Systems approach to the design of locomotive fatigue management technologies

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Aeronautics and Astronautics, 2006.Includes bibliographical references (p. 145-148).Falling asleep while operating a vehicle leads to serious accidents and loss of lives. The challenge of detecting drowsiness nonintrusively stems from the absence of a single marker, and the existence of diverse signs and symptoms that collectively but not uniquely characterize it. Current alerters for locomotive cabs are inadequate partly because they a) often monitor one modality b) fail to consider the inherent characteristics of the locomotive operator tasks and physical environment, and c) are typically developed without quantitative techniques to assess performance and optimize components as part of an overall system, rather than at the individual level. Based on an estimation theory framework, a new systems approach is here proposed to design locomotive cab alerting technologies. The main idea is to combine information from an infrared eyelid monitor and a generic Train Sentry class activity monitor, to isolate the common drowsiness component and obtain an improved estimate of the operator's state. A study first quantified the important physical aspects of the locomotive cab and engineer behavior pertinent to the performance of image-based eye closure monitors.(cont.) A bench test study evaluated Attention Technology's current infrared eye closure monitor prototype front-end image analysis, Model DD-850, to verify whether its performance was a good match to the locomotive physical environment and engineer behavioral characteristics. Data from these studies were used to develop a simulation software tool in MATLAB/SIMULINK. The goal was to assess the proposed tandem detector solution and to support rational design, development and optimization of future locomotive alerting systems. A signal detection theory (SDT) approach was employed. However, the detectors were nonlinear, had multiple alerting levels and displayed non-Gaussian noise characteristics. Therefore, Monte Carlo methods were used to compute their SDT parameters on both a standalone and tandem basis. Investigation through simulation showed that adopting an architecture using tandem detectors and an "AND" logic based arbiter reduces the false alarm rate by an order of magnitude and improves the total time to alert, at the expense of only a few percent in missed alarm probability. Detection performance may be further enhanced using a speed dependent arbiter with "AND" logic above a speed threshold and "OR" logic below it.(cont.) In the simulation, the speed threshold was found to be 25 mph. This system-level study provides enough ground to build a prototype system and test the proposed solution in a simulator. Supported by FRA through Department of Transportation Volpe Research Center Contract DTRS57-04-Q-80164 PR 79-3354 and by a Postgraduate Scholarship from the Natural Sciences and Engineering Research Council of Canada.by Anton Aboukhalil.S.M

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses, and disease, testing enhancer activity in animals remains tedious, with a minority of enhancers having been characterized. Here, we have developed ‘enhancer-FACS-Seq’ (eFS) technology for highly parallel identification of active, tissue-specific enhancers in Drosophila embryos. Analysis of enhancers identified by eFS to be active in mesodermal tissues revealed enriched DNA binding site motifs of known and putative, novel mesodermal transcription factors (TFs). Naïve Bayes classifiers using TF binding site motifs accurately predicted mesodermal enhancer activity. Application of eFS to other cell types and organisms should accelerate the cataloging of enhancers and understanding how transcriptional regulation is encoded within them

An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud

To elucidate the transcriptional regulation of Bmp4 expression during organogenesis, we used phylogenetic footprinting and transgenic reporter analyses to identify Bmp4 cis-regulatory modules (CRMs). These analyses identified a regulatory region located ∼46 kb upstream of the mouse Bmp4 transcription start site that had previously been shown to direct expression in lateral plate mesoderm. We refined this regulatory region to a 396-bp minimal enhancer, and show that it recapitulates features of endogenous Bmp4 expression in developing mandibular arch ectoderm and incisor epithelium during the initiation-stage of tooth development. In addition, this enhancer directs expression in the apical ectodermal ridge (AER) of the developing limb and in anterior and posterior limb mesenchyme. Transcript profiling of E11.5 mouse incisor dental lamina, together with protein binding microarray (PBM) analyses, allowed identification of a conserved DNA binding motif in the Bmp4 enhancer for Pitx homeoproteins, which are also expressed in the developing mandibular and incisor epithelium. In vitro electrophoretic mobility shift assays (EMSA) and in vivo transgenic reporter mutational analyses revealed that this site supports Pitx binding and that the site is necessary to recapitulate aspects of endogenous Bmp4 expression in developing craniofacial and limb tissues. Finally, Pitx2 chromatin immunoprecipitation (ChIP) demonstrated direct binding of Pitx2 to this Bmp4 enhancer site in a dental epithelial cell line. These results establish a direct molecular regulatory link between Pitx family members and Bmp4 gene expression in developing incisor epithelium

Computationally-guided inference of cis-regulatory codes in metazoans

Thesis: Sc. D., Massachusetts Institute of Technology, Department of Aeronautics and Astronautics, 2014.Cataloged from PDF version of thesis.Includes bibliographical references.The biomedical problems of spaceflight pose a formidable challenge for the future of long-duration human space exploration. Besides the effects of radiation, astronauts experience muscle atrophy, cardiovascular deconditioning, bone demineralization, cataracts, as well as sensorimotor and immune disruptions. Existing countermeasures are ineffective partly because they focus on the symptoms, rather than on the underlying biological circuitry. Deciphering the networks of genes, their regulatory proteins (transcription factors (TFs)) and their regulatory DNA elements (cis-regulatory modules (CRMs)) is fundamental to the understanding of the biological processes they underlie. These processes include the formation and maintenance of cells, tissues and organs in healthy conditions, in disease, and in response to environmental perturbations, such as spaceflight. A better understanding of these networks can thus aid the development of specific and effective molecular therapeutics. Towards this goal, this thesis focuses on the computational inference of the cis-regulatory codes (combinations of TF binding site motifs) that drive the precise spatio-temporal expression of different sets of genes. The problem of cis-regulatory code inference is notoriously difficult in multicellular organisms (metazoans) because of their large repertoires of TFs and because of their vast genomes, where biological discovery and validation is laborious and costly, requiring computational decision aids to guide and prioritize experiments. First, I present a novel computational approach to control for length-dependent artifacts encountered by popular CRM discovery algorithms in the field. This LOESS-based method is flexible in capturing diverse score-length relationships and is more effective at correcting for length-dependent artifacts, compared with four available competing approaches. Application of this method in the context of Drosophila melanogaster embryonic muscle and larval neural development resulted in a more accurate inference of their biologically validated cis-regulatory codes. This method is broadly applicable for the detection of other types of patterns in biological sequences. Second, I computationally identified the Forkhead (Fkh) family of TFs as putative regulators in the development of different D. melanogaster mesodermal tissues, including cardiac, somatic and visceral muscle. The LOESS method was used to identify the Fkh family as part of general cis-regulatory codes driving the development of the embryonic heart, which otherwise could not have been identified. This study has also found that the same CRM in different cell types can be targeted by different TFs of the same family, a finding that improves our understanding of the principles of gene regulation. Third, I developed Archimedes, a novel efficient algorithm to infer high-order cisregulatory codes of up to arity 10 using large input collections of TF binding site motifs (-100s). An exhaustive search of the exponential space of motif combinations is computationally intractable. Existing brute-force algorithms are limited to small collections of input TF binding site motifs (less than 20) or to low-order combinations (single or pairwise). Many other algorithms make assumptions that are biologically invalid or are unsuitable for metazoans with vast genomes. Archimedes achieves an average of -7 orders of magnitude savings in the number of motif combinations explored, with respect to a brute-force approach. These substantial savings are achieved by the use of (a) a qualitative model of gene regulation, and (b) concepts from combinatorial optimization and constraint satisfaction to eliminate large regions of the search space that lead to non-promising or to suboptimal solutions. Archimedes performs as well as Lever, a brute-force algorithm, with -85% mean positive predictive value at a 20% false positive rate, and outperforms its two other best competitors, Compo and CPModule, in identifying known regulatory motif combinations for different gene sets in D. melanogaster. In sum, the computational tools developed in this thesis can be used as decision aids to expedite biological discovery of cis-regulatory codes involved in health, in disease, and in the environmental perturbations of spaceflight. A better understanding of the underlying molecular circuitry of muscle atrophy, cataracts, and immune suppression, for instance, will ultimately inform and pave the way for the development of novel therapeutics to treat the health problems of humans when they are sick on Earth and as they push the frontiers of space exploration.by Anton Aboukhalil.Sc. D

Reducing false alarm rates for critical arrhythmias using the arterial blood pressure waveform

Abstract Background. Over the past two decades, high false alarm (FA) rates have remained an important yet unresolved concern in the Intensive Care Unit (ICU). High FA rates lead to desensitization of the attending staff to such warnings, with associated slowing in response times and detrimental decreases in the quality of care for the patient. False arrhythmia alarms are commonly due to single channel ECG artifacts and low voltage signals, and therefore it is likely that the FA rates may be reduced if information from other independent signals is used to form a more robust hypothesis of the alarm's etiology. Methods. A large multi-parameter ICU database (PhysioNet's MIMIC II database) was used to investigate the frequency of five categories of false critical ("red" or "life-threatening") ECG arrhythmia alarms produced by a commercial ICU monitoring system, namely: asystole, extreme bradycardia, extreme tachycardia, ventricular tachycardia and ventricular fibrillation/tachycardia. Non-critical ("yellow") arrhythmia alarms were not considered in this study. Multiple expert reviews of 5,386 critical ECG arrhythmia alarms from a total of 447 adult patient records in the MIMIC II database were made using the associated 41,301 hours of simultaneous ECG and arterial blood pressure (ABP) waveforms. An algorithm to suppress false critical ECG arrhythmia alarms using morphological and timing information derived from the ABP signal was then tested. Results. An average of 42.7% of the critical ECG arrhythmia alarms were found to be false, with each of the five alarm categories having FA rates between 23.1% and 90.7%. The FA suppression algorithm developed was able to suppress 59.7% of the false alarms, with FA reduction rates as high as 93.5% for asystole and 81.0% for extreme bradycardia. FA reduction rates were lowest for extreme tachycardia (63.7%) and ventricular-related alarms (58.2% for ventricular fibrillation/tachycardia 2 and 33.0% for ventricular tachycardia). True alarm (TA) reduction rates were all 0%, except for ventricular tachycardia alarms (9.4%). Conclusions. The FA suppression algorithm reduced the incidence of false critical ECG arrhythmia alarms from 42.7% to 17.2%, where simultaneous ECG and ABP data were available. The present algorithm demonstrated the potential of data fusion to reduce false ECG arrhythmia alarms in a clinical setting, but the non-zero TA reduction rate for ventricular tachycardia indicates the need for further refinement of the suppression strategy. To avoid suppressing any true alarms, the algorithm could be implemented for all alarms except ventricular tachycardia. Under these conditions the FA rate would be reduced from 42.7% to 22.7%. This implementation of the algorithm should be considered for prospective clinical evaluation. The public availability of a real-world ICU database of multiparameter physiologic waveforms, together with their associated annotated alarms is a new and valuable research resource for algorithm developers

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification, Supplemental Table S2

<p>Supplemental Table S2 for the manuscript "Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification" by </p> <p>Shaad M. Ahmad, Brian W. Busser, Di Huang, Elizabeth J. Cozart,</p> <p>Sébastien Michaud, Xianmin Zhu, Neal Jeffries, Anton Aboukhalil, Martha L.</p> <p>Bulyk, Ivan Ovcharenko and Alan M. Michelson</p> <p> </p> <p>article in press, DOI: 10.1242/dev.101709</p> <p> </p

<i>Bmp4^lacZneo</i> and <i>Tg^CONS3</i> β-galactosidase activity in the limb and orofacial region.

<p>(<b>A</b>) Lateral views of developing fore- or hindlimbs of <i>Bmp4^lacZneo</i> control mouse embryos (<i>upper row</i>). <i>Tg^CONS3</i> transgenic embryos from permanent transgenic line TL3459 (<i>lower</i> row). The CONS3 transgene expression largely recapitulates endogenous <i>Bmp4</i> expression in the AER from E9.5–13.5. (<b>B</b>) Frontal views of the developing head of <i>Bmp4^lacZneo</i> and <i>Tg^CONS3</i> transgenic embryos from permanent line TL3459. From E9.5 to E11.0, <i>Bmp4</i> is expressed in the epithelium overlying the distal first branchial arch, maxillary and mandibular processes and medial and lateral nasal processes. At these stages, the CONS3 enhancer recapitulates endogenous expression in the ectoderm overlying the distal part of the first branchial arch at E9.5 and the mandibular process at E10.5. At E12.5, endogenous <i>Bmp4</i> expression shifts to the mesenchyme, while CONS3 expression persists in the epithelium overlying the mandibular arch and premaxilla, including incisor tooth germs. At E12.5 and 13.5, endogenous <i>Bmp4</i> is concentrated in the mesenchyme of the midface including the whisker follicles. CONS3 transgene expression persists in the epithelium that overlies the mandible, pre-maxilla and nasal pits, and fails to shift to the underlying mesenchyme. Abbreviations: MxP, maxillary process; MdP, mandibular process; MNP, medial nasal process; LNP, lateral nasal process; NP, nasal pit; Mx, maxilla; Md, mandible.</p

Conserved region driven β-galactosidase activity in the orofacial region and limb.

<p>(<b>A</b>) Schematic of the transgenic reporter construct used in transient transgenic analyses. The black rectangle denotes the location of CONS region insertions upstream of the human beta globin promoter in pGLKS (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038568#s4" target="_blank">Materials and Methods</a>). (<b>B</b>) Schematic of the <i>Bmp4^lacZneo</i> allele <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038568#pone.0038568-Lawson1" target="_blank">[45]</a> (white boxes, exons; gray boxes, coding regions). (<b>C</b>) Number of transient transgenic embryos with various CONS derivative constructs that supported β-galactosidase expression in limb or orofacial tissue.</p