Enabling remote design and troubleshooting experiments using the ilab shared architecture

12th Biennial International Conference on Engineering, Construction, and Operations in Challenging Environments; and Fourth NASA/ARO/ASCE Workshop on Granular Materials in Lunar and Martian Exploration Honolulu, Hawaii, United States March 14-17, 2010The MIT iLab Project is dedicated to the goal of increasing laboratory experimentation opportunities for engineering students worldwide. Since its inception in 1998, the project has furthered this goal through the development of individual remote laboratories, or iLabs, as well as a distributed software infrastructure designed to streamline the implementation and sharing of remote laboratories. iLabs are designed to complement traditional, hands-on laboratories by providing practical educational experiences where they would not otherwise be available. Such remote labs, developed and hosted by MIT and other institutions within the iLab Consortium, have been successfully used by instructors at schools across the educational spectrum and around the world. While certainly valuable, many of the original experiments available through the iLab platform provide a limited experience in that they are observational in nature. They only provide students the ability to study the behavior of a pre-defined system under test. Such labs have proven to be valuable additions to engineering curricula, but do not have the flexibility that is inherent in a traditional laboratory experience. To address this, the MIT iLab Project has begun focusing on the development of iLabs that provide students with the ability to design or troubleshoot experimental systems. Through two particular remote labs, focusing on electronic control system analysis and basic electronics test and measurement respectively, the project is designing remote labs that provide a more flexible learning experience for students and are more attractive to instructors in a broad set of disciplines.National Science Foundation (U.S.) (award 0702735)Singapore-MIT Alliance for Research and Technology CenterMicrosoft CorporationCarnegie Corporation of New YorkMaricopa County Community College District. Maricopa Advanced Technology Education Cente

Hot Electron Capture Dissociation Distinguishes Leucine from Isoleucine in a Novel Hemoglobin Variant, Hb Askew, β54(D5)Val→Ile

Population migration has led to the global dispersion of human hemoglobinopathies and has precipitated a need for their identification. An effective mass spectrometry-based procedure involves analysis of the intact α- and β-globin chains to determine their mass, followed by location of the variant amino acid residue by direct analysis of the enzymatically digested chains and low-energy collision induced dissociation of the variant peptide. Using this procedure, a variant was identified as either β54Val→Leu or β54Val→Ile, since the amino acids leucine and isoleucine cannot be distinguished using low-energy collisions. Here, we describe how hot electron capture dissociation on a Fourier transform-ion cyclotron resonance mass spectrometer was used to distinguish isoleucine from leucine and identify the mutation as β54(D5)Val→Ile. This is a novel variant, and we have named it Hb Askew

A general pattern of trade-offs between ecosystem resistance and resilience to tropical cyclones

Tropical cyclones drive coastal ecosystem dynamics, and their frequency, intensity, and spatial distribution are pre-dicted to shift with climate change. Patterns of resistance and resilience were synthesized for 4138 ecosystem time series from n = 26 storms occurring between 1985 and 2018 in the Northern Hemisphere to predict how coastal ecosystems will respond to future disturbance regimes. Data were grouped by ecosystems (fresh water, salt water, terrestrial, and wetland) and response categories (biogeochemistry, hydrography, mobile biota, sedentary fauna, and vascular plants). We observed a repeated pattern of trade-offs between resistance and resilience across analyses. These patterns are likely the outcomes of evolutionary adaptation, they conform to disturbance theories, and they indicate that consistent rules may govern ecosystem susceptibility to tropical cyclones

Searching a bitstream in linear time for the longest substring of any given density

Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method involves (i) reformulating the problem as a constrained walk through a sparse matrix, and then (ii) developing a data structure for this sparse matrix that allows us to perform each step of the walk in amortised constant time. We also give a linear time algorithm to find the longest substring whose ratio of ones to zeroes is bounded below by a given value. Both problems have practical relevance to cryptography and bioinformatics.Comment: 22 pages, 19 figures; v2: minor edits and enhancement

Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals

Background: Vertebrate alpha (α)- and beta (β)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the α- and β-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil β-globin gene (ω) in the marsupial α-cluster, however, suggested that duplication of the α-β cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous α- and β-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation. Results: The platypus α-globin cluster (chromosome 21) contains embryonic and adult α- globin genes, a β-like ω-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-ζ-ζ'-αD-α3-α2-α1-ω-GBY-3'. The platypus β-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-ε-β-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate α-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal β-globin clusters are embedded in olfactory genes. Thus, the mammalian α- and β-globin clusters are orthologous to the bird α- and β-globin clusters respectively. Conclusion: We propose that α- and β-globin clusters evolved from an ancient MPG-C16orf35-α-β-GBY-LUC7L arrangement 410 million years ago. A copy of the original β (represented by ω in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of β-globin genes with different expression profiles in different lineages.Vidushi S. Patel, Steven J.B. Cooper, Janine E. Deakin, Bob Fulton, Tina Graves, Wesley C. Warren, Richard K. Wilson and Jennifer A.M. Grave

Evaluation of a Policy, Systems, and Environmental-Focused Faith-Based Health Promotion Program

Objective: This study assessed the impact and lessons learned from implementing policy, systems, and environmental (PSE) changes through Faithful Families Thriving Communities (Faithful Families), a faith-based health promotion program, in 3 southern states. Methods: Faithful Families classes and PSE changes were implemented through a coordinated effort between the Expanded Food and Nutrition Education Program (EFNEP) and Supplemental Nutrition Assistance Program–Education (SNAP-Ed). Changes were measured using a faith community assessment, site reports, and annual reporting. Results: Thirteen faith communities participated in the intervention. A total of 34 PSE changes were implemented across the 3 states, affecting 11 faith communities with 4,810 members across sites. Conclusions and Implications: Programs such as Faithful Families can allow EFNEP and SNAP-Ed to coordinate to implement PSE changes in community settings. However, these types of coordinated programs to support faith communities require time for relationship building and trust, adequate training, and strong support for faith-based lay leaders as they carry out this work

Lactate signalling regulates fungal β-glucan masking and immune evasion

AJPB: This work was supported by the European Research Council (STRIFE, ERC- 2009-AdG-249793), The UK Medical Research Council (MR/M026663/1), the UK Biotechnology and Biological Research Council (BB/K017365/1), the Wellcome Trust (080088; 097377). ERB: This work was supported by the UK Biotechnology and Biological Research Council (BB/M014525/1). GMA: Supported by the CNPq-Brazil (Science without Borders fellowship 202976/2014-9). GDB: Wellcome Trust (102705). CAM: This work was supported by the UK Medical Research Council (G0400284). DMM: This work was supported by UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC/K000306/1). NARG/JW: Wellcome Trust (086827, 075470,101873) and Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology (097377). ALL: This work was supported by the MRC Centre for Medical Mycology and the University of Aberdeen (MR/N006364/1).Peer reviewedPostprin

Fatal Disseminated Cryptococcus gattii Infection in New Mexico

We report a case of fatal disseminated infection with Cryptococcus gattii in a patient from New Mexico. The patient had no history of recent travel to known C. gattii-endemic areas. Multilocus sequence typing revealed that the isolate belonged to the major molecular type VGIII. Virulence studies in a mouse pulmonary model of infection demonstrated that the strain was less virulent than other C. gattii strains. This represents the first documented case of C. gattii likely acquired in New Mexico

Beyond microarrays: Finding key transcription factors controlling signal transduction pathways

BACKGROUND: Massive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function. Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments. RESULTS: We developed a novel approach to find key transcription factors that may explain concerted expression changes of specific components of the signal transduction network. The approach aims at revealing evidence of positive feedback loops in the signal transduction circuits through activation of pathway-specific transcription factors. We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways. Application of the approach to the microarray gene expression data on TNF-alpha stimulated primary human endothelial cells helped to reveal novel key transcription factors potentially involved in the regulation of the signal transduction pathways of the cells. CONCLUSION: We developed a novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC(® )and TRANSPATH(®)). The corresponding software and databases are available at

Defining functional DNA elements in the human genome

With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease