Consequences of placing an intramolecular crosslink in myosin S1

This paper describes the placement of a crosslinking agent (dibromobimane) between two thiols (Cys-522 and Cys-707) of a fragment, “S1,” of the motor protein, myosin. It turns out that fastening the first anchor of the crosslinker is easy and rapid, but fastening the second anchor (Cys-522) is very temperature dependent, taking 30 min at room temperature but about a week on ice. Moreover, crystallography taken at 4°C would seem to predict that the linkage is impossible, because the span of the crosslinking agent is much less than the interthiol distance. The simplest resolution of this seeming paradox is that structural fluctuations of the protein render the linkage increasingly likely as the temperature increases. Also, measurements of the affinity of MgADP for the protein, as well as the magnetic resonance of the P-atoms of the ADP once emplaced, suggest that binding the first reagent anchor to Cys-707 initiates an influence that travels to the rather distant ADP-binding site, and it is speculated what this “path of influence” might be.

The interphotoreceptor retinoid binding protein gene in therian mammals: Implications for higher level relationships and evidence for loss of function in the marsupial mole

The subclass Theria of Mammalia includes marsupials (infraclass Metatheria) and placentals (infraclass Eutheria). Within each group, interordinal relationships remain unclear. One limitation of many studies is incomplete ordinal representation. Here, we analyze DNA sequences for part of exon 1 of the interphotoreceptor retinoid binding protein gene, including 10 that are newly reported, for representatives of all therian orders. Among placentals, the most robust clades are Cetartiodactyla, Paenungulata, and an expanded African clade that includes paenungulates, tubulidentates, and macroscelideans. Anagalida, Archonta, Altungulata, Hyracoidea + Perissodactyla, Ungulata, and the “flying primate” hypothesis are rejected by statistical tests. Among marsupials, the most robust clade includes all orders except Didelphimorphia. The phylogenetic placement of the monito del monte and the marsupial mole remains unclear. However, the marsupial mole sequence contains three frameshift indels and numerous stop codons in all three reading frames. Given that the interphotoreceptor retinoid binding protein gene is a single-copy gene that functions in the visual cycle and that the marsupial mole is blind with degenerate eyes, this finding suggests that phenotypic degeneration of the eyes is accompanied by parallel changes at the molecular level as a result of relaxed selective constraints.

The root of the universal tree and the origin of eukaryotes based on elongation factor phylogeny.

The genes for the protein synthesis elongation factors Tu (EF-Tu) and G (EF-G) are the products of an ancient gene duplication, which appears to predate the divergence of all extant organismal lineages. Thus, it should be possible to root a universal phylogeny based on either protein using the second protein as an outgroup. This approach was originally taken independently with two separate gene duplication pairs, (i) the regulatory and catalytic subunits of the proton ATPases and (ii) the protein synthesis elongation factors EF-Tu and EF-G. Questions about the orthology of the ATPase genes have obscured the former results, and the elongation factor data have been criticized for inadequate taxonomic representation and alignment errors. We have expanded the latter analysis using a broad representation of taxa from all three domains of life. All phylogenetic methods used strongly place the root of the universal tree between two highly distinct groups, the archaeons/eukaryotes and the eubacteria. We also find that a combined data set of EF-Tu and EF-G sequences favors placement of the eukaryotes within the Archaea, as the sister group to the Crenarchaeota. This relationship is supported by bootstrap values of 60-89% with various distance and maximum likelihood methods, while unweighted parsimony gives 58% support for archaeal monophyly.

Multiple origins of the yucca-yucca moth association.

The association of species of yucca and their pollinating moths is considered one of the two classic cases of obligate mutualism between floral hosts and their pollinators. The system involves the active collection of pollen by females of two prodoxid moth genera and the subsequent purposeful placement of the pollen on conspecific stigmas of species of Yucca. Yuccas essentially depend on the moths for pollination and the moths require Yucca ovaries for oviposition. Because of the specificity involved, it has been assumed that the association arose once, although it has been suggested that within the prodoxid moths as a whole, pollinators have arisen from seed predators more than once. We show, by using phylogenies generated from three molecular data sets, that the supposed restriction of the yucca moths and their allies to the Agavaceae is an artifact caused by an incorrect circumscription of this family. In addition we provide evidence that Yucca is not monophyletic, leading to the conclusion that the modern Yucca-yucca moth relationship developed independently more than once by colonization of a new host.

THE DESIGN OF A POWER SYSTEM FOR A WIRELESS SENSOR NETWORK FOR LONG-TERM OPERATION

Wireless sensor networks (WSNs) have shown wide applicability to many fields including monitoring of environmental, civil, and industrial settings. WSNs however are resource constrained by many competing factors that span their hardware, software, and networking. One of the central resource constrains is the charge consumption of WSN nodes. With finite energy supplies, low charge consumption is needed to ensure long lifetimes and success of WSNs. This thesis details the design of a power system to support long-term operation of WSNs. The power system’s development occurs in parallel with a custom WSN from the Queen’s MEMS Lab (QML-WSN), with the goal of supporting a 1+ year lifetime without sacrificing functionality. The final power system design utilizes a TPS62740 DC-DC converter with AA alkaline batteries to efficiently supply the nodes while providing battery monitoring functionality and an expansion slot for future development. Testing tools for measuring current draw and charge consumption were created along with analysis and processing software. Through their use charge consumption of the power system was drastically lowered and issues in QML-WSN were identified and resolved including the proper shutdown of accelerometers, and incorrect microcontroller unit (MCU) power pin connection. Controlled current profiling revealed unexpected behaviour of nodes and detailed current-voltage relationships. These relationships were utilized with a lifetime projection model to estimate a lifetime between 521-551 days, depending on the mode of operation. The power system and QML-WSN were tested over a long term trial lasting 272+ days in an industrial testbed to monitor an air compressor pump. Environmental factors were found to influence the behaviour of nodes leading to increased charge consumption, while a node in an office setting was still operating at the conclusion of the trail. This agrees with the lifetime projection and gives a strong indication that a 1+ year lifetime is achievable. Additionally, a light-weight charge consumption model was developed which allows charge consumption information of nodes in a distributed WSN to be monitored. This model was tested in a laboratory setting demonstrating +95% accuracy for high packet reception rate WSNs across varying data rates, battery supply capacities, and runtimes up to full battery depletion.

Foraminiferal oxygen and carbon isotopic measurements from 5 sites of southern Atlantic and Pacific

The stratigraphy and paleoceanography of the late Miocene and early Pliocene have been examined at six sites in the South Atlantic and southwest Pacific oceans: Deep Sea Drilling Project (DSDP) sites 284, 516A, 519, 588, and 590 and two piston cores from Chain cruise 115. A consistent stratigraphy was developed among sites using graphic correlation, which resulted in age models for all sites that are tied to the revised paleomagnetic time scale of Berggren et al. (1985). Applying these chronologies, we assessed latitudinal and interocean contrasts in the stratigraphic ranges of late Miocene-early Pliocene planktonic foraminiferal and nanno - fossil datums. Salient stratigraphic results include (1) The last appearance datum (LAD) of Globoquadrina dehiscens is a late Miocene (approx. 6.4 Ma) event in the subtropics and is not useful for the placement of the Miocene/Pliocene (M/P) boundary in this biogeographic province. (2) The first appearance datum (FAD) of Globorotalia crassaformis occurred at 5.1 Ma in the South Atlantic near the M/P boundary, suggesting that Gr. crassaformis may have first evolved in the South Atlantic and later migrated to other regions. (3) In the southwest Pacific, the FADs of Gr. margaritae (5.97 Ma), Gr. puncticulata (5.09 Ma), and Gr. crassaformis (4.87 Ma) are significantly time transgressive between temperate and warm subtropical regions. Time lags of 1.0 m.y. were required for these species to adapt to physical and/or biotic conditions peripheral to their endemic biogeographic provinces. (4) Between the subtropics of the South Atlantic and southwest Pacific, many planktonic foraminiferal datums (FAD of Dentogloboquadrina altispira, Gr. cibaoensis, Gr. conomiozea, Gr. margaritae, and Gq. dehiscens and LAD of Gr. cibaoensis) markedly depart from the correlation suggested by magnetostratigraphy, indicating that these datum levels are unreliable for correlation between these ocean basins. (5) In contrast, available calcareous nannofossil datum levels fall on or near the paleomagnetic correlation line, indicating synchroneity of events within the subtropics. (6) Biostratigraphic, magnetic, and 87Sr/86Sr correlation between sites 588 and 519 and the M/P neostratotype at Capo Rossello, Sicily, suggests that the base of the Zanclean stratotype occurs at 5.1-5.0 Ma in the lower reversed subchron of the Gilbert, about 2-3 * 10**5 years above the Gilbert/Chron 5 boundary. Oxygen isotopic results from DSDP sites 284, 519, and CH115 piston cores confirm a prolonged benthic d18O increase in the latest Miocene between 5.6 and 5.0 Ma, as originally proposed by Shackleton and Kennett (1975). At DSDP site 588, the benthic d18O record in the latest Miocene is marked by high-frequency fluctuations with amplitude variations of 0.5per mill, and a long-period wavelength component of 400,000 years. Maximum d18O values, however, occurred during the late Miocene (Kapitean Stage) between 5.5 and 5.1 Ma. The late Miocene d18O changes resulted from mid- and high-latitude cooling and pulses of ice sheet expansion and contraction. Glacial events were most intense during the latest Miocene (Kapitean Stage), and occurred at 5.50-5.35 Ma and at 5.10 Ma. Glacial events are estimated to have lowered sea level by 40 to 60 m and contributed to the isolation and desiccation of the Mediterranean Basin during the late Messinian. Interglacial conditions prevailed at 5.2 Ma and between 5.0 and 4.1 Ma in the early Pliocene. The beginning of the Pliocene was marked by changes in many proxy climatic indicators at all sites, suggesting a prolonged interval of warm, interglacial conditions between 5.0 and 4.1 Ma during the earliest Pliocene.

Calcareous nannofossil biostratigraphy of ODP Hole 108-667A and DSDP Site 85-574

Detailed quantitative analyses of selected calcareous nannofossil species were used to determine the placement of zonal boundaries. In Hole 667A in the equatorial Atlantic Ocean, Zones CP19 through CN5 were recognized, whereas at Site 574 in the equatorial Pacific Ocean, only the CN4/CN5 boundary could be determined. Boundaries were identified by sharp rises and declines in abundance at the beginnings and ends, respectively, of index fossil ranges. The sharp rise in abundance at the beginning of the range of Triquetrorhabdulus rugosus provided a good datum level in both regions; the same is true for the sharp decline in abundance at the end of the range of Cyclicargolithus floridanus. The last occurrence of Helicosphaera ampliaperta was used to mark the CN3/CN4 boundary in Hole 667A, while at Site 574, H. ampliaperta was absent. The abundance pattern of Triquetrorhabdulus carinatus obtained from Hole 667A makes it impossible to observe a distinct disappearance level. Age/depth plots reveal uniform sedimentation rates at both sites during early Miocene times. At Site 667 in the Atlantic the mean sedimentation rate was 14.90 m/m.y., and at Site 574 in the Pacific it was 16.17 m/m.y. during this same period. One new nannofossil species, Triquetrorhabdulus rioensis, is described; and one species, Triquetrorhabdulus serratus, is recombined.

Village of Rosemont special project report : Willow-Higgins Creek Flood Mitigation Project phases III & IV, Cook County, Illinois.

Report by the Illinois Office of Water Resources on Phases III & IV of a flood hazard mitigation project in Rosemont, Illinois. Phase III of the Willow-Higgins Flood Mitigation Project consists of widening and improving a 340-foot reach of Willow-Higgins Creek upstream of River Road. The improvement will include the replacement of 340 lineal feet of vertical floodwall along both sides of Willow-Higgins Creek. Phase IV of the Willow-Higgins Flood Mitigation Project consists of widening and improving a reach of Willow-Higgins Creek between the downstream end of Phase II, which is 2565 feet downstream of Higgins Road, and Granville Road; and also between Willow Creek Road and a point 160 feet downstream of Willow Creek Road. The improvement will include placement of 2200 lineal feet of vertical floodwall along the north side of Willow-Higgins Creek and 160 feet of vertical floodwall along both sides of Willow-Higgins Creek downstream of Willow Creek Road.

Under the Bridge: Utilizing Covered Liminal Spaces for Sanctioned Homeless Encampments in the City of Seattle

Thesis (Master's)--University of Washington, 2016-06

Optimally distributed actuator placement and control for a slewing single-link flexible manipulator

A method is proposed for determining the optimal placement and controller design for multiple distributed actuators to reduce the vibrations of flexible structures. In particular, application of piezoceramic patches to a horizontally-slewing single-link flexible manipulator modeled using the assumed modes method is investigated. The optimization method uses simulated annealing and allows placement of any number of distributed actuators of unequal length, although piezoceramics of fixed equal lengths are used in the example. It also designs an linear-quadratic-regulator controller as part of the optimization procedure. The measures of performance used in the investigation to determine optimality are the total mass of the system and the time integral of the absolute value of the hub and tip position error. This study also varies the relative weightings for each of these performance measures to observe the effects on the controller designs and piezoceramic patch positions in the optimized solutions.

Investigation of in vitro transdermal absorption of fentanyl from patches placed on skin samples obtained from various anatomic regions of dogs

Objective-To investigate in vitro transdermal absorption of fentanyl from patches through skin samples obtained from various anatomic regions of dogs. Sample Population-Skin samples from 5 Greyhounds. Procedure-Skin samples from the dogs' thoracic, neck, and groin regions were collected postmortem and frozen. After samples were thawed, circular sections were cut and placed in Franz-type diffusion cells in a water bath (32degreesC). A commercial fentanyl patch, attached to an acetate strip with a circular hole, was applied to each skin sample. Cellulose strips were used as control membranes. Samples of receptor fluid in the diffusion cells were collected at intervals for 48 hours, and fentanyl concentrations were analyzed by use of high-performance liquid chromatography. Results-Mean +/- SD release rate of fentanyl from the patch, defined by its absorption rate through the non-rate-limiting cellulose membrane, was linear during the first 8 hours (2.01 +/- 0.05 pg/cm(2) of cellulose membrane/h) and then decreased. Fentanyl passed through skin from the groin region at a faster rate and with a significantly shorter lag time, compared with findings in neck or thoracic skin samples. Conclusions and Clinical Relevance-In vitro, fentanyl from a patch was absorbed more quickly and to a greater extent through skin collected from the groin region of dogs, compared with skin samples from the thoracic and neck regions. Placement of fentanyl patches in the groin region of dogs may decrease the lag time to achieve analgesia perioperatively; however, in vivo studies are necessary to confirm these findings.

Preliminary study of shunt related death in paediatric patients

Hydrocephalus is a condition commonly encountered in paediatric and adult neurosurgery and cerebrospinal fluid (CSF) shunting remains the treatment of choice for many cases. Despite improvements in shunt technology and technique, morbidity and mortality remain. The incidence of early shunt obstruction is high with later failures seen less frequently. This review aims to examine mortality associated with mechanical failure of CSF shunts within Queensland. Neurosurgical and Intensive Care databases were reviewed for cases of mortality associated with shunt failure. Eight cases were identified between the years of 1992 and 2002 with the average age at death 7.7 years. Deaths occurred on average 2 years after last shunt revision. Seven of the eight patients lived outside the metropolitan area. Shunting remains an imperfect means of treating hydrocephalus. Mortality may be encountered at any time post surgery and delays to surgical intervention influence this. Alternative measures such as third ventriculostomy or the placement of a separate access device should be considered. In the event of emergency, a spinal needle could be used to access the ventricle along the course of the ventricular catheter. (C) 2004 Elsevier Ltd. All rights reserved.

A probabilistic switch model of information flow in social networks: Application for virtual circuits to organizational design

Network building and exchange of information by people within networks is crucial to the innovation process. Contrary to older models, in social networks the flow of information is noncontinuous and nonlinear. There are critical barriers to information flow that operate in a problematic manner. New models and new analytic tools are needed for these systems. This paper introduces the concept of virtual circuits and draws on recent concepts of network modelling and design to introduce a probabilistic switch theory that can be described using matrices. It can be used to model multistep information flow between people within organisational networks, to provide formal definitions of efficient and balanced networks and to describe distortion of information as it passes along human communication channels. The concept of multi-dimensional information space arises naturally from the use of matrices. The theory and the use of serial diagonal matrices have applications to organisational design and to the modelling of other systems. It is hypothesised that opinion leaders or creative individuals are more likely to emerge at information-rich nodes in networks. A mathematical definition of such nodes is developed and it does not invariably correspond with centrality as defined by early work on networks.

Temperature changes in dental pulp associated with use of power grinding equipment on equine teeth

Objective To quantify the temperature changes in the dental pulp associated with equine dental procedures using power grinding equipment. Design A matrix experimental design with replication on the same sample was followed to allow the following independent variables to be assessed: horse age (young or old), tooth type (premolar or molar), powered grinding instrument (rotating disc or die grinder), grinding time (15 or 20 seconds) and the presence or absence of water coolant. Procedure Sound premolar and molar teeth from a 6-year-old horse and a 15-year-old horse, which had been removed postmortem, were sectioned parallel to the occlusal plane to allow placement of a miniature thermocouple at the level of the dental pulp. The maximum temperature increase, the time taken to reach this maximum and the cooling time were measured (n=10 in each study). The teeth were placed in a vice and the instrument used on the tooth as per clinical situation. Results Significant differences were recorded for horse age (P < 0.001), instrument type (P < 0.001), grinding time (P < 0.001) and presence or absence of coolant (P < 0.001). There was no significant difference for tooth type. Conclusion Thermal insult to the dental pulp from the use of power instruments poses a significant risk to the tooth. This risk can be reduced or eliminated by appropriate selection of treatment time and by the use of water irrigation as a coolant. The increased dentine thickness in older horses appears to mitigate against thermal injury from frictional heat.

Ultrastructure of the spermatozoon of Apus apus (Linnaeus 1758), the common swift (Aves; Apodiformes; Apodidae), with phylogenetic implications

The spermatozoon of Apus apus is typical of non-passerines in many respects. Features shared with palaeognaths and the Galloanserae are the conical acrosome, shorter than the nucleus; the presence of a proximal as well as distal centriole; the elongate midpiece with mitochondria grouped around an elongate distal centriole; and the presence of a fibrous or amorphous sheath around the principal piece of the axoneme. The perforatorium and endonuclear canal are lost in A. apus as in some other non-passerines. All non-passerines differ from palaeognaths in that the latter have a transversely ribbed fibrous sheath whereas in non-passerines it is amorphous, as in Apus, or absent. The absence of an annulus is an apomorphic but homoplastic feature of swift, psittaciform, gruiform and passerine spermatozoa. The long distal centriole, penetrating the entire midpiece, is a remarkably plesiomorphic feature of the swift spermatozoa, known elsewhere only in palaeognaths. The long centriole of Apus, if not a reversal, would be inconsistent with the former placement of the Apodiformes above the Psittaciformes from DNA-DNA hybridization. In contrast to passerines, in A. apus the microtubules in the spermatid are restricted to a transient single row encircling the cell. The form of the spermatozoon fully justifies the exclusion of swifts from the passerine family Hirundinidae.