gebhart/patrepeval huggingface dataset:
Generation and characterisation of the carbon G-centre in silicon (2015)

Silicon photonics has gained more popularity in the last decade stimulated by a series of recent breakthroughs and attractive potential applications in the integrated-optics. One of the great challenges is to modify the silicon lattice so as to enhance the light emission properties. Moreover, by referring to Moore’s Law, there are concerns of the increase in interconnect time delay which can surpass the switching time if the gate length in transistors are continued to scale down. By implementing the silicon optical emitter on the integrated circuit, it will eliminate this major problem thus enhancing the performance and speed of the computer. This work will focus on researching the point defect especially the G-centre in silicon as a potential technique to emit coherent light from silicon. We have investigated and presented a new approach to incorporate high levels of the emissive G-centre peaking sharply at 1280 nm by implanting carbon and protons into the silicon lattice. Significantly this technique utilizes fully ULSI technology compatible processes such as ion implantation and high temperature annealing.\n\nRutherford backscattering spectrometry (RBS) and transmission electron microscopy (TEM) techniques were used along with the photoluminescence measurement to correlate the optical and structural properties of the G-centre formed by the carbon implantation and high energy ion irradiation. The analysis reveals that the silicon interstitials generated after proton irradiation are an essential factor in forming the G-centre complex. \n\nWe have also introduced the dislocation engineering technique into the silicon lattice with the G-centre complexes. The results are promising and with optimization of the technique to introduce the dislocation loops into the G-centre technique, the temperature quenching problem often related to the optically active point-defect centre, may be solved. Electroluminescence (EL) measurements were carried out after the fabrication of the LED devices. Results from the sample with the G-centre luminescence is the most crucial as it shows that by using the proposed technique in this research, luminescence from silicon is indeed possible when electrically pumped. This is an essential key result for the future research of the optically active point-defect especially the G-centre towards the possibility of an electrically pumped, efficient silicon laser.
Genetic Studies with the Fission Yeast <i>Schizosaccharomyces pombe</i> Suggest Involvement of Wee1, Ppa2, and Rad24 in Induction of Cell Cycle Arrest by Human Immunodeficiency Virus Type 1 Vpr (2000)

Accessory protein Vpr of human immunodeficiency virus type 1 (HIV-1) arrests cell cycling at G(2)/M phase in human and simian cells. Recently, it has been shown that Vpr also causes cell cycle arrest in the fission yeast Schizosaccharomyces pombe, which shares the cell cycle regulatory mechanisms with higher eukaryotes including humans. In this study, in order to identify host cellular factors involved in Vpr-induced cell cycle arrest, the ability of Vpr to cause elongated cellular morphology (cdc phenotype) typical of G(2)/M cell cycle arrest in wild-type and various mutant strains of S. pombe was examined. Our results indicated that Vpr caused the cdc phenotype in wild-type S. pombe as well as in strains carrying mutations, such as the cdc2-3w, Deltacdc25, rad1-1, Deltachk1, Deltamik1, and Deltappa1 strains. However, other mutants, such as the cdc2-1w, Deltawee1, Deltappa2, and Deltarad24 strains, failed to show a distinct cdc phenotype in response to Vpr expression. Results of these genetic studies suggested that Wee1, Ppa2, and Rad24 might be required for induction of cell cycle arrest by HIV-1 Vpr. Cell proliferation was inhibited by Vpr expression in all of the strains examined including the ones that did not show the cdc phenotype. The results supported the previously suggested possibility that Vpr affects the cell cycle and cell proliferation through different pathways.
σ-Organyl complexes of ruthenium and osmium supported by a mixed-donor ligand (2005)

A series of vinyl, aryl, acetylide and silyl complexes [Ru(R)(kappa2-MI)(CO)(PPh3)2] (R = CH=CH2, CH=CHPh, CH=CHC6H4CH3-4, CH=CH(t)Bu, CH=2OH, C(C triple bond CPh)=CHPh, C6H5, C triple bond CPh, SiMe2OEt; MI = 1-methylimidazole-2-thiolate) were prepared from either [Ru(R)Cl(CO)(PPh3)2] or [Ru(R)Cl(CO)(BTD)(PPh3)2](BTD = 2,1,3-benzothiadiazole) by reaction with the nitrogen-sulfur mixed-donor ligand, 1-methyl-2-mercaptoimidazole (HMI), in the presence of base. In the same manner, [Os(CH=CHPh)(kappa2-MI)(CO)(PPh3)2] was prepared from [Os(CH=CHPh)(CO)Cl(BTD)(PPh3)2]. The in situ hydroruthenation of 1-ethynylcyclohexan-1-ol by [RuH(CO)Cl(BTD)(PPh3)2] and subsequent addition of the HMI ligand and excess sodium methoxide yielded the dehydrated 1,3-dienyl complex [Ru(CH=CHC6H9)(kappa2-MI)(CO)(PPh3)2]. Dehydration of the complex [Ru(CH=CHCPh2OH)(kappa2-MI)(CO)(PPh3)2] with HBF4 yielded the vinyl carbene [Ru(=CHCH=CPh2)(kappa2-MI)(CO)(PPh3)2]BF4. The hydride complexes [MH(kappa2-MI)(CO)(PPh3)2](M = Ru, Os) were obtained from the reaction of HMI and KOH with [RuHCl(CO)(PPh3)3] and [OsHCl(CO)(BTD)(PPh3)2], respectively. Reaction of [Ru(CH=CHC6H4CH3-4)(kappa2-MI)(CO)(PPh3)2] with excess HC triple bond CPh leads to isolation of the acetylide complex [Ru(C triple bond CPh)(kappa2-MI)(CO)(PPh3)2], which is also accessible by direct reaction of [Ru(C triple bond CPh)Cl(CO)(BTD)(PPh3)2] with 1-methyl-2-mercaptoimidazole and NaOMe. The thiocarbonyl complex [Ru(CPh = CHPh)Cl(CS)(PPh3)2] reacted with HMI and NaOMe without migration to yield [Ru(CPh= CHPh)(kappa2-MI)(CS)(PPh3)2], while treatment of [Ru(CH=CHPh)Cl(CO)2(PPh3)2] with HMI yielded the monodentate acyl product [Ru{eta(1)-C(=O)CH=CHPh}(kappa2-MI)(CO)(PPh3)2]. The single-crystal X-ray structures of five complexes bearing vinyl, aryl, acetylide and dienyl functionality are reported.
5′ isomiR variation is of functional and evolutionary importance (2014)

We have sequenced miRNA libraries from human embryonic, neural and foetal mesenchymal stem cells. We report that the majority of miRNA genes encode mature isomers that vary in size by one or more bases at the 3' and/or 5' end of the miRNA. Northern blotting for individual miRNAs showed that the proportions of isomiRs expressed by a single miRNA gene often differ between cell and tissue types. IsomiRs were readily co-immunoprecipitated with Argonaute proteins in vivo and were active in luciferase assays, indicating that they are functional. Bioinformatics analysis predicts substantial differences in targeting between miRNAs with minor 5' differences and in support of this we report that a 5' isomiR-9-1 gained the ability to inhibit the expression of DNMT3B and NCAM2 but lost the ability to inhibit CDH1 in vitro. This result was confirmed by the use of isomiR-specific sponges. Our analysis of the miRGator database indicates that a small percentage of human miRNA genes express isomiRs as the dominant transcript in certain cell types and analysis of miRBase shows that 5' isomiRs have replaced canonical miRNAs many times during evolution. This strongly indicates that isomiRs are of functional importance and have contributed to the evolution of miRNA genes.
Symmetry of spin excitation spectra in the tetragonal paramagnetic and superconducting phases of 122-ferropnictides (2010)

We study the symmetry of spin excitation spectra in 122-ferropnictide superconductors by comparing the results of first-principles calculations with inelastic neutron-scattering (INS) measurements on ${\text{BaFe}}_{1.85}{\text{Co}}_{0.15}{\text{As}}_{2}$ and ${\text{BaFe}}_{1.91}{\text{Ni}}_{0.09}{\text{As}}_{2}$ samples that exhibit neither static magnetic phases nor structural phase transitions. In both the normal and superconducting (SC) states, the spectrum lacks the three-dimensional ${4}_{2}/m$ screw symmetry around the $(\frac{1}{2}\frac{1}{2}L)$ axis that is implied by the $I4/mmm$ space group. This is manifest both in the in-plane anisotropy of the normal- and SC-state spin dynamics and in the out-of-plane dispersion of the spin-resonance mode. We show that this effect originates from the higher symmetry of the magnetic Fe sublattice with respect to the crystal itself, hence the INS signal inherits the symmetry of the unfolded Brillouin zone (BZ) of the Fe sublattice. The in-plane anisotropy is temperature independent and can be qualitatively reproduced in normal-state density-functional-theory calculations without invoking a symmetry-broken (``nematic'') ground state that was previously proposed as an explanation for this effect. Below the SC transition, the energy of the magnetic resonant mode ${\ensuremath{\omega}}_{\text{res}}$, as well as its intensity and the SC spin gap inherit the normal-state intensity modulation along the out-of-plane direction $L$ with a period twice larger than expected from the body-centered-tetragonal BZ symmetry. The amplitude of this modulation decreases at higher doping, providing an analogy to the splitting between even and odd resonant modes in bilayer cuprates. Combining our and previous data, we show that at odd $L$ a universal linear relationship $\ensuremath{\hbar}{\ensuremath{\omega}}_{\text{res}}\ensuremath{\approx}4.3\text{ }{k}_{\text{B}}{T}_{\text{c}}$ holds for all the studied Fe-based superconductors, independent of their carrier type. Its validity down to the lowest doping levels is consistent with weaker electron correlations in ferropnictides as compared to the underdoped cuprates.
The first step of aminoacylation at the atomic level in histidyl-tRNA synthetase (1997)

The crystal structure of an enzyme-substrate complex with histidyl-tRNA synthetase from Escherichia coli, ATP, and the amino acid analog histidinol is described and compared with the previously obtained enzyme-product complex with histidyl-adenylate. An active site arginine, Arg-259, unique to all histidyl-tRNA synthetases, plays the role of the catalytic magnesium ion seen in seryl-tRNA synthetase. When Arg-259 is substituted with histidine, the apparent second order rate constant (kcat/Km) for the pyrophosphate exchange reaction and the aminoacylation reaction decreases 1,000-fold and 500-fold, respectively. Crystals soaked with MnCl2 reveal the existence of two metal binding sites between beta- and gamma-phosphates; these sites appear to stabilize the conformation of the pyrophosphate. The use of both conserved metal ions and arginine in phosphoryl transfer provides evidence of significant early functional divergence of class II aminoacyl-tRNA synthetases.
Serum soluble interleukin 6 (IL-6) receptor and IL-6/soluble IL-6 receptor complex in systemic juvenile rheumatoid arthritis. (1994)

By using a sandwich ELISA, soluble human IL-6 receptor (sIL-6 R) levels were measured in the sera of 20 healthy children and of 25 patients with systemic juvenile rheumatoid arthritis (JRA). In patients with systemic JRA, serum sIL-6 R levels (114.6 +/- 37.7 ng/ml) were significantly lower (P < 0.01) than those of healthy children (161.2 +/- 45.5 ng/ml). Serum sIL-6 R levels were negatively correlated (r = -0.610, P < 0.001) with serum IL-6 levels measured with the B9 cells. The serum IL-6/sIL-6 R complex was detected using an ELISA based on a monoclonal antibody to IL-6 for capture and on a monoclonal antibody to human sIL-6 R for detection. Healthy controls had little, if any, detectable serum IL-6/sIL-6 R complex (OD 0.024 +/- 0.027), while the majority of patients with systemic JRA presented measurable serum IL-6/sIL-6 R complex (OD 0.492 +/- 0.546). IL-6 levels estimated in the circulating IL-6/sIL-6 R complexes were in the range of nanograms per milliliter and approximately 20-fold higher than those measured by the B9 cells. Since serum C-reactive protein concentrations were much more correlated with serum levels of IL-6/sIL-6 R complexes (r = 0.713, r2 = 0.51, P < 0.0001) than with the serum IL-6 levels measured with the B9 cells (r = 0.435, r2 = 0.19, P = 0.05), the large quantities of serum IL-6 present in IL-6/sIL-6 R complexes appear to be biologically relevant in vivo, at least as far as the induction by IL-6 of acute phase protein production.
ABL Tyrosine Kinase Inhibition Variable Effects on the Invasive Properties of Different Triple Negative Breast Cancer Cell Lines (2015)

The non-receptor tyrosine kinase ABL drives myeloid progenitor expansion in human chronic myeloid leukemia. ABL inhibition by the tyrosine kinase inhibitor nilotinib is a first-line treatment for this disease. Recently, ABL has also been implicated in the transforming properties of solid tumors, including triple negative (TN) breast cancer. TN breast cancers are highly metastatic and several cell lines derived from these tumors display high invasive activity in vitro. This feature is associated with the activation of actin-rich membrane structures called invadopodia that promote extracellular matrix degradation. Here, we investigated nilotinib effect on the invasive and migratory properties of different TN breast cancer cell lines. Nilotinib decreased both matrix degradation and invasion in the TN breast cancer cell lines MDA-MB 231 and MDA-MB 468. However, and unexpectedly, nilotinib increased by two-fold the invasive properties of the TN breast cancer cell line BT-549 and of Src-transformed fibroblasts. Both display much higher levels of ABL kinase activity compared to MDA-MB 231. Similar effects were obtained by siRNA-mediated down-regulation of ABL expression, confirming ABL central role in this process. ABL anti-tumor effect in BT-549 cells and Src-transformed fibroblasts was not dependent on EGF secretion, as recently reported in neck and squamous carcinoma cells. Rather, we identified the TRIO-RAC1 axis as an important downstream element of ABL activity in these cancer cells. In conclusion, the observation that TN breast cancer cell lines respond differently to ABL inhibitors could have implications for future therapies.
Risk-Aversive Behavior Planning under Multiple Situations with Uncertainty (2015)

This paper addresses the problem of future behavior evaluation and planning for upcoming ADAS, especially for inner city traffic scenarios. Situations in inner city traffic scenarios are generally highly complex and of high uncertainty. The behavior in such complex scenarios differs strongly depending on the actually occurring situation. In general the current situation can only be determined with high uncertainty based on current and past sensory measurements of the ego entity and the other involved entities. Additionally a situation can change very quickly, e.g. if a traffic participant suddenly changes its behavior. Here we propose an approach how to plan safe, but still efficient future behavior under consideration of multiple possible situations with different occurrence probabilities. For each situation we predict prototypical future trajectories of all involved entities using a highly general, interaction aware model Foresighted Driver Model (FDM). Then, based on a continuous, probabilistic model for future risk, we build so-called predictive risk maps, one for each possible situation, and plan the own behavior while minimizing overall risk and utility. We show that our approach generates efficient behavior for situations with high probability, while generating a "plan b" to safely deal with improbable but risky situations.
Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains (2016)

Sweet and umami tastes are perceived by T1r taste receptors in oral cavity. T1rs are class C G-protein coupled receptors (GPCRs), and the extracellular ligand binding domains (LBDs) of T1r1/T1r3 and T1r2/T1r3 heterodimers are responsible for binding of chemical substances eliciting umami or sweet taste. However, molecular analyses of T1r have been hampered due to the difficulties in recombinant expression and protein purification, and thus little is known about mechanisms for taste perception. Here we show the first molecular view of reception of a taste substance by a taste receptor, where the binding of the taste substance elicits a different conformational state of T1r2/T1r3 LBD heterodimer. Electron microscopy has showed a characteristic dimeric structure. Förster resonance energy transfer and X-ray solution scattering have revealed the transition of the dimerization manner of the ligand binding domains, from a widely spread to compactly organized state upon taste substance binding, which may correspond to distinct receptor functional states.
Imaging properties of Gaussian beams with a nonlinear graded-index rod lens (1992)

The imaging properties of Gaussian beams of light passing through a nonlinear graded-index rod are studied for the first time to our knowledge. The beam-width parameter, the distance of the focal plane, and the linear magnification in terms of the beam power, diffraction, and the rod dimensions are derived by using the variational approach and the ABCD law of Gaussian beam propagation. A comparison of these results with those derived from the ray equation and the linear case shows that the effects of the beam power on the imaging characteristics are significant.
Can yield potential be increased by manipulation of reproductive partitioning in quinoa (Chenopodium quinoa)? Evidence from gibberellic acid synthesis inhibition using Paclobutrazol (2011)

One factor conditioning quinoa (Chenopodium quinoa Willd.) adoption is the need to increase yield. This paper analyses the effect that Paclobutrazol, a GA synthesis inhibitor, produces on yield, biomass, partitioning, seed number and weight in quinoa. Two experiments were conducted under field conditions: one compared a tall genotype (2-Want) with a shorter genotype (NL-6); while the other analysed seed yield and its components using the 2-Want genotype. As a consequence of Paclobutrazol application in the one-genotype experiment, plant height decreased from 197 to 138cm, yield increased from 517 to 791gm-2, seed numbers rose from 308000 to 432000seedsperm2, and the harvest index increased from 0.282 to 0.398gg-1. Biomass accumulation and seed weight were not affected. The leaf area index was reduced by Paclobutrazol but radiation interception was only marginally reduced; soil plant analysis development (SPAD) values and specific leaf weight were increased, but radiation use efficiency was not affected by treatments. Root biomass and lateral roots tended to increase under Paclobutrazol treatment. Genotypes were compared until the end of flowering and similar responses were obtained. Higher yields could be obtained in quinoa if reproductive partitioning was increased, turning it into a good candidate in the search for high quality protein sources.
Recent developments of maritime law : Korean Collision Avoidance Rules and Apportionment of Liability (2011)

The author explains on the Korean collision avoidance rules in this article. It includes Korean statutory laws regarding collision avoidance rules and legal mechanism established by the Korean Marine Safety Tribunal (KMST) for apportionment of liability as well. The author introduces several issues in Korea involved in the interpretation of collision avoidance rules such as legal status of anchored vessel, vessel lying at sea, tug-barge, cuttlefish catching fishing boat, and recommend course. The author recommends that three countries including Korea, Japan and China should work together to unify the collision avoidance rules in order to give safe navigation in the East Asian region.
Antibody-mediated inhibition of the growth of larvae from an insect causing cutaneous myiasis in a mammalian host (1997)

Many insects feed on blood or tissue from mammalian hosts. One potential strategy for the control of these insects is to vaccinate the host with antigens derived from the insect. The larvae of the fly Lucilia cuprina feed on ovine tissue and tissue fluids causing a cutaneous myiasis associated with considerable host morbidity and mortality. A candidate vaccine antigen, peritrophin 95, was purified from the peritrophic membrane, which lines the gut of these larvae. Serum from sheep vaccinated with peritrophin 95 inhibited growth of first-instar L. cuprina larvae that fed on this serum. Growth inhibition was probably caused by antibody-mediated blockage of the normally semipermeable peritrophic membrane and the subsequent development of an impervious layer of undefined composition on the gut lumen side of the peritrophic membrane that restricted access of nutrients to the larvae. The amino acid sequence of peritrophin 95 was determined by cloning the DNA complementary to its mRNA. The deduced amino acid sequence codes for a secreted protein containing a distinct Cys-rich domain of 317 amino acids followed by a mucin-like domain of 139 amino acids. The Cys-rich domain may be involved in binding chitin. This report describes a novel immunological strategy for the potential control of L. cuprina larvae that may have general application to the control of other insect pests.
Aberrant phenylalanine metabolism in phenylketonuria heterozygotes (1998)

The wide variation in phenylalanine hydroxylating capacity observed among patients with phenylketonuria (PKU) is primarily due to allelic heterogeneity at the phenylalanine hydroxylase (PAH) locus. In this study, we examined phenylalanine metabolism after an oral phenylalanine load in 148 carriers of known PAH gene mutations. As a group, heterozygotes formed less tyrosine than normozygotes (p < 0.001), and there was a tendency that carriers of a severe PAH mutation formed less tyrosine than carriers of a mild mutation. Nevertheless, the interindividual variation was extensive, and we identified a group of individuals who formed no or very little tyrosine after the phenylalanine load. This tyrosine response was accompanied by a decreased ability to eliminate the phenylalanine test dose but did not correlate with the intrinsic severity of the mutant PAH allele. Examination of the entire coding region of the PAH gene revealed no additional sequence alterations in these subjects. Our data suggest that a subset of PKU heterozygotes have reduced phenylalanine hydroxylating capacity approaching or equalling the levels observed in genetic compounds with non-PKU mild hyperphenylalaninaemia (MHP). Awareness of this phenotypic overlap between PKU carriers and genetic compounds with two mutant alleles may be useful for clinicians and paediatricians involved in diagnosis and genetic counselling.
Identification of a nuclear factor that binds to a conserved sequence of the I-A <i>beta</i> gene. (1988)

Human and murine class II genes of the MHC show a striking homology 50 to 120 bp upstream of the transcription start site. This area is composed of two conserved sequences (a 13-mer and an 8-mer separated by 19 to 20 bp). Recently, these conserved sequences have been identified as cis-acting transcriptional regulatory elements. We have sought nuclear factors that bind specifically to an upstream fragment (-245 to +75 bp) of the murine I-A beta chain gene that contains the conserved sequences by application of a modified gel electrophoresis DNA binding assay. We report here the identification of a nuclear factor whose binding site overlaps the 8-mer conserved sequence. This factor is present in murine B and T lymphocytes, macrophages, mastocytes, fibroblasts, and human B lymphocytes and macrophages. The binding site was defined by using DNase I and dimethylsulfate protection assays. The putative binding sequence is closely related to the sequence, CCAAT, which is often found associated with the promoter of a gene and is recognized by the transcriptional factors CCAAT-binding transcription factor and nuclear factor I. Oligonucleotides that contain the binding site sequences for nuclear factor I and the alpha-globin CCAAT element, however, do not compete for binding of the nuclear factor to the sequence identified here, suggesting that, in spite of the similarity of the binding sequence, the nuclear factor identified in this report may be different. This nuclear protein may be one of the trans-acting factors that mediate transcription of class II genes.