Life Sciences Commons^™

Tree-Based Multivariate Regression And Density Estimation With Right-Censored Data , Annette M. Molinaro, Sandrine Dudoit, Mark J. Van Der Laan

U.C. Berkeley Division of Biostatistics Working Paper Series

We propose a unified strategy for estimator construction, selection, and performance assessment in the presence of censoring. This approach is entirely driven by the choice of a loss function for the full (uncensored) data structure and can be stated in terms of the following three main steps. (1) Define the parameter of interest as the minimizer of the expected loss, or risk, for a full data loss function chosen to represent the desired measure of performance. Map the full data loss function into an observed (censored) data loss function having the same expected value and leading to an efficient estimator …

Design And Standards For Genetic Evaluation Of Swine Seedstock Populations, T. J. Baas, R. N. Goodwin, L. L. Christian, R. K. Johnson, O. W. Robison, J. W. Mabry, K. Clark, M. Tokach, S. Henry, P. J. Berger

Department of Animal Science: Faculty Publications

The purpose of this article is to describe a program for evaluation of seedstock populations in the swine industry. Differences among seedstock populations for economically important traits must be identified in order for pork producers to efficiently use available genetic resources. National genetic evaluation programs have the potential to identify the important differences among populations and to increase the rate of genetic improvement in a population. Program results provide performance benchmarks that stimulate testing and selection procedures by seedstock suppliers that further increase the rate of genetic improvement. A Terminal Sire Line Genetic Evaluation Program was designed and conducted in …

The Complete Genome Sequence Of The Arabidopsis And Tomato Pathogen Pseudomonas Syringae Pv. Tomato Dc3000, C. Robin Buell, Vinita Joardar, Magdalen Lindeberg, Jeremy Selengut, Ian T. Paulsen, Michelle L. Gwinn, Robert J. Dodson, Robert T. Deboy, A. Scott Durkin, James F. Kolonay, Ramana Radupu, Sean Daugherty, Lauren Brinkac, Maureen J. Beanan, Daniel H. Haft, William C. Nelson, Tanja Davidsen, Nikhat Zafar, Liwei Zhou, Jia Liu, Qiaoping Yuan, Hoda Khouri, Nadia Fedorova, Bao Tran, Daniel Russell, Kristi Berry, Teresa Utterback, Susan E. Van Aken, Tamara V. Feldblyum, Mark D'Ascenzo, Wen-Ling Deng, Adela R. Ramos, James R. Alfano, Samuel Cartinhour, Arn K. Chatterjee, Terrence P. Delaney, Sondra G. Lazarowitz, Gregory B. Martin, David J. Schneider, Xiaoyan Tang, Carol L. Bender, Owen White, Claire M. Fraser, Alan Collmer

Department of Plant Pathology: Faculty Publications

We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise7%of the DC3000 genome. The bacterium possesses a large repertoire of transporters for …

Hexapod Herald - Vol. 15, No. 4, September 2003

Hexapod Herald and Other Entomology Department Newsletters

Congratulations

Welcome

Farewell

Faculty news

Graduate student news

From the office

Grants

Museum news

Publications

Travel

Condolences

This and that

Direct Marketing Of Agroforestry Products, Stefanie Aschmann

Agroforestry Notes (USDA-NAC)

Agroforestry can enhance cash flow on many farms through the production of high-value forest products. The greatest challenge, however, is often marketing rather than production. Unlike commodity crops that have a readily available, but relatively uncompromising, market; the market for some agroforestry products is not always apparent. Landowners may need to take an active role in marketing to reap the benefits of their production. Producer goals, resources, and products, as well as local customer needs and habits usually dictate marketing strategies. This Note describes several different direct marketing strategies that might be used to market agroforestry products. Many variations on …

The Relationship Between Health Status And Hope In Individuals With Hiv Disease, Celine Meera Chohan

All-Inclusive List of Electronic Theses and Dissertations

This study examined the relationship between hope and health status over a two-year period in individuals who were HIV -infected. One hundred and three individuals completed the surveys at entry into the study, at 12 months, and at 24 months. The Health Status Questionnaire (Wu et.al., 1991) measured Cognitive Functioning, Emotional Functioning, and Physical Functioning. Additionally, the Hope Scale (Snyder, 1991) and the Client Information Form were used to collect data. Results suggested hope at entry into the study was a significant predictor of physical functioning initially, at 12 months, and at 24 months. This finding suggests a link between …

Characterization Of Six Polymorphic Microsatellites For The Polychaete Tubeworm Hydroides Elegans And Cross-Species Amplification In The Congener Hydroides Hexagonus, J. B. Pettengill, M. G. Hadfield, M. D. Schug, D. E. Wendt

Biological Sciences

We isolated and characterized six polymorphic microsatellite loci for the polychaete tubeworm, Hydroides elegans. Two additional loci were not reliably scorable and estimates of heterozygosity were obtained for the other six. In addition, cross-species amplification was successful for two loci using the congener H. hexagonus. Given that few microsatellite loci are available for polychaetes, these markers will be useful in assessing dispersal and gene flow in H. elegans and probably also other polychaetes.

Blackwood Catchment : Beaufort Zone (Zone 4) : Catchment Appraisal 2002, Henry Brockman, Blackwood Rapid Catchment Appraisal Team (Wa ), Natural Heritage Trust (Australia)

Resource management technical reports

Using the Rapid Catchment Appraisal process, this report summarises current information for the Beaufort zone, located in the mid to southern part of the Blackwood basin, including parts of the shires of Kojonup, West Arthur, Woodanilling, Katanning, Broomehill, Wagin and Boyup Brook, Western Australia. Assesses the condition of, and future risks to agricultural and natural resources, provides information for reducing those risks and identifies the most suitable options to manage the risk.

Predicting The Effectiveness Of Farm Planning At The Byenup Hill Catchment Using A Groundwater Model, Gregory Paul Raper, L M. Guppy

Resource management technical reports

A catchment model was constructed for the Byenup Hill catchment based on detailed hydrogeological mapping, information on land mapping units and land use collected from landholders. The aim of this work was to assess the likely impact of proposed land management changes to soil salinisation and recharge in the Byenup Hill Catchment.

Converting A Pasture To A Silvopasture In The Pacific Northwest, Steven H. Sharrow, Rick Fletcher

Agroforestry Notes (USDA-NAC)

Forestry and livestock production are mainstays of the natural resource-based economies of many rural communities in the western United States and Canada. Regenerating mixed conifer forests may produce considerable amounts of ground vegetation that is suitable as livestock feed, while open-canopied pine forests in more arid conditions produce forage throughout their lives. Not surprisingly, there is a strong tradition of livestock grazing within western forests. Silvopasture, the combination of forest management and improved forage species, is a more intensive, controlled application of this traditional use. It is most often implemented to increase profitability, reduce risk, and augment environmental benefits from …

Context-Aware Semantic Association Ranking, Boanerges Aleman-Meza, Christian Halaschek-Wiener, I. Budak Arpinar, Amit P. Sheth

Kno.e.sis Publications

Discovering complex and meaningful relationships, which we call Semantic Associations, is an important challenge. Just as ranking of documents is a critical component of today's search engines, ranking of relationships will be essential in tomorrow's semantic search engines that would support discovery and mining of the Semantic Web. Building upon our recent work on specifying types of Semantic Associations in RDF graphs, which are possible to create through semantic metadata extraction and annotation, we discuss a framework where ranking techniques can be used to identify more interesting and more relevant Semantic Associations. Our techniques utilize alternative ways of specifying the …

Social Learning Of Prey Location In Hatchery-Reared Atlantic Salmon, C. Brown, A. Markula, K. Laland

Aquaculture Collection

Naïve, hatchery-reared Atlantic salmon Salmo salar parr were paired with demonstrators that had been pre-trained to accept live prey from the surface or from the benthos. After 6 days of observing demonstrators through a clear perspex partition the naïve fish’s benthic foraging skills were tested. The results revealed that hatchery-reared Atlantic salmon can be taught to target benthic prey items by observation alone and social learning protocols can be utilized to dramatically increase benthic foraging success. The results are discussed with reference to refining hatchery-rearing practices with a view to improving the post-release survival of hatchery fishes. The role of …

Csrees School Of Natural Resources Comprehensive Five-Year Review

School of Natural Resources: Documents and Reviews

No abstract provided.

A National Early Detection And Rapid Response System For Invasive Plants In The United States, Conceptual Design, Federal Interagency Committee For The Management Of Noxious And Exotic Weeds

All U.S. Government Documents (Utah Regional Depository)

No abstract provided.

Annuals For Utah Gardens, Teresa Cerny, Debbie Amundsen, Loralie Cox

Gardening

No abstract provided.

Aggiecology- Usu Thinks Green, Utah State University

Agriculture

No abstract provided.

Fisheries Research Contract Report No. 4 - Determining Waste Excretion Parameters From Barramundi Aquaculture: Final Report For Aquaculture Development Fund Of Wa, Brett Glencross, Neil Rutherford, Wayne Hawkins

Fisheries Research Contract Reports

This study was undertaken to evaluate the nutrient excretion budgets for each of three key commercial diets when fed to barramundi (Lates calcarifer). The diets differed primarily in their energy density ranging from 21.3 MJ/kg DM to 23.0 MJ/kg DM, with the protein content of each diet being relatively constant at around 550 g/kg DM. The determination of the nutrient excretion budgets required the assessment of the digestibilities of key nutrients from each of the diets and also the specific retention of nutrients over a prolonged period. This necessitated two digestibility trials and a growth trial.

An examination was also …

Freshwater Wetlands Inventory Outreach Activities, West, M, West Environmental, Inc., Carex Ecosystem Sciences

PREP Reports & Publications

West Environmental, Inc. together with Carex Ecosystem Sciences and Doucet Survey, under contract with the NH Estuaries Project, have identified and mapped potential freshwater wetland mitigation opportunities in nineteen (19) communities that border coastal or estuarine habitats.

Successful Field Pea Harvesting, Glen Riethmuller, Ian Pritchard

Bulletins 4000 -

Many thousands of hectares of field peas are harvested trouble free each year. Growers experience together with recent machinery innovations and modifications have solved the majority of harvesting difficulties. Optimum harvesting conditions are in a crop of uniform density on a level soil surface with the machine either working into or across the direction that the crop has been laid by the wind.

To make harvest easier the receival standard for moisture in pulses has been lifted to 14 per cent, which allows harvest to begin sooner when the crop is the range of 14 to 15 per cent moisture. …

Differences In Hyporheic-Zone Microbial Community Structure Along A Heavy-Metal Contamination Gradient, Kevin P. Feris, Philip W. Ramsey, Frazar Chris, Johnnie N. Moore, James E. Gannon, William E. Holben

Biological Sciences Faculty Publications

Heavy metals contaminate numerous freshwater streams and rivers worldwide. Previous work by this group demonstrated a relationship between the structure of hyporheic microbial communities and the fluvial deposition of heavy metals along a contamination gradient during the fall season. Seasonal variation has been documented in microbial communities in numerous terrestrial and aquatic environments, including the hyporheic zone. The current study was designed to assess whether relationships between hyporheic microbial community structure and heavy-metal contamination vary seasonally by monitoring community structure along a heavy-metal contamination gradient for more than a year. No relationship between total bacterial abundance and heavy metals was …

Selective Plating Underestimates Abundance And Shows Differential Recovery Of Bifidobacterial Species From Human Feces, Juha H. A. Apajalahti, Anu Kettunen, Päivi H. Nurminen, Hanna Jatila, William E. Holben

Biological Sciences Faculty Publications

The aim of the present work was to compare the efficacies and levels of selectivity of different culture-dependent and -independent methods for analyzing bifidobacteria in human stool samples. The three different culture media used here significantly differed from each other, particularly with regard to the recovery of Bifidobacterium adolescentis. Bifidobacterium medium failed to recover B. adolescentis; Beerens medium recovered some B. adolescentis organisms (17% of total bifidobacteria), whereas tomato-Eugon medium recovered mainly B. adolescentis organisms (58% of total bifidobacteria). A culture-independent method that combines GC fractionation of bacterial community DNA and 16S rRNA sequencing indicated that B. adolescentis organisms accounted …

The Effects Of The Trawl Fishery On The Stock Of Pink Snapper, Pagrus Auratus, In Denham Sound, Shark Bay, M. Moran, M. I. Kangas

Fisheries Research Bulletins

Snapper stocks in the inner gulfs of Shark Bay are in a depleted condition, both in trawled and non-trawled areas, with the main factor contributing to the depletion considered to be recreational fishing for adult snapper, including some mortality of undersized snapper returned to the water. The commercial prawn trawl fishery catches many small fish species, including small juvenile pink snapper, as part of its unintended bycatch. Some members of the local community believe that mortality of juvenile snapper due to trawling has also been a significant factor in depletion of the adult stock in Denham Sound, Shark Bay. While …

Nebraska Vine Lines, Vol. Vi, No. September/October 2003.

Nebraska Vine Lines (2003–2006)

Contents

• Water Management and More

• The Freezer - Faux Pas?

• AUTUMN NOTES – A Review of Happenings in Nebraska’s Grape and Wine Industry.

• Summer Field Days Successful

• STATE FAIR WINE FESTIVAL

• Notes From the University of Nebraska Viticulture Program Research Vineyards

• NWGGA NEWS

Forage News [2003-09], Department Of Plant And Soil Sciences, University Of Kentucky

Forage News

• Grazing School in Paris October 14-15
• Kentucky Grazing Conference
• KFGC Awards
• Influence of Nitrogen Rate and Pasture Composition on Toxicity, Quality and Yield of Stockpiled Tall Fescue
• Revised Publications
• Variety Information Available on Web
• Feed Cost #1
• Can It Pay to Graze High Value Land?
• Upcoming Events

Nebraska Bird Review (September 2003) 71(3), Whole Issue

Nebraska Bird Review

Summer Field Report, June–July 2003 ... 106

Autumn Roosting Habitat for Chimney Swifts in Eastern Omaha ... 127 [Article not included at the request of the author]

2002 (14th) Report of the NOU Records Committee ... 136

Subscription and Organization Information ... 143

Taxonomic Changes For Fifteen Species Of North American Mordellidae (Coleoptera), Anneke E. Lisberg

Insecta Mundi

In an attempt to more consistently apply generic concepts, 13 species of Mordellidae are transferred to different genera. Mordellistena bihamata (Melsheimer) and Mordellistena discolor (Melsheimer) are transferred to Falsomordellistena Ermisch, 1941, while 11 species (Mordellistena ancilla LeConte, Mordellistena floridensis Smith, Mordellistena guttulata Helmuth, Mordellistena impatiens LeConte, Mordellistena infima LeConte, Mordellistena lecontei Ermisch, Mordellistena minutalis Liljeblad, Mordellistena nigricans Melsheimer, Mordellistena parva Liljeblad, Mordellistena semiusta LeConte, and Mordellistena testacea Blatchley) are transferred to Mordellina Schilsky, 1908. Two species, Mordellistena rufa Liljeblad and Mordellina ustulata (LeConte), are proposed as junior synonyms of Mordellina ancilla (LeConte).

Pentatomidae (Heteroptera) Of Honduras: A Checklist With Description Of A New Ochlerine Genus, Nolberto Arismendi, Donald B. Thomas

Insecta Mundi

Abstract:
Through collecting, surveys of museum collections, and search of the literature, we are able to list 181 species of Pentatomidae as occurring within the boundaries of the Republic of Honduras. Most of these, 129, around 70%, are widespread in the American tropics. Twenty-nine species are new country records, reported for Honduras for the first time. Four species of pentatomids are endemic to Honduras including a new genus and species of ochlerine (Discocephalinae) herein described. Although a few species extend from South America into Honduras (the Gondwanan element), and a few from North America extend into Honduras (the Nearctic element), …

External Morphology Of The First And Second Instars Of Lecanodiaspis Tingtunensis (Coccoidea: Lecanodiaspididae), P. L. Lambdin, Elzbieta Podsiadlo

Insecta Mundi

The first and second instars of Lecanodiaspis tingtunensis are described and illustrated. First instars are distinguished from other species of Lecanodiaspis by the arrangement of dorsal 8-shaped pores in six complete longitudinal rows and a partial row in the thoracic region and the number of labial, anal plate, and spiracular setae. Second instars are dimorphic with males possessing well developed 5-segmented legs, dorsal tubular ducts, and long hair-like setae on the venter between the antennae and on the abdominal segments. Females have fewer 8-shaped pores in transverse rows on the dorsum, as well as legs reduced to stubs and only …

First Records Of Melanichneumon Dreisbachi Heinrich In Florida (Hymenoptera: Ichneumonidae: Ichneumoninae: Ichneumonini), Charles C. Porter

Insecta Mundi

Melanichneumon dreisbachi was described by Heinrich (1962) on the basis of material from Maine and Michigan. No further records of this species have been published, even though Heinrich subsequently (1977) provided an exhaustive treatment of the Florida Ichneumoninae, but more recent collecting in the Gainesville area of north-central Florida has turned up 2 additional specimens.

First Record Of Labium (Hymenoptera: Ichneumonidae: Labiini) In South America With Description Of A New Species From Brasil, Charles C. Porter

Insecta Mundi

Abstract:
Labium is a primitive transantarctic genus which parasitizes ground-nesting halictid bees and until now has been known only from the Australian Region. Diagnostic features include its large exposed labrum (as long as clypeus) ; elongate mandible with upper tooth much shorter and smaller than lower tooth; slender 1st gastric tergite with spiracle distad of middle; and short, concealed ovipositor which is slender, depressed, and without notch or nodus. Labium wahli is now described from south Brazilian rain forest. It differs from the Australian species by its longer flagellum which is only slightly thickened apicad and because it has no …