bluuebunny/crossref_metadata_2025_split huggingface dataset:
A70 Viromes of two migratory birds as support for identifying the influence of molecular biology and bioinformatics settings
Authors: Tirera S , Salmier A , Donato D , Frigerio J M , Therond S , Lacoste V , de Thoisy B , Franc A , Lavergne A 
Published: August 2019

Abstract
Thanks to high-throughput sequencing (HTS) and dedicated bioinformatics tools, it is possible to study all viruses present in a sample with an unprecedented detection of viral diversity. Applied to wildlife and humans, HTS becomes a powerful means to understand viral emerging infectious diseases. BLAST searches to find remote homolog sequences after an assembly of shotgun-generated sequences are often used to analyze virome datasets. However, this process might be biased by molecular biology approaches (use of whole genome/transcriptome amplification) and bioinformatics assembly that can induce chimeric sequences formation. Our objective was to identify confounding factors (molecular biology and bioinformatics) that can bias virome composition. Hence, we studied the viromes from cloacal swab samples of two migratory birds. Viral DNA and RNA were extracted using three different methods (easymag®, phenol, and trizol), followed by whole genome amplification (WGA)/WTA amplifications, before Illumina MiSeq sequencing. After trimming and assembly, sequences underwent BLAST (BLASTn and BLASTx). At the end of the first BLAST (n/x), some portions of sequences were uncovered and unassigned. We, then, implemented a novel recursive split-resubmit python program that searched for homologs of > 50 base pairs (bp), uncovering parts for a better exploitation of the datasets. Thirty-eight known viral families were detected in our samples. Circoviridae, Parvoviridae, and Microviridae were found in the majority of the results from easymag® and Phenol extracted samples, while trizol samples resulted in a majority of Picornaviridae and Coronaviridae. These results show that the viromes are of different composition depending on extraction methods. Most of the viral sequences were predominantly identified at the blastx step reflecting a high level of divergence with known viral sequences. Compared to a unique BLAST search, our resubmission pipeline allowed the assignment of up to 23 per cent of the viral sequences. Most of these sequences belonged to taxa already observed at the first blast step and few viral sequences of different families were detected. Knowing the complementarities between extraction methods and a better identification of viral sequences using our pipeline, the next step will be to get a precise position of each viral genomic segment in phylogenetic distance-based tree that will give a more accurate representation of viral diversity.
Predicting Forest Road and Bridge Construction Costs
Authors: Jackson David H. , Loveless Robert 
Published: August 2019

Abstract
Using market-transactions evidence revealed by transportation project contracts, the authors develop forest road and bridge cost equations. The "quality" variable for bridge contracts is bridge size. In the case of roads, the amount of excavation, clearing and grubbing, haul, culverts and surfacing (aggregate) all explain variation in winning contract bids. The resulting equations should be useful in transportation planning as well as in timber-bidding studies. West. J. Appl. For. 1:76-79, July 1986.
Firewood Use on National Forests in the Western United States
Authors: Force Jo Ellen 
Published: August 2019

Abstract
USDA Forest Service personnel from 81 of the 87 national forests in the 11 western states responded to an April 1984 mail survey on firewood for personal use. Firewood use increased steadily from 1970 to 1982 when 655,000 permits were issued, and forest managers estimate 2.8 million cords were cut. In 1983, there were 462,000 permits issued and an estimated 2 0 million cords cut. Forest managers say the decrease may reflect more accurate records being kept because of permit fees in 1983. Until reliable, accurate firewood use data are available, utilization of this forest resource cannot be fully understood, and the ability to predict future trends is limited. However, 93 percent of the forest managers predict that the demand for fire-wood will increase during the next five years. Managers believe the major factors influencing supply and demand are accessibility, the amount of timber harvested, and the cost of conventional fuels for home heating. Adoption of 15 firewood management practices was examined and provides guidance to forest managers responsible for the firewood resource. West. J. Appl. For. 1:111-115, Oct. 86.
Responses of Red Alder to Thinning
Authors: Hibbs David E. , Emmingham William H. , Bondi Michael C. 
Published: August 2019

Abstract
Responses of red alder (Alnus rubra Bong.) to thinning were observed at two sites in the Oregon Coast Range. Five years after thinning in the 20-yr-old stand, mortality was observed only in control plots. Diameter growth of crop trees increased up to 54% with thinning. Trends toward less height growth at wider spacings and increased growth in basal area compared to controls appeared to be developing in thinned plots. Ten years after thinning in the 14-yr-old stand, the problems of flashback seen at year 5 in the chemically thinned plots had largely been overcome. Reduction in height growth in all thinned plots had been overcome. Net basal area growth was up to 60% greater in thinned treatments. Thinning appears effective for 10 to 15 yr in the narrow spacings and 15 to 20 yr in the wide spacings. West. J. Appl. For. 10(1): 17-23.
Effects of Bigleaf Maple Sprout Clumps on Diameter and Height Growth of Douglas-Fir
Authors: Knowe Steven A. , Carrier Byron D. , Dobkowski Alex 
Published: August 2019

Abstract
Diameter and height growth of 7- to 11-yr-old Douglas-fir (Pseudotsuga menziesii) were examined in relation to bigleaf maple (Acer macrophyllum) competition. Growth models were developed for plantations in Oregon and Washington by joining a distance-dependent model with a model that excluded competition effects. The fitted equations were based on Douglas-fir size at plantation age 7 yr and distance from the stump and crown diameter of the bigleaf maple clump. The models suggest that bigleaf maple clumps between 5.7-14.6 m from planted Douglas-firs decrease the latter's dbh and height growth, and that this decrease becomes greater with increasing size of the clump. A procedure is suggested to use the models to guide vegetation management prescriptions on sites with bigleaf maple sprout clumps. West. J. Appl. For. 10(1):5-11.
Pruning Costs for Four Northern Rocky Mountain Species with Three Equipment Combinations
Authors: O'Hara Kevin L. , Larvik Darin A. , Valappil Narayanan I. 
Published: August 2019

Abstract
A time and motion study was conducted to determine the cost to prune ponderosa pine (Pinus ponderosa), interior Douglas-fir (Pseudotsuga menziesii var. glauca), western larch (Larix occidentalis), and lodgepole pine (Pinus contorta) with loppers, pole saws, and Power Pruners. Costs to prune up to 8 ft ranged from $0.61 to $2.35/tree, and from $2.34 to $6.42/tree to prune to 18 ft depending upon species, equipment, and wage assumptions. Pole saws were the recommended equipment based on cost, ease of use, and damage to trees. Multivariate models were unable to explain much variation in pruning time because of the confounding effects of so many variables. Results suggest more than three trees could be pruned to a height of 9 ft for the same cost as pruning one tree to 18 ft. Pruning more trees to a 9 ft height would therefore increase clearwood production overpruning fewer trees to 18 ft, but may necessitate some modification of current log grading standards. West. J. Appl. For. 10(2):59-65.
Timber Harvesting by Nonindustrial Private Forest Landowners in Western Oregon
Authors: Cleaves David A. , Bennett Max 
Published: August 2019

Abstract
A survey of nonindustrial private forest (NIPF) landowners in Western Oregon was analyzed to gain insights about their harvesting activity. Past participation in harvesting, harvest type, and future intentions for harvest were related to ownership size, tenure, residence, form of organization, method of acquisition, occupation, age, and income. Thirty percent of the respondents reported harvesting at least once during the 1979-1989 period. Higher rates of harvest participation were found for larger ownership sizes, longer tenure, corporate organization, farm ownership, and higher personal income. At least some of the influence of size on reported participation came from the natural tendency of larger ownerships to have a greater variety of acres eligible for harvest. Ownership size combined with a variety of demographic factors--tenure, residence, form of organization, acquisition method, occupation, and income--influenced whether the harvest was a clearcut or a commercial thinning. Commercial thinning and thinning/clearcutting combination harvests were more common than clearcutting. Landowners were generally willing to harvest in the future; more than two-thirds of the NIPF acreage is controlled by owners with definite harvest plans. Owners who reported no intentions to harvest had little past harvesting activity. The predominance of thinning and other forms of partial cutting by smaller NIPF owners may indicate opportunities to improve the condition of NIPFs through assistance in selective cutting. West. J. Appl. For. 10(2):66-71.
Reliability of Tanoak Volume Equations when applied to different areas
Authors: Pillsbury Norman H. , McDonald Philip M. , Simon Victor 
Published: August 2019

Abstract
Tree volume equations for tanoak (Lithocarpus densiflorus) were developed for seven stands throughout its natural range and compared by a volume prediction and a parameter difference method. The objective was to test if volume estimates from a species growing in a local, relatively uniform habitat could be applied more widely. Results indicated that they could not. Diameter slope coefficients and intercepts differed at the 5% probability level. Tree height slope coefficients did not differ, but when all slope coefficients (dbh and height) were combined, a significant difference was present. Overall, volume equations from different populations were significantly different, and the general rule of matching standard volume tables to specific stands is reinforced. West. J. Appl. For. 10(2):72-78.
Porcupine Feeding Damage in Precommercially Thinned Conifer Stands of Central Southeast Alaska
Authors: Eglitis Andris , Hennon Paul E. 
Published: August 2019

Abstract
This study describes feeding damage by porcupines (Erethizon dorsatum) in precommercially thinned young growth stands of Sitka spruce (Picea sitchensis) and western hemlock (Tsuga heterophylla) on Mitkof Island in central southeast Alaska. We examined 641 trees from 54 sampling plots along transect lines in three 12 to 20 yr old stands. Porcupine feeding was monitored each spring and fall from 1985 to 1987. Four categories of feeding damage are described: complete girdling of the bole, partial girdling (bole scars), branch clipping, and "tasting wounds" (small basal bole scars). Sitka spruce, the primary crop tree in these thinned stands, sustained significantly higher damage (52% of trees affected) than western hemlock (26% of trees affected). Porcupine feeding was greater on taller than shorter Sitka spruce. Although only 8 of 59 trees initially girdled in 1985 were killed, many later sustained additional feeding damage. Following the 1987 season 3 yr after thinning, nearly 30% of the spruce and 14% of the western hemlock crop trees had been partially or completely girdled. Issues deserving future attention include the role of thinning in predisposing stands to porcupine damage, methods of population assessment, and mechanisms of host selection by porcupines. West. J. Appl. For. 12(4):115-121.
Early Height Growth of Western White Pine Provenances in British Columbia Plantations
Authors: Meagher M. D. , Hunt R. S. 
Published: August 2019

Abstract
To estimate the limits of seed transfer to and within British Columbia, heights of 36 western white pine (Pinus monticola) provenances 5-13 yr after planting on 24 sites, comprising 4 studies, were analyzed for geographic patterns. Thirty-six provenances were tested, with a maximum of 17 on a site. California and Oregon sources are not recommended due to poor height growth. Percentage differences between tallest and shortest provenances varied from 16% to 31%, depending on plantation series. Washington State and Idaho sources can be used on coastal sites but are not recommended on northern-interior sites. Northern-interior provenances are recommended for local sites, especially those beyond the species' natural range. The data support establishment of separate seed orchards, one for each of the coastal and interior portions of this disjunct species. West. J. Appl. For. 13(2):47-53.
Lumber Recovery from Beetle-Killed Spruce Trees, Kenai Peninsula, Alaska
Authors: Lowell Eini C. , Willits Susan A. 
Published: August 2019

Abstract
A four-level, visual classification system based on tree condition was developed for the beetle-killed spruce on Alaska's Kenai Peninsula. The lumber recovery study estimated lumber volume and value recovery for each of the deterioration classes. Trees were selected by dbh and deterioration class from a wide geographic range on the Kenai Peninsula. Defect present prior to attack by beetles (existing defect) played a significant role in recovery results. Both volume and value of logs from live and dead trees decreased significantly. Volume and value recovery did not statistically differ among deterioration classes 2, 3, and 4. Models were developed for each deterioration class that incorporate losses from existing defect. Each 1% of existing defect translates to a decrease of 0.3% in cubic recovery and a loss of $1.92 per hundred cubic feet (CCF) of gross log volume. The recommendation is to have two deterioration classes: one for live and infested trees and a second for dead trees. Information on individual deterioration classes is also provided. West. J. Appl. For. 13(2):54-59.
Shifting Public Values for Forest Management: Making Sense of Wicked Problems
Authors: Shindler Bruce , Cramer Lori A. 
Published: August 2019

Abstract
Wicked problems typify many of the natural resource debates in the United States and certainly describe the management of forestlands in the Pacific Northwest. Wicked problems are interrelated ones of organized complexity that cannot be solved in isolation from one another, but also hinge on differing sociopolitical values that clash in the political arena. Forestry professionals frequently find themselves caught up in the dilemma of making decisions in this era of social change and much scrutiny. This paper examines what shifting social values mean for forest management and research by (1) providing a conceptual context for forest policy decisions, (2) examining relevant problems facing management and research institutions, and (3) characterizing the implication for public forest management given the nature of wicked problems. West. J. Appl. For. 14(1):28-34.
Response of Planted Ponderosa Pine Seedlings to Weed Control by Herbicide in Western Montana
Authors: Uzoh Fabian C. C. 
Published: August 2019

Abstract
The effects of competing herbaceous vegetation on the growth of ponderosa pine seedlings with and without the herbicide Pronone were characterized in this 1987-1990 study. Study areas were established in 36 plantations across western Montana on Champion International Corporation's timberland (currently owned by Plum Creek Timber Company). The study sites were divided into three precipitation classes: low, medium, and high. Mean percent stem volume growth was calculated for 3 yr by precipitation class. Split-plot analyses of variance for precipitation class, treatment, and interaction were conducted across sites between treated and untreated seedlings to test for significant (a = 0.05) differences in growth. A two-dimensional plot of precipitation class by treated versus untreated trees was constructed to show growth rate trends. After 3 growing seasons, the treated seedlings showed significantly higher stem volume growth than their untreated counterparts regardless of precipitation class. The difference between treated and untreated seedlings was statistically significant. West. J. Appl. For. 14(1):48-52.
Growth of Douglas-Fir and Ponderosa Pine Seedlings with Foliar Applications of Methanol and Ethanol
Authors: Joseph Gladwin , Kelsey Rick G. 
Published: August 2019

Abstract
To test whether methanol or ethanol stimulated growth of coast Douglas-fir (Pseudotsuga menziesii vat. menziesii) or ponderosa pine (Pinus ponderosa) seedlings, we sprayed concentrations of 1 to 10% (v/v) on the foliage twice a week for 13 wk during the growing season. Foliar applications of methanol and ethanol neither significantly stimulated nor inhibited growth, and signs of damage at these concentrations were lacking. West. J. Appl. For. 14(4):183-185.
Boreal Plant Community Diversity 10 Years After Glyphosate Treatment
Authors: Boateng Jacob O. , Haeussler Sybille , Bedford Lorne 
Published: August 2019

Abstract
This study examined 10 and 12 yr posttreatment effects of broadcast and spot application of glyphosate for site preparation on structural diversity, species richness and diversity, and crop tree growth in two boreal forest plant communities in northeastern British Columbia. At the broadcast-sprayed site, reduced dominance of the tall shrub layer was associated with increased structural diversity and increased richness of the herb layer 10 yr after treatment. At the spot-sprayed site, no significant differences in plant community structure or diversity could be detected after 12 yr. At both sites, glyphosate application increased the growth of planted white spruce (Picea glauca) seedlings without eliminating deciduous trees and shrubs. The results indicate that a single application of glyphosate to prepare sites for reforestation can improve crop tree performance without adversely affecting vascular plant community diversity. West. J. Appl. For. 15(1):15-26.
Height Growth Models for High-Elevation Subalpine Fir, Engelmann Spruce, and Lodgepole Pine in British Columbia
Authors: Chen Han Y. H. , Klinka Karel 
Published: August 2019

Abstract
To estimate potential productivity of the high-elevation Engelmann Spruce and Subalpine Fir (ESSF) zone of British Columbia forests, the height growth models developed from low-elevation forests are currently used to estimate site indices of subalpine fir (Abies lasiocarpa), Engelmann spruce (Picea engelmannii), and lodgepole pine (Pinus contorta). Whether these models are adequate to describe height growth of high-elevation forests is of concern. We sampled a total of 319 naturally established, even-aged, and undamaged stands with breast height age ≥50 yr (165 for subalpine fir, 87 for Engelmann spruce, and 67 for lodgepole pine) ranging widely in climate and available soil moisture and nutrients. In each sampled stand, three dominant trees were destructively sampled for stem analysis. Height growth models developed from fitting data to a conditioned logistic function explained > 97% variation in height for all three study species. Examined by residual analysis, no models showed lack of fit. These models provided more accurate estimates of site index than the currently used models developed from low-elevation stands or different species. It is recommended that the models developed in this study be applied to estimate site index of the three species in the ESSF zone in British Columbia. West. J. Appl. For. 15(2):62-69.
Cold Hardiness Testing for Douglas-Fir Tree Improvement Programs: Guidelines for a Simple, Robust, and Inexpensive Screening Method
Authors: Anekonda T. S. , Adams W. T. , Aitken S. N. 
Published: August 2019

Abstract
Operational methods are needed for screening genotypes in breeding programs for adaptive traits. In this article, we present a detailed description of one procedure for screening improved coastal Douglas-fir seedlings and saplings for cold hardiness, based on research results of the Pacific Northwest Tree Improvement Research Cooperative. Artificial freeze testing of detached shoots from genetic tests, followed by visual scoring of injury, has proved to be an efficient, reliable, and cost-effective method of screening large numbers of genotypes. Relevant research results are summarized, and practical details of this methodology are presented for straightforward implementation by Douglas-fir breeders and researchers. West. J. Appl. For. 15(3):129-136.
The Influence of Weeding on Growth of Browsed Seedlings in Douglas-Fir Plantations
Authors: O'Dea M. E. , Newton M. , Cole E. C. , Gourley M. 
Published: August 2019

Abstract
Large Douglas-fir (Pseudotsuga menziesii) transplants were exposed to heavy browsing pressure under various weeding regimes in two experiments continued 4 and 5 yr, respectively. Browsing had relatively little effect on seedlings that did not receive weed control because potential growth was modest. With increasing degrees of weed control, seedlings that escaped browsing grew more rapidly. Weeding facilitated escapement from reach of browsing and increased net growth significantly because of both escapement and increased rates of recovery after herbivory. When subjected to repeated browsing, seedlings were similar in size in plots weeded both the first year and for 2 yr. Seedlings in plots weeded at both levels were larger than those in unweeded plots. Intensive weeding after planting appears to be a useful and integrative method of protecting seedlings from browsing losses. West. J. Appl. For. 15(3):163-168.
Forest Service Spatial Information Use for Planning Prescribed Fires
Authors: Barrett T.M. , Jones J.G. , Wakimoto R.H. 
Published: August 2019

Abstract
Forest management decision support systems (FMDSS) and geographic information systems have improved the incorporation of spatial information into forest planning. However, most FMDSS have been designed to implement silvicultural treatments rather than prescribed fire and fuel treatments. Results from a survey of 277 Forest Service employees in the western US show FMDSS need modifications to be better adapted to the needs of prescribed fire planners. Survey responses indicate that, on average, prescribed fire planners would like to increase the area treated annually by 12 times current levels. Available time windows for burning provide the most severe constraint for managers, while funding and personnel constraints were rated as comparably less important. Given these results, FMDSS may be most appropriately designed to help managers develop a long-term strategy for prioritizing prescribed fire treatments. Necessary FMDSS modifications may include different methods of delineating treatment boundaries, improved integration with wildlife habitat models, emphasis on short-term costs, and flexible intervals between repeated treatments. West. J. Appl. For. 15(4):200–207.