Surface science motivated by heating of trapped ions from the quantum ground state.

For the past two and a half decades, anomalous heating of trapped ions from nearby electrode surfaces has continued to demonstrate unexpected results. Caused by electric-field noise, this heating of the ions' motional modes remains an obstacle for scalable quantum computation with trapped ions. One of the anomalous features of this electric-field noise is the reported nonmonotonic behavior in the heating rate when a trap is incrementally cleaned by ion bombardment. Motivated by this result, the present work reports on a surface analysis of a sample ion-trap electrode treated similarly with incremental doses of Ar+ ion bombardment. Kelvin probe force microscopy and x-ray photoelectron spectroscopy were used to investigate how the work functions on the electrode surface vary depending on the residual contaminant coverage between each treatment. It is shown that the as-fabricated Au electrode is covered with a hydrocarbon film that is modified after the first treatment, resulting in work functions and core-level binding energies that resemble that of atomic-like carbon on Au. Changes in the spatial distribution of work functions with each treatment, combined with a suggested phenomenological coverage and surface-potential roughness dependence to the heating, appear to be related to the nonmonotonic behavior previously reported.

All-Mechanical Polarization Control and Anomalous (Electro)Mechanical Responses in Ferroelectric Nanowires.

Piezoelectric and ferroelectric nanowires exhibit properties and phases that are not available in the bulk. They are extremely promising for functional nanoscale application. On the basis of atomistic first-principles-based simulations, we predict an all-mechanical polarization control in ferroelectric nanowires. We report that the application of uniaxial compressive stress to ferroelectric nanowires with poor surface charge compensation leads to a reversible phase switching between the polar phase with axial polarization and macroscopically nonpolar flux-closure phase. The phase switching is associated with anomalously large changes in polarization and piezoelectric and mechanical response. In particular, in PbTiO3 nanowires the values as large as 5400 pC/N and 140 TPa-1 are predicted for the piezoelectric coefficient and elastic constant, respectively. Remarkably, the effect persists up to the gigahertz frequency which is potentially promising for nanoscale applications, such as nanogenerators, biomedical electronics, monitoring devices, nanosensors, nanotransducers, and nanoactuators.

Significant variation between SNP-based HLA imputations in diverse populations: the last mile is the hardest.

Four single nucleotide polymorphism (SNP)-based human leukocyte antigen (HLA) imputation methods (e-HLA, HIBAG, HLA*IMP:02 and MAGPrediction) were trained using 1000 Genomes SNP and HLA genotypes and assessed for their ability to accurately impute molecular HLA-A, -B, -C and -DRB1 genotypes in the Human Genome Diversity Project cell panel. Imputation concordance was high (>89%) across all methods for both HLA-A and HLA-C, but HLA-B and HLA-DRB1 proved generally difficult to impute. Overall, <27.8% of subjects were correctly imputed for all HLA loci by any method. Concordance across all loci was not enhanced via the application of confidence thresholds; reliance on confidence scores across methods only led to noticeable improvement (+3.2%) for HLA-DRB1. As the HLA complex is highly relevant to the study of human health and disease, a standardized assessment of SNP-based HLA imputation methods is crucial for advancing genomic research. Considerable room remains for the improvement of HLA-B and especially HLA-DRB1 imputation methods, and no imputation method is as accurate as molecular genotyping. The application of large, ancestrally diverse HLA and SNP reference data sets and multiple imputation methods has the potential to make SNP-based HLA imputation methods a tractable option for determining HLA genotypes.

Which spinal lesions are associated with new bone formation in patients with ankylosing spondylitis treated with anti-TNF agents? A long-term observational study using MRI and conventional radiography.

OBJECTIVE: To study the relationship of spinal inflammation and fatty degeneration (FD) as detected by MRI and new bone formation seen on conventional radiographs (CRs) in ankylosing spondylitis (AS). METHODS: CRs at baseline, 2 years and 5 years and spinal MRIs at baseline and 2 years of 73 AS patients treated with infliximab in European AS Infliximab Cohort were available. Relative risks (RR) were calculated with a general linear model after adjustment for within-patient variation. RESULTS: In a total of 1466 vertebral edges (VEs) without baseline syndesmophytes, 61 syndesmophytes developed at 5 years, the majority of which (57.4%) had no corresponding detectable MRI lesions at baseline. VEs with both inflammation and FD at baseline had the highest risk (RR 3.3, p=0.009) for syndesmophyte formation at 5 years, followed by VEs that developed new FD or did not resolve FD at 2 years (RR=2.3, p=0.034), while inflammation at baseline with no FD at 2 years had the lowest risk for syndesmophyte formation at 5 years (RR=0.8). Of the VEs with inflammation at baseline, >70% resolved completely, 28.8% turned into FD after 2 years, but only 1 syndesmophyte developed within 5 years. CONCLUSIONS: Parallel occurrence of inflammation and FD at baseline and development of FD without prior inflammation after 2 years were significantly associated with syndesmophyte formation after 5 years of anti-tumour necrosis factor (TNF) therapy. However, the sequence 'inflammation-FD-new bone formation' was rarely observed, an argument against the TNF-brake hypothesis. Whether an early suppression of inflammation leads to a decrease of the risk for new bone formation remains to be demonstrated.

Frequency comb generation in superconducting resonators.

We have generated frequency combs spanning 0.5 to 20 GHz in superconducting λ/2 resonators at T=3 K. Thin films of niobium-titanium nitride enabled this development due to their low loss, high nonlinearity, low frequency dispersion, and high critical temperature. The combs nucleate as sidebands around multiples of the pump frequency. Selection rules for the allowed frequency emission are calculated using perturbation theory, and the measured spectrum is shown to agree with the theory. Sideband spacing is measured to be accurate to 1 part in 10(8). The sidebands coalesce into a continuous comb structure observed to cover at least several frequency octaves.

Measuring a topological transition in an artificial spin-1/2 system.

We present measurements of a topological property, the Chern number (C_{1}), of a closed manifold in the space of two-level system Hamiltonians, where the two-level system is formed from a superconducting qubit. We manipulate the parameters of the Hamiltonian of the superconducting qubit along paths in the manifold and extract C_{1} from the nonadiabatic response of the qubit. By adjusting the manifold such that a degeneracy in the Hamiltonian passes from inside to outside the manifold, we observe a topological transition C_{1}=1→0. Our measurement of C_{1} is quantized to within 2% on either side of the transition.

Genetic burden in multiple sclerosis families.

A previous study using cumulative genetic risk estimations in multiple sclerosis (MS) successfully tracked the aggregation of susceptibility variants in multi-case and single-case families. It used a limited description of susceptibility loci available at the time (17 loci). Even though the full roster of MS risk genes remains unavailable, we estimated the genetic burden in MS families and assess its disease predictive power using up to 64 single-nucleotide polymorphism (SNP) markers according to the most recent literature. A total of 708 controls, 3251 MS patients and their relatives, as well as 117 twin pairs were genotyped. We validated the increased aggregation of genetic burden in multi-case compared with single-case families (P=4.14e-03) and confirm that these data offer little opportunity to accurately predict MS, even within sibships (area under receiver operating characteristic (AUROC)=0.59 (0.55, 0.53)). Our results also suggest that the primary progressive and relapsing-type forms of MS share a common genetic architecture (P=0.368; difference being limited to that corresponding to ± 2 typical MS-associated SNPs). We have confirmed the properties of individual genetic risk score in MS. Comparing with previous reference point for MS genetics (17 SNPs), we underlined the corrective consequences of the integration of the new findings from GWAS and meta-analysis.

100-fold reduction of electric-field noise in an ion trap cleaned with in situ argon-ion-beam bombardment.

Motional heating of trapped atomic ions is a major obstacle to their use as quantum bits in a scalable quantum computer. The detailed physical origin of this heating is not well understood, but experimental evidence suggests that it is caused by electric-field noise emanating from the surface of the trap electrodes. In this study, we have investigated the role of adsorbates on the electrodes by identifying contaminant overlayers, implementing an in situ argon-ion-beam cleaning treatment, and measuring ion heating rates before and after treating the trap electrodes' surfaces. We find a 100-fold reduction in heating rate after treatment. The experiments described here are sensitive to low levels of electric-field noise in the MHz frequency range. Therefore, this approach could become a useful tool in surface science that complements established techniques.

The effects of microcystin-LR in Oryza sativa root cells: F-actin as a new target of cyanobacterial toxicity.

Microcystins are toxins produced by cyanobacteria, notorious for negatively affecting a wide range of living organisms, among which several plant species. Although microtubules are a well-established target of microcystin toxicity, its effect on filamentous actin (F-actin) in plant cells has not yet been studied. Τhe effects of microcystin-LR (MC-LR) and an extract of a microcystin-producing freshwater cyanobacterial strain (Microcystis flos-aquae TAU-MAC 1510) on the cytoskeleton (F-actin and microtubules) of Oryza sativa (rice) root cells were studied with light, confocal, and transmission electron microscopy. Considering the role of F-actin in endomembrane system distribution, the endoplasmic reticulum and the Golgi apparatus in extract-treated cells were also examined. F-actin in both MC-LR- and extract-treated meristematic and differentiating root cells exhibited time-dependent alterations, ranging from disorientation and bundling to the formation of ring-like structures, eventually resulting in a collapse of the F-actin network after longer treatments. Disorganization and eventual depolymerization of microtubules, as well as abnormal chromatin condensation were observed following treatment with the extract, effects which could be attributed to microcystins and other bioactive compounds. Moreover, cell cycle progression was inhibited in extract-treated roots, specifically affecting the mitotic events. As a consequence of F-actin network disorganization, endoplasmic reticulum elements appeared stacked and diminished, while Golgi dictyosomes appeared aggregated. These results support that F-actin is a prominent target of MC-LR, both in pure form and as an extract ingredient. Endomembrane system alterations can also be attributed to the effects of cyanobacterial bioactive compounds (including microcystins) on the F-actin cytoskeleton.

Materials loss measurements using superconducting microwave resonators.

The performance of superconducting circuits for quantum computing is limited by materials losses. In particular, coherence times are typically bounded by two-level system (TLS) losses at single photon powers and millikelvin temperatures. The identification of low loss fabrication techniques, materials, and thin film dielectrics is critical to achieving scalable architectures for superconducting quantum computing. Superconducting microwave resonators provide a convenient qubit proxy for assessing performance and studying TLS loss and other mechanisms relevant to superconducting circuits such as non-equilibrium quasiparticles and magnetic flux vortices. In this review article, we provide an overview of considerations for designing accurate resonator experiments to characterize loss, including applicable types of losses, cryogenic setup, device design, and methods for extracting material and interface losses, summarizing techniques that have been evolving for over two decades. Results from measurements of a wide variety of materials and processes are also summarized. Finally, we present recommendations for the reporting of loss data from superconducting microwave resonators to facilitate materials comparisons across the field.

Longitudinal system-based analysis of transcriptional responses to type I interferons.

Type I interferons (IFNs) are pleiotropic cytokines that modulate both innate and adaptive immune responses. They have been used to treat autoimmune disorders, cancers, and viral infection and have been demonstrated to elicit differential responses within cells, despite sharing a single receptor. The molecular basis for such differential responses has remained elusive. To identify the mechanisms underlying differential type I IFN signaling, we used whole genome microarrays to measure longitudinal transcriptional events within human CD4(+) T cells treated with IFN-alpha(2b) or IFN-beta(1a). We identified differentially regulated genes, analyzed them for the enrichment of known promoter elements and pathways, and constructed a network module based on weighted gene coexpression network analysis (WGCNA). WGCNA uses advanced statistical measures to find interconnected modules of correlated genes. Overall, differential responses to IFN in CD4(+) T cells related to three dominant themes: migration, antigen presentation, and the cytotoxic response. For migration, WGCNA identified subtype-specific regulation of pre-mRNA processing factor 4 homolog B and eukaryotic translation initiation factor 4A2, which work at various levels within the cell to affect the expression of the chemokine CCL5. WGCNA also identified sterile alpha-motif domain-containing 9-like (SAMD9L) as critical in subtype-independent effects of IFN treatment. RNA interference of SAMD9L expression enhanced the migratory phenotype of activated T cells treated with IFN-beta compared with controls. Through the analysis of the dynamic transcriptional events after differential IFN treatment, we were able to identify specific signatures and to uncover novel genes that may underpin the type I IFN response.

Atom counting at surfaces.

Multiphoton resonance ionization has been combined with energetic ion bombardment to examine dopant concentrations ofindium on the surface of silicon. The results yield a linear relation between the indium concentration and the known bulk values and a detection limit of 9 parts per trillion, at a mass resolution exceeding 160. This measurement, which surpasses the limits of any previous surface analysis by a factor of 100, has been made possible with an experimental configuration that optimizes sampling and detection efficiency while reducing background noise to virtually zero. During the analysis, submonolayer quantities of the surface are removed, so that as few as 180 surface atoms may be counted.

Crystallographic orientation dependence of work function: carbon adsorption on Au surfaces.

We investigate the work function (WF) variation of different Au crystallographic surface orientations with carbon atom adsorption. Ab initio calculations within density-functional theory are performed on carbon deposited (100), (110), and (111) gold surfaces. The WF behaviour with carbon coverage for the different surface orientations is explained by the resultant electron charge density distributions. The dynamics of carbon adsorption at sub-to-one- monolayer (ML) coverage depends on the landscape of the potential energy surfaces. At higher ML coverage, because of adsorption saturation, the WF will have weak surface orientation dependence. This systematic study has consequential bearing on studies of electric-field noise emanating from polycrystalline gold ion-trap electrodes that have been largely employed in microfabricated electrodes.

256-channel magnetic imaging system.

We present the design and fabrication of a magnetoresistive imaging system capable of scanning 256 channels simultaneously along linear ranges of either 4 or 13 mm. High speed electronics read the channels and transfer the data to a computer that builds and displays the images. The system was successfully used to image magnetic tapes for real-time forensic validation purposes and can also be applied in other noninvasive imaging applications.

Development of a Thin Film Magnetic Moment Reference Material.

In this paper we present the development of a magnetic moment reference material for low moment magnetic samples. We first conducted an inter-laboratory comparison to determine the most useful sample dimensions and magnetic properties for common instruments such as vibrating sample magnetometers (VSM), SQUIDs, and alternating gradient field magnetometers. The samples were fabricated and then measured using a vibrating sample magnetometer. Their magnetic moments were calibrated by tracing back to the NIST YIG sphere, SRM 2853.

Functional interaction between Ssu72 and the Rpb2 subunit of RNA polymerase II in Saccharomyces cerevisiae.

SSU72 is an essential gene encoding a phylogenetically conserved protein of unknown function that interacts with the general transcription factor TFIIB. A recessive ssu72-1 allele was identified as a synthetic enhancer of a TFIIB (sua7-1) defect, resulting in a heat-sensitive (Ts(-)) phenotype and a dramatic downstream shift in transcription start site selection. Here we describe a new allele, ssu72-2, that confers a Ts(-) phenotype in a SUA7 wild-type background. In an effort to further define Ssu72, we isolated suppressors of the ssu72-2 mutation. One suppressor is allelic to RPB2, the gene encoding the second-largest subunit of RNA polymerase II (RNAP II). Sequence analysis of the rpb2-100 suppressor defined a cysteine replacement of the phylogenetically invariant arginine residue at position 512 (R512C), located within homology block D of Rpb2. The ssu72-2 and rpb2-100 mutations adversely affected noninduced gene expression, with no apparent effects on activated transcription in vivo. Although isolated as a suppressor of the ssu72-2 Ts(-) defect, rpb2-100 enhanced the transcriptional defects associated with ssu72-2. The Ssu72 protein interacts directly with purified RNAP II in a coimmunoprecipitation assay, suggesting that the genetic interactions between ssu72-2 and rpb2-100 are a consequence of physical interactions. These results define Ssu72 as a highly conserved factor that physically and functionally interacts with the RNAP II core machinery during transcription initiation.

Laser-assisted atom probe tomography of Ti/TiN films deposited on Si.

Laser-assisted atom probe tomography (L-APT) was used to examine superconducting TiN/Ti/TiN trilayer films with nominal respective thicknesses of 5/5/5 (nm). Such materials are of interest for applications that require large arrays of microwave kinetic inductance detectors. The trilayers were deposited on Si substrates by reactive sputtering. Electron energy loss microscopy performed in a scanning transmission electron microscope (STEM/EELS) was used to corroborate the L-APT results and establish the overall thicknesses of the trilayers. Three separate batches were studied where the first (bottom) TiN layer was deposited at 500°C (for all batches) and the subsequent TiN/Ti bilayer was deposited at ambient temperature, 250°C, and 500°C, respectively. L-APT rendered an approximately planar TiN/Si interface by making use of plausible mass-spectral assignments to N31+, SiN1+, and SiO1+. This was necessary since ambiguities associated with the likely simultaneous occurrence of Si1+ and N21+ prevented their use in rendering the TiN/Si interface upon reconstruction. The non-superconducting Ti2N phase was also revealed by L-APT. Neither L-APT nor STEM/EELS rendered sharp Ti/TiN interfaces and the contrast between these layers diminished with increased film deposition temperature. L-APT also revealed that hydrogen was present in varying degrees in all samples including control samples that were composed of single layers of Ti or TiN.

Low-noise kinetic inductance traveling-wave amplifier using three-wave mixing.

We have fabricated a wide-bandwidth, high dynamic range, low-noise cryogenic amplifier based on a superconducting kinetic inductance traveling-wave device. The device was made from NbTiN and consisted of a long, coplanar waveguide on a silicon chip. By adding a DC current and an RF pump tone we are able to generate parametric amplification using three-wave mixing. The devices exhibit gain of more than 15 dB across an instantaneous bandwidth from 4 to 8 GHz. The total usable gain bandwidth, including both sides of the signal-idler gain region, is more than 6 GHz. The noise referred to the input of the devices approaches the quantum limit, with less than 1 photon excess noise. Compared to similarly constructed four-wave mixing amplifiers, these devices operate with the RF pump at ~20 dB lower power and at frequencies far from the signal. This will permit easier integration into large scale qubit and detector applications.

Experimental increase in brain HIPDM uptake by hypercapnia.

The 30-min brain uptake of [125I]HIPDM was measured in conscious rats--normocapnic (n = 8), hypercapnic (n = 12), and hyperoxic (n = 6). A mean 41.2% higher uptake was found in the brains of hypercapnic animals (p less than 0.01). In the three groups of rats, brain HIPDM uptake had a negative correlation with body weight (p less than 0.001) and a positive correlation with arterial pCO2 (p less than 0.01), when adjusted for body weight. These results indicate that HIPDM uptake with hypercapnia may be used as a provocative test to measure cerebral blood flow reserves.

Differential relationships between positive and negative symptoms and neuropsychological deficits in schizophrenia.

UNLABELLED: This study assessed the relationships between positive and negative clinical symptoms and specific neuropsychological deficits in a group of stable schizophrenic patients. METHOD: Thirty patients were assessed using the Positive and Negative Syndrome Scale (PANSS) for schizophrenia and a battery of cognitive tests. The PANSS assessments were done by a group of raters blind to the results of cognitive tests, while the cognitive tests were conducted by a different group of raters who remained blind to the PANSS scores. RESULTS: We found that, although positive and negative symptoms showed a trend toward direct correlation with each other, they correlated with distinct cognitive deficits. Patients with higher negative scores had more perseverative responses, perservative errors, and completed fewer categories on the Wisconsin Card Sorting Test; they also experienced more difficulties on trail making and verbal fluency tests. On the other hand, positive symptoms were associated with poor performance on the Digit Span, particularly the Digit Span Forward. CONCLUSIONS: Our findings are in agreement with previous reports that negative symptoms may be associated with poor performance on cognitive tests reflecting particularly frontal function. Positive symptoms, on the other hand, seem to be associated with poor attention, specifically of auditory type, and thus, possibly with dysfunction within the more widespread neural networks underlying attention. Our findings support the hypothesis that positive and negative symptoms may be associated with distinct neuropsychological deficits and thus with distinct neurological substrates and point to the need to address both positive and negative dimensions when studying schizophrenia.