Strain induced stabilization of stepped Si and Ge surfaces near (001)

We report on calculations of the formation energies of several [100] and [110] oriented step structures on biaxially stressed Si and Ge (001) surfaces. It is shown that a novel rebonded [100] oriented single-height step is strongly stabilized by compressive strain compared to most well-known step structures. We propose that the side walls of ``hut''-shaped quantum dots observed in recent experiments on SiGe/Si films are made up of these steps. Our calculations provide an explanation for the nucleationless growth of shallow mounds, with steps along the [100] and [110] directions in low- and high-misfit films, respectively, and for the stability of the (105) facets under compressive strain.Comment: to appear in Appl. Phys. Lett.; v2=minor corrections,figs resize

Rapidly Rotating Fermi Gases

We show that the density profile of a Fermi gas in rapidly rotating potential will develop prominent features reflecting the underlying Landau level like energy spectrum. Depending on the aspect ratio of the trap, these features can be a sequence of ellipsoidal volumes or a sequence of quantized steps.Comment: 4 pages, 1 postscript fil

Functional and evolutionary analysis of host Synaptogyrin-2 in porcine circovirus type 2 susceptibility

Mammalian evolution has been influenced by viruses for millions of years, leaving signatures of adaptive evolution within genes encoding for viral interacting proteins. Synaptogyrin- 2 (SYNGR2) is a transmembrane protein implicated in promoting bacterial and viral infections. A genome-wide association study of pigs experimentally infected with porcine circovirus type 2b (PCV2b) uncovered a missense mutation (SYNGR2 p.Arg63Cys) associated with viral load. In this study, CRISPR/Cas9-mediated gene editing of the porcine kidney 15 (PK15, wtSYNGR2+p.63Arg) cell line generated clones homozygous for the favorable SYNGR2 p.63Cys allele (emSYNGR2+p.63Cys). Infection of edited clones resulted in decreased PCV2 replication compared to wildtype PK15 (P\u3c0.05), with consistent effects across genetically distinct PCV2b and PCV2d isolates. Sequence analyses of wild and domestic pigs (n\u3e700) revealed the favorable SYNGR2 p.63Cys allele is unique to domestic pigs and more predominant in European than Asian breeds. A haplotype defined by the SYNGR2 p.63Cys allele was likely derived from an ancestral haplotype nearly fixed within European (0.977) but absent from Asian wild boar. We hypothesize that the SYNGR2 p.63Cys allele arose post-domestication in ancestral European swine. Decreased genetic diversity in homozygotes for the SYNGR2 p.63Cys allele compared to SYNGR2 p.63Arg, corroborates a rapid increase in frequency of SYGNR2 p.63Cys via positive selection. Signatures of adaptive evolution across mammalian species were also identified within SYNGR2 intraluminal loop domains, coinciding with the location of SYNGR2 p.Arg63Cys. Therefore, SYNGR2 may reflect a novel component of the host-virus evolutionary arms race across mammals with SYNGR2 p.Arg63Cys representing a species-specific example of putative adaptive evolution

How Should We Measure? A Review of Circular Cities Indicators

As the world continues to urbanize, it is necessary to identify and implement new urban development models and strategies in order to meet the challenges of sustainable development. As cities continue to face challenges in becoming fully circular, the need to establish a framework to measure the circular economy in urban areas grows. Many definitions for circular cities have been developed and addressed in recent years, as have numerous indicators. To make the transition to a circular city, we must integrate the findings and develop a general definition and measurement framework. This article aims at outlining a framework for circular cities indicators based on their key characteristics, as well providing directions for fostering circularity at the city level. To accomplish this goal, we conducted a systematic review and analyzed key papers published in the field of circular economy to determine how circular cities are measured. Choosing the right indicators to use for developing, monitoring, and evaluating circular cities is a difficult task for urban policymakers, managers, and planners. This highlights the significance of standardized frameworks for urban indicators. As a result, the authors propose a framework and highlight some key points about circular cities and smart urban metabolism

Qualitative modelling and analysis of regulations in multi-cellular systems using Petri nets and topological collections

In this paper, we aim at modelling and analyzing the regulation processes in multi-cellular biological systems, in particular tissues. The modelling framework is based on interconnected logical regulatory networks a la Rene Thomas equipped with information about their spatial relationships. The semantics of such models is expressed through colored Petri nets to implement regulation rules, combined with topological collections to implement the spatial information. Some constraints are put on the the representation of spatial information in order to preserve the possibility of an enumerative and exhaustive state space exploration. This paper presents the modelling framework, its semantics, as well as a prototype implementation that allowed preliminary experimentation on some applications.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Host-genetic-based outcome of co-infection by PCV2b and PRRSV in pigs

Replication of porcine circovirus type 2 (PCV2), an important worldwide swine pathogen, has been demonstrated to be influenced by host genotype. Specifically, a missense DNA polymorphism (SYNGR2 p.Arg63Cys) within the SYNGR2 gene was demonstrated to contribute to variation in PCV2b viral load and subsequent immune response following infection. PCV2 is known to induce immunosuppression leading to an increase in susceptibility to subsequent infections with other viral pathogens such as porcine reproductive and respiratory syndrome virus (PRRSV). In order to assess the role of SYNGR2 p.Arg63Cys in co-infections, pigs homozygous for the favorable SYNGR2 p.63Cys (N = 30) and unfavorable SYNGR2 p.63Arg (N = 29) alleles were infected with PCV2b followed a week later by a challenge with PRRSV. A lower PCV2b viremia (P \u3c 0.001) and PCV2-specific IgM antibodies (P \u3c 0.005) were observed in SYNGR2 p.63Cys compared to SYNGR2 p.63Arg genotypes. No significant differences in PRRSV viremia and specific IgG antibodies were observed between SYNGR2 genotypes. Lung histology score, an indicator of disease severity, was lower in the pigs with SYNGR2 p.63Cys genotypes (P \u3c 0.05). Variation in the lung histology scores within SYNGR2 genotypes suggests that additional factors, environmental and/or genetic, could be involved in disease severity. Lay Summary: Porcine circovirus type 2 (PCV2) is an important virus involved in the onset of a group of severe disease symptoms commonly known as porcine circovirus associated diseases (PCVAD). Vaccination options exist for PCV2, though the severity of PCVAD can be influenced by the presence of additional co-infecting pathogens, such as porcine reproductive and respiratory syndrome virus (PRRSV), for which vaccination is still a challenge. Host genetic resistance is a potential avenue for solving this problem. Previously, a genetic polymorphism in the SYNGR2 gene was found to be associated with PCV2b viremia and immune response. The aim of this study was to determine the impact of this polymorphism in pigs experimentally co-infected with PCV2b and PRRSV. Pigs were weighed, and blood was collected at various days following infection to measure viremia and antibodies. Histological analysis was performed at the experiment completion to assess disease severity in lungs and lymph nodes. The results showed that variation within the SYNGR2 gene is involved in PCV2b disease progression including lung histology scores, but no evidence was seen in response to PRRSV infection

Dynamics of spin-2 Bose condensate driven by external magnetic fields

Dynamic response of the F=2 spinor Bose-Einstein condensate (BEC) under the influence of external magnetic fields is studied. A general formula is given for the oscillation period to describe population transfer from the initial polar state to other spin states. We show that when the frequency and the reduced amplitude of the longitudinal magnetic field are related in a specific manner, the population of the initial spin-0 state will be dynamically localized during time evolution. The effects of external noise and nonlinear spin exchange interaction on the dynamics of the spinor BEC are studied. We show that while the external noise may eventually destroy the Rabi oscillations and dynamic spin localization, these coherent phenomena are robust against the nonlinear atomic interaction.Comment: 16 pages, 7 figures. accepted by Phys. Rev.

Evaluation of genotype quality parameters for \u3ci\u3eSowPro90\u3c/i\u3e, a new genotyping array for swine

Understanding early predictors of sow fertility has the potential to improve genomic predictions. A custom SNP array (SowPro90 produced by Affymetrix) was developed to include genetic variants overlapping quantitative trait loci for age at puberty, one of the earliest indicators of sow fertility, as well as variants related to innate and adaptive immunity. The polymorphisms included in the custom genotyping array were identified using multiple genomic approaches including deep genomic and transcriptomic sequencing and genome-wide associations. Animals from research and commercial populations (n = 2,586) were genotyped for 103,476 SNPs included in SowPro90. To assess the quality of data generated, genotype concordance was evaluated between the SowPro90 and Porcine SNP60 BeadArray using a subset of common SNP (n = 44,708) and animals (n = 277). The mean genotype concordance rate per SNP was 98.4%. Differences in distribution of data quality were observed between the platforms indicating the need for platform specific thresholds for quality parameters. The optimal thresholds for SowPro90 (≥97% SNP and ≥93% sample call rate) were obtained by analyzing the data quality distribution and genotype concordance per SNP across platforms. At ≥97% SNP call rate, there were 42,151 SNPs (94.3%) retained with a mean genotype concordance of 98.6% across platforms. Similarly, ≥94% SNPs and ≥85% sample call rates were established as thresholds for Porcine SNP60 BeadArray. At ≥94% SNPs call rate, there were 41,043 SNPs (91.8%) retained with a mean genotype concordance of 98.6% across platforms. Final evaluation of SowPro90 array content (n = 103,476) at ≥97% SNPs and ≥93% sample call rates allowed retention of 89,040 SNPs (86%) for downstream analysis. The findings and strategy for quality control could be helpful in identifying consistent, high-quality genotypes for genomic evaluations, especially when integrating genotype data from different platforms

Protocol for single-cell isolation and genome amplification of environmental microbial eukaryotes for genomic analysis

We describe environmental microbial eukaryotes (EMEs) sample collection, single-cell isolation, lysis, and genome amplification, followed by the rDNA amplification and OTU screening for recovery of high-quality species-specific genomes for de novo assembly. These protocols are part of our pipeline that also includes bioinformatic methods. The pipeline and its application on a wide range of phyla of different sample complexity are described in our complementary paper. In addition, this protocol describes optimized lysis, genome amplification, and OTU screening steps of the pipeline. For complete details on the use and execution of this protocol, please refer to Ciobanu et al. (2021)

Matter-Wave Solitons in an F=1 Spinor Bose-Einstein Condensate

Following our previous work [J. Ieda, T. Miyakawa, M. Wadati, cond-mat/0404569] on a novel integrable model describing soliton dynamics of an F=1 spinor Bose--Einstein condensate, we discuss in detail the properties of the multi-component system with spin-exchange interactions. The exact multiple bright soliton solutions are obtained for the system where the mean-field interaction is attractive (c_0 < 0) and the spin-exchange interaction is ferromagnetic (c_2 < 0). A complete classification of the one-soliton solution with respect to the spin states and an explicit formula of the two-soliton solution are presented. For solitons in polar state, there exists a variety of different shaped solutions including twin peaks. We show that a "singlet pair" density can be used to distinguish those energetically degenerate solitons. We also analyze collisional effects between solitons in the same or different spin state(s) by computing the asymptotic forms of their initial and final states. The result reveals that it is possible to manipulate the spin dynamics by controlling the parameters of colliding solitons.Comment: 12 pages, 9 figures, to appear in J. Phys. Soc. Jpn. Vol.73 No.11 (2004