Engineering Purely Nonlinear Coupling between Superconducting Qubits Using a Quarton.

Strong nonlinear coupling of superconducting qubits and/or photons is a critical building block for quantum information processing. Because of the perturbative nature of the Josephson nonlinearity, linear coupling is often used in the dispersive regime to approximate nonlinear coupling. However, this dispersive coupling is weak and the underlying linear coupling mixes the local modes, which, for example, distributes unwanted self-Kerr nonlinearity to photon modes. Here, we use the quarton to yield purely nonlinear coupling between two linearly decoupled transmon qubits. The quarton's zero ϕ^{2} potential enables an ultrastrong gigahertz-level cross-Kerr coupling, which is an order of magnitude stronger compared to existing schemes, and the quarton's positive ϕ^{4} potential can cancel the negative self-Kerr nonlinearity of qubits to linearize them into resonators. This ultrastrong cross-Kerr coupling between bare modes of qubit-qubit, qubit-photon, and even photon-photon is ideal for applications such as single microwave photon detection, ultrafast two-qubit gates, and readout.

Effects of the local environment on CNT-based nanoelectronics: development of a microenvironment probe station.

In this study, we report the development of a microenvironment probe station capable of detecting the effect of small changes to the local environment around a carbon nanotube conduction channel. The microenvironment probe station is highly versatile and is used to characterize alterations in carbon nanotube field effect transistor electrical behavior in response to changes in temperature, gas species, infrared and ultraviolet light. All devices were electrically characterized in atmospheric, ultrahigh vacuum and oxygen-rich environments. The results suggest that devices could be changed from n-type at 1 x 10(-8) torr through an intermediate ambipolar state at 1 x 10(-4) torr to p-type at atmosphere solely by increasing the oxygen concentration. The average resistance of these carbon nanotube field effect transistors after annealing was observed to decrease by approximately 54% from their initial value under ultrahigh vacuum to their final value in the presence of pure oxygen while corresponding threshold voltages shifts were also observed. Illumination with infrared light resulted in a approximately 10% increase in drain current with an estimated response time <1 fs due to photon-induced electron-hole pair generation. Illumination with ultraviolet light resulted in approximately 5-15% reduction in drain current due to photon-induced desorption of oxygen adsorbate.

Low temperature synthesis of vertically aligned carbon nanotubes with electrical contact to metallic substrates enabled by thermal decomposition of the carbon feedstock.

Growth of vertically aligned carbon nanotube (CNT) carpets on metallic substrates at low temperatures was achieved by controlled thermal treatment of ethylene and hydrogen at a temperature higher than the substrate temperature. High-resolution transmission electron microscopy showed that nanotubes were crystalline for a preheating temperature of 770 degrees C and a substrate temperature of 500 degrees C. Conductive atomic force microscopy measurements indicated electrical contact through the CNT carpet to the metallic substrate with an approximate resistance of 35 kOmega for multiwall carpets taller than two micrometers. An analysis of the activation energies indicated that thermal decomposition of the hydrocarbon/hydrogen gas mixture was the rate-limiting step for low-temperature chemical vapor deposition growth of CNTs. These results represent a significant advance toward the goal of replacing copper interconnects with nanotubes using CMOS-compatible processes.

Connecting single molecule electrical measurements to ensemble spectroscopic properties for quantification of single-walled carbon nanotube separation.

We directly compared ensemble spectroscopic measurements to a statistically rigorous single molecule electrical characterization of individual SWNT devices using a high throughput electrical probe station and reported, for the first time, a highly accurate extinction coefficient ratio for metallic to semiconducting SWNTs of 0.352 +/- 0.009. The systematic counting of metallic and semiconducting types from solution also allows us to examine the variances associated with device properties and therefore provide the first measure of potential defect generation during processing methods.

Inparanoid: a comprehensive database of eukaryotic orthologs.

The Inparanoid eukaryotic ortholog database (http://inparanoid.cgb.ki.se/) is a collection of pairwise ortholog groups between 17 whole genomes; Anopheles gambiae, Caenorhabditis briggsae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Takifugu rubripes, Gallus gallus, Homo sapiens, Mus musculus, Pan troglodytes, Rattus norvegicus, Oryza sativa, Plasmodium falciparum, Arabidopsis thaliana, Escherichia coli, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Complete proteomes for these genomes were derived from Ensembl and UniProt and compared pairwise using Blast, followed by a clustering step using the Inparanoid program. An Inparanoid cluster is seeded by a reciprocally best-matching ortholog pair, around which inparalogs (should they exist) are gathered independently, while outparalogs are excluded. The ortholog clusters can be searched on the website using Ensembl gene/protein or UniProt identifiers, annotation text or by Blast alignment against our protein datasets. The entire dataset can be downloaded, as can the Inparanoid program itself.

OrthoDisease: a database of human disease orthologs.

One of the greatest promises of genome sequencing projects is to further the understanding of human diseases and to develop new therapies. Model organism genomes have been sequenced in parallel to human genomes to provide effective tools for the investigation of human gene function. Many of their genes share a common ancestry and function with human genes, and this is particularly true for orthologous genes. Here we present OrthoDisease, a comprehensive database of model organism genes that are orthologous to human disease genes. OrthoDisease was constructed by applying the Inparanoid ortholog detection algorithm to disease genes derived from the Online Mendelian Inheritance in Man database (OMIM). Pairwise whole genome/proteome comparisons between Homo sapiens and six other organisms were performed to identify ortholog clusters. OMIM numbers were extracted from the OMIM Morbid Map and were converted to gene sequences using the Locuslink mim2loc and loc2acc tables. These were mapped to Inparanoid ortholog clusters using Blast. The number of ortholog clusters in OrthoDisease with each respective species is currently: M. musculus, 1,354; D. melanogaster, 724; C. elegans, 533; A. thaliana, 398; S. cerevisiae, 290; and E. coli, 153. The database is accessible online at http://orthodisease.cgb.ki.se, and can be searched with disease or protein names. The web interface presents all ortholog clusters that include a selected disease gene. A capability to download the entire dataset is also provided.

Prevalence and factors associated with asymptomatic gonococcal and chlamydial infection among US Navy and Marine Corps men infected with the HIV: a cohort study.

OBJECTIVES: Neisseria gonorrhoeae (GC) and Chlamydia trachomatis (CT) can facilitate transmission of HIV. Men who have sex with men (MSM) may harbour infections at genital and extragenital sites. Data regarding extragenital GC and CT infections in military populations are lacking. We examined the prevalence and factors associated with asymptomatic GC and CT infection among this category of HIV-infected military personnel. DESIGN: Cross-sectional cohort study (pilot). SETTING: Infectious diseases clinic at a single military treatment facility in San Diego, CA. PARTICIPANTS: Ninety-nine HIV-positive men were evaluated-79% men who had sex with men, mean age 31 years, 36% black and 33% married. INCLUSION CRITERIA: male, HIV-infected, Department of Defense beneficiary. EXCLUSION CRITERIA: any symptom related to the urethra, pharynx or rectum. PRIMARY OUTCOME MEASURES: GC and CT screening results. RESULTS: Twenty-four per cent were infected with either GC or CT. Rectal swabs were positive in 18% for CT and 3% for GC; pharynx swabs were positive in 8% for GC and 2% for CT. Only one infection was detected in the urine (GC). Anal sex (p=0.04), male partner (OR 7.02, p=0.04) and sex at least once weekly (OR 3.28, p=0.04) were associated with infection. Associated demographics included age <35 years (OR 6.27, p=0.02), non-Caucasian ethnicity (p=0.03), <3 years since HIV diagnosis (OR 2.75, p=0.04) and previous sexually transmitted infection (STI) (OR 5.10, p=0.001). CONCLUSIONS: We found a high prevalence of extragenital GC/CT infection among HIV-infected military men. Only one infection was detected in the urine, signalling the need for aggressive three-site screening of MSM. Clinicians should be aware of the high prevalence in order to enhance health through comprehensive STI screening practices.

Effect of layer stacking on the electronic structure of graphene nanoribbons.

The evolution of electronic structure of graphene nanoribbons (GNRs) as a function of the number of layers stacked together is investigated using ab initio density functional theory (DFT), including interlayer van der Waals interactions. Multilayer armchair GNRs (AGNRs), similar to single-layer AGNRs, exhibit three classes of band gaps depending on their width. In zigzag GNRs (ZGNRs), the geometry relaxation resulting from interlayer interactions plays a crucial role in determining the magnetic polarization and the band structure. The antiferromagnetic (AF) interlayer coupling is more stable compared to the ferromagnetic (FM) interlayer coupling. ZGNRs with the AF in-layer and AF interlayer coupling have a finite band gap, while ZGNRs with the FM in-layer and AF interlayer coupling do not have a band gap. The ground state of the bilayer ZGNR is nonmagnetic with a small but finite band gap. The magnetic ordering is less stable in multilayer ZGNRs compared to that in single-layer ZGNRs. The quasiparticle GW corrections are smaller for bilayer GNRs compared to single-layer GNRs because of the reduced Coulomb effects in bilayer GNRs compared to single-layer GNRs.

HLA-Cw*0602 associates more strongly to psoriasis in the Swedish population than variants of the novel 6p21.3 gene PSORS1C3.

The PSORS1 locus in the major histocompatibility complex region on chromosome 6p21.3 contains a major predisposing factor for psoriasis for which several candidate genes have been tested. The analyses are complicated by strong linkage disequilibrium in the region and the complex genetic background of psoriasis. In the search for an alternative to HLA-C we have identified a novel gene, PSORS1C3, and characterized it with regard to psoriasis. PSORS1C3 is located approximately 7 kb centromeric to POU5F1. A putative protein of 58 amino acids was predicted and expression was detected in both normal and psoriasis skin. Sequencing of the coding region revealed a total of 11 single nucleotide polymorphisms. When comparing the frequencies of PSORS1C3 variants in a case-control material in the Swedish population, three single nucleotide polymorphisms displayed significant association with psoriasis. This association appeared to be HLA-Cw*0602-dependent due to linkage disequilibrium, thus HLA-C remains the strongest associating factor in the region.

STG does not associate with psoriasis in the Swedish population.

Psoriasis is a chronic inflammatory skin disease that is known to have a strong genetic predisposition. Several psoriasis-susceptibility loci have been previously found through genomic scans. Of these, psoriasis-susceptibility region 1 (PSORS1) on chromosome 6p21 remains the most consistently identified region across populations with the highest association with disease. STG is a gene that was previously isolated from rhesus monkey taste buds, and its ortholog in humans was found to be part of the cluster of genes in PSORS1, which is telomeric to HLA-C. Upon characterization of STG, we identified several sequence variants and investigated their association with psoriasis in cases and controls from the Swedish population. None of these STG single-nucleotide polymorphisms were found to be significantly associated with psoriasis. However, HLA-Cw*0602 status was strongly associated with disease. STG expression was investigated in human tissues and found not to be restricted to taste buds, with signals also being detected in skin and tonsils.

Polymorphisms in the SEEK1 and SPR1 genes on 6p21.3 associate with psoriasis in the Swedish population.

Psoriasis is a chronic skin disease that results in red and scaly lesions. Several psoriasis susceptibility loci have been identified across the genome, of which PSORS1 on 6p21.3 is predominant. There is an ongoing debate regarding whether the HLA-C allele, Cw*0602, can be considered the major predisposing factor in this region. Investigation of other genes in the PSORS1 region with regard to psoriasis may provide alternate candidates to HLA-C. We have characterized two overlapping genes, SEEK1 and SPR1. SEEK1 encodes two putative protein isoforms: the first being one of 152 amino acids from the full-length splice-isoform (exon 1-6), and the second being one of 100 amino acids from an alternate splice-isoform (exon 1 and 6). SPR1 encodes a highly conserved protein of 134 amino acids, and in addition to characterization of human SPR1 we report the cloning of its orthologs in mouse and pig. Both SEEK1 and SPR1 are expressed in normal and psoriasis skin. In a case-control study, five of the nine single nucleotide polymorphisms (SNPs) found in SEEK1 were associated with psoriasis, while one of the four SNPs found in SPR1 showed association. Testing the Cw*0602 confounding status revealed that two of the SEEK1 SNPs showed Cw*0602-independent association, while the SPR1 SNP showed Cw*0602-dependent association. The second exon of SEEK1, containing the two Cw*0602-independent SNPs, showed the highest concentration of the psoriasis-associating SNPs, but did not appear to be translated.

Neutrophil gelatinase-associated lipocalin is a marker for dysregulated keratinocyte differentiation in human skin.

Neutrophil gelatinase-associated lipocalin (NGAL) is a 25-kDa protein initially isolated from the specific granules of human neutrophils. It is a member of the highly heterogeneous lipocalin protein family, which shares a common tertiary structure. Its synthesis is induced in gastrointestinal epithelium in association with inflammation and malignancy. To gain insight into its potential role in other epithelia we have investigated the expression of NGAL in human skin embryonic development, in normal adult skin, and in skin associated with inflammation and neoplastic transformation. In the present study we report that the embryonic expression of NGAL appears to be regulated in a spatio-temporal pattern. It was induced in the interfollicular epidermis at 20-24 weeks of gestational age but thereafter progressively receded towards the hair follicles. In normal adult skin, NGAL was detected solely in association with hair follicles. However, strong induction of NGAL in the epidermis was seen in a variety of skin disorders characterized by dysregulated epithelial differentiation such as psoriasis, pityriasis rubra and squamous cell carcinoma. In these tissues production of NGAL was confined to spatially distinct subpopulations of keratinocytes underlying areas of parakeratosis, whereas skin samples lacking parakeratotic epithelium such as lichen ruber planus, acute contact eczema and basal cell carcinoma were negative for NGAL. Consistent with being a marker for disturbed terminal differentiation, NGAL immunoreactivity showed an inverse pattern when compared with that of the differentiation marker filaggrin. The biologic functions of NGAL in epithelia are not fully known, although an immunomodulatory role in host defense has been proposed. In addition, the transient interfollicular NGAL expression during skin embryogenesis along with the induction of NGAL in adult parakeratotic epidermis suggests it play a role in epithelial differentiation pathways.