First record of hatchling overwintering inside the natal nest of a chelid turtle

Hatchling overwintering inside the natal nest is a strategy used by several Northern Hemisphere species of freshwater turtles. We recorded hatchling overwintering in the nest by Chelodina longicollis (Chelidae) in southeastern Australia, during three reproductive seasons. Hatchlings spent, on average, 320 days inside the nest from the date eggs were laid until emergence. Some nests were carefully opened adjacent to the nest plug, one during winter and one in spring, to confirm that eggs had hatched and were not in diapause, although we could not precisely confirm hatching dates. Despite our small sample size, we observed a dichotomous overwintering strategy, with hatchlings from one nest emerging in autumn and spending their first winter in the aquatic environment, and hatchlings from three nests overwintering in the nest and emerging in spring. These findings expand the phylogenetic range of turtles exhibiting hatchling overwintering behaviour. Future research should evaluate whether this strategy is widespread among other long-necked turtles in temperate regions and examine physiological mechanisms involved in coping with winter temperatures

Predicting bycatch hotspots for endangered leatherback turtles on longlines in the Pacific Ocean

Fisheries bycatch is a critical source of mortality for rapidly declining populations of leatherback turtles, Dermochelys coriacea. We integrated use-intensity distributions for 135 satellite-tracked adult turtles with longline fishing effort to estimate predicted bycatch risk over space and time in the Pacific Ocean. Areas of predicted bycatch risk did not overlap for eastern and western Pacific nesting populations, warranting their consideration as distinct management units with respect to fisheries bycatch. For western Pacific nesting populations, we identified several areas of high risk in the north and central Pacific, but greatest risk was adjacent to primary nesting beaches in tropical seas of Indo-Pacific islands, largely confined to several exclusive economic zones under the jurisdiction of national authorities. For eastern Pacific nesting populations, we identified moderate risk associated with migrations to nesting beaches, but the greatest risk was in the South Pacific Gyre, a broad pelagic zone outside national waters where management is currently lacking and may prove difficult to implement. Efforts should focus on these predicted hotspots to develop more targeted management approaches to alleviate leatherback bycatch

Benefits of a Rail-Trail in Rural Appalachia: A Mixed Methods Study of the Virginia Creeper Trail in Damascus, Virginia

Since the 1980s numerous abandoned railbeds have been converted to multi-use trails across the United States. These trails are commonly referred to as “rail-trails.” They accommodate pedestrians and bicyclists most frequently but may also be used for a wide range of non-motorized traffic. Rail-trails preserve cultural heritage and wildlife corridors that benefit local economies by promoting small businesses and tourism while providing a safe and enjoyable means of active recreation and transportation. Because of the subtle grade of former railbeds, rail-trails commonly provide a gentle slope that allows access to users with a wide range of physical ability. One such rail-trail, the Virginia Creeper Trail in Damascus, Virginia, was the focus of a mixed method research project from September 2011 until December 2012. The research focused on two key components for building a case to further extend rail-trails in Appalachia. Through a wide reaching review of literature, in-depth interviews with local residents, and an economic impact survey of trail users, the many benefits of a rail-trail came to light

The host metabolite D-serine contributes to bacterial niche specificity through gene selection

Escherichia coli comprise a diverse array of both commensals and niche-specific pathotypes. The ability to cause disease results from both carriage of specific virulence factors and regulatory control of these via environmental stimuli. Moreover, host metabolites further refine the response of bacteria to their environment and can dramatically affect the outcome of the host–pathogen interaction. Here, we demonstrate that the host metabolite, D-serine, selectively affects gene expression in E. coli O157:H7. Transcriptomic profiling showed exposure to D-serine results in activation of the SOS response and suppresses expression of the Type 3 Secretion System (T3SS) used to attach to host cells. We also show that concurrent carriage of both the D-serine tolerance locus (dsdCXA) and the locus of enterocyte effacement pathogenicity island encoding a T3SS is extremely rare, a genotype that we attribute to an ‘evolutionary incompatibility’ between the two loci. This study demonstrates the importance of co-operation between both core and pathogenic genetic elements in defining niche specificity

The Social and Political Dimensions of the Ebola Response: Global Inequality, Climate Change, and Infectious Disease

The 2014 Ebola crisis has highlighted public-health vulnerabilities in Liberia, Sierra Leone, and Guinea – countries ravaged by extreme poverty, deforestation and mining-related disruption of livelihoods and ecosystems, and bloody civil wars in the cases of Liberia and Sierra Leone. Ebola’s emergence and impact are grounded in the legacy of colonialism and its creation of enduring inequalities within African nations and globally, via neoliberalism and the Washington Consensus. Recent experiences with new and emerging diseases such as SARS and various strains of HN influenzas have demonstrated the effectiveness of a coordinated local and global public health and education-oriented response to contain epidemics. To what extent is international assistance to fight Ebola strengthening local public health and medical capacity in a sustainable way, so that other emerging disease threats, which are accelerating with climate change, may be met successfully? This chapter considers the wide-ranging socio-political, medical, legal and environmental factors that have contributed to the rapid spread of Ebola, with particular emphasis on the politics of the global and public health response and the role of gender, social inequality, colonialism and racism as they relate to the mobilization and establishment of the public health infrastructure required to combat Ebola and other emerging diseases in times of climate change

Efficient tagged memory

We characterize the cache behavior of an in-memory tag table and demonstrate that an optimized implementation can typically achieve a near-zero memory traffic overhead. Both industry and academia have repeatedly demonstrated tagged memory as a key mechanism to enable enforcement of powerful security invariants, including capabilities pointer integrity, watchpoints, and information-flow tracking. A single-bit tag shadowspace is the most commonly proposed requirement, as one bit is the minimum metadata needed to distinguish between an untyped data word and any number of new hardware-enforced types. We survey various tag shadowspace approaches and identify their common requirements and positive features of their implementations. To avoid non-standard memory widths, we identify the most practical implementation for tag storage to be an in-memory table managed next to the DRAM controller. We characterize the caching performance of such a tag table and demonstrate a DRAM traffic overhead below 5\% for the vast majority of applications. We identify spatial locality on a page scale as the primary factor that enables surprisingly high table cache-ability. We then demonstrate tag-table compression for a set of common applications. A hierarchical structure with elegantly simple optimizations reduces DRAM traffic overhead to below 1\% for most applications. These insights and optimizations pave the way for commercial applications making use of single-bit tags stored in commodity memory

Fast Protection-Domain Crossing in the CHERI Capability-System Architecture

Capability Hardware Enhanced RISC Instructions (CHERI) supplement the conventional memory management unit (MMU) with instruction-set architecture (ISA) extensions that implement a capability system model in the address space. CHERI can also underpin a hardware-software object-capability model for scalable application compartmentalization that can mitigate broader classes of attack. This article describes ISA additions to CHERI that support fast protection-domain switching, not only in terms of low cycle count, but also efficient memory sharing with mutual distrust. The authors propose ISA support for sealed capabilities, hardware-assisted checking during protection-domain switching, a lightweight capability flow-control model, and fast register clearing, while retaining the flexibility of a software-defined protection-domain transition model. They validate this approach through a full-system experimental design, including ISA extensions, a field-programmable gate array prototype (implemented in Bluespec SystemVerilog), and a software stack including an OS (based on FreeBSD), compiler (based on LLVM), software compartmentalization model, and open-source applications.This work is part of the CTSRD and MRC2 projects sponsored by the Defense Advanced Research Projects Agency (DARPA) and the Air Force Research Laboratory (AFRL), under contracts FA8750-10-C-0237 and FA8750-11-C-0249. We also acknowledge the Engineering and Physical Sciences Research Council (EPSRC) REMS Programme Grant [EP/K008528/1], the EPSRC Impact Acceleration Account [EP/K503757/1], EPSRC/ARM iCASE studentship [13220009], Microsoft studentship [MRS2011-031], the Isaac Newton Trust, the UK Higher Education Innovation Fund (HEIF), Thales E-Security, and Google, Inc.This is the author accepted manuscript. The final version of the article can be found at: http://ieeexplore.ieee.org/document/7723791

CheriABI: Enforcing Valid Pointer Provenance and Minimizing Pointer Privilege in the POSIX C Run-time Environment

The CHERI architecture allows pointers to be implemented as capabilities (rather than integer virtual addresses) in a manner that is compatible with, and strengthens, the semantics of the C language. In addition to the spatial protections offered by conventional fat pointers, CHERI capabilities offer strong integrity, enforced provenance validity, and access monotonicity. The stronger guarantees of these architectural capabilities must be reconciled with the real-world behavior of operating systems, run-time environments, and applications. When the process model, user-kernel interactions, dynamic linking, and memory management are all considered, we observe that simple derivation of architectural capabilities is insufficient to describe appropriate access to memory. We bridge this conceptual gap with a notional \emph{abstract capability} that describes the accesses that should be allowed at a given point in execution, whether in the kernel or userspace. To investigate this notion at scale, we describe the first adaptation of a full C-language operating system (FreeBSD) with an enterprise database (PostgreSQL) for complete spatial and referential memory safety. We show that awareness of abstract capabilities, coupled with CHERI architectural capabilities, can provide more complete protection, strong compatibility, and acceptable performance overhead compared with the pre-CHERI baseline and software-only approaches. Our observations also have potentially significant implications for other mitigation techniques.This work was supported by the Defense Advanced Research Projects Agency (DARPA) and the Air Force Research Laboratory (AFRL), under contracts FA8750-10-C-0237 (``CTSRD'') and HR0011-18-C-0016 (``ECATS''). The views, opinions, and/or findings contained in this report are those of the authors and should not be interpreted as representing the official views or policies of the Department of Defense or the U.S. Government. We also acknowledge the EPSRC REMS Programme Grant (EP/K008528/1), the ERC ELVER Advanced Grant (789108), Arm Limited, HP Enterprise, and Google, Inc. Approved for Public Release, Distribution Unlimited

Increased S-nitrosylation and proteasomal degradation of caspase-3 during infection contribute to the persistence of adherent invasive escherichia coli (AIEC) in immune cells

Adherent invasive Escherichia coli (AIEC) have been implicated as a causative agent of Crohn's disease (CD) due to their isolation from the intestines of CD sufferers and their ability to persist in macrophages inducing granulomas. The rapid intracellular multiplication of AIEC sets it apart from other enteric pathogens such as Salmonella Typhimurium which after limited replication induce programmed cell death (PCD). Understanding the response of infected cells to the increased AIEC bacterial load and associated metabolic stress may offer insights into AIEC pathogenesis and its association with CD. Here we show that AIEC persistence within macrophages and dendritic cells is facilitated by increased proteasomal degradation of caspase-3. In addition S-nitrosylation of pro- and active forms of caspase-3, which can inhibit the enzymes activity, is increased in AIEC infected macrophages. This S-nitrosylated caspase-3 was seen to accumulate upon inhibition of the proteasome indicating an additional role for S-nitrosylation in inducing caspase-3 degradation in a manner independent of ubiquitination. In addition to the autophagic genetic defects that are linked to CD, this delay in apoptosis mediated in AIEC infected cells through increased degradation of caspase-3, may be an essential factor in its prolonged persistence in CD patients

Contingent Kernel Density Estimation

Kernel density estimation is a widely used method for estimating a distribution based on a sample of points drawn from that distribution. Generally, in practice some form of error contaminates the sample of observed points. Such error can be the result of imprecise measurements or observation bias. Often this error is negligible and may be disregarded in analysis. In cases where the error is non-negligible, estimation methods should be adjusted to reduce resulting bias. Several modifications of kernel density estimation have been developed to address specific forms of errors. One form of error that has not yet been addressed is the case where observations are nominally placed at the centers of areas from which the points are assumed to have been drawn, where these areas are of varying sizes. In this scenario, the bias arises because the size of the error can vary among points and some subset of points can be known to have smaller error than another subset or the form of the error may change among points. This paper proposes a “contingent kernel density estimation” technique to address this form of error. This new technique adjusts the standard kernel on a point-by-point basis in an adaptive response to changing structure and magnitude of error. In this paper, equations for our contingent kernel technique are derived, the technique is validated using numerical simulations, and an example using the geographic locations of social networking users is worked to demonstrate the utility of the method