ArrayBridge: Interweaving declarative array processing with high-performance computing

Scientists are increasingly turning to datacenter-scale computers to produce and analyze massive arrays. Despite decades of database research that extols the virtues of declarative query processing, scientists still write, debug and parallelize imperative HPC kernels even for the most mundane queries. This impedance mismatch has been partly attributed to the cumbersome data loading process; in response, the database community has proposed in situ mechanisms to access data in scientific file formats. Scientists, however, desire more than a passive access method that reads arrays from files. This paper describes ArrayBridge, a bi-directional array view mechanism for scientific file formats, that aims to make declarative array manipulations interoperable with imperative file-centric analyses. Our prototype implementation of ArrayBridge uses HDF5 as the underlying array storage library and seamlessly integrates into the SciDB open-source array database system. In addition to fast querying over external array objects, ArrayBridge produces arrays in the HDF5 file format just as easily as it can read from it. ArrayBridge also supports time travel queries from imperative kernels through the unmodified HDF5 API, and automatically deduplicates between array versions for space efficiency. Our extensive performance evaluation in NERSC, a large-scale scientific computing facility, shows that ArrayBridge exhibits statistically indistinguishable performance and I/O scalability to the native SciDB storage engine.Comment: 12 pages, 13 figure

The careless use of language in quantum information

An imperative aspect of modern science is that scientific institutions act for the benefit of a common scientific enterprise, rather than for the personal gain of individuals within them. This implies that science should not perpetuate existing or historical unequal social orders. Some scientific terminology, though, gives a very different impression. I will give two examples of terminology invented recently for the field of quantum information which use language associated with subordination, slavery, and racial segregation: 'ancilla qubit' and 'quantum supremacy'.Comment: 2 page

The Valuation of Contaminated Land

This paper presents a Monte Carlo based method for explicitly accounting for uncertainty in the valuation of contaminated property. Environmental risk is being quantified by the scientific methods described in this paper. Financial risk is also quantifiable by these techniques. A 1993 Supreme Court case known as Daubert has changed the admission requirements for scientific evidence by expert witnesses. Hoyt (1997) notes that it is "imperative that real estate appraisers who testify be sure that their scientific evidence will stand up to the scrutiny of Daubert of their testimony may be rejected." A scientific method of quantifying the unique financial risk of this type of asset is used for the valuation of contaminated land.

Arctic–CHAMP: A program to study Arctic hydrology and its role in global change

The Arctic constitutes a unique and important environment that is central to the dynamics and evolution of the Earth system. The Arctic water cycle, which controls countless physical, chemical, and biotic processes, is also unique and important. These processes, in turn, regulate the climate, habitat, and natural resources that are of great importance to both native and industrial societies. Comprehensive understanding of water cycling across the Arctic and its linkage to global biogeophysical dynamics is a scientific as well as strategic policy imperative

Arctic–CHAMP: A program to study Arctic hydrology and its role in global change

The Arctic constitutes a unique and important environment that is central to the dynamics and evolution of the Earth system. The Arctic water cycle, which controls countless physical, chemical, and biotic processes, is also unique and important. These processes, in turn, regulate the climate, habitat, and natural resources that are of great importance to both native and industrial societies. Comprehensive understanding of water cycling across the Arctic and its linkage to global biogeophysical dynamics is a scientific as well as strategic policy imperative

Bridging the Gap Between Schools and Non-Formal Science Institutions: Using New York City\u27s Non-Formal Resources to Teach Science

Effective science teaching and learning needs to take place in an environment in which the formal and non-formal worlds of science combine their expertise and resources. Science learning and ultimately, scientific literacy for all depends on the teaching that occurs both in schools and in non-formal settings. As we move towards the attainment of scientific literacy for all, it is becoming more imperative that we recognize and utilize the media, industry education programs, non-formal science centers, museums, and other science learning outlets as valuable segments of our nation’s science education infrastructure. This paper describes the context, rationale, and outline of the non-formal science education course developed at New York University under the auspices of New York Collaborative for Excellence in Teacher Preparation (NYCETP) and the subsequently developed non-formal science education specialization

Neuroimaging Research into Disorders of Consciousness: Moral Imperative or Ethical and Legal Failure?

This article explores the ethical and legal implications of enrolling individuals with disorders of consciousness (DOC) in neuroimaging research studies. Many scientists have strongly emphasized the need for additional neuroimaging research into DOC, characterizing the conduct of such studies as morally imperative. On the other hand, institutional review boards charged with approving research protocols, scientific journals deciding whether to publish study results, and federal agencies that disburse grant money have limited the conduct, publication, and funding of consciousness investigations based on ethical and legal concerns. Following a detailed examination of the risks and benefits of neuroimaging research involving individuals with DOC, the author urges IRBs, scientific journals, and funding agencies to no longer stall the conduct, publication, and funding of neuroimaging research into DOC if certain criteria designed to protect the health and safety of individuals with DOC are satisfied

Do Alternative Therapies Have a Role in Autism?

Interventions considered to be branches of Complementary & Alternative Medicine (CAM) for autism are on the rise. Many new treatments have emerged & traditional beliefs of Ayurveda, Yoga, Behavioral therapy, Speech therapy and Homoeopathy have gained popularity and advocacy among parents. It is imperative that data supporting new treatments should be scrutinized for scientific study design, clinical safety, and scientific validity, before embarking on them as modes of therapy. Practitioners take care in explaining the rationale behind the various approaches that they practice, it is important to indicate possible limitations too during the initial clinical examination and interactive session. Clinicians must remember that parents may have different beliefs regarding the effectiveness of treatment since their information is derived more from the ‘hear-say’ route when they compare benefits/effects of CAM therapies on other children and often underestimate differential tolerance for treatment risks. It is thus significant that practitioners do not assume a "don't ask, don't tell" posture. The scientific validation and support for many interventions is incomplete and very different from the recommendations of the American Academy of Pediatrics Policy Statement. In this article, we discuss the various modes of CAM and their utilities and limitations in relation to autism

Methodology and ontology in microbiome research

Research on the human microbiome has gen- erated a staggering amount of sequence data, revealing variation in microbial diversity at the community, species (or phylotype), and genomic levels. In order to make this complexity more manageable and easier to interpret, new units—the metagenome, core microbiome, and entero- type—have been introduced in the scientific literature. Here, I argue that analytical tools and exploratory statisti- cal methods, coupled with a translational imperative, are the primary drivers of this new ontology. By reducing the dimensionality of variation in the human microbiome, these new units render it more tractable and easier to interpret, and hence serve an important heuristic role. Nonetheless, there are several reasons to be cautious about these new categories prematurely ‘‘hardening’’ into natural units: a lack of constraints on what can be sequenced metagenomically, freedom of choice in taxonomic level in defining a ‘‘core microbiome,’’ typological framing of some of the concepts, and possible reification of statistical constructs. Finally, lessons from the Human Genome Project have led to a translational imperative: a drive to derive results from the exploration of microbiome variation that can help to articulate the emerging paradigm of per- sonalized genomic medicine (PGM). There is a tension between the typologizing inherent in much of this research and the personal in PGM