gebhart/patrepeval huggingface dataset:
Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies (2015)

MicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNAs' Target Sites (poly-miRTS)-centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)-, and femoral neck (FN)-bone mineral density (BMD). In stage I, 41,102 poly-miRTSs were meta-analyzed in 7 cohorts with a genome-wide significance (GWS) α=0.05/41,102=1.22×10. By applying α=5×10 (suggestive significance), 11 poly-miRTSs were selected, with FGFRL1 rs4647940 and PRR5 rs3213550 as top signals for FN-BMD (P-value=7.67×10 and 1.58×10) in gender-combined sample. In stage II in silico replication (two cohorts), FGFRL1 rs4647940 was the only signal marginally replicated for FN-BMD (P-value=5.08×10) at α=0.10/11=9.09×10. PRR5 rs3213550 was also selected based on biological significance. In stage III de novo genotyping replication (two cohorts), FGFRL1 rs4647940 was the only signal significantly replicated for FN-BMD (P-value=7.55×10) at α=0.05/2=0.025 in gender-combined sample. Aggregating three stages, FGFRL1 rs4647940 was the single stage I-discovered and stages II- and III-replicated signal attaining GWS for FN-BMD (P-value=8.87×10). Dual-luciferase reporter assays demonstrated that FGFRL1 3' untranslated region harboring rs4647940 appears to be hsa-miR-140-5p's target site. In a zebrafish microinjection experiment, dre-miR-140-5p is shown to exert a dramatic impact on craniofacial skeleton formation. Taken together, we provided functional evidence for a novel FGFRL1 poly-miRTS rs4647940 in a previously known 4p16.3 locus, and experimental and clinical genetics studies have shown both FGFRL1 and hsa-miR-140-5p are important for bone formation.
Analysis of <i>N</i> <sup>1</sup> ‐acetyl‐ <i>N</i> <sup>2</sup> ‐formyl‐5‐methoxykynuramine/ <i>N</i> <sup>1</sup> ‐acetyl‐5‐methoxy‐kynuramine formation from melatonin in mice (2010)

The interactions of melatonin, a potent endogenous antioxidant, with reactive oxygen species generate several products that include N(1)-acetyl-N(2)-formyl-5-methoxykynuramine (AFMK) and N(1)-acetyl-5-methoxy-kynuramine (AMK). The physiological or pathological significance of AFMK/AMK formation during the process of melatonin metabolism in mammals has not been clarified. Using a metabolomic approach in the current study, the AFMK/AMK pathway was thoroughly investigated both in mice and humans. Unexpectedly, AFMK and AMK were not identified in the urine of humans nor in the urine, feces or tissues (including liver, brain, and eyes) in mice under the current experimental conditions. Metabolomic analysis did identify novel metabolites of AMK, i.e. hydroxy-AMK and glucuronide-conjugated hydroxy-AMK. These two newly identified metabolites were, however, not found in the urine of humans. In addition, oxidative stress induced by acetaminophen in the mouse model did not boost AFMK/AMK formation. These data suggest that AFMK/AMK formation is not a significant pathway of melatonin disposition in mice, even under conditions of oxidative stress.
Two-color two-dimensional Fourier transform electronic spectroscopy with a pulse-shaper (2008)

We report two-color two-dimensional Fourier transform electronic spectroscopy obtained using an acousto-optic pulse-shaper in a pump-probe geometry. The two-color setup will facilitate the study of energy transfer between electronic transitions that are widely separated in energy. We demonstrate the method at visible wavelengths on the laser dye LDS750 in acetonitrile. We discuss phase-cycling and polarization schemes to optimize the signal-to-noise ratio in the pump-probe geometry. We also demonstrate that phase-cycling can be used to separate rephasing and nonrephasing signal components.
A Conceptually New Approach to DNA Sequencing Without Gel Electrophoresis (1993)

Journal Article A Conceptually New Approach to DNA Sequencing Without Gel Electrophoresis Get access Kevin Burgess, Kevin Burgess 1Department of Chemistry, Texas A & M University, College Station,TX 77843-3255 Search for other works by this author on: Oxford Academic PubMed Google Scholar Andrew Civitell0, Andrew Civitell0 2Institute of Molecular Genetics, Baylor College of Medicine,Houston TX 77030 Search for other works by this author on: Oxford Academic PubMed Google Scholar RichardA. Gibbs, RichardA. Gibbs 2Institute of Molecular Genetics, Baylor College of Medicine,Houston TX 77030 Search for other works by this author on: Oxford Academic PubMed Google Scholar MichaelL. Metzker, MichaelL. Metzker 2Institute of Molecular Genetics, Baylor College of Medicine,Houston TX 77030 Search for other works by this author on: Oxford Academic PubMed Google Scholar Ramesh Raghavachari Ramesh Raghavachari 1Department of Chemistry, Texas A & M University, College Station,TX 77843-3255 Search for other works by this author on: Oxford Academic PubMed Google Scholar Protein Engineering, Design and Selection, Volume 6, Issue Supplement, 1993, Page 111, https://doi.org/10.1093/protein/6.Supplement.111-a Published: 01 January 1993
Two different 16S rRNA genes in a mycobacterial strain (1996)

Sequencing of the gene coding for 16S rRNA (16S rDNA) is a well-established method used to identify bacteria, particularly mycobacteria. Unique sequences allow identification of a particular genus and species. If more than one 16S rDNA is present on one mycobacterial genome, their sequences are assumed to be strictly or almost identical. We have isolated a slowly growing Mycobacterium strain, "X", identified by conventional biochemical tests as Mycobacterium terrae. Identification by amplification and direct sequencing of 16S rDNA yielded ambiguous results in two variable regions, suggesting the presence of different copies of the sequenced gene. Total DNA was digested by restriction enzymes and hybridized after Southern blotting to a probe representing about two-thirds of the 16S rDNA. Two copies of 16S rDNA were identified and cloned. By sequencing, the clones were of two different types, A and B, differing in 18 positions. Oligonucleotides specific to each copy of the 16S rDNA were used to distinguish the positions of the two genes observed in the Southern blot. We conclude that Mycobacterium strain "X" has two different copies of 16S rDNA. Variations in the sequence between two copies of 16S rDNA gene have been described in archaeobacteria, but not in mycobacteria. When placed in a phylogenetic tree together with other slowly growing mycobacteria gene A shows a common root with M. terrae, whereas gene B is placed separately.
ChemInform Abstract: Progress Towards Viridin: Synthesis of the Pentacyclic Furanosteroid Ring System via o‐Benzoquinonoid Cycloadditions. (2000)

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.
Effect of Hepatocyte Growth Factor in Alveolar Epithelial Cells (2012)

Lung inflammatory diseases, such as chronic obstructive pulmonary disease (COPD), are the third leading cause of death in United States. The disruption of gas exchange observed in COPD is a consequence of alveolar enlargement. Previous results from our laboratory showed that hepatocyte growth factor (HGF) administration in both an elastase‐induced emphysema mouse model and a genetic emphysema model significantly reduced airspace damage. Since hepatocyte growth factor (HGF) is a pleiotrophic cytokine that promotes epithelial proliferation, morphogenesis, migration, angiogenesis and survival, we investigated the cell‐autonomous effects of HGF in alveolar epithelial cell line. MLE‐12 cells were treated with HGF to study downstream mediators, proliferation, protection against apoptosis and scattering. We found that the prosurvival ERK and AKT pathways were activated in the presence of HGF. Using specific inhibitors, we found that basal and HGF‐induced proliferation was mediated through ERK signaling. However, HGF was shown to confer protection against cell death principally by AKT signaling. Finally, we demonstrated that HGF could induce MLE12 cell scattering after 1 hour of treatment. Together, the results obtained in this study showed that MLE12 cells are a good model system to dissect the role of HGF in the critical events of alveolar septation. Supported by grant to E.R.N (RO1‐HL085312).
A Taxonomy for Trusted Services (2005)

Electronic commerce must be trustworthy. This includes (technical) trust in the computerised systems and networks, and (organisational) trust in the honest intent of the counterparts. To establish trust, in general one has to rely upon infrastructures consisting of trusted services. In particular for organisational trust, a plethora of different services may be needed. This paper suggests a taxonomy to characterise trusted services in general. The virtues of a taxonomy are easier comparison and a common terminology, increased understanding, and facilitation of tasks like requirements specifications.
A REDUCED-SCALE MODEL TO EVALUATE THE RESPONSE OF TALL TOWERS HIT BY LIGHTNING (2001)

We present a reduced-scale model developed to analyze the surge response of tall towers hit by a lightning return stroke. The height of the reduced-scale tower model could be varied from 40 cm to 1 m and the minimum rise-time of the injected voltage at its top is about 500 ps. The response of a simple configuration, namely a vertical cone is analyzed and compared with theory. One of the aims of the system is the study of the contamination of lightning current measured using instrumented towers.
Mutagen sensitivity and environmental exposures as contributing causes of chromosome 3p losses in head and neck cancers (2000)

The interaction between environmental exposures and host susceptibility may lead to specific mutational events within head and neck squamous cell carcinoma (HNSCC). Furthermore, this interplay may determine not only the probability of cancer development but also the biologic characteristics of the tumor once it occurs. To better understand the relationship of mutagen sensitivity and tobacco and/or alcohol consumption on HNSCC carcinogenesis, we examined loss of heterozygosity on chromosome 3p in 58 HNSCCs using 10 microsatellite markers. Mutagen sensitivity was determined in vitro by quantitating bleomycin-induced chromatid breaks utilizing peripheral blood lympocytes from respective patients. Forty-six of the 58 invasive cancers showed allelic loss at one or more loci. Consistent with previous investigations, three discrete regions of deletions were identified: 3p13–14.2, 3p21.1–21.2, and 3p25.1–26.1. The frequency and types of deletions were dependent upon tobacco and alcohol exposures. The distal region of 3p but not the remaining two regions was most frequently influenced by tobacco exposure. In contrast, heavy alcohol use when combined with tobacco use was associated with whole-arm loss of 3p rather than identifiable site-specific damage. Furthermore, this combined influence of alcohol and tobacco exposures on whole-arm loss was most apparent in those patients who expressed mutagen-sensitivity; the odds ratio of whole-arm loss increasing from 2.67 (95% CI 0.21–33.49) in those individuals who were mutagen resistant to 13.5 (95% CI 1.3–136.0; P = 0.02 by Fisher's exact test) in those who were mutagen sensitive. An assessment of clinical parameters in this population demonstrated that patients with whole-arm loss were more likely to present with cervical lymph node metastases and advanced stage disease than patients with partial losses. Results indicate that various environmental exposures as well as the expression of mutagen sensitivity will influence the types of chromosome 3p allelic losses in head and neck cancers as well as the behavior of disease once it develops.
Autoantibodies to a collagen-specific molecular chaperone, heat-shock protein 47, in systemic sclerosis (2004)

SUMMARY Heat-shock proteins are highly conserved and immunogenic proteins, which may be involved in the initiation and perpetuation of autoimmune diseases. Heat-shock protein 47 (HSP47) is expressed by collagen-secreting cells such as fibroblasts and serves as a collagen-specific molecular chaperone that plays a crucial role in collagen metabolism. Abnormal collagen accumulation and autoimmunity are characteristics of systemic sclerosis (SSc). We determined the presence and prevalence of autoantibodies to HSP47 in patients with SSc and also in tight-skin (TSK/+) mice, an animal model for SSc. Anti-HSP47 autoantibodies were present in SSc patients with a frequency of 26%, while patients with systemic lupus erythematosus, those with dermatomyositis, those with keloid and healthy subjects did not have anti-HSP47 antibodies. IgG1 and IgG2 were the major Ig isotypes of the autoantibodies. Patients positive for anti-HSP47 had a significantly shorter duration of disease than those who were negative. Anti-HSP47 autoantibodies were also positive in 79% of TSK/+ mice. Thus, autoantobodies to HSP47 were present in the sera from SSc patients as well as those from TSK mice, and may be associated with the pathogenesis of SSc.
Immunotherapy of Murine Hepatocellular Carcinoma by <i>α</i> -Fetoprotein DNA Vaccination Combined with Adenovirus-Mediated Chemokine and Cytokine Expression (2008)

Most hepatocellular carcinomas (HCCs) express oncofetal alpha-fetoprotein (AFP). We and others have demonstrated efficient tumor control mediated by cellular immune responses in mice bearing subcutaneous tumors derived from the AFP-expressing murine HCC cell line Hepa 1-6 by DNA vaccination against AFP. In the present study, we examined AFP DNA vaccination in the AFP-expressing primary murine HCC model BW7756. In this model AFP DNA vaccination resulted in only minimal lymphocytic infiltration and failed to control tumor growth. To augment the AFP-specific cellular immune response, intratumoral expression of chemokine IP-10 (interferon-inducible protein-10) and the proinflammatory cytokine interleukin (IL)-12 by adenoviral vectors (AdmIL-12 and AdmIP-10) was analyzed. Intratumoral injection of AdmIL-12 and AdmIP-10 resulted in transient tumor regressions, without prolongation of animal survival. By contrast, AFP DNA vaccination followed by intratumoral injection of AdmIL-12 and AdmIP-10 resulted in tumor regression in all animals and in prolongation of animal survival; in 25% of animals the tumors became undetectable. This study demonstrates for the first time that activation of effector cells against a tumor antigen induced by the combination of DNA vaccination and intratumoral chemokine and cytokine expression is superior to the respective treatment strategies alone. This effect may be mediated by attraction of activated effector cells to the tumor tissue.
Temperature dependence of capacitance–voltage characteristics of germanium telluride thin films (2022)

Temperature-dependent capacitance–voltage and conductance–voltage measurements of 200-nm-thick germanium telluride (GeTe) thin films deposited via direct current magnetron sputtering were investigated. Measurements were performed across a temperature range of 27–357 °C, with a sweep of voltage values from −20 to +20 V at an operating frequency of 1 MHz. An amorphous–crystalline transition temperature (Tc) of 197 °C was found. Below Tc, the GeTe films were highly resistive, and their capacitance was insensitive to the applied bias voltage and temperature. Above Tc, the capacitance showed strong dependence on temperature, owing to the triggering of GeTe crystallization incorporating nucleation and growth processes. Applied bias voltage did not show a profound impact on the GeTe capacitance even after crystallization, but it had an observable impact on the film conductance beyond 250 °C. Moreover, the GeTe thin film capacitance increased by a factor of 13 upon crystallization. Hall-effect measurements revealed that the film conductivity increased upon crystallization, as did the hole concentration and mobility. Cross-sectional transmission electron microscopy demonstrated that the GeTe thin films crystallize via a nucleation-dominated crystallization mechanism.
From biological pathways to regulatory networks (2010)

This paper presents a general theoretical framework for generating Boolean networks whose state transitions realize a set of given biological pathways or minor variations thereof. This ill-posed inverse problem, which is of crucial importance across practically all areas of biology, is solved by using Karnaugh maps which are classical tools for digital system design. It is shown that the incorporation of prior knowledge, presented in the form of biological pathways, can bring about a dramatic reduction in the cardinality of the network search space. Constraining the connectivity of the network, the number and relative importance of the attractors, and concordance with observed time-course data are additional factors that can be used to further reduce the cardinality of the search space. The networks produced by the approaches developed here should facilitate the understanding of multivariate biological phenomena and the subsequent design of intervention approaches that are more likely to be successful in practice. As an example, the results of this paper are applied to the widely studied p53 pathway and it is shown that the resulting network exhibits dynamic behavior consistent with experimental observations from the published literature.
0 Serogroup and Virulence Factors of Motile Aeromonas (1992)

A total of 182 isolates of motile Aeromonas from patients with diarrhea and environmental sources was investigated for hemolytic activity to rabbit erythrocyte and cytotoxicity to HeLa 229 cell. Furthermore, the relation between O serogroup and virulence factors, which were lethal to mouse and autoagglutination, were investigated. There were many strains possessing both the hemolytic and cytotoxic activities in A. hydrophila from overseas traveller's diarrhea, suggesting that these activities were associated with intestinal pathogenecity. Although there was a clear correlation between hemolytic and cytotoxic activities in A. hydrophila from overseas traveller's diarrhea, the correlation was not found in A. hydrophila from domestic cases of diarrhea and A. sobria from overseas traveller's diarrhea. Especially, some A. hydrophila isolates from domestic case of diarrhea produced only hemolysin. These results indicated that there was a difference in specificity between the toxins accounted for hemolytic and cytotoxic activities, and more than two different toxins were developed. O serogroups 11, 34, 14, 16, and 35 in that order were the most frequent serogroups. About half of O11 and O34 strains possessed lethal activity to mouse. Autoagglutination phenomenon did not seem to be associated with the lethal activity. In O11 strains, high cytotoxic titer was more frequently found in lethal activity positive-strains than in the activity negative-strains, suggesting that cytotoxicity contributed preferentially to lethal activity to mouse. But such a correlation was not found in O34 strains, so other virulence factors than hemolysin and cytotoxin may be associated with the lethal activity.
Molecular Characterization of Rice OsLCB2a1 Gene and Functional Analysis of its Role in Insect Resistance (2016)

In plants, sphingolipids, such as long-chain bases (LCBs), act as bioactive molecules in stress responses. Until now, it is still not clear if these lipids are involved in biotic stress responses to herbivore. Herein we report that a rice LCB gene, <i>OsLCB2a1</i> encoding a subunit of serine palmitoyltransferase (SPT), a key enzyme responsible for the <i>de novo</i> biosynthesis of sphingolipids, plays a critical role in plant defense response to the brown planthopper (BPH) attack and that its up-regulation protects plants from herbivore infestation. Transcripts of <i>OsLCB2a1</i> gene in rice seedlings were increased at 4 h, but decreased at 8-24 h after BPH attack. Sphingolipid measurement profiling revealed that overexpression of <i>OsLCB2a1</i> in <i>Arabidopsis thaliana</i> increased trihydroxylated LCB phytosphingosine (t18:0) and phytoceramide by 1.7 and 1.3-fold, respectively, compared with that of wild type (WT) plants. Transgenic Arabidopsis plants also showed higher callose and wax deposition in leaves than that of WT. Overexpression of <i>OsLCB2a1</i> gene in <i>A. thaliana</i> reduced the population size of green peach aphid (<i>Myzus persicae</i>). Moreover, the electrical penetration graph (EPG) results indicated that the aphids encounter resistance factors while reaching for the phloem on the transgenic plants. The defense response genes related to salicylic acid signaling pathway, remained uplgulated in the <i>OsLCB2a1</i>-overexpressing transgenic plants. Our data highlight the key functions of <i>OsLCB2a1</i> in biotic stress response in plants.
Effects of Melatonin and 6‐Methoxybenzoxazolinone on Photoperiodic Control of Testis Size in Adult Male Golden Hamsters (1988)

Consumption of young plants containing 6-methoxybenzoxazolinone (6-MBOA) appears to play an important role in the initiation of reproduction each spring in wild populations of the montane vole. Following its identification, 6-MBOA has been found to stimulate the reproductive system in a number of rodent species, but the mechanism of action remains unknown. The chemical structure of 6-MBOA is similar to melatonin, which, in addition to its well-known antigonadal effects, can exert a progonadal influence under certain experimental conditions. To determine if 6-MBOA might act as a melatonin agonist, four experiments were conducted to compare the effect of these two compounds on testis size in the golden hamster, a rodent whose responses to melatonin are well characterized. 1) Hamsters exposed to 14 h light per day (14L:10D) received a daily injection of melatonin (25.0 micrograms) or 6-MBOA (17.8 micrograms). 2) Hamsters exposed to 6L:18D received Silastic capsules (50 or 200 mm) containing melatonin or 6-MBOA. 3) Hamsters exposed to 6L:18D received chow containing melatonin (21.1 or 42.2 micrograms/gm chow) or 6-MBOA (15.0 or 30.0 micrograms/gm). 4) Hamsters exposed to 6L:18D received drinking water containing melatonin (15.5 micrograms/ml) or 6-MBOA (11.0 micrograms/ml). Testis widths were determined at 2--3 week intervals, and after 66-73 days testes were removed and weighed. Melatonin significantly influenced testis size in each experiment, but treatment with 6-MBOA had no effect in any of these experimental paradigms, indicating that 6-MBOA does not act as a melatonin agonist in the hamster. However, these results indicate that the consumption of melatonin (and presumably melatonin agonists) could serve as an environmental stimulus for reproductive activity.
The Effects of Steroids on Survival of Mouse and Human Tympanic Membrane Fibroblasts (2020)

Steroids found in commercial ear drops reduce survival of mouse and human TM fibroblasts. Hydrocortisone appears to be more cytotoxic than the more potent steroids, dexamethasone and fluocinolone. These findings should be considered when assessing clinical outcomes of ototopical preparations.