Tuning Jammed Frictionless Disk Packings from Isostatic to Hyperstatic

We perform extensive computational studies of two-dimensional static bidisperse disk packings using two distinct packing-generation protocols. The first involves thermally quenching equilibrated liquid configurations to zero temperature over a range of thermal quench rates $r$ and initial packing fractions followed by compression and decompression in small steps to reach packing fractions $\phi_J$ at jamming onset. For the second, we seed the system with initial configurations that promote micro- and macrophase-separated packings followed by compression and decompression to $\phi_J$. We find that amorphous, isostatic packings exist over a finite range of packing fractions from $\phi_{\rm min} \le \phi_J \le \phi_{\rm max}$ in the large-system limit, with $\phi_{\rm max} \approx 0.853$. In agreement with previous calculations, we obtain $\phi_{\rm min} \approx 0.84$ for $r > r^*$, where $r^*$ is the rate above which $\phi_J$ is insensitive to rate. We further compare the structural and mechanical properties of isostatic versus hyperstatic packings. The structural characterizations include the contact number, bond orientational order, and mixing ratios of the large and small particles. We find that the isostatic packings are positionally and compositionally disordered, whereas bond-orientational and compositional order increase with contact number for hyperstatic packings. In addition, we calculate the static shear modulus and normal mode frequencies of the static packings to understand the extent to which the mechanical properties of amorphous, isostatic packings are different from partially ordered packings. We find that the mechanical properties of the packings change continuously as the contact number increases from isostatic to hyperstatic.Comment: 11 pages, 15 figure

Attributing Tropical Cyclogenesis to Equatorial Waves in the Western North Pacific

The direct influences of equatorial waves on the genesis of tropical cyclones are evaluated. Tropical cyclogenesis is attributed to an equatorial wave when the filtered rainfall anomaly exceeds a threshold value at the genesis location. For an attribution threshold of 3 mm/day, 51% of warm season western North Pacific tropical cyclones are attributed to tropical depression (TD)-type disturbances, 29% to equatorial Rossby waves, 26% to mixed Rossby-Gravity waves, 23% to Kelvin waves, 13% to the Madden-Julian oscillation (MJO), and 19% are not attributed to any equatorial wave. The fraction of tropical cyclones attributed to TD-type disturbances is consistent with previous findings. Past studies have also demonstrated that the MJO significantly modulates tropical cyclogenesis, but fewer storms are attributed to the MJO than any other wave type. This disparity arises from the difference between attribution and modulation. The MJO produces broad regions of favorable conditions for cyclogenesis, but the MJO alone might not determine when and where a storm will develop within these regions. Tropical cyclones contribute less than 17% of the power in any portion of the equatorial wave spectrum because tropical cyclones are relatively uncommon equatorward of 15deg latitude. In regions where they are active, however, tropical cyclones can contribute more than 20% of the warm season rainfall and up to 50% of the total variance. Tropical cyclone-related anomalies can significantly contaminate wave-filtered precipitation at the location of genesis. To mitigate this effect, the tropical cyclone-related rainfall anomalies were removed before filtering in this study

Photonic Band Gaps in 3D Network Structures with Short-range Order

We present a systematic study of photonic band gaps (PBGs) in three-dimensional (3D) photonic amorphous structures (PAS) with short-range order. From calculations of the density of optical states (DOS) for PAS with different topologies, we find that tetrahedrally connected dielectric networks produce the largest isotropic PBGs. Local uniformity and tetrahedral order are essential to the formation of PBGs in PAS, in addition to short-range geometric order. This work demonstrates that it is possible to create broad, isotropic PBGs for vector light fields in 3D PAS without long-range order.Comment: 6 pages, 8 figure

Combining and Aggregating Environmental Data for Status and Trend Assessments: Challenges and Approaches

Increasingly, natural resource management agencies and nongovernmental organizations are sharing monitoring data across geographic and jurisdictional boundaries. Doing so improves their abilities to assess local-, regional-, and landscape-level environmental conditions, particularly status and trends, and to improve their ability to make short-and long-term management decisions. Status monitoring assesses the current condition of a population or environmental condition across an area. Monitoring for trends aims at monitoring changes in populations or environmental condition through time. We wrote this paper to inform agency and nongovernmental organization managers, analysts, and consultants regarding the kinds of environmental data that can be combined with suitable techniques and statistically aggregated for new assessments. By doing so, they can increase the (1) use of available data and (2) the validity and reliability of the assessments. Increased awareness of the difficulties inherent in combining and aggregating data for local-and regional-level analyses can increase the likelihood that future monitoring efforts will be modified and/or planned to accommodate data from multiple sources

Urban and Rural-residential Land Uses: Their Role in Watershed Health and the Rehabilitation of Oregon’s Wild Salmonids

This technical report by the Independent Multidisciplinary Science Team (IMST) is a comprehensive review of how human activities in urban and rural-residential areas can alter aquatic ecosystems and resulting implications for salmonid recovery, with a geographic focus on the state of Oregon. The following topics are considered in the form of science questions, and comprise the major components of this report: The effects of urban and rural-residential development on Oregon’s watersheds and native wild salmonids. Actions that can be used to avoid or mitigate undesirable changes to aquatic ecosystems near developing urban and rural-residential areas. The benefits and pitfalls of salmonid habitat rehabilitation within established urban or rural-residential areas. Suggested research and monitoring focus areas that will facilitate the recovery of salmonid populations affected by development. The fundamental concepts presented in this report should be applicable to most native salmonid populations across the state. IMST encourages managers and policy-makers with interest in a specific species or geographic region to carefully research local ecological conditions, as well as specific life history characteristics of salmonids in the region. Conserving watershed condition and salmonids in the face of increasing development requires consideration of two distinct sets of processes. First are the human social and economic processes that drive patterns in land use change. Second are the ecological processes, altered by land use, that underlie salmonid habitat changes. This report focuses on the latter and summarizes the effects of rural-residential and urban development on native, wild salmonid populations and the watersheds upon which they depend

Effects of juvenile steelhead on juvenile chinook salmon behavior and physiology

Experiments were designed to determine whether and how steelhead Oncorhynchus mykiss affect chinook salmon O. tshawytscha when the two species are confined together. In a behavioral experiment, we observed groups of juvenile chinook salmon and steelhead together and groups of chinook salmon alone to determine whether the steelhead were aggressive and their presence changed the behavior of chinook salmon. We also performed two runs of a physiological experiment to determine whether the addition of steelhead to tanks containing chinook salmon would stress the chinook salmon, as determined by a change in their plasma cortisol levels. Behavioral changes were observed in the chinook salmon when they were held with steelhead; they reduced their movements, darted less, were attacked up to 16 times as often, and were found less frequently in the shade than chinook salmon held without steelhead. Steelhead were found to establish territories and defend them with chases, charges, and nips. In their attempts to establish and defend territories, the steelhead attacked the chinook salmon as often as they attacked other steelhead, but the chinook salmon showed little aggression toward the steelhead. Cortisol concentrations were significantly higher for chinook salmon in tanks receiving steelhead than in tanks receiving additional chinook salmon or no additional fish after 2 h (in one of the two experimental runs) and after 32 h (in both experimental runs; combined data). These results suggest that confining steelhead and chinook salmon together, such as in raceways and barges in the Columbia River system and in other situations, is stressful to the chinook salmon

The response to forced decompression in six species of Pacific rockfish

Pacific rockfish experience high discard mortality when captured owing to a condition called barotrauma,which is caused by the change in pressure during capture. This condition appears to be species specific at the macroscopic level; however, little is known about the microscopic tissue-level effects of barotrauma. Determining whether tissue-level injuries are also species specific or influenced by factors such as life history and phylogenetic relatedness can improve our management of discard mortality. We evaluated the responses of six species of Pacific rockfish (black rockfish Sebastes melanops, blue rockfish S. mystinus, yellowtail rockfish S. flavidus, quillback rockfish S. maliger, canary rockfish S. pinniger, and yelloweye rockfish S. ruberrimus) captured from varying depths to forced decompression at the histological level (heart ventricle, rete mirabile, head kidney, liver, gill, and eye) as well as the macroscopic level. At the macroscopic level we focused on injuries caused by barotrauma, namely, everted esophaguses, exophthalmia, ocular emphysema, and ruptured swim bladders. Yellowtail and quillback rockfish experienced the fewest macroscopic injuries. Depth of capture influenced the presence of exophthalmia in quillback rockfish and ocular emphysema in quillback and yelloweye rockfish. Tissue injuries as a result of forced decompression included emphysema in the heart ventricle, emboli in the vessels of the rete mirabile, and emboli in the vessels of the head kidney. No injuries were observed at the histological level in the liver, gill, or eye owing to barotrauma. We could not detect a difference in the tissue-level response to barotrauma among the six species, suggesting that all species are susceptible to high internal gas pressure during forced decompression

Discard Mortality of Trawl-Caught Lingcod in Relation to Tow Duration and Time on Deck

The lingcod Ophiodon elongatus is a benthic marine fish commonly caught by groundfish trawlers and discarded due to low catch limits. Managers must account for the mortality of bycatch to assess population status accurately. Our objectives were to estimate the actual mortality of trawl-discarded lingcod (50- 84 cm) and describe their physiological stress response to capture. We investigated three major factors of the trawling operation that may influence lingcod survival: tow duration, fish size, and the amount of time fish were on the deck of the vessel. Survival was monitored for 21 d and each surviving animal was then physically and physiologically evaluated. The results showed that regardless of the duration of the tow, lingcod survival was 100% for animals discarded immediately after the cod end was emptied on deck. All lingcod captured during a tow of average commercial duration demonstrated a maximal stress response, measured by plasma cortisol, glucose, and lactate concentrations. As expected, lingcod from an average duration tow showed decreased survival with increased time on deck, though still had 50% survival after 30 min. This study suggests that discard mortality of lingcod is determined mainly by on-deck sorting and can be minimized by releasing fish quickly upon capture. Accurate estimation of mortality rates for lingcod will depend on the documentation of normal fishing behavior and on-deck sorting procedures.Keywords: lethal limits, Ophiodon elongatus, trawling, bycatc

Maturation characteristics and life-history strategies of the Pacific lamprey, Entosphenus tridentatus

Lampreys (Petromyzontiformes) have persisted over millennia and now suffer a recent decline in abundance. Complex life histories may have factored in their persistence; anthropogenic perturbations in their demise. The complexity of life histories of lampreys is not understood, particularly for the anadromous Pacific lamprey, Entosphenus tridentatus Gairdner, 1836. Our goals were to describe the maturation timing and associated characteristics of adult Pacific lamprey, and to test the null hypothesis that different life histories do not exist. Females exhibited early vitellogenesis – early maturation stages; males exhibited spermatogonia – spermatozoa. Cluster analyses revealed an “immature” group and a “maturing–mature” group for each sex. We found statistically significant differences between these groups in the relationships between (i) body mass and total length in males; (ii) Fulton’s condition factor and liver lipids in males; (iii) the gonadosomatic index (GSI) and liver lipids in females; (iv) GSI and total length in females; (v) mean oocyte diameter and liver lipids; and (vi) mean oocyte diameter and GSI. We found no significant difference between the groups in the relationship of muscle lipids and body mass. Our analyses support rejection of the hypothesis of a single life history. We found evidence for an “ocean-maturing” life history that would likely spawn within several weeks of entering fresh water, in addition to the formerly recognized life history of spending 1 year in fresh water prior to spawning—the “stream-maturing” life history. Late maturity, semelparity, and high fecundity suggest that Pacific lamprey capitalize on infrequent opportunities for reproduction in highly variable environments.Keywords: Primitive, Petromyzontiformes, Life histor