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.

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.

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.

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.

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.

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.

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.

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.

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.

Transcriptional expression patterns triggered by chemically distinct neuroprotective molecules.

Glutamate-mediated excitotoxicity has been purported to underlie many neurodegenerative disorders. A subtype of glutamate receptors, namely N-methyl-d-aspartate (NMDA) receptors, has been recognized as potential targets for neuroprotection. To increase our understanding of the mechanisms that underlie this neuroprotection, we employed a mouse model of glutamate receptor-induced excitotoxic injury. Primary cortical neurons derived from postnatal day-0 CD-1 mice were cultured in the presence or absence of neuroprotective molecules and exposed to NMDA. Following a recovery period, whole genome expression was measured by microarray analysis. We used a combination of database and text mining, as well as systems modeling to identify signatures within the differentially expressed genes. While molecules differed in their mechanisms of action, we found significant overlap in the expression of a core group of genes and pathways. Many of these molecules have clear links to neuronal protection and survival, including ion channels, transporters, as well as signaling pathways including the mitogen-activated protein kinase (MAPK), the Toll-like receptor (TLR), and the hypoxic inducible factor (HIF). Within the TLR pathway, we also discovered a significant enrichment of interferon regulatory factor 7 (IRF7)-regulated genes. Knockdown of Irf7 by RNA interference resulted in reduced survival following NMDA treatment. Given the prominent role that IRF7 plays in the transduction of type-I interferons (IFNs), we also tested whether type-I IFNs alone functioned as neuroprotective agents and found that type-I IFNs were sufficient to promote neuronal survival. Our data suggest that the TLR/IRF7/IFN axis plays a significant role in recovery from glutamate-induced excitotoxicity.

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.

Cholelithiasis in a neonate with chylous ascites.

A case of a neonate with congenital chylous ascites resulting from primary lymphatic dysplasia is described. The baby also presented with a sludge ball in the gallbladder that eventually progressed to gallstones. The association of chylous ascites with cholelithiasis in this neonate is discussed.

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.

Gigantic hepatic amebic abscess presenting as acute abdomen: a case report.

INTRODUCTION: Amebiasis is a parasitic disease caused by Entamoeba histolytica. It most commonly results in asymptomatic colonization of the gastrointestinal tract, but some patients develop intestinal invasive or extra-intestinal diseases. Liver abscess is the most common extra-intestinal manifestation. The large number of clinical presentations of amebic liver abscess makes the diagnosis very challenging in non-endemic countries. Late diagnosis of the amebic abscess may lead to perforation and amebic peritonitis, resulting in high mortality rates. CASE PRESENTATION: This report describes a 37-year-old white man, suffering from hepatitis B, with a gigantic amebic liver abscess presenting as an acute abdomen due to its rupture. Rapid deterioration of the patient's condition and acute abdomen led to an emergency operation. A large volume of free fluid together with debris was found at the moment of entry into the peritoneal cavity because of a rupture of the hepatic abscess at the position of the segment VIII. Surgical drainage of the hepatic abscess was performed; two wide drains were placed in the remaining hepatic cavities and one on the right hemithorax. The patient was hospitalized in the ICU for 14 days and for another 14 days in our department. The diagnosis of amebic abscess was made by the pathologists who identified E. histolytica in the debris. CONCLUSION: Acute abdomen due to a ruptured amebic liver abscess is extremely rare in western countries where the parasite is not endemic. Prompt diagnosis and treatment are fundamental to preserving the patient's life since the mortality rates remain extremely high when untreated, even nowadays.

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.

Akinetic mutism followed by a manic reaction on introduction of steroid replacement for Addison's disease.

Neuropsychiatric changes during exogenous corticosteroid administration are well-recognized. However, reports of neuropsychiatric reactions to corticosteroid replacement for Addison's disease are distinctively rare. We report on a patient with primary adrenocortical insufficiency, initially presenting with depressive symptoms, who developed akinetic mutism followed by acute manic illness shortly after the initiation of steroid replacement. Both disorders occurred with physiological doses of hydrocortisone and resolved spontaneously. The pathogenesis of the above neuropsychiatric reactions is discussed in the context of glucocorticoid receptor-related brain effects of glucocorticoids. In addition, this report points to the need for accurate psychiatric assessment of patients with Addison's disease upon introduction of replacement therapy.