytoskeleton. In REF52 cells, we have observed that activation of MAP kinases is accompanied by redistribution of the protein to the nucleus, suggesting that the activated kinases may impinge on factors regulating gene expression. Thus, integrin-mediated cell adhesion seems a sufficient stimulus to cause activation and nuclear translocation of MAP kinases. This may have important implications for the regulation of cell growth and differentiation by the extracellular matrix.
TTA codons in some genes prevent their expression in a class of developmental, antibiotic-negative, Streptomyces mutants. (1991)

In Streptomyces coelicolor A3(2) and the related species Streptomyces lividans 66, aerial mycelium formation and antibiotic production are blocked by mutations in bldA, which specifies a tRNA(Leu)-like gene product which would recognize the UUA codon. Here we show that phenotypic expression of three disparate genes (carB, lacZ, and ampC) containing TTA codons depends strongly on bldA. Site-directed mutagenesis of carB, changing its two TTA codons to CTC (leucine) codons, resulted in bldA-independent expression; hence the bldA product is the principal tRNA for the UUA codon. Two other genes (hyg and aad) containing TTA codons show a medium-dependent reduction in phenotypic expression (hygromycin resistance and spectinomycin resistance, respectively) in bldA mutants. For hyg, evidence is presented that the UUA codon is probably being translated by a tRNA with an imperfectly matched anticodon, giving very low levels of gene product but relatively high resistance to hygromycin. It is proposed that TTA codons may be generally absent from genes expressed during vegetative growth and from the structural genes for differentiation and antibiotic production but present in some regulatory and resistance genes associated with the latter processes. The codon may therefore play a role in developmental regulation.
Studies on the Chemical Constituents of the Bulbs of Lilium mackliniae. (1991)

Chemical study on the bulbs of Lilium (L.) mackliniae has led to the isolation of a total of 27 compounds, including nine new phenolics. The structures of the new compounds have been shown by spectral analysis and chemical degradation to be 4, 4'-di-O-acetyl-3, 6'-di-O-feruloylsucrose, 3, 4'-di-O-p-coumaroylsucrose, 3, 6'-di-O-p-coumaroylsucrose, 2'-O-acetyl-3, 4'-di-O-p-coumaroylsucrose, 3'-O-acetyl-3, 4'-di-O-p-coumaroylsucrose, (2S)-1-O-p-methoxycinnamoyl-2-O-β-D-glucopyranosylglycerol (methylregaloside D), (2S)-1-O-cinnamoyl-2-O-β-D-glucopyranosyl (regaloside J), (2S)-l-O-caffeoyl-2-Oβ-D-glucopyranosylglycerol (regaloside K) and (2R)-1-O-β-D-glucopyranosyl-2-O-caffeoylgly-cerol (regaloside L). In addition, several previously reported phenolic glycosides, steroidal saponins and steroidal alkaloid have been isolated and identified. The presence of the steroidal alkaloid supported the idea that L. mackliniae is taxonomically related to the genus Fritillaria.