An update on the biological control of rabbits

When myxomatosis was introduced into Western Australia in the early 1950s, farmers, pastoralists and government alike thought it was an answer to the rabbit problem. The disease was devastatingly effective in the short term and initially had a 99 per cent kill rate. With time, the virus declined in strength, and the surviving rabbits have multiplied. There have been many recent reports about new forms of biological control for rabbits and potential improvements in old ones. This article summarises each of the prospective methods and improvements, and assesses the potential usefulness of each

Easily searched encodings for number partitioning

Can stochastic search algorithms outperform existing deterministic heuristics for the NP-hard problem Number Partitioning if given a sufficient, but practically realizable amount of time? In a thorough empirical investigation using a straightforward implementation of one such algorithm, simulated annealing, Johnson et al. (Ref. 1) concluded tentatively that the answer is negative. In this paper, we show that the answer can be positive if attention is devoted to the issue of problem representation (encoding). We present results from empirical tests of several encodings of Number Partitioning with problem instances consisting of multiple-precision integers drawn from a uniform probability distribution. With these instances and with an appropriate choice of representation, stochastic and deterministic searches can—routinely and in a practical amount of time—find solutions several orders of magnitude better than those constructed by the best heuristic known (Ref. 2), which does not employ searching. We thank David S. Johnson of AT&T Bell Labs for generously and promptly sharing his test instances. For stimulating discussions, we thank members of the Harvard Animation/Optimization Group (especially Jon Christensen), the Computer Science Department at the University of New Mexico, the Santa Fe Institute, and the Berkeley CAD Group. The anonymous referees made numerous constructive suggestions. We thank Rebecca Hayes for comments concerning the figures. The second author is grateful for a Graduate Fellowship from the Fannie and John Hertz Foundation. We thank the Free Software Foundation for making the GNU Multiple Precision package available. The research described in this paper was conducted mostly while the third author was at Digital Equipment Corporation Cambridge Research Lab. This work was supported in part by the National Science Foundation, principally under Grants IRI-9157996 and IRI-9350192 to the fourth author, and by matching grants from Digital Equipment Corporation and Xerox Corporation.Engineering and Applied Science

A seed-growth heuristic for graph bisection

We present a new heuristic algorithm for graph bisection, based on an implicit notion of clustering. We describe how the heuristic can be combined with stochastic search procedures and a postprocess application of the Kernighan-Lin algorithm. In a series of time-equated comparisons with large-sample runs of pure Kernighan-Lin, the new algorithm demonstrates significant superiority in terms of the best bisections found.Engineering and Applied Science

Easily searched encodings for number partitioning

Can stochastic search algorithms outperform existing deterministic heuristics for the NP-hard problem Number Partitioning if given a sufficient, but practically realizable amount of time? In a thorough empirical investigation using a straightforward implementation of one such algorithm, simulated annealing, Johnson et al. (Ref. 1) concluded tentatively that the answer is negative. In this paper, we show that the answer can be positive if attention is devoted to the issue of problem representation (encoding). We present results from empirical tests of several encodings of Number Partitioning with problem instances consisting of multiple-precision integers drawn from a uniform probability distribution. With these instances and with an appropriate choice of representation, stochastic and deterministic searches can—routinely and in a practical amount of time—find solutions several orders of magnitude better than those constructed by the best heuristic known (Ref. 2), which does not employ searching. We thank David S. Johnson of AT&T Bell Labs for generously and promptly sharing his test instances. For stimulating discussions, we thank members of the Harvard Animation/Optimization Group (especially Jon Christensen), the Computer Science Department at the University of New Mexico, the Santa Fe Institute, and the Berkeley CAD Group. The anonymous referees made numerous constructive suggestions. We thank Rebecca Hayes for comments concerning the figures. The second author is grateful for a Graduate Fellowship from the Fannie and John Hertz Foundation. We thank the Free Software Foundation for making the GNU Multiple Precision package available. The research described in this paper was conducted mostly while the third author was at Digital Equipment Corporation Cambridge Research Lab. This work was supported in part by the National Science Foundation, principally under Grants IRI-9157996 and IRI-9350192 to the fourth author, and by matching grants from Digital Equipment Corporation and Xerox Corporation.Engineering and Applied Science

Design gallery browsers based on 2D and 3D graph drawing

Many problems in computer-aided design and graphics involve the process of setting and adjusting input parameters to obtain desirable output values. Exploring different parameter settings can be a difficult and tedious task in most such systems. In the Design GalleryTM (DG) approach, parameter setting is made easier by dividing the task more equitably between user and computer. DG interfaces present the user with the broadest selection, automatically generated and organized, of perceptually different designs that can be produced by varying a given set of input parameters. The DG approach has been applied to several difficult parameter-setting tasks from the field of computer graphics: light selection and placement for image rendering; opacity and color transfer-function specification for volume rendering; and motion control for articulated-figure and particle-system animation. The principal technical challenges posed by the DG approach are dispersion (finding a set of input-parameter vectors that optimally disperses the resulting output values) and arrangement (arranging the resulting designs for easy browsing by the user). We show how effective arrangement can be achieved with 2D and 3D graph drawing. While navigation is easier in the 2D interface, the 3D interface has proven to be surprisingly usable, and the 3D drawings sometimes provide insights that are not so obvious in the 2D drawings.Engineering and Applied Science

Acute Renal Replacement Therapy in Pediatrics

Acute kidney injury (AKI) independently increases morbidity and mortality in children admitted to the hospital. Renal replacement therapy (RRT) is an essential therapy in the setting of AKI and fluid overload. The decision to initiate RRT is complex and often complicated by concerns related to patient hemodynamic and thermodynamic instability. The choice of which RRT modality to use depends on numerous criteria that are both patient and treatment center specific. Surprisingly, despite decades of use, no randomized, controlled trial study involving RRT in pediatrics has been performed. Because of these factors, clear-cut consensus is lacking regarding key questions surrounding RRT delivery. In this paper, we will summarize existing data concerning RRT use in children. We discuss the major modalities and the data-driven specifics of each, followed by controversies in RRT. As no standard of care is in widespread use for RRT in AKI or in multiorgan disease, we conclude in this paper that prospective studies of RRT are needed to identify best practice guidelines

BOSS-LDG: A Novel Computational Framework that Brings Together Blue Waters, Open Science Grid, Shifter and the LIGO Data Grid to Accelerate Gravitational Wave Discovery

We present a novel computational framework that connects Blue Waters, the NSF-supported, leadership-class supercomputer operated by NCSA, to the Laser Interferometer Gravitational-Wave Observatory (LIGO) Data Grid via Open Science Grid technology. To enable this computational infrastructure, we configured, for the first time, a LIGO Data Grid Tier-1 Center that can submit heterogeneous LIGO workflows using Open Science Grid facilities. In order to enable a seamless connection between the LIGO Data Grid and Blue Waters via Open Science Grid, we utilize Shifter to containerize LIGO's workflow software. This work represents the first time Open Science Grid, Shifter, and Blue Waters are unified to tackle a scientific problem and, in particular, it is the first time a framework of this nature is used in the context of large scale gravitational wave data analysis. This new framework has been used in the last several weeks of LIGO's second discovery campaign to run the most computationally demanding gravitational wave search workflows on Blue Waters, and accelerate discovery in the emergent field of gravitational wave astrophysics. We discuss the implications of this novel framework for a wider ecosystem of Higher Performance Computing users.Comment: 10 pages, 10 figures. Accepted as a Full Research Paper to the 13th IEEE International Conference on eScienc

Cortical AAV-CNTF gene therapy combined with intraspinal mesenchymal precursor cell transplantation promotes functional and morphological outcomes after spinal cord injury in adult rats

Ciliary neurotrophic factor (CNTF) promotes survival and enhances long-distance regeneration of injured axons in parts of the adult CNS. Here we tested whether CNTF gene therapy targeting corticospinal neurons (CSN) in motor-related regions of the cerebral cortex promotes plasticity and regrowth of axons projecting into the female adult F344 rat spinal cord after moderate thoracic (T10) contusion injury (SCI). Cortical neurons were transduced with a bicistronic adeno-associated viral vector (AAV1) expressing a secretory form of CNTF coupled to mCHERRY (AAV-CNTFmCherry) or with control AAV only (AAV-GFP) two weeks prior to SCI. In some animals, viable or nonviable F344 rat mesenchymal precursor cells (rMPCs) were injected into the lesion site two weeks after SCI to modulate the inhibitory environment. Treatment with AAV-CNTFmCherry, as well as with AAV-CNTFmCherry combined with rMPCs, yielded functional improvements over AAV-GFP alone, as assessed by open-field and Ladderwalk analyses. Cyst size was significantly reduced in the AAV-CNTFmCherry plus viable rMPC treatment group. Cortical injections of biotinylated dextran amine (BDA) revealed more BDA-stained axons rostral and alongside cysts in the AAV-CNTFmCherry versus AAV-GFP groups. After AAV-CNTFmCherry treatments, many sprouting mCherry-immunopositive axons were seen rostral to the SCI, and axons were also occasionally found caudal to the injury site. These data suggest that CNTF has the potential to enhance corticospinal repair by transducing parent CNS populations

Transcriptome-pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS.

Sporadic amyotrophic lateral sclerosis (sALS) is the most common form of ALS, however, the molecular mechanisms underlying cellular damage and motor neuron degeneration remain elusive. To identify molecular signatures of sALS we performed genome-wide expression profiling in laser capture microdissection-enriched surviving motor neurons (MNs) from lumbar spinal cords of sALS patients with rostral onset and caudal progression. After correcting for immunological background, we discover a highly specific gene expression signature for sALS that is associated with phosphorylated TDP-43 (pTDP-43) pathology. Transcriptome-pathology correlation identified casein kinase 1ε (CSNK1E) mRNA as tightly correlated to levels of pTDP-43 in sALS patients. Enhanced crosslinking and immunoprecipitation in human sALS patient- and healthy control-derived frontal cortex, revealed that TDP-43 binds directly to and regulates the expression of CSNK1E mRNA. Additionally, we were able to show that pTDP-43 itself binds RNA. CK1E, the protein product of CSNK1E, in turn interacts with TDP-43 and promotes cytoplasmic accumulation of pTDP-43 in human stem-cell-derived MNs. Pathological TDP-43 phosphorylation is therefore, reciprocally regulated by CK1E activity and TDP-43 RNA binding. Our framework of transcriptome-pathology correlations identifies candidate genes with relevance to novel mechanisms of neurodegeneration

Reply to Fischer et al

We welcome the correspondence from Fischer and colleagues regarding our recent paper on vocal learning in chimpanzee food grunts [1]. Fischer et al. make two challenges to our paper's conclusions, which we address here