gebhart/patrepeval huggingface dataset:
ATR/ATM Targets Are Phosphorylated by ATR in Response to Hypoxia and ATM in Response to Reoxygenation (2003)

The ATR kinase phosphorylates both p53 and Chk1 in response to extreme hypoxia (oxygen concentrations of less than 0.02%). In contrast to ATR, loss of ATM does not affect the phosphorylation of these or other targets in response to hypoxia. However, hypoxia within tumors is often transient and is inevitably followed by reoxygenation. We hypothesized that ATR activity is induced under hypoxic conditions because of growth arrest and ATM activity increases in response to the oxidative stress of reoxygenation. Using the comet assay to detect DNA damage, we find that reoxygenation induced significant amounts of DNA damage. Two ATR/ATM targets, p53 serine 15 and histone H2AX, were both phosphorylated in response to hypoxia in an ATR-dependent manner. These phosphorylations were then maintained in response to reoxygenation-induced DNA damage in an ATM-dependent manner. The reoxygenation-induced p53 serine 15 phosphorylation was inhibited by the addition of N-acetyl-l-cysteine (NAC), indicating that free radical-induced DNA damage was mediated by reactive oxygen species. Taken together these data implicate both ATR and ATM as critical roles in the response of hypoxia and reperfusion in solid tumors.
Targeted gene expression in transgenic Xenopus using the binary Gal4-UAS system (2002)

The transgenic technique in Xenopus allows one to misexpress genes in a temporally and spatially controlled manner. However, this system suffers from two experimental limitations. First, the restriction enzyme-mediated integration procedure relies on chromosomal damage, resulting in a percentage of embryos failing to develop normally. Second, every transgenic embryo has unique sites of integration and unique transgene copy number, resulting in variable transgene expression levels and variable phenotypes. For these reasons, we have adapted the Gal4-UAS method for targeted gene expression to Xenopus. This technique relies on the generation of transgenic lines that carry "activator" or "effector" constructs. Activator lines express the yeast transcription factor, Gal4, under the control of a desired promoter, whereas effector lines contain DNA-binding motifs for Gal4-(UAS) linked to the gene of interest. We show that on intercrossing of these lines, the effector gene is transcribed in the temporal and spatial manner of the activator's promoter. Furthermore, we use the Gal4-UAS system to misexpress Xvent-2, a transcriptional target of bone morphogenetic protein 4 (BMP4) signaling during early embryogenesis. Embryos inheriting both the Gal4 activator and Xvent-2 effector transgenes display a consistent microcephalic phenotype. Finally, we exploit this system to characterize the neural and mesodermal defects obtained from early misexpression of Xvent-2. These results emphasize the potential of this system for the controlled analyses of gene function in Xenopus.
Size of radial and ulnar artery in local population. (2010)

We conclude that ulnar artery diameter is larger than the radial artery in our population. Knowing the size will guide the interventional cardiologist in using appropriate size sheaths and guide catheters. Cardiac surgeons can utilize ulnar artery for bypass grafting when it is deemed unsafe to harvest the radial artery.
Plasmon-Enhanced Upconversion in Single NaYF4:Yb3+/Er3+ Codoped Nanocrystals (2009)

In this Letter we report the plasmon-enhanced upconversion in single NaYF(4) nanocrystals codoped with Yb(3+)/Er(3+). Single nanocrystals and gold nanospheres are investigated and assembled in a combined confocal and atomic force microscope setup. The nanocrystals show strong upconversion emission in the green and red under excitation with a continuous wave laser in the near-infrared at 973 nm. By the use of the atomic force microscope, we couple single nanocrystals with gold spheres (30 and 60 nm in diameter) to obtain enhanced upconversion emission. An overall enhancement factor of 3.8 is reached. A comparison of time-resolved measurements on the bare nanocrystal and the coupled nanocrystal-gold sphere systems unveil that faster excitation as well as faster emission occurs in the nanocrystals.
Marrow stromal cells migrate throughout forebrain and cerebellum, and they differentiate into astrocytes after injection into neonatal mouse brains (1999)

Stem cells are a valuable resource for treating disease, but limited access to stem cells from tissues such as brain restricts their utility. Here, we injected marrow stromal cells (MSCs) into the lateral ventricle of neonatal mice and asked whether these multipotential mesenchymal progenitors from bone marrow can adopt neural cell fates when exposed to the brain microenvironment. By 12 days postinjection, MSCs migrated throughout the forebrain and cerebellum without disruption to the host brain architecture. Some MSCs within the striatum and the molecular layer of the hippocampus expressed glial fibrillary acidic protein and, therefore, differentiated into mature astrocytes. MSCs also populated neuron rich regions including the Islands of Calleja, the olfactory bulb, and the internal granular layer of the cerebellum. A large number of MSCs also were found within the external granular layer of the cerebellum. In addition, neurofilament positive donor cells were found within the reticular formation of the brain stem, suggesting that MSCs also may have differentiated into neurons. Therefore, MSCs are capable of producing differentiated progeny of a different dermal origin after implantation into neonatal mouse brains. These results suggest that MSCs are potentially useful as vectors for treating a variety of central nervous system disorders.
LYα TRANSIT SPECTROSCOPY AND THE NEUTRAL HYDROGEN TAIL OF THE HOT NEPTUNE GJ 436b (2014)

To date, more than 750 planets have been discovered orbiting stars other than the Sun. Two sub-classes of these exoplanets, "hot Jupiters" and their less massive counterparts "hot Neptunes," provide a unique opportunity to study the extended atmospheres of planets outside of our solar system. We describe here the first far-ultraviolet transit study of a hot Neptune, specifically GJ436b, for which we use HST/STIS Lyman-$\alpha$ spectra to measure stellar flux as a function of time, observing variations due to absorption from the planetary atmosphere during transit. This analysis permits us to derive information about atmospheric extent, mass-loss rate from the planet, and interactions between the star and planet. We observe an evolution of the Lyman-$\alpha$ lightcurve with a transit depth of GJ436b from $8.8\pm4.5\%$ near mid-transit, to $22.9\pm3.9\%$ $\sim2$ hours after the nominal geometric egress of the planet. Using data from the time-tag mode and considering astrophysical noise from stellar variability, we calculate a post-egress occultation of $23.7\pm4.5\%$, demonstrating that the signature is statistically significant and of greater amplitude than can be attributed to stellar fluctuations alone. The extended egress absorption indicates the probable existence of a comet-like tail trailing the exoplanet. We calculate a mass-loss rate for GJ436b in the range of $3.7\times10^6 -1.1\times10^{9}$ g s$^{-1}$, corresponding to an atmospheric lifetime of $4\times10^{11}-2\times10^{14}$ years.
Differential cyclophosphamide sensitivity of precursor cells in allogeneic and H-2 restricted cytotoxic responses. (1979)

Spleen cells from cyclophosphamide-treated mice responded in vitro to allogeneic stimulator cells but not to TNP-coupled syngeneic spleen cells. Similarly, cells from female mice, primed in vivo with syngeneic male cells, could not respond in vitro to male spleen cell stimulation if the mice were pretreated with cyclophosphamide. These results suggest that the precursor cells for H-2-restricted cytotoxic responses belong to a different T-cell subpopulation than the precursor cells for allogeneic responses.
Nanoscale thickness double-gated field effect silicon sensors for sensitive pH detection in fluid (2008)

In this work, we report on the optimization of a double-gate silicon-on-insulator field effect device operation to maximize pH sensitivity. The operating point can be fine tuned by independently biasing the fluid and the back gate of the device. Choosing the bias points such that device is nearly depleted results in an exponential current response—in our case, 0.70decade per unit change in pH. This value is comparable to results obtained with devices that have been further scaled in width, reported at the forefront of the field, and close to the ideal value of 1decade∕pH. By using a thin active area, sensitivity is increased due to increased coupling between the two conducting surfaces of the devices.
Structural Studies of Human Histone Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors, (2008)

Metal-dependent histone deacetylases (HDACs) require Zn(2+) or Fe(2+) to regulate the acetylation of lysine residues in histones and other proteins in eukaryotic cells. Isozyme HDAC8 is perhaps the archetypical member of the class I HDAC family and serves as a paradigm for studying structure-function relationships. Here, we report the structures of HDAC8 complexes with trichostatin A and 3-(1-methyl-4-phenylacetyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide (APHA) in a new crystal form. The structure of the APHA complex reveals that the hydroxamate CO group accepts a hydrogen bond from Y306 but does not coordinate to Zn(2+) with favorable geometry, perhaps due to the constraints of its extended pi system. Additionally, since APHA binds to only two of the three protein molecules in the asymmetric unit of this complex, the structure of the third monomer represents the first structure of HDAC8 in the unliganded state. Comparison of unliganded and liganded structures illustrates ligand-induced conformational changes in the L2 loop that likely accompany substrate binding and catalysis. Furthermore, these structures, along with those of the D101N, D101E, D101A, and D101L variants, support the proposal that D101 is critical for the function of the L2 loop. However, amino acid substitutions for D101 can also trigger conformational changes of Y111 and W141 that perturb the substrate binding site. Finally, the structure of H143A HDAC8 complexed with an intact acetylated tetrapeptide substrate molecule confirms the importance of D101 for substrate binding and reveals how Y306 and the active site zinc ion together bind and activate the scissile amide linkage of acetyllysine.
Mammalian cell survival and processing in supercritical CO 2 (2006)

We demonstrate that mammalian cells can survive for 5 min within high-pressure CO(2)(.) Cell survival was investigated by exposing a range of mammalian cell types to supercritical CO(2) (scCO(2)) (35 degrees C, 74 bar; 1 bar = 100 kPa) for increasing exposure and depressurization times. The myoblastic C2C12 cell line, 3T3 fibroblasts, chondrocytes, and hepatocytes all displayed appreciable but varying metabolic activity with exposure times up to 1 min. With depressurization times of 4 min, cell population metabolic activity was >/=70% of the control population. Based on survival data, we developed a single-step scCO(2) technique for the rapid production of biodegradable poly(dl-lactic acid) scaffolds containing mammalian cells. By using optimum cell-survival conditions, scCO(2) was used to process poly(dl-lactic acid) containing a cell suspension, and, upon pressure release, a polymer sponge containing viable mammalian cells was formed. Cell functionality was demonstrated by retention of an osteogenic response to bone morphogenetic protein-2 in C2C12 cells. A gene microarray analysis showed no statistically significant changes in gene expression across 4,418 genes by a single-class t test. A significance analysis of microarrays revealed only eight genes that were down-regulated based on a delta value of 1.0125 and a false detection rate of 0.
Targeted Gene Disruption by Homologous Recombination in the Hyperthermophilic ArchaeonThermococcus kodakaraensisKOD1 (2002)

In contrast to the high accumulation in sequence data for hyperthermophilic archaea, methodology for genetically manipulating these strains is still at an early stage. This study aimed to develop a gene disruption system for the hyperthermophilic euryarchaeon Thermococcus kodakaraensis KOD1. Uracil-auxotrophic mutants with mutations in the orotidine-5'-monophosphate decarboxylase gene (pyrF) were isolated by positive selection using 5-fluoroorotic acid (5-FOA) and used as hosts for further transformation experiments. We then attempted targeted disruption of the trpE locus in the host strain by homologous recombination, as disruption of trpE was expected to result in tryptophan auxotrophy, an easily detectable phenotype. A disruption vector harboring the pyrF marker within trpE was constructed for double-crossover recombination. The host cells were transformed with the exogenous DNA using the CaCl(2) method, and several transformants could be selected based on genetic complementation. Genotypic and phenotypic analyses of a transformant revealed the unique occurrence of targeted disruption, as well as a phenotypic change of auxotrophy from uracil to tryptophan caused by integration of the wild-type pyrF into the host chromosome at trpE. As with the circular plasmid, gene disruption with linear DNA was also possible when the homologous regions were relatively long. Shortening these regions led to predominant recombination between the pyrF marker in the exogenous DNA and the mutated allele on the host chromosome. In contrast, we could not obtain trpE disruptants by insertional inactivation using a vector designed for single-crossover recombination. The gene targeting system developed in this study provides a long-needed tool in the research on hyperthermophilic archaea and will open the way to a systematic, genetic approach for the elucidation of unknown gene function in these organisms.
LGR4 and LGR5 Function Redundantly During Human Endoderm Differentiation (2016)

Our results show that <i>LGR5</i> is induced during DE differentiation, LGR receptors are functionally required for DE induction, and that they function to potentiate WNT signaling during this process.
Function of the Escherichia coli msbB Gene, a Multicopy Suppressor of htrB Knockouts, in the Acylation of Lipid A (1997)

Overexpression of the Escherichia coli msbB gene on high copy plasmids suppresses the temperature-sensitive growth associated with mutations in the htrB gene. htrB encodes the lauroyl transferase of lipid A biosynthesis that acylates the intermediate (Kdo)2-lipid IVA (Brozek, K. A., and Raetz, C. R. H. (1990) J. Biol. Chem. 265, 15410-15417). Since msbB displays 27.5% identity and 42.2% similarity to htrB, we explored the possibility that msbB encodes a related acyltransferase. In contrast to htrB, extracts of strains with insertion mutations in msbB are not defective in transferring laurate from lauroyl acyl carrier protein to (Kdo)2-lipid IVA. However, extracts of msbB mutants do not efficiently acylate the product formed by HtrB, designated (Kdo)2-(lauroyl)-lipid IVA. Extracts of strains harboring msbB+ bearing plasmids acylate (Kdo)2-(lauroyl)-lipid IVA very rapidly compared with wild type. We solubilized and partially purified MsbB from an overproducing strain, lacking HtrB. MsbB transfers myristate or laurate, activated on ACP, to (Kdo)2-(lauroyl)-lipid IVA. Decanoyl, palmitoyl, palmitoleoyl, and (R)-3-hydroxymyristoyl-ACP are poor acyl donors. MsbB acylates (Kdo)2-(lauroyl)-lipid IVA about 100 times faster than (Kdo)2-lipid IVA. The slow, but measurable, rate whereby MsbB acts on (Kdo)2-lipid IVA may explain why overexpression of MsbB suppresses the temperature-sensitive phenotype of htrB mutations. Presumably, the acyloxyacyl group generated by excess MsbB substitutes for the one normally formed by HtrB.
Novel polysiloxane and polycarbosilane aerogels via hydrosilylation of preceramic polymers (2012)

We report new polysiloxane and polycarbosilane aerogels, which have been obtained by crosslinking Si–H-containing polymers with a CC-containing crosslinker via hydrosilylation reactions. The crosslinking reaction has been carried out in a highly diluted solution using up to 97 vol% of solvent. The obtained aerogels have a colloidal structure with meso- and macropores. Density as low as 0.17 g cm−3 has been reached, which implies a porosity of ca. 84 vol%.
Vascular Endothelial Growth Factor Receptor Family Genes: When Did the Three Genes Phylogenetically Segregate? (2002)

The vascular endothelial growth factor (VEGF) receptor family in mammals contains three members, VEGFR1(Flt-1), VEGFR2(KDR/Flk-1) and VEGFR3 (Flt-4), which directly regulate the formation of blood vessels and lymphatic vessels. These two circular systems are essential for the supply of O2 and nutrients to all tissues of the body as well as the drainage of excess fluids with waste metabolites from peripheral tissues. VEGF receptors have a characteristic structure with 7 Ig-like domains in the extracellular domain and a cytoplasmic tyrosine kinase domain with a long kinase insert region. Recently, some novel findings on the phylogenetical conservation of VEGF receptor genes in animals were reported: the conservation of the VEGFR1/soluble-VEGFR1 gene in birds, and the conservation of the VEGFR-PDGFR-like receptor gene in nonvertebrates. Based on this new information as well as established observations, here the possibility is discussed that the three VEGFR genes phylogenetically segregated not at once when the vertebrates established, but in a step-wise manner: two genes first (the VEGFR1/R2 progenitor and the VEGFR3 gene), and subsequently the three genes VEGFR1, R2 and R3.
High power silicon RF LDMOSFET technology for 2.1GHz power amplifier applications (2004)

In this paper, RF LDMOSFET is demonstrated with excellent RF performance. It achieves high power gain of 14.5dB with a high power of 130W at 2.1GHz. Its high efficiency and high linearity makes it to be highly desired by applications. 2mil substrate enables the best-in-class of thermal stability. Low HCI degradation, integrated ESD and gold metal ensure a good long-term reliability.
Transgene-based, female-specific lethality system for genetic sexing of the silkworm, Bombyx mori (2013)

Transgene-based genetic sexing methods are being developed for insects of agricultural and public health importance. Male-only rearing has long been sought in sericulture because males show superior economic characteristics, such as better fitness, lower food consumption, and higher silk yield. Here we report the establishment of a transgene-based genetic sexing system for the silkworm, Bombyx mori. We developed a construct in which a positive feedback loop regulated by sex-specific alternative splicing leads to high-level expression of the tetracycline-repressible transactivator in females only. Transgenic animals show female-specific lethality during embryonic and early larval stages, leading to male-only cocoons. This transgene-based female-specific lethal system not only has wide application in sericulture, but also has great potential in lepidopteran pest control.
CARBON‐14 LABELING AND BIOLOGICAL ACTIVITY OF THE TUMOR‐LOCALIZING DERIVATIVE OF HEMATOPORPHYRIN (1988)

Abstract— Carbon‐14‐labeled hematoporphyrin ([ 14 C]HP) was synthesized by two methods, (i) Using an in vitro avian whole‐blood system, [ 14 C]protoheme was obtained biosynthetically by incorporating [ 4 C]aminolevulinic acid into the porphyrin ring structure. Subsequently, the [ 14 C]protoheme was converted to [ 4 C]HP by standard procedures, (ii) By adopting several well‐characterized chemical reactions, deuteroporphyrin was treated with [ 14 C]acetyl chloride, giving [ 14 C]diacetyl deuteroporphy‐rin which was readily reduced and hydrolyzed to [ 14 C]HP (with thecarbon–14 label on the hydroxyethyl side‐chains). These two methods are simple and afford good yields of [ 14 C]HP with moderate to high specific activities. The [ 14 C]HP was then treated with acetic acid/sulfuric acid followed by sodium hydroxide to give [ 14 C]HPD. Upon gel‐ and ultra‐filtration, the [ 14 C]HPD was enriched in the so‐called tumor‐localizing fraction of HPD, giving [ 14 C]PII with specific activities of 0.4 Ci/mol (biosynthesis) and 10 Ci/mol (chemical synthesis). These [ 14 C]PII preparations were equivalent with respect to chromatographic and spectrophotometric characteristics, as well as tumoricidal photodynamic activity in the DBA/2 Ha‐DD mouse: SMT‐F tumor system, to the unlabeled commercial product Photofrin ™ II. The distribution of [ 14 C]PII in mouse tissues was in close agreement to that previously reported, after adjustment for dose, for [ 14 C]HPD biosynthetically labeled in vivo (Gomer and Dougherty, 1979), as well as for Photofrin ™ II, where tissue levels were determined spectrophotometrically after extraction (Dougherty and Mang, unpublished).
Single Injection of CD34+ Progenitor-Derived Dendritic Cell Vaccine Can Lead to Induction of T-Cell Immunity in Patients With Stage IV Melanoma (2003)

There is evidence that dendritic cell (DC) vaccines induce tumor-specific immune responses that correlate with clinical responses. Little is known, however, about the kinetics of T-cell responses to antigens presented on DC vaccines. The authors vaccinated 18 HLA A*0201+ patients with stage IV melanoma with CD34 HPC-derived DCs pulsed with six antigens: influenza matrix peptide (Flu-MP), KLH, and peptides derived from the four melanoma antigens: MART-1/Melan A, gp100, tyrosinase, and MAGE-3. A single DC vaccination was sufficient for induction of KLH-specific CD4 T-cell responses in five patients and Flu-MP-specific CD8 T-cell responses in eight patients. A single DC vaccine was sufficient for induction of tumor-specific effectors to at least one melanoma antigen in five patients. Thus, a single injection of CD34 HPC-derived DCs can lead to rapid immune response to CD4 epitopes or to melanoma antigens.
Efficacy of lotilaner (Credelio™), a novel oral isoxazoline against naturally occurring mange mite infestations in dogs caused by Demodex spp. (2017)

In this study lotilaner administered at a minimum oral dose of 20 mg/kg was highly effective in reducing and eliminating live mite counts in dogs with natural infestations of Demodex spp.
Twenty-four percent efficient silicon solar cells with double layer antireflection coatings and reduced resistance loss (1995)

Significant performance increase for silicon solar cells is reported. This has been achieved by a combination of several mechanisms. One is the reduction of recombination at cell surfaces using atomic hydrogen passivation of silicon/silicon dioxide interfaces. Joule resistive losses in the cell have been reduced by a process which allows different thickness for fine and coarse features in the top cell metallization. Finally, reflection losses have been reduced by the use of a double layer antireflection coating. For successful incorporation, this required the development of techniques for growing the surface passivating oxide very thin, without reducing its passivation qualities. The cells display a monochromatic light energy conversion efficiency of 46.3% for 1.04 μm wavelength light, also the highest ever for a silicon devices.