High temperature luminescence of Dy3+ in crystalline silicon in the optical communication and eye-safe spectral regions.

We report on photoluminescence in the 1.3 and 1.7 µm spectral ranges in silicon doped with dysprosium. This is attributed to the Dy3+ internal transitions between the second Dy3+ excited state and the ground state, and between the third Dy3+ excited state and the ground state. Luminescence is achieved by Dy implantation into Si substrates codoped with boron, to form dislocation loops, and show a strong dependence on fabrication process. The spectra consist of several sharp lines with the strongest emission at 1736 nm, observed up to 200 K. No Dy3+ luminescence is observed in samples without B codoping, showing the paramount importance of dislocation loops to enable the Dy emission.

Sub-ångstrom experimental validation of molecular dynamics for predictive modeling of extended defect structures in Si.

In this Letter we present the detailed, quantitative comparison between experimentally and theoretically derived structures of the extended {311} defect in silicon. Agreement between experimental and theoretical column positions of better than ±0.05 nm has been achieved for all 100 atomic columns in the defect structure. This represents a calculated density of 5.5×10(14) silicon interstitials per cm(2) on {311} planes, in agreement with previous work [S. Takeda, Jpn. J. Appl. Phys., Part 2, 30, L639 (1991)]. We show that although the {311} defect is made up of five-, six-, seven-, and eight-member rings, the shape of these rings varies as a function of position along the defect, and these variations can be determined experimentally with high precision and accuracy. The excellent agreement between the calculated and experimentally derived structure, including the position of atomic columns and the shape of the distinct structural units of the defect, provides strong evidence for the quality and robustness of the molecular dynamics simulation approach for structural studies of defects. The experimental approach is straightforward, without the need for complicated image processing methods, and is therefore widely applicable.

Insights into the genetic architecture of osteoarthritis from stage 1 of the arcOGEN study.

OBJECTIVES: The genetic aetiology of osteoarthritis has not yet been elucidated. To enable a well-powered genome-wide association study (GWAS) for osteoarthritis, the authors have formed the arcOGEN Consortium, a UK-wide collaborative effort aiming to scan genome-wide over 7500 osteoarthritis cases in a two-stage genome-wide association scan. Here the authors report the findings of the stage 1 interim analysis. METHODS: The authors have performed a genome-wide association scan for knee and hip osteoarthritis in 3177 cases and 4894 population-based controls from the UK. Replication of promising signals was carried out in silico in five further scans (44,449 individuals), and de novo in 14 534 independent samples, all of European descent. RESULTS: None of the association signals the authors identified reach genome-wide levels of statistical significance, therefore stressing the need for corroboration in sample sets of a larger size. Application of analytical approaches to examine the allelic architecture of disease to the stage 1 genome-wide association scan data suggests that osteoarthritis is a highly polygenic disease with multiple risk variants conferring small effects. CONCLUSIONS: Identifying loci conferring susceptibility to osteoarthritis will require large-scale sample sizes and well-defined phenotypes to minimise heterogeneity.

Bone mineral density, osteoporosis, and osteoporotic fractures: a genome-wide association study.

BACKGROUND: Osteoporosis is diagnosed by the measurement of bone mineral density, which is a highly heritable and multifactorial trait. We aimed to identify genetic loci that are associated with bone mineral density. METHODS: In this genome-wide association study, we identified the most promising of 314 075 single nucleotide polymorphisms (SNPs) in 2094 women in a UK study. We then tested these SNPs for replication in 6463 people from three other cohorts in western Europe. We also investigated allelic expression in lymphoblast cell lines. We tested the association between the replicated SNPs and osteoporotic fractures with data from two studies. FINDINGS: We identified genome-wide evidence for an association between bone mineral density and two SNPs (p<5x10(-8)). The SNPs were rs4355801, on chromosome 8, near to the TNFRSF11B (osteoprotegerin) gene, and rs3736228, on chromosome 11 in the LRP5 (lipoprotein-receptor-related protein) gene. A non-synonymous SNP in the LRP5 gene was associated with decreased bone mineral density (rs3736228, p=6.3x10(-12) for lumbar spine and p=1.9x10(-4) for femoral neck) and an increased risk of both osteoporotic fractures (odds ratio [OR] 1.3, 95% CI 1.09-1.52, p=0.002) and osteoporosis (OR 1.3, 1.08-1.63, p=0.008). Three SNPs near the TNFRSF11B gene were associated with decreased bone mineral density (top SNP, rs4355801: p=7.6x10(-10) for lumbar spine and p=3.3x10(-8) for femoral neck) and increased risk of osteoporosis (OR 1.2, 95% CI 1.01-1.42, p=0.038). For carriers of the risk allele at rs4355801, expression of TNFRSF11B in lymphoblast cell lines was halved (p=3.0x10(-6)). 1883 (22%) of 8557 people were at least heterozygous for these risk alleles, and these alleles had a cumulative association with bone mineral density (trend p=2.3x10(-17)). The presence of both risk alleles increased the risk of osteoporotic fractures (OR 1.3, 1.08-1.63, p=0.006) and this effect was independent of bone mineral density. INTERPRETATION: Two gene variants of key biological proteins increase the risk of osteoporosis and osteoporotic fracture. The combined effect of these risk alleles on fractures is similar to that of most well-replicated environmental risk factors, and they are present in more than one in five white people, suggesting a potential role in screening.

Free carrier lifetime modification for silicon waveguide based devices.

We investigate the effect of silicon ion irradiation on free carrier lifetime in silicon waveguides, and thus its ability to reduce the density of two-photon-absorption (TPA) generated free carriers. Our experimental results show that free carrier lifetime can be reduced significantly by silicon ion implantation. Associated excess optical absorption from the implanted ions can be reduced to an acceptable level if irradiation energy and dose are correctly chosen. Simulations of Raman scattering suggest that net gain can be achieved in certain cases without the need for an integrated diode in reverse bias to remove the photo-generated free carriers.

Collective electronic excitations in the ultra violet regime in 2-D and 1-D carbon nanostructures achieved by the addition of foreign atoms.

Plasmons in the visible/UV energy regime have attracted great attention, especially in nano-materials, with regards to applications in opto-electronics and light harvesting; tailored enhancement of such plasmons is of particular interest for prospects in nano-plasmonics. This work demonstrates that it is possible, by adequate doping, to create excitations in the visible/UV regime in nano-carbon materials, i.e., carbon nanotubes and graphene, with choice of suitable ad-atoms and dopants, which are introduced directly into the lattice by low energy ion implantation or added via deposition by evaporation. Investigations as to whether these excitations are of collective nature, i.e., have plasmonic character, are carried out via DFT calculations and experiment-based extraction of the dielectric function. They give evidence of collective excitation behaviour for a number of the introduced impurity species, including K, Ag, B, N, and Pd. It is furthermore demonstrated that such excitations can be concentrated at nano-features, e.g., along nano-holes in graphene through metal atoms adhering to the edges of these holes.

Super-enhancement of 1.54 µm emission from erbium codoped with oxygen in silicon-on-insulator.

We report on the super enhancement of the 1.54 µm Er emission in erbium doped silicon-on-insulator when codoped with oxygen at a ratio of 1:1. This is attributed to a more favourable crystal field splitting in the substitutional tetrahedral site favoured for the singly coordinated case. The results on these carefully matched implant profiles show that optical response is highly determined by the amount and ratio of erbium and oxygen present in the sample and ratios of O:Er greater than unity are severely detrimental to the Er emission. The most efficient luminescence is forty times higher than in silicon-on-insulator implanted with Er only. This super enhancement now offers a realistic route not only for optical communication applications but also for the implementation of silicon photonic integrated circuits for sensing, biomedical instrumentation and quantum communication.

Coherent creation and destruction of orbital wavepackets in Si:P with electrical and optical read-out.

The ability to control dynamics of quantum states by optical interference, and subsequent electrical read-out, is crucial for solid state quantum technologies. Ramsey interference has been successfully observed for spins in silicon and nitrogen vacancy centres in diamond, and for orbital motion in InAs quantum dots. Here we demonstrate terahertz optical excitation, manipulation and destruction via Ramsey interference of orbital wavepackets in Si:P with electrical read-out. We show milliradian control over the wavefunction phase for the two-level system formed by the 1s and 2p states. The results have been verified by all-optical echo detection methods, sensitive only to coherent excitations in the sample. The experiments open a route to exploitation of donors in silicon for atom trap physics, with concomitant potential for quantum computing schemes, which rely on orbital superpositions to, for example, gate the magnetic exchange interactions between impurities.

Physical mapping of chromosome 6: a strategy for the rapid generation of sequence-ready contigs.

The development of radiation hybrid (RH) mapping (Cox et al., 1990) and the availability of large numbers of STS markers, together with extensive bacterial clone resources provided a means to accelerate the process of mapping a human chromosome and preparing bacterial clone contigs ready to sequence. Our aim is to construct physical clone maps covering those regions of chromosome 6 that are not currently extensively mapped, and use these to determine the DNA sequence of the whole chromosome. We report here a strategy which initially involves establishing a high density framework map using RH mapping. The framework markers are then used for the identification of bacterial genomic clones covering the chromosome. The bacterial clones are analysed by restriction enzyme fingerprinting and STS-content analysis to identify sequence-ready contigs. Contig gap closure will also be performed by clone walking.

[Molecular cloning of some components of the translation apparatus of fission yeast Schizosaccharomyces pombe and a list of its cytoplasm ic proteins genes]. / Molekuliarnoe klonirovanie nekotorykh komponentov apparata transliatsii deliashchikhsia drozhzhei Schizosaccharomyces pombe i pervichnyi unifitsirovannyi spisok genov tsitoplasmaticheskikh ribosomnykh belkov etogo mikroorganizma.

Full-length cDNAs of four new genes encoding cytoplasmic ribosomal proteins L14 and L20 (large ribosomal subunit) and S1 and S27 (small ribosomal subunit) were isolated and sequenced during the analysis of the fission yeast Schizosaccharomyces pombe genome. One of the Sz. pombe genes encoding translation elongation factor EF-2 was also cloned and its precise position on chromosome I established. A unified nomenclature was proposed, and the list of all known genetic determinants encoding cytoplasmic ribosomal proteins of Sz. pombe was compiled. By now, 76 genes/cDNAs encoding different ribosomal proteins have been identified in the fission yeast genome. Among them, 35 genes are duplicated and three homologous genes are identified for each of the ribosomal proteins L2, L16, P1, and P2.

Kinetics and morphological instabilities of stressed solid-solid phase transformations.

An atomistic model of the growth kinetics of stressed solid-solid phase transformations is presented. Solid phase epitaxial growth of (001) Si was used for comparison of new and prior models with experiments. The results indicate that the migration of crystal island ledges in the growth interface may involve coordinated atomic motion. The model accounts for morphological instabilities during stressed solid-solid phase transformations.

Lumbar vertebral and femoral neck bone mineral density are higher in postmenopausal women with the alpha 2HS-glycoprotein 2 phenotype.

alpha 2HS-glycoprotein (AHSG) is a plasma protein which becomes concentrated in the organic matrix of bone. The two most common alleles, AHSG*1 and AHSG*2, give rise to three common phenotypes. A recent report showed that a group of postmenopausal white North American women with different AHSG phenotypes differed significantly with respect to their oestrogen status. We have studied variations in bone mineral density, measured by DEXA, and levels of sex hormones and biochemical markers of bone metabolism in a group of 88 post-menopausal women unselected as to their health status. Lumbar vertebral and femoral neck bone mineral density (BMD), and the free oestradiol index were all significantly higher (P < 0.05) in women with the AHSG 2 phenotype. Values of these three parameters were lowest in the AHSG 1 phenotype and intermediate in the AHSG 2-1 phenotype. Because the differences in BMD between the AHSG 2 and 1 phenotypes represent at least a 40% difference in fracture risk, the AHSG phenotype may be of some clinical relevance as a risk factor for osteoporosis.

Wavelength conversion of 1.53-microm-wavelength picosecond pulses in an ion-implanted multiple-quantum-well all-optical switch.

An ultrafast high-contrast all-optical switch produced from a metal-organic vapor phase epitaxy-grown wafer incorporating a 50-period InGaAsP/InGaAsP multiple-quantum-well (MQW) saturable absorber (SA) and a distributed Bragg reflector is described. Postgrowth implantation with 4-MeV nitrogen ions reduces the MQW free-carrier lifetime, and hence the switch recovery time, to 5.2 ps. Incorporation of the MQW SA in an optical cavity results in switching contrast ratios greater than 10 dB. The all-optical switch is used to perform wavelength conversion of 2-ps pulses.

An efficient room-temperature silicon-based light-emitting diode.

There is an urgent requirement for an optical emitter that is compatible with standard, silicon-based ultra-large-scale integration (ULSI) technology. Bulk silicon has an indirect energy bandgap and is therefore highly inefficient as a light source, necessitating the use of other materials for the optical emitters. However, the introduction of these materials is usually incompatible with the strict processing requirements of existing ULSI technologies. Moreover, as the length scale of the devices decreases, electrons will spend increasingly more of their time in the connections between components; this interconnectivity problem could restrict further increases in computer chip processing power and speed in as little as five years. Many efforts have therefore been directed, with varying degrees of success, to engineering silicon-based materials that are efficient light emitters. Here, we describe the fabrication, using standard silicon processing techniques, of a silicon light-emitting diode (LED) that operates efficiently at room temperature. Boron is implanted into silicon both as a dopant to form a p-n junction, as well as a means of introducing dislocation loops. The dislocation loops introduce a local strain field, which modifies the band structure and provides spatial confinement of the charge carriers. It is this spatial confinement which allows room-temperature electroluminescence at the band-edge. This device strategy is highly compatible with ULSI technology, as boron ion implantation is already used as a standard method for the fabrication of silicon devices.

Quasi-phase-matched second-harmonic generation in a GaAs/AlAs superlattice waveguide by ion-implantation-induced intermixing.

We report type I second-harmonic generation by use of first-order quasi-phase matching in a GaAs/AlAs symmetric superlattice structure with femtosecond fundamental pulses at 1.55 microm. Periodic spatial modulation of the bulklike second-order susceptibility chi(zxy)(2) was achieved with quantum-well intermixing for which the group III vacancies were created by As+-ion implantation. A narrow second-harmonic bandwidth of approximately 0.9 nm (FWHM) with an average power of approximately 1.5 microW was detected, corresponding to an internal conversion efficiency of approximately 0.06%, which was considerably limited by the spectral bandwidth of the fundamental.

Enhancement of the high-magnetic-field critical current density of superconducting MgB2 by proton irradiation.

Magnesium diboride, MgB2, has a relatively high superconducting transition temperature, placing it between the families of low- and high-temperature (copper oxide based) superconductors. Supercurrent flow in MgB2 is unhindered by grain boundaries, making it potentially attractive for technological applications in the temperature range 20-30 K. But in the bulk material, the critical current density (Jc) drops rapidly with increasing magnetic field strength. The magnitude and field dependence of the critical current are related to the presence of structural defects that can 'pin' the quantized magnetic vortices that permeate the material, and a lack of natural defects in MgB2 may be responsible for the rapid decline of Jc with increasing field strength. Here we show that modest levels of atomic disorder induced by proton irradiation enhance the pinning of vortices, thereby significantly increasing Jc at high field strengths. We anticipate that either chemical doping or mechanical processing should generate similar levels of disorder, and so achieve performance that is technologically attractive in an economically viable way.

The t(X;1)(p11.2;q21.2) translocation in papillary renal cell carcinoma fuses a novel gene PRCC to the TFE3 transcription factor gene.

The specific chromosomal translocation t(X;1)(p11.2;q21.2) has been observed in human papillary renal cell carcinomas. In this study we demonstrated that this translocation results in the fusion of a novel gene designated PRCC at 1q21.2 to the TFE3 gene at Xp11.2. TFE3 encodes a member of the basic helix-loop-helix (bHLH) family of transcription factors originally identified by its ability to bind to microE3 elements in the immunoglobin heavy chain intronic enhancer. The translocation is predicted to result in the fusion of the N-terminal region of the PRCC protein, which includes a proline-rich domain, to the entire TFE3 protein. Notably the generation of the chimaeric PRCC-TFE3 gene appears to be accompanied by complete loss of normal TFE3 transcripts. This work establishes that the disruption of transcriptional control by chromosomal translocation is important in the development of kidney carcinoma in addition to its previously established role in the aetiology of sarcomas and leukaemias.

Analysis of 114 kb of DNA sequence from fission yeast chromosome 2 immediately centromere-distal to his5.

One hundred and fourteen kilobase pairs (kb) of contiguous genomic sequence have been determined immediately distal to the his5 genetic marker located about 0.9 Mb from the centromere on the long arm of Schizosaccharomyces pombe chromosome 2. The sequence is contained in overlapping cosmid clones c16H5, c12D12, c24C6 and c19G7, of which 20 kb are identical to previously reported sequence from clone c21H7. The remaining 93 781 bp of sequence contains 10 known genes (cdc14, cdm1, cps1, gpa1, msh2, pck2, rip1, rps30-2, sad1 and ubl1), 32 open reading frames (ORFs) capable of coding for proteins of at least 100 amino acid residues in length, one 5S rRNA gene, one tRNA(Pro) gene, one lone Tf1-type long terminal repeat (LTR) and one lone Tf2-type LTR. There is a density of one protein-coding gene per 2.2 kb and 22 of the 42 ORFs (52%) incorporate one or more introns. Twenty-one of the novel ORFs show sequence similarities which suggest functions of their products, including a cyclin C, a MADS box transcription factor, mad2-like protein, telomere binding protein, topoisomerase II-associated protein, ATP-dependent DEAH box RNA helicase, G10 protein, ubiquitin-activating e1-like enzyme, nucleoporin, prolyl-tRNA synthetase, peptidylprolyl isomerase, delta-1-pyrroline-5-carboxylate dehydrogenase, protein transport protein, coatomer epsilon, TCP-1 chaperonin, beta-subunit of 6-phosphofructokinase, aminodeoxychorismate lyase, a phosphate transport protein and a thioredoxin.