Transcription Factor-DNA Binding Via Machine Learning Ensembles

We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif, collected from the component algorithms. Using dimension reduction, we identify significant PWM-based subspaces for analysis. Within each subspace a machine classifier is built for identifying the TF's gene (promoter) targets (Problem 1). These PWM-based subspaces form an ML-based sequence analysis tool. Problem 2 (finding binding motifs) is solved by agglomerating k-mer (string) feature PWM-based subspaces that stand out in identifying gene targets. We approach Problem 3 (binding sites) with a novel machine learning approach that uses promoter string features and ML importance scores in a classification algorithm locating binding sites across the genome. For target gene identification this method improves performance (measured by the F1 score) by about 10 percentage points over the (a) motif scanning method and (b) the coexpression-based association method. Top motif outperformed 5 component algorithms as well as two other common algorithms (BEST and DEME). For identifying individual binding sites on a benchmark cross species database (Tompa et al., 2005) we match the best performer without much human intervention. It also improved the performance on mammalian TFs. The ensemble can integrate orthogonal information from different weak learners (potentially using entirely different types of features) into a machine learner that can perform consistently better for more TFs. The TF gene target identification component (problem 1 above) is useful in constructing a transcriptional regulatory network from known TF-target associations. The ensemble is easily extendable to include more tools as well as future PWM-based information.Comment: 33 page

A Framework for teaching Ethics to ICS Students and Practitioners using Open Educational Resources

This project has exploited findings of a pilot study funded by The Open University's (OU) CETL known as COLMSCT (Centre for Open Learning of Maths, Science, Computing and Technology – http://open.ac.uk/colmsct) and carried out under the auspices of OpenLearn (http://www.open.ac.uk/openlearn), the OU's open content initiative. The project has used the experience gained in that study to create a multimedia self-study course introducing ethics in ICS to advanced students and practitioners. The course has been made openly and freely available as an OpenLearn unit that can be studied, re-used and re-purposed by the wider community involved in the area

Tracking implicit trajectories

Output tracking of implcitly defined reference trajectories is examined. A continuous-time nonlinear dynamical system is constructed that produces explicit estimates of time-varying implicit trajectories. We prove that incorporation of this "dynamic inverter" into a tracking controller provides exponential output tracking of the implicitly defined trajectory for nonlinear control systems having vector relative degree and well-behaved internal dynanmics

A 60-million-year Cenozoic history of western Amazonian ecosystems in Contamana, eastern Peru

Weprovide a synopsis of ~60million years of life history in Neotropical lowlands, based on a comprehensive survey of the Cenozoic deposits along the Quebrada Cachiyacu near Contamana in PeruvianAmazonia. The 34 fossilbearing localities identified have yielded a diversity of fossil remains, including vertebrates,mollusks, arthropods, plant fossils, and microorganisms, ranging from the early Paleocene to the lateMiocene–?Pliocene (N20 successive levels). This Cenozoic series includes the base of the Huchpayacu Formation (Fm.; early Paleocene; lacustrine/ fluvial environments; charophyte-dominated assemblage), the Pozo Fm. (middle + ?late Eocene; marine then freshwater environments; most diversified biomes), and complete sections for the Chambira Fm. (late Oligocene–late early Miocene; freshwater environments; vertebrate-dominated faunas), the Pebas Fm. (late early to early late Miocene; freshwater environments with an increasing marine influence; excellent fossil record), and Ipururo Fm. (late Miocene–?Pliocene; fully fluvial environments; virtually no fossils preserved). At least 485 fossil species are recognized in the Contamana area (~250 ‘plants’, ~212 animals, and 23 foraminifera). Based on taxonomic lists from each stratigraphic interval, high-level taxonomic diversity remained fairly constant throughout themiddle Eocene–Miocene interval (8-12 classes), ordinal diversity fluctuated to a greater degree, and family/species diversity generally declined, with a drastic drop in the early Miocene. The Paleocene–?Pliocene fossil assemblages from Contamana attest at least to four biogeographic histories inherited from (i) Mesozoic Gondwanan times, (ii) the Panamerican realm prior to (iii) the time of South America’s Cenozoic “splendid isolation”, and (iv) Neotropical ecosystems in the Americas. No direct evidence of any North American terrestrial immigrant has yet been recognized in the Miocene record at Contamana.Facultad de Ciencias Naturales y Muse

Migration pattern of silver eel (Anguilla anguilla, L.) in an obstructed river system.

The downstream migration of European silver eels in the River Frémur was examined to determine the potential effects of the numerous migration barriers that exist on waterways in western France. The Frémur has a 14 m high dam which creates a 3 · 106 m3 water supply reservoir, 6 km from tidal limit. Based on 8-year records (1996–2004) of migrant silver eels captured in a Wolf trap located about 1 km below the dam, the influence of this dam on the migration was examined. These records indicate that 91% of silver eels were captured when the dam was overtopped (i.e. when the water reservoir was full). The timings of the overflow periods varied greatly between years mainly because they are function of the duration of the filling period which in turn is dependent on the level of summer water abstraction and annual hydrological conditions. Consequently, migration periods occurred at variable dates (between November and April) which is late in comparison with nonobstructed European river systems (generally between August and December). During overflow periods the migration of silver eels increased markedly during rain events (increasing river flow). This indicates that flow flushes, are essential so that settled silver eels can orientate themselves and pass over the dam. The hypothesis of a ‘dam effect’ that could stop temporarily or permanently some of silver eels in the reservoir is discussed. Finally, the influence of the migration delays on the condition of silver eels is considered

Cycle II.5 aircraft aero-optical turbulent boundary-layer/shear-layer measurements

The aero-optical effects associated with propagating a laser beam through aircraft turbulent boundary layers and shear layers were examined. Observed laser optical performance levels were compared with those inferred from aerodynamic measurements of unsteady densities and correlation lengths within these random flows. Optical instrumentation included a fast shearing interferometer (FSI). A 9 cm diameter collimated helium neon laser beam made a double pass through the aircraft random flow via an airfoil mirror located one meter from the fuselage. Typical aircraft turbulent boundary layer thickness measured 0.3 meters. Averaging many FSI generated modulation transfer functions (MTFs) and Fourier transforming, this average yields the expected far field intensity degradation associated with an aircraft mounted laser system. Aerodynamic instrumentation included fine wire probes to measure unsteady temperature and mass flux. A laser doppler velocimeter measured unsteady velocity within the flows. An analysis of these data yielded point measurements of unsteady density and correlation length

Medusan Morphospace: Phylogenetic Constraints, Biomechanical Solutions, and Ecological Consequences

Medusae were the earliest animals to evolve muscle-powered swimming in the seas. Although medusae have achieved diverse and prominent ecological roles throughout the world\u27s oceans, we argue that the primitive organization of cnidarian muscle tissue limits force production and, hence, the mechanical alternatives for swimming bell function. We use a recently developed model comparing the potential force production with the hydrodynamic requirements of jet propulsion, and conclude that jet production is possible only at relatively small bell diameters. In contrast, production of a more complex wake via what we term rowing propulsion permits much larger sizes but requires a different suite of morphological features. Analysis of morphometric data from all medusan taxa independently confirms size-dependent patterns of bell forms that correspond with model predictions. Further, morphospace analysis indicates that various lineages within the Medusozoa have proceeded along either of two evolutionary trajectories. The first alternative involved restriction of jet-propelled medusan bell diameters to small dimensions. These medusae may be either solitary individuals (characteristic of Anthomedusae and Trachymedusae) or aggregates of small individual medusan units into larger colonial forms (characteristic of the nectophores of many members of the Siphonophorae). The second trajectory involved use of rowing propulsion (characteristic of Scyphozoa and some hydromedusan lineages such as the Leptomedusae and Narcomedusae) that allows much larger bell sizes. Convergence on either of the differing propulsive alternatives within the Medusozoa has emerged via parallel evolution among different medusan lineages. The distinctions between propulsive modes have important ecological ramifications because swimming and foraging are interdependent activities for medusae. Rowing swimmers are characteristically cruising predators that select different prey types from those selected by jet-propelled medusae, which are predominantly ambush predators. These relationships indicate that the different biomechanical solutions to constraints on bell function have entailed ecological consequences that are evident in the prey selection patterns and trophic impacts of contemporary medusan lineages

La Boheme, Thursday, April 22, 1999

This is the concert program of the La Boheme performance on Thursday - Friday, April 22 - 24, 1999 at 8:00 p.m. and Saturday, April 25, 1999 at 2:00 p.m., at the Boston University Theater, 264 Huntington Avenue, Boston, Massachusetts. The work performed was La Boheme by Giacomo Puccini. Digitization for Boston University Concert Programs was supported by the Boston University Humanities Library Endowed Fund