Using SMT to accelerate nested virtualization

IaaS datacenters offer virtual machines (VMs) to their clients, who in turn sometimes deploy their own virtualized environments, thereby running a VM inside a VM. This is known as nested virtualization. VMs are intrinsically slower than bare-metal execution, as they often trap into their hypervisor to perform tasks like operating virtual I/O devices. Each VM trap requires loading and storing dozens of registers to switch between the VM and hypervisor contexts, thereby incurring costly runtime overheads. Nested virtualization further magnifies these overheads, as every VM trap in a traditional virtualized environment triggers at least twice as many traps. We propose to leverage the replicated thread execution resources in simultaneous multithreaded (SMT) cores to alleviate the overheads of VM traps in nested virtualization. Our proposed architecture introduces a simple mechanism to colocate different VMs and hypervisors on separate hardware threads of a core, and replaces the costly context switches of VM traps with simple thread stall and resume events. More concretely, as each thread in an SMT core has its own register set, trapping between VMs and hypervisors does not involve costly context switches, but simply requires the core to fetch instructions from a different hardware thread. Furthermore, our inter-thread communication mechanism allows a hypervisor to directly access and manipulate the registers of its subordinate VMs, given that they both share the same in-core physical register file. A model of our architecture shows up to 2.3× and 2.6× better I/O latency and bandwidth, respectively. We also show a software-only prototype of the system using existing SMT architectures, with up to 1.3× and 1.5× better I/O latency and bandwidth, respectively, and 1.2--2.2× speedups on various real-world applications

Assessing the requirements of prenatal UBE3A expression for rescue of behavioral phenotypes in a mouse model for Angelman syndrome

Background: Angelman syndrome (AS) is a rare neurodevelopmental disorder caused by the loss of functional ubiquitin protein ligase E3A (UBE3A). In neurons, UBE3A expression is tightly regulated by a mechanism of imprinting which suppresses the expression of the paternal UBE3A allele. Promising treatment strategies for AS are directed at activating paternal UBE3A gene expression. However, for such strategies to be successful, it is important to know when such a treatment should start, and how much UBE3A expression is needed for normal embryonic brain development. Methods: Using a conditional mouse model of AS, we further delineated the critical period for UBE3A expression during early brain development. Ube3a gene expression was induced around the second week of gestation and mouse phenotypes were assessed using a behavioral test battery. To investigate the requirements of embryonic UBE3A expression, we made use of mice in which the paternal Ube3a allele was deleted. Results: We observed a full behavioral rescue of the AS mouse model phenotypes when Ube3a gene reactivation was induced around the start of the last week of mouse embryonic development. We found that full silencing of the paternal Ube3a allele was not completed till the first week after birth but that deletion of the paternal Ube3a allele had no significant effect on the assessed phenotypes. Limitations: Direct translation to human is limited, as we do not precisely know how human and mouse brain development aligns over gestational time. Moreover, many of the assessed phenotypes have limited translational value, as the underlying brain regions involved in these tasks are largely unknown. Conclusions: Our findings provide further important insights in the requirement of UBE3A expression during brain development. We found that loss o

Intrinsic dynamic behavior of fascin in filopodia

Author Posting. © American Society for Cell Biology, 2007. This article is posted here by permission of American Society for Cell Biology for personal use, not for redistribution. The definitive version was published in Molecular Biology of the Cell 18 (2007): 3928-3940, doi:10.1091/mbc.E07-04-0346.Recent studies showed that the actin cross-linking protein, fascin, undergoes rapid cycling between filopodial filaments. Here, we used an experimental and computational approach to dissect features of fascin exchange and incorporation in filopodia. Using expression of phosphomimetic fascin mutants, we determined that fascin in the phosphorylated state is primarily freely diffusing, whereas actin bundling in filopodia is accomplished by fascin dephosphorylated at serine 39. Fluorescence recovery after photobleaching analysis revealed that fascin rapidly dissociates from filopodial filaments with a kinetic off-rate of 0.12 s–1 and that it undergoes diffusion at moderate rates with a coefficient of 6 µm2s–1. This kinetic off-rate was recapitulated in vitro, indicating that dynamic behavior is intrinsic to the fascin cross-linker. A computational reaction–diffusion model showed that reversible cross-linking is required for the delivery of fascin to growing filopodial tips at sufficient rates. Analysis of fascin bundling indicated that filopodia are semiordered bundles with one bound fascin per 25–60 actin monomers.This work was supported by a National Institutes of Health F31National Research Service Award NS055565-01 (to Y.S.A.), Northwestern University Pulmonary and Critical Care Division T32 (to T.E.S.), and National Institutes of Health grant GM-70898 (to G.G.B.)

Deinococcus geothermalis: The Pool of Extreme Radiation Resistance Genes Shrinks

Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis

Current Output Filter for State Estimation of Scalar Nonlinear Systems with Application to Chaotic Communication

A novel nonlinear state estimation technique called Current Output Filter is proposed in this paper. By taking two successive measurements into account and optimizing the coefficients of the proposed filter structure, an unbiased minimum variance state estimation algorithm with guaranteed estimation error performance is derived for scalar nonlinear systems. The performance of this filter is shown to be superior to the Extended Kalman Filter (EKF) in simulations. An application to a chaotic communication scheme is also presented in this work

The comparison of dispersal rate between invasive and native species varied by plant life form and functional traits.

A long dispersal distance is widely used to indicate high invasiveness, but it ignores the temporal dimensions of plant invasion. Faster dispersal rates (= distance/time) of invasive species than native ones have been widely used in modeling species invasion and planning control management. However, the comparison of dispersal rate between invasive and native plants, particularly for dispersal on a local or landscape scale, has not been tested with a comprehensive dataset. Moreover, both the effects of plant functional traits on the dispersal rate and variation in the functional-trait effects between invasive and native plants remain elusive. Compiling studies from 30 countries globally, we compared seed dispersal rates (km/year) on a local or landscape scale between 64 observations of invasive and 78 observations of native plants given effects of plant life forms, disturbance levels, and measurement methods. Furthermore, we compared the effects of functional traits on dispersal rate between invasive and native species. We found that: (1) Trait values were similar between the invasive and native plants except for the greater height of woody native plants than woody invasive ones; (2) Compared within the same plant life form, the faster dispersal rates of invasive species were found in herbaceous plants, not in woody plants, and disturbance level and measurement methods did not affect the rate comparison; (3) Plant height and seed length had significant effects on dispersal rates of both invasive and native plants, but the effect of leaf dry matter content (LDMC) was only significant on herbaceous invasive plants. The comparison of dispersal rate between invasive and native plants varied by plant life form. The convergent values but divergent dispersal effects of plant traits between invasive and native species suggest that the trait effects on invasiveness could be better understood by trait association with key factors in invasiveness, e.g., dispersal rate, than the direct trait comparison between invasive and native plants

Current Output Observer for Discrete-Time Nonlinear Stochastic Systems

A Current Output Observer is presented and its estimation error performance is compared to that of the Extended Kalman Filter. It is shown that performance improvement can be obtained by this new scheme with minor increase in computational load. In order to obtain stronger results, scalar nonlinear stochastic systems are focused on. These systems are categorized based on the derivatives of their nonlinear functions. It is shown that different state estimation performance is achieved when the Current Output Observer is applied to scalar nonlinear systems in these different categories, which allows the convergence property to be known before its implementation. This provides insight into what is going to happen in applications, e.g. for a nonlinear estimator used in chaotic synchronization. Simulation studies involving nonlinear estimation - based chaotic synchronization complement the theory presented

The comparison of dispersal rate between invasive and native species varied by plant life form and functional traits

Abstract A long dispersal distance is widely used to indicate high invasiveness, but it ignores the temporal dimensions of plant invasion. Faster dispersal rates (= distance/time) of invasive species than native ones have been widely used in modeling species invasion and planning control management. However, the comparison of dispersal rate between invasive and native plants, particularly for dispersal on a local or landscape scale, has not been tested with a comprehensive dataset. Moreover, both the effects of plant functional traits on the dispersal rate and variation in the functional-trait effects between invasive and native plants remain elusive. Compiling studies from 30 countries globally, we compared seed dispersal rates (km/year) on a local or landscape scale between 64 observations of invasive and 78 observations of native plants given effects of plant life forms, disturbance levels, and measurement methods. Furthermore, we compared the effects of functional traits on dispersal rate between invasive and native species. We found that: (1) Trait values were similar between the invasive and native plants except for the greater height of woody native plants than woody invasive ones; (2) Compared within the same plant life form, the faster dispersal rates of invasive species were found in herbaceous plants, not in woody plants, and disturbance level and measurement methods did not affect the rate comparison; (3) Plant height and seed length had significant effects on dispersal rates of both invasive and native plants, but the effect of leaf dry matter content (LDMC) was only significant on herbaceous invasive plants. The comparison of dispersal rate between invasive and native plants varied by plant life form. The convergent values but divergent dispersal effects of plant traits between invasive and native species suggest that the trait effects on invasiveness could be better understood by trait association with key factors in invasiveness, e.g., dispersal rate, than the direct trait comparison between invasive and native plants

Plants Used in Chinese Medicine for the Treatment of Male Infertility Possess Antioxidant and Anti-Oestrogenic Activity

In this study Chinese herbs commonly used in the treatment of male infertility were investigated for relevant biochemical activity. Male factor infertility predominantly arises via barriers to, or defects in, spermatogenesis. The process of spermatogenesis is under strict endocrine control; in addition oxidative stress has been implicated in male infertility with significant levels of reactive oxygen species detected in 25% of infertile males. A total of 37 individual herbs and seven herb decoctions used in the treatment of male factor infertility were therefore tested for endocrine activity using a recombinant yeast based assay and antioxidant activity using the FRAP (ferric reducing antioxidant potential) assay. Individual herbs tested did not show androgenic properties, 20 showed strong and 10 weak anti-oestrogenic activity (per g of dried herb tamoxifen equivalents ranged from 1.18-1280.66 mg and 0.06-0.98 mg, respectively). Oestrogenic responses were elicited for two herbs (85.30-550 g oestradiol equivalents/g dried herb), with seven and three herbs exhibiting a strong or weak anti-androgenic response (per g of dried herb DHT equivalents ranged from 1.54-66.78 mg and 0.17-0.32 mg), respectively. Of these 37 herbs, strong (15 herbs), intermediate (7 herbs) and weak/no (15 herbs) antioxidant activity was detected (ranging from 0.912-1.26; 0.6-0.88 and 0-0.468 g ascorbate equivalent/mg dried herb, respectively). The seven decoctions (previously used to treat patients) tested elicited strong (5 herbs) and weak (2 herbs) anti-oestrogenic responses (per g of dried herb tamoxifen equivalents ranged from 1.14-13.23 mg and 0.22-0.26 mg, respectively), but not oestrogenic, androgenic nor anti-androgenic, consistent with their individual composition. With regard to antioxidant activity the following responses were recorded: three strong, three intermediate and one weak (ranging from 1.02-1.2; 0.72-0.76 and 0.44 g ascorbate equivalent/mg dried herb, respectively). The prospects for introducing Chinese herbal treatments into the Western-based medicine are discussed

Angiotensin-Converting Enzyme 2-Based Biosensing Modalities and Devices for Coronavirus Detection

Rapid and cost-effective diagnostic tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are a critical and valuable weapon for the coronavirus disease 2019 (COVID-19) pandemic response. SARS-CoV-2 invasion is primarily mediated by human angiotensin-converting enzyme 2 (hACE2). Recent developments in ACE2-based SARS-CoV-2 detection modalities accentuate the potential of this natural host-virus interaction for developing point-of-care (POC) COVID-19 diagnostic systems. Although research on harnessing ACE2 for SARS-CoV-2 detection is in its infancy, some interesting biosensing devices have been developed, showing the commercial viability of this intriguing new approach. The exquisite performance of the reported ACE2-based COVID-19 biosensors provides opportunities for researchers to develop rapid detection tools suitable for virus detection at points of entry, workplaces, or congregate scenarios in order to effectively implement pandemic control and management plans. However, to be considered as an emerging approach, the rationale for ACE2-based biosensing needs to be critically and comprehensively surveyed and discussed. Herein, we review the recent status of ACE2-based detection methods, the signal transduction principles in ACE2 biosensors and the development trend in the future. We discuss the challenges to development of ACE2-biosensors and delineate prospects for their use, along with recommended solutions and suggestions