Supersymmetry on the honeycomb lattice: resonating charge stripes, superfrustration, and domain walls

We study a model of spinless fermions on the honeycomb lattice with nearest-neighbor exclusion and extended repulsive interactions that exhibits `lattice supersymmetry' [P. Fendley, K. Schoutens, and J. de Boer, Phys. Rev. Lett. 90, 120402 (2003)]. Using a combination of exact diagonalization of large ($N\leq56$ site) systems, mean-field numerics, and symmetry analysis, we establish a rich phase structure as a function of fermion density, that includes non-Fermi liquid behavior, resonating charge stripes, domain-wall and bubble physics, and identify a finite range of fillings with extensive ground state degeneracy and both gapped and gapless spectra. We comment on the stability of our results to relaxing the stringent requirements for supersymmetry, and on their possible broader relevance to systems of strongly-correlated electrons with extended repulsive interactions.Comment: 15 pages, 12 figures, 1 tabl

Conserved syntenic clusters of protein coding genes are missing in birds

BACKGROUND: Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood. RESULTS: Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal rearrangements, and are largely present in crocodiles, suggesting that their loss occurred subsequent to the split of dinosaurs/birds from crocodilians. Many of these genes are associated with lethality in rodents, human genetic disorders, or biological functions targeting various tissues. Functional enrichment analysis combined with orthogroup analysis and paralog searches revealed enrichments that were shared by non-avian species, present only in birds, or shared between all species. CONCLUSIONS: Together these results provide a clearer definition of the genetic background of extant birds, extend the findings of previous studies on missing avian genes, and provide clues about molecular events that shaped avian evolution. They also have implications for fields that largely benefit from avian studies, including development, immune system, oncogenesis, and brain function and cognition. With regards to the missing genes, birds can be considered ‘natural knockouts’ that may become invaluable model organisms for several human diseases. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0565-1) contains supplementary material, which is available to authorized users

Numerical modeling and design decisions for aerostatic bearings with relatively large nozzle sizes in Magic-Angle Spinning (MAS) systems

The work was supported by an ERC Advanced Grant (B.H.M., grant number 741863, FASTER), and by the Swiss National Science Foundation (B.H.M., grant number 200020_188711).Numerical stability analysis for aerostatic bearings was performed to obtain optimized design parameters for small submillimeter to millimeter range diameter cylindrical rotors. Such rotors are used in nuclear magnetic resonance (NMR) application to rotate sample around an axis inclined by magic angle (54.74) relative to the magnetic field direction at rotational frequencies of about 100 kHz (magic-angle spinning, MAS). The governing Reynolds equation for the fluid film between rotor and bearing was modified for small size aerostatic bearings with relatively large nozzle diameters. The modified Reynolds equation was solved using a finite-volume method to obtain pressure and film thickness around the rotor. This led to the solution of the maximum stable inertial force as a function of rotational frequency and design parameters. The comparison with aerostatic bearings with infinitesimal nozzle sizes was obtained for supported rotor weight and critical vibrational frequency of the rotor. The stable inertial force was found to correspond to a specific nozzle diameter and a specific rotor–bearing clearance. Numerical investigation also shows an enhancement of stable inertial force with decreasing nozzle number or increasing molecular mass of the impinging gas for a specific range of nozzle parameters. Experimental observations further confirmed the role of nozzle diameter, nozzle number and molecular weight of the gas in enhancing the rotor spinning frequency. Further, design decisions were made based on such analysis and were tested for varying rotor size and bearing properties. Using design optimization based on numerical simulation, the maximum frequency of rotation for a home-built 0.4 mm MAS rotor could be enhanced from 25 kHz up to 110 kHz, still below the extrapolation from large rotors

An Index of Biotic Integrity for Macroinvertebrate Stream Bioassessment Conducted by Community Scientists

Community science bioassessment has great potential to inform comprehensive stream management plans, but regional analytical tools are needed to evaluate macroinvertebrate data collected through community science programs. To this end, we modified a pre-existing professional index of biotic integrity (IBI) to create a community science IBI (CS-IBI), designed for stream macroinvertebrate data collected by community scientists with minimal training. We used data collected by both professional and community scientists to develop, calibrate, and validate the CS-IBI at 76 streamsites in the Puget Lowland andWillamette Valley ecoregions of the PacificNorthwest in theUnited States. Community science data were taxonomically coarser andmore variable than data generated by professionals; however, IBI scores and assemblage data were statistically similar between community science and professional data. Stream impairment categories classified by family-level CS-IBI scores matched genus-level professional classifications 65% of the time and never diverged by \u3e1 category. CS-IBI scores were negatively related to the percentage of agriculture and land development in the watershed, although this relationship was weaker than for professional IBI scores. Despite increased variability in data generated by community scientists, our findings suggest the CS-IBI performs similarly to a professional IBI across a gradient of human influence. Although we do not advocate using the CS-IBI in regulatory settings, we believe the development of community science IBIs enhances, expands, and strengthens public partnerships, thereby supporting environmental managers’ efforts to monitor and restore degraded streams and rapidly respond to pollution events. Our hope is that the CS-IBI will improve the applicability of community science bioassessment data and serve as a model for how agencies can develop regionalized macroinvertebrate IBIs for use in comprehensive watershed management plans. Key words: citizen science, community science, stream macroinvertebrates, stream bioassessment, index of biotic integrity, watershed stressor

Abbreviated dignity therapy for adults with advanced-stage cancer and their family caregivers: Qualitative analysis of a pilot study

Objective Dignity therapy (DT) is designed to address psychological and existential challenges that terminally ill individuals face. DT guides patients in developing a written legacy project in which they record and share important memories and messages with those they will leave behind. DT has been demonstrated to ease existential concerns for adults with advanced-stage cancer; however, lack of institutional resources limits wide implementation of DT in clinical practice. This study explores qualitative outcomes of an abbreviated, less resource-intensive version of DT among participants with advanced-stage cancer and their legacy project recipients. Method Qualitative methods were used to analyze postintervention interviews with 11 participants and their legacy recipients as well as the created legacy projects. Direct content analysis was used to assess feedback from the interviews about benefits, barriers, and recommendations regarding abbreviated DT. The legacy projects were coded for expression of core values. Result Findings suggest that abbreviated DT effectively promotes (1) self-expression, (2) connection with loved ones, (3) sense of purpose, and (4) continuity of self. Participants observed that leading the development of their legacy projects promoted independent reflection, autonomy, and opportunities for family interaction when reviewing and discussing the projects. Consistent with traditional DT, participants expressed “family” as the most common core value in their legacy projects. Expression of “autonomy” was also a notable finding. Significance of results Abbreviated DT reduces resource barriers to conducting traditional DT while promoting similar benefits for participants and recipients, making it a promising adaptation warranting further research. The importance that patients place on family and autonomy should be honored as much as possible by those caring for adults with advanced-stage cancer

The Science of Sungrazers, Sunskirters, and Other Near-Sun Comets

This review addresses our current understanding of comets that venture close to the Sun, and are hence exposed to much more extreme conditions than comets that are typically studied from Earth. The extreme solar heating and plasma environments that these objects encounter change many aspects of their behaviour, thus yielding valuable information on both the comets themselves that complements other data we have on primitive solar system bodies, as well as on the near-solar environment which they traverse. We propose clear definitions for these comets: We use the term near-Sun comets to encompass all objects that pass sunward of the perihelion distance of planet Mercury (0.307 AU). Sunskirters are defined as objects that pass within 33 solar radii of the Sun’s centre, equal to half of Mercury’s perihelion distance, and the commonly-used phrase sungrazers to be objects that reach perihelion within 3.45 solar radii, i.e. the fluid Roche limit. Finally, comets with orbits that intersect the solar photosphere are termed sundivers. We summarize past studies of these objects, as well as the instruments and facilities used to study them, including space-based platforms that have led to a recent revolution in the quantity and quality of relevant observations. Relevant comet populations are described, including the Kreutz, Marsden, Kracht, and Meyer groups, near-Sun asteroids, and a brief discussion of their origins. The importance of light curves and the clues they provide on cometary composition are emphasized, together with what information has been gleaned about nucleus parameters, including the sizes and masses of objects and their families, and their tensile strengths. The physical processes occurring at these objects are considered in some detail, including the disruption of nuclei, sublimation, and ionisation, and we consider the mass, momentum, and energy loss of comets in the corona and those that venture to lower altitudes. The different components of comae and tails are described, including dust, neutral and ionised gases, their chemical reactions, and their contributions to the near-Sun environment. Comet-solar wind interactions are discussed, including the use of comets as probes of solar wind and coronal conditions in their vicinities. We address the relevance of work on comets near the Sun to similar objects orbiting other stars, and conclude with a discussion of future directions for the field and the planned ground- and space-based facilities that will allow us to address those science topics

RefGenes: identification of reliable and condition specific reference genes for RT-qPCR data normalization

Background RT-qPCR is a sensitive and increasingly used method for gene expression quantification. To normalize RT-qPCR measurements between samples, most laboratories use endogenous reference genes as internal controls. There is increasing evidence, however, that the expression of commonly used reference genes can vary significantly in certain contexts. Results Using the Genevestigator database of normalized and well-annotated microarray experiments, we describe the expression stability characteristics of the transciptomes of several organisms. The results show that a) no genes are universally stable, b) most commonly used reference genes yield very high transcript abundances as compared to the entire transcriptome, and c) for each biological context a subset of stable genes exists that has smaller variance than commonly used reference genes or genes that were selected for their stability across all conditions. Conclusion We therefore propose the normalization of RT-qPCR data using reference genes that are specifically chosen for the conditions under study. RefGenes is a community tool developed for that purpose. Validation RT-qPCR experiments across several organisms showed that the candidates proposed by RefGenes generally outperformed commonly used reference genes. RefGenes is available within Genevestigator at http://www.genevestigator.com

Kidney function, endothelial activation and atherosclerosis in black and white Africans with rheumatoid arthritis

OBJECTIVE: To determine whether kidney function independently relates to endothelial activation and ultrasound determined carotid atherosclerosis in black and white Africans with rheumatoid arthritis (RA). METHODS: We calculated the Jelliffe, 5 Cockcroft-Gault equations, Salazar-Corcoran, Modification of Diet in Renal Disease (MDRD) and Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) estimated glomerular filtration rate (EGFR) equations in 233 (112 black) RA patients. RESULTS: The CKD-EPI eGFR was 0.1 for comparisons of AUC (SE)) for the other 8 equations. Based on optimal eGFR cutoff values with sensitivities and specificities ranging from 42 to 60% and 70 to 91% respectively, as determined in ROC curve analysis, a low eGFR increased the odds ratio for plaque 2.2 to 4.0 fold. CONCLUSION: Reduced kidney function is independently associated with atherosclerosis and endothelial activation in black and white Africans with RA, respectively. CKD is highly prevalent in black Africans with RA. Apart from the MDRD, eGFR equations are useful in predicting carotid plaque presence, a coronary heart disease equivalent, amongst black African RA patients

Copy Number Variation in Patients with Disorders of Sex Development Due to 46,XY Gonadal Dysgenesis

Disorders of sex development (DSD), ranging in severity from mild genital abnormalities to complete sex reversal, represent a major concern for patients and their families. DSD are often due to disruption of the genetic programs that regulate gonad development. Although some genes have been identified in these developmental pathways, the causative mutations have not been identified in more than 50% 46,XY DSD cases. We used the Affymetrix Genome-Wide Human SNP Array 6.0 to analyse copy number variation in 23 individuals with unexplained 46,XY DSD due to gonadal dysgenesis (GD). Here we describe three discrete changes in copy number that are the likely cause of the GD. Firstly, we identified a large duplication on the X chromosome that included DAX1 (NR0B1). Secondly, we identified a rearrangement that appears to affect a novel gonad-specific regulatory region in a known testis gene, SOX9. Surprisingly this patient lacked any signs of campomelic dysplasia, suggesting that the deletion affected expression of SOX9 only in the gonad. Functional analysis of potential SRY binding sites within this deleted region identified five putative enhancers, suggesting that sequences additional to the known SRY-binding TES enhancer influence human testis-specific SOX9 expression. Thirdly, we identified a small deletion immediately downstream of GATA4, supporting a role for GATA4 in gonad development in humans. These CNV analyses give new insights into the pathways involved in human gonad development and dysfunction, and suggest that rearrangements of non-coding sequences disturbing gene regulation may account for significant proportion of DSD cases

A Phase II Trial of Sorafenib in Metastatic Melanoma with Tissue Correlates

Sorafenib monotherapy in patients with metastatic melanoma was explored in this multi-institutional phase II study. In correlative studies the impact of sorafenib on cyclin D1 and Ki67 was assessed. mutational status and clinical activity. No significant changes in expression of cyclin D1 or Ki67 with sorafenib treatment were demonstrable in the 15 patients with pre-and post-treatment tumor samples. mutational status of the tumor was not associated with clinical activity and no significant effect of sorafenib on cyclin D1 or Ki67 was seen, suggesting that sorafenib is not an effective BRAF inhibitor or that additional signaling pathways are equally important in the patients who benefit from sorafenib