bluuebunny/crossref_metadata_2025 huggingface dataset:
A2 Phylogenetic investigation of transmitted HIV-1 drug resistance mutations in Denmark, 2009–17
Authors: Fonager J , Fischer T K
Published: August 2019

Transmission of HIV-1 resistance mutations among therapy-naïve patients impairs the efficiency of antiretroviral therapy (ART). Therefore, genotypic resistance testing of patients is recommended at baseline, as this both allows for the selection of the correct ART regimen and for surveillance of transmitted drug resistance mutations (TDRM) among therapy naive HIV-1 patients. In Denmark, the occurrence of TDRM in newly diagnosed and therapy naïve HIV-1 patients is monitored through the SERO project. Here, we investigated if the prevalence of TDRM differed between patients within and outside of phylogenetically identified transmission clusters. Samples from 1,227 newly diagnosed HIV-1 patients were sent along with epidemiological information to the Virological Surveillance and Research group at Statens Serum Institut. HIV-1 RNA extraction, RT-PCR and Sanger sequencing of the pol gene was performed using an in-house assay. The sequences were analyzed using BioNumerics v. 6.6 and manually checked for the presence of mixed mutations and analyzed for mutations using the HIVDB 8.4 algorithm implemented at the Stanford database. Sequence alignments were performed in Mafft, and phylogenetic analysis was performed using Mega 6.0 using the Maximum likelihood general time reversible model with 100 bootstrap replicates. Clusters were identified with ClusterPicker at default settings (cluster support = 90%, genetic distance 4.5%). Active clusters contained newly diagnosed patients from the 2015 to 2017 period. HIV-1 sequences from 588 patients belonged to one of 154 clusters, and sequences from 639 patients did not belong to a cluster. Patients in clusters were significantly more likely to be men who have sex with men and subtype B and significantly less likely to be late presenters (Fisher’s test P < 0.05). The TDRM prevalence was significantly higher for patients outside of clusters than within clusters, 16.6 per cent versus 12.1 per cent, respectively (Fisher’s test P < 0.05); however, no significant differences were found in the TDRM prevalence between the 75 active and 79 inactive clusters, nor between small (<3 patients) and large (≥3 patients) clusters. E138A, V179D, and K103N were the three most prevalent TDRMs for both patient groups, whereas M41L differed between them. In Denmark, the TDRM prevalence is lower within clusters than outside, indicating that TDRM cases are either imported and/or belong to yet unidentified clusters.
A8 Epidemiological study of transmission clusters in a local HIV-1 cohort
Authors: González Domenech Carmen M , Viciana-Ramos Isabel , Sena-Corrales Gabriel , Mora Navas Laura , Ojeda Guillermo , Nuño Enrique , Clavijo Encarnación , Palacios Rosario , Santos Jesus
Published: August 2019

Integration of molecular, clinical, and demographic data represents a powerful tool to understand the dynamics of local HIV-1 transmission chains (TCs). The aim of our study was the phylogenetic analysis of the TCs within a HIV-1 cohort and the description of the relevant patient data within a TC. We performed a phylogenetic analysis of 757 sequences from newly HIV-1 diagnosed patients in Málaga (Southern Spain) during the period 2004–15. We used partial pol gene sequences in a preliminary phylogenetic reconstruction using the Neighbour Joining method (MEGA v6.06 program). After eliminating branches with bootstrap values <80 per cent, we constructed a new phylogeny by Maximum likelihood method (FastTree program). We considered as TC any cluster with bootstrap values ≥ 90 per cent. Patient sequences within and outside TCs were compared. Resistance mutations in the protease (PR) and reverse transcriptase (RT) sequences were analyzed using the Stanford algorithm. Four hundred and fifty-one out of 757 patients (59.6%) were grouped into fifty-three TCs, seventeen of them with five or more subjects. The largest number of patients associated within a TC was ninety. Patients younger than 40 years [odds ratio (OR) 1.75, 95% confidence interval (95% CI) 1.2–2.4, P = 0.002], men who have sex with men (MSM) (OR 2.14, 95% CI 1.3–3.2, P < 0.0001), non-Spanish (OR 1.48, 95% CI 1.0–2.1, P = 0.038), with a non-B subtype HIV-1 (OR 3.12, 95% CI 2.0–4.8, P < 0.0001), and presenting primary resistance mutations (OR 14.1, 95% CI 3.1–62.6, P = 0.001) were more likely to be associated within a cluster. Ninety-four out of 118 patients (79.6%) with transmission resistance mutations were included in some TC. The most frequent mutations associated with clusters were T69D/N, L210W, and K219E/Q, for NRTIs, K103N, and G190A/S for NNRTIs, and the I54L/M and L90M mutations for PIs. The prevalence for resistance to NNRTIs in TCs was 13.7 per cent. There were two TCs of rarer non-B subtypes: CRF19_cpx, with twenty-one individuals, sixteen of them (76.2%) with mutation G190A; and CRF51_01B with thirty-nine patients, twenty of them with the K103N mutation. Approximately 60 per cent of newly HIV-1 diagnosed patients were included in a TC. Younger patients, MSM, non-Spanish, with non-B subtype HIV-1 and primary resistance mutations were more likely to belong to a cluster. NNRTI mutations were the most frequent ones among patients in TCs. We observed two TCs represented by infrequent non-B subtypes in our area—CRF19_cpx and CRF51_01B—both of which were associated to the transmission of primary resistance.
A23 Population level diversification of hepatitis C viral strains over time among people who inject drugs in Baltimore, MD
Authors: Hackman J , Falade-Nwulia O , Mehta S , Downing Z , Kirk G , Ray S , Thomas D , Laeyendecker O
Published: August 2019

Hepatitis C virus (HCV) infection occurs in 30–90 per cent of people who inject drugs (PWID). Although cure rates can exceed 95 per cent, treatment access is limited and approximately 400,000 people die each year due to complications of chronic infection. A temporal analysis of cluster networks among PWID can be used to inform strategies to interdict transmission. In Baltimore, PWID have been recruited for The AIDS Linked to the IntraVenous Experience (ALIVE) cohort. A demographic questionnaire was administered and recorded for baseline and recent participants. Viral RNA underwent PCR with primers targeting the core and envelope-1 protein (CE1) and sequenced via Sanger sequencing. Sequences with > 400 bp reads and Q-scores >370 were used for downstream analysis resulting in 322 ALIVE baseline participants (1988–9) and 548 recently diagnosed subjects enrolled approximately two decades later (2005–16). Cluster networks were rendered with a threshold of 4 per cent in MicrobeTRACE, and statistical analyses were performed in R Studio. Of the 1988–9 subjects, the majority (259/317, 81.7%) were a part of cluster. There were nine clusters and fifty-eight singletons, with two large clusters containing most sequences of genotype 1a (73.5%). Two decades later, a minority of recently diagnosed individuals (235/512, 44.1%) were part of a cluster. There were seventeen clusters with 286 singletons with two large clusters containing 1a genotype individuals (21.5%). Additional clustering was done by parsing the two datasets by subtype 1a (n = 714) and 1b (n = 151). The genotype 1a network demonstrates a majority, 65.8 per cent, of participants in clusters. Moreover, two large clusters can be observed with baseline participants towards the center and recent participants on the outskirts indicative of high linkage at baseline. The genotype 1b network produced a single large cluster but subclusters were observed. The sequences between the two time points co-mingled but subclusters were also observed. Interestingly, the two large clusters from 1988 to 1989 were still evident in the 2005–16 viral sequences. We observed greater cluster diversity in more recently diagnosed individuals, indicative of a less connected network of individuals sharing transmission risk, though major viral strains did persist over time in this cohort.
A47 Reconstructing the evolutionary history of pandemic foot-and-mouth disease viruses: The impact of recombination within the emerging O/ME-SA/Ind-2001 lineage
Authors: Bachanek-Bankowska K , Di Nardo A , Wadsworth J , King D , Knowles N
Published: August 2019

Foot-and-mouth disease (FMD) is a highly contagious disease of livestock affecting animal production and trade throughout Asia and Africa. Understanding FMD virus (FMDV) global movements and evolution can help to reconstruct the disease spread between endemic regions and predict the risks of incursion into FMD-free countries. Global expansion of a single FMDV lineage is rare but can result in severe economic consequences. Using extensive sequence data, we have reconstructed the global space-time transmission history of the O/ME-SA/Ind-2001 lineage (which normally circulates in the Indian sub-continent) providing evidence of at least fifteen independent escapes during 2013–7 that have led to outbreaks in North Africa, the Middle East, Southeast Asia, and the Far East and the FMD-free islands of Mauritius. We demonstrated that sequence heterogeneity of this emerging FMDV lineage is accommodated within two co-evolving divergent sublineages, and that recombination by exchange of capsid-coding sequences can impact upon the reconstructed evolutionary histories. Thus, we recommend that only sequences encoding the outer capsid proteins should be used for broad-scale phylogeographical reconstruction. These data emphasize the importance of the Indian subcontinent as a source of FMDV that can spread across large distances and illustrates the impact of FMDV genome recombination on FMDV molecular epidemiology.
A58 Epidemic dynamics of ancient disease outbreaks
Authors: Esquivel Gomez Luis R , Spyrou Maria A , Keller Marcel , Herbig Alexander , Bos Kirsten I , Krause Johannes , Kühnert Denise
Published: August 2019

Bayesian phylogenetic analysis allows for the estimation of the time to the most recent common ancestor (tMRCA) of sequences sampled at different times, as long as they prove to be ‘measurably evolving’, which means that the time between sampling dates was long enough to allow the appearance of a measurable amount of genetic changes. This ‘temporal signal’ can be tested with the software TempEst (Rambaut et al. 2016), which generates a regression of the root-to-tip genetic distance on sampling times and finds the best-fitting root that produces the lowest residual sum of squares. For the case of pathogen single nucleotide polymorphism (SNP) alignments, containing both modern and ancient sequences, it is common to find positions with unknown nucleotides (gaps) that could generate problems in the phylogenetic reconstruction. Thus, the use of complete deletion alignments is fairly common. This practice, however, could cause the loss of potentially important information, so we aim to identify the most suitable deletion threshold for the proportion of unknown sites allowed for a given alignment before proceeding to analyze the data in BEAST. Here, I present the temporal signal of 204 whole-genome sequences of Yersinia pestis, a zoonotic gram-negative bacteria and causal agent of the bubonic, pneumonic, and systemic plagues. I demonstrate measurable temporal signal for the alignment with thresholds of 0–10 per cent for the proportion of unknown sites per SNP. The results showed that a complete deletion alignment presented the lowest correlation and greatest residual mean squared values. The best threshold depends on the method used to find the best root, but appears to be between 7–9 per cent.
A69 Phylodynamics of language evolution
Authors: Hoffmann K , Kühnert D
Published: August 2019

We used Bayesian evolutionary analysis to study linguistic data and infer phylogenetic trees of language evolution. Languages were encoded as binary strings indicating the presence or absence of members of cognate classes, the equivalence of classes of words with similar meaning, and shared ancestry. These strings formed the alignment data used to compute the posterior likelihood of a tree with respect to Bayes’ formula. Informative priors are crucial for testing hypotheses regarding the age of common ancestry and divergence times and should include as much available information as possible. Here, we investigated the birth–death process as a method to construct tree priors specifically suitable for modeling the evolution of cognate data. To test these models, we will use a dataset of the languages from Vanuatu, an island nation featuring world’s highest language density.
Calculating the Maximum Grade a Log Truck Can Climb
Authors: Sessions John , Stewart Rod , Anderson Paul , Tuor Brian
Published: August 2019

Steep road grades provide managers with a new way to reduce economic and environmental costs of transportation systems. Equations for maximum grade-climbing ability (gradeability) of both loaded and unloaded log trucks are presented. They were derived by considering rolling resistance, vehicle geometry, and weight-distribution changes among axles as the truck negotiates different grades. West. Appl. For. 1:43-45 April 1986
Analyzing Fuel Treatment Costs
Authors: González-Cabán Armando , McKetta Charles W.
Published: August 2019

Economically sound decisions on fuel treatment require knowledge of treatment costs. Fuel treatment costs derived using an economic cost concept on two National Forests were found to be higher than reported by accounting methods. Costs are sufficiently high and variable to question the economic feasibility of fuel treatments. Regression analysis did not show a strong relationship between fuel treatment costs and the physical characteristics of treatment sites. Management behavior and organization constraints may more successfully explain the magnitude and variability of fuel treatment costs. There are economies of scale in larger fuel treatment projects. Fuels managers emphasized hazard reduction over silvicultural objectives but believe that hazard targets could be achieved with lower fuel treatment levels. West. J. Appl. For 1:116-121, Oct. 1986.
How Much Timber Quality can we afford in Coast Douglas-Fir Stands?
Authors: Fight Roger D. , Johnston Stuart , Briggs David G. , Fahey Thomas D. , Bolon Natalie A. , Cahill James M.
Published: August 2019

Once site and genetic stock are selected, management of stocking, rotation age, and pruning are the principal means available to foresters to affect wood quality and value in stands of coast Douglas-fir (Pseudotsuga menziesii var menziesii). Financial evaluation was used to test whether or not improvements in wood quality and value by these means justify the costs of doing so. This analysis showed in general that improving quality through high levels of stocking or extending rotations were costly ways to improve wood quality while pruning was a cost-effective way to improve wood quality. West. J. Appl. For. 10(1):12-16.
Technical Commentary: Management of Lodgepole Pine Stand Density to Reduce Susceptibility to Mountain Pine Beetle Attack
Authors: Anhold J. A. , Jenkins M. J. , Long J. N.
Published: August 2019

Silvicultural strategies to reduce tree losses from mountain pine beetle attacks typically seek to reduce relative densities in order to increase tree resistance and thus lower potential beetle attacks. For lodgepole pine stands, however, the tree mortality/relative density relationship is nonlinear. We describe three relative density zones corresponding to different levels of resistance to beetle attack. In the density management of young lodgepole pine stands, we propose two alternative strategies to reduce future losses from mountain pine beetle attacks. The first density management regime involves a low density (i.e., SDI < 140) throughout the rotation. The second density management regime is designed to maintain relative density above a threshold level (i.e., SDI > 245). West. J. Appl. For. 11(2):50-53.
Survival and Growth of Douglas-Fir Relating to Weeding, Fertilization, and Seed Source
Authors: Roth Brian E. , Newton Michael
Published: August 2019

The goal of this study was to quantitatively evaluate the individual and interactive effects of weed control, nitrogen fertilization, and seed source on Douglas-fir (Pseudotsuga menziesii) survival and growth in a range of sites and growing conditions in western Oregon. Weed control was the dominant factor influencing seedling survival and growth and accounted for 49% of the explained variation in seedling volume after 2 yr. Nitrogen fertilization had no effect when used in conjunction with weed control and a negative effect when used without weed control. Seedlings from a seed orchard source were significantly larger in diameter and volume than those from a wild local source after two growing seasons, but second-year heights were similar for the two seedling types. Initial seedling size was positively correlated with growth rate. West. J. Appl. For. 11(2):00-00.
A Comparison of Logging Planning, Felling, and Skyline Yarding Costs Between Clearcutting and Five Group-Selection Harvesting Methods
Authors: Kellogg Loren D. , Bettinger Pete , Edwards Richard M.
Published: August 2019

Logging planning, felling, and cable yarding costs were determined for five group-selection treatments and a clearcut in a 90 yr old Douglas-fir (Pseudotsuga menziesii) stand in western Oregon. The harvesting system included manual felling and a yarder rigged in a standing skyline configuration with a mechanical slackpulling carriage. The clearcut treatment had the lowest total harvest cost; costs of the group-selection treatments were 7.3 to 31.5% higher than the clearcut. Yarding cost associated with road and landing changes, plus the cost of equipment moving, set up, and tear down allocated over different treatment volumes removed had the biggest influence on total cost for each silvicultural treatment. West. J. Appl. For. 11(3):90-96.
Deterioration of Fire-Killed Timber in Southern Oregon and Northern California
Authors: Lowell Eini C. , Cahill James M.
Published: August 2019

Deterioration of fire-killed timber in the coastal mountains of southern Oregon and northern California was monitored over a 3 yr period (1988-1990). Defect was identified and measured on felled and bucked sample trees by using Scribner and cubic scaling rules. Douglas-fir (Pseudotsuga menziesii), grand fir (Abies grandis), white fir (A. concolor),ponderosa pine (Pinus ponderosa), and sugar pine (Pinus lambertiana), covering a wide range of geographic areas, site conditions, and tree size and age, were studied. One year after death, Douglas-fir, sugar pine, and ponderosa pine had lost about 1% and the true firs 5% of their cubic volume. The sapwood of the pines was heavily stained. The occurrence of sap rot and weather checks increased the second year. Percent loss in all species was correlated with small-end scaling diameter. A logistic regression model predicting the incidence of cull was developed for use on logs that have been dead for 3 yr. West. J. Appl. For. 11(4):125-131.
Tanoak Sprout Development After Cutting and Burning in a Shade Environment
Authors: Wilkinson William H. , McDonald Philip M. , Morgan Penelope
Published: August 2019

Mean height and number of sprouts from tanoak (Lithocarpus densiflorus) stumps treated by repeated burning (propane weed burner) and by double decapitation (cutting twice within 24 hr) were compared to sprouts from untreated stumps in a shaded environment on the Hoopa Valley Indian Reservation in northern California. Much is known about tanoak sprout growth in full sunlight, but little is known about its development in shade. Four years after burning or cutting, sprouts from stumps treated by burning were significantly (P < 0.001) more numerous and shorter than sprouts in the double decapitation and control treatments. Double decapitation was ineffective as a sprout manipulation technique. Some natural events affected the treatments. Mold negatively affected vigor and growth of sprouts in the control and double-decapitation treatments; deer browsing shortened sprout length in the burning treatment; shade delayed sprouting for up to 1 yr after treatment. West. J. Appl. For. 12(1):21-26.
Laminated Root Rot: New Considerations For Surveys
Authors: Thies Walter G. , Nelson Earl E.
Published: August 2019

In 1981, Douglas-fir (Pseudotsuga menziesii) trees were placed into 3 disease classes of 45 trees each based on signs and symptoms of Phellinus weirii infection: infected, probably infected, and probably not infected. Trees that died during the course of the study were felled and their stumps and roots removed from the soil, cleaned carefully, dissected, and examined. In August 1991, the remaining study trees were similarly treated. Eight trees recorded as infected in 1981, based on the presence of ectotrophic mycelium, were found to be not infected in 1991. Only one-third of the trees near inoculum sources, and thus expected to be infected, were infected. Of the trees thought to be not infected, one-third were infected. Based on limited observations, laminated root rot appears to be distributed both as "pockets" (aggregated) that appear as openings early in stand development and in a more "diffuse" manner that may lead to openings late in stand development. These findings have implications for disease survey and disease management. West. J. Appl. For. 12(2):49-51.
Evaluation of Tree Height Prediction Models for Stand Inventory
Authors: Martin Fred C. , Flewelling James W.
Published: August 2019

The study appraised nine models that predict total tree height from diameter by species within individual stands. Models were fitted with nonlinear least squares by species within individual stands using inventory data from western Washington. Stand-level models were examined with respect to species, geographic regions, dominance characteristics, and sample sizes. Models were evaluated for mean square error, bias by diameter class, overfitting, and consistency in relative ranking. No substantial differences in model performance were noted with respect to geographic regions, but small differences were evident by species, dominance characteristics, and sample sizes. Model bias occurred with some but not all models. Overfitting was detected and considered a problem in fitting three-parameter models with the often small height sample in some stands. Some models were consistently good across species and sample sizes, whereas others were consistently poor. Yet the performance of other models varied by species and sample sizes. For predicting heights by species within individual stands, a single model was recommended Height = 1.37 + b0eb1dbh-1.0 A method was examined for constraining height predictions for trees beyond the range of sample data. West. J. Appl. For. 13(4):109-119.
Assessing the Salability of Timber Offerings
Authors: Gebert Krista M. , Niccolucci Michael J. , Schuster Ervin G.
Published: August 2019

Given the complex and expensive nature of timber sale planning, timber offerings that receive no bids waste valuable time and resources for the managers of national forests. This article compares several tools for predicting the salability of timber offerings. These tools include probability-based techniques and appraisal-based techniques. The probability-based techniques include probit regression and discriminant analysis. The appraisal-based techniques use various modifications of the standard transaction evidence appraisal equations to predict salability. Results show probability-based techniques do better at correctly classifying timber offerings as sold or unsold. They correctly classify nearly 100% of the sold offerings, which constitute most of the offerings in the sample. However, if the user's primary interest is to predict unsold offerings correctly, appraisal-based techniques outperform probability-based techniques. West. J. Appl. For. 13(4):129-136.
The Impact of Environment and Nursery on Survival and Early Growth of Douglas-fir, Noble Fir, and White Pine--A Case Study
Authors: Randall William , Johnson G. R.
Published: August 2019

Survival and third-year height were examined on 2,383 reforestation units from 1983 to 1994 to determine which factors impact reforestation success. Survival of Douglas-fir (Pseudotsuga menziesii) varied by as much as 20% from year to year. The most significant factor affecting reforestation success was the nursery that provided the seedlings. Nursery impacted both survival and height of Douglas-fir and impacted height for noble fir (Abies procera) and white pine (Pinus monticola). No nursery was best for all species. Other factors that were important for all three species were the administrative unit where the seedlings were planted, initial plant height, aspect, and length of storage prior to planting. Other significant factors that were important for Douglas-fir were seed origin, planting month, protection, stock type, and aspect. For noble fir, other important factors were planting month and stock type; for white pine, the other important factor was slope. Elevation of the seed source and the planting unit affected Douglas-fir survival and height but did not affect the other two species. This supports the smaller elevational bands for Douglas-fir compared with noble fir and white pine. West. J. Appl. For. 13(4):137-143.
The Transferability of Western White Pine to and within British Columbia Based on Early Survival, Environmental Damage, and Juvenile Height
Authors: Meagher M. D. , Hunt R. S.
Published: August 2019

Survival, environmental damage, and juvenile height of 27 provenances of western white pine (Pinus monticola) in three plantation series were analyzed after 5 to 13 yr on site to assist in evaluating seed-transfer practices. Survival averaged 79.2% on nine sites in the "root-rot" series and 84.1% on six sites in the "provenance-test" series. Trends of survival on seed-source parameters differed between series, generally increasing with both elevation and latitude in the root-rot series, while generally decreasing with latitude in the provenance-test series. Analysis by seed zone (coast or interior) and plantation region (coast, southern interior, or northern interior) showed that coastal sources on interior sites caused much of these anomalies. Substantial environmental damage was found only on sites near to or beyond the species' northern limit. Differences in the trend of damage with source parameters were found between the test series: interior sources were damaged less than coastal sources on two root-rot sites, whereas interior sources were damaged more heavily than coastal sources on the provenance-test site exhibiting substantial damage. Damage increased with increasing provenance latitude and elevation in the root-rot series, while it dropped with increasing elevation in the "provenance-test" series. In general, taller seedlings in taller provenances were damaged. Coastal seed should not be used on interior sites, but transfer of seed from the BC interior to the BC coast seems safe. We recommend that the present limits for latitudinal transfer be doubled, except where late-spring-frost risk is high, and that elevational transfer of seeds for the interior zone be reduced by about half West. J. Appl. For. 14(1)41-47.
Wildlife Use of Dwarf Mistletoe Brooms in Douglas-Fir in Northeast Oregon
Authors: Parks Catherine G. , Bull Evelyn L. , Tinnin Robert O. , Shepherd Jay F. , Blumton Arlene K.
Published: August 2019

Douglas-fir (Pseudotsuga menziesii) trees with and without dwarf mistletoe (Arceuthobium douglasii) brooms were examined for evidence of use by wildlife. Evidence of foraging occurred in 51% of the broomed trees and in 29% of the trees without brooms. Evidence of nesting by mammals occurred in 18% of the broomed trees and in none of the trees without brooms. Brooms used and those not used by wildlife were significantly different in type and volume. These findings suggest that retaining mistletoe brooms in stands may be important to provide nesting, foraging, resting and roosting habitat for mammals and birds. West. J. Appl. For. 14(2):100-105.
Influence of Streamside Cover and Stream Features on Temperature Trends in Forested Streams of Western Oregon
Authors: Zwieniecki Maciej A. , Newton Michael
Published: August 2019

Clearcut harvesting along low-elevation western Oregon streams with forest buffers (8.6 to 30.5 m wide) was followed by little direct local effect on water temperature. A study of 14 streams demonstrated that all have a tendency to warm with downstream direction even under full forest cover. After the natural warming trend of the stream water was accounted for, water at slightly higher temperatures within the buffered clearcut zones cooled to the trend line of temperature by 150 m downstream. Because of the natural warming trends in streams, estimating the net temperature effect associated with management practices requires use of a warming trend line as the norm for fully covered forests for each general level of discharge. West. J. Appl. For. 14(2):106-113.
Evaluations of Plastic Mesh Tubes for Protecting Conifer Seedlings from Pocket Gophers in Three Western States
Authors: Engeman Richard M. , Anthony Richard M. , Barnes Victor G. , Krupa Heather W. , Evans James
Published: August 2019

The efficacy of plastic mesh tubes for protecting conifer seedlings from pocket gopher damage was evaluated on three national forest lands in three states. In each area, cohorts of 640 protected seedlings and 640 unprotected seedlings (3,840 total) were individually monitored for damage, survival, and growth twice each summer for 5 yr after planting. Substantial differences were found between protected and unprotected seedlings for time until occurrence of damage, survival time, proportion damaged and proportion surviving, as well as differences in growth. Over the three forest study sites, the proportion of unprotected seedlings damaged ranged from 60-89%, whereas the proportion of protected seedlings damaged after 5 yr ranged from 18-27%. The proportion of unprotected seedlings that died of gopher damage over 5 yr ranged from 46-64%, versus 1-19% for protected seedlings. Height growth was 25% greater for protected seedlings. Even when only undamaged seedlings were considered, protected seedlings exhibited superior height growth, possibly due to a more favorable microclimate provided by the tubes. These results were reflected in the higher and more uniform stocking rates for protected seedlings. West. J. Appl. For. 14(2):86-90.
Antelope Bitterbrush and Scouler's Willow Response to a Shelterwood Harvest and Prescribed Burn in Western Montana
Authors: Ayers Dayna M. , Bedunah Donald J. , Harrington Michael G.
Published: August 2019

In many western Montana ponderosa pine (Pinus ponderosa) stands, fire suppression and past selective logging of large trees have resulted in conditions favoring succession to dense stands of shade-tolerant, but insect- and disease-prone Douglas-fir (Pseudotsuga menziesii). Stand thinning and understory prescribed burning have been proposed as surrogates for pre-Euro-American settlement ecological processes and as potential treatments to improve declining forest condition and reduce the probability of severe wildfire. To test the effectiveness of these silvicultural techniques on overstory and understory conditions, research is ongoing in the Lick Creek Demonstration Site in the Bitterroot National Forest, Montana. Our research examined the response (mortality and vigor) of the dominant browse species, antelope bitterbrush (Purshia tridentata) and Scouler's willow (Salix scouleriana), to a ponderosa pine stand restoration project utilizing four treatments: (1) a shelterwood cut that removed 53% of the tree basal area; (2) a shelterwood cut with a low fuel consumption burn; (3) a shelterwood cut with a high fuel consumption burn; and (4) a control. Prior to the application of treatments, 1,856 bitterbrush and 871 willow were located, and their survival and vigor subsequently monitored for 2 yr posttreatment. The cut and burn treatments resulted in the greatest reduction in antelope bitterbrush and Scouler's willow density averaging 66% and 24% of pretreatment density, respectively. The shelterwood cut reduced bitterbrush and Scouler's willow density by 35% and 14%, respectively. On treatments receiving a shelterwood cut (all treatments but the control), but where antelope bitterbrush and Scouler's willow did not have fire damage, mortality was 45% for bitterbrush and 20% for willow, respectively. For bitterbrush and Scouler's willow plants that received fire damage, mortality was 72% for bitterbrush and 19% for willow. Although the burn and shelterwood harvest treatments resulted in reduced density of antelope bitterbrush and Scouler's willow 2 yr posttreatment, these treatments increased vigor of both species and created mineral seedbeds that may be necessary for establishment of seedlings. West. J. Appl. For. 14(3):137-143.
Precommercial Thinning in a Ponderosa Pine Stand Affected by Armillaria Root Disease in Central Oregon: 30 Years of Growth and Mortality
Authors: Filip Gregory M. , Fitzgerald Stephen A. , Ganio Lisa M.
Published: August 2019

A 30-yr-old stand of ponderosa pine was precommercially thinned in 1966 to determine the effects of thinning on tree growth and mortality caused by Armillaria root disease in central Oregon. After 30 yr, crop tree mortality was significantly (P = 0.02) less in thinned plots than in unthinned plots. Tree diameter growth was not significantly (P = 0.17) increased by thinning. Crop-tree basal area/ac growth was significantly (P = 0.03) greater in thinned plots. Apparently, from a root disease perspective, precommercial thinning of pure ponderosa stands significantly decreases the incidence of crop-tree mortality after 30 yr and significantly increases basal area/ac growth but not individual tree diameter growth. Recommendations for thinning based on stand density index (SDI) are given. West. J. Appl. For. 14(3):144-148.
The Influence of Temporal and Spatial Factors on Clearcut Use by White-Tailed Deer in Northern Idaho
Authors: Secord Mark L. , Zager Peter E. , Pletscher Daniel H.
Published: August 2019

Relatively little is known about the response of white-tailed deer (Odocoileus virginianus) to forest management practices currently used in northern Idaho. We used pellet group surveys and radiotelemetry to assess the influence of season, clearcut age, and clearcut size on deer use in the Priest Lake watershed of northern Idaho. Deer use of 14 clearcuts ranging from 1 to 25 yr in age and 4.05 to 14.75 ha in size was investigated. No association between pellet group density and clearcut size or age was found. Both pellet group and telemetry data, however, indicated seasonal shifts in white-tailed deer habitat use patterns. Deer displayed strong avoidance of nonforested sites during winter and concentrated on low elevation winter ranges characterized by dense overstories. With the advent of warm weather and reduced snow depths, nonforested sites received increasing use. Clearcut use peaked during early spring and declined with the onset of summer as deer migrated to higher elevations. Spring use of clearcuts was significantly higher than summer use on all sites sampled. Spring pellet group densities averaged 1.52 groups/plot, whereas summer densities averaged 0.50 groups/plot. In the Priest Lake drainage, cutting units should be restricted to less critical sites adjacent to wintering areas. Clearcuts within winter habitats will further fragment existing forested stands and will be at the expense of critical thermal cover. In other regions, vegetation structure and composition should not be the only criteria used to evaluate the influence of clearcutting on white-tailed deer habitat use. West. J. Appl. For. 14(4):177-182.
A Comparison of Felling Techniques on Stump Height and Log Damage with Economic Interpretations
Authors: Boston Kevin , Dysart Gerald
Published: August 2019

This study investigated two of the many potential sources of value loss that occur during logging operations: stump heights and butt log damage. The potential value loss was determined for manual felling and five different felling heads for logging sites located in the central north island of New Zealand. Manual felling produced the highest stumps and three different felling heads (Hultdin, Timbco, and Warratah) produced second highest stumps. The group with the lowest stumps was felled with AFM Magnum and Koehring felling heads. The Warratah felling head had the lowest incidence of butt log damage, while manual felling had the highest proportion of damaged butt logs. The majority of the damage to the butt logs was slabbing damage; all felling techniques produced little stump pull damage. A comparison of the potential value loss showed that the Koehring produced the lowest potential value loss at US$128/ac, while manual felling had the highest potential value loss at over US$420/ac. West. J. Appl. For. 15(2):59-61.
Estimating Large Snag Recruitment Needs in Regeneration Timber Harvests
Authors: Harris Richard B.
Published: August 2019

Retaining snags after timber harvest is now a common silvicultural practice. However, little is known about silvicultural practices necessary to ensure timber-rotation length equilibrium of snag densities (existing snags all fall eventually). Large diameter snags in particular are important to many wildlife species and require long time periods to develop. Where timber harvest removes most of the existing stand, estimates of required retention density must be made ahead of time if long-term equilibrium in snag abundance is desired.A simple simulation model was used to investigate potential dynamics of snags for 80-120 yr following timber harvest. Parameters resulting in recovery of the initial number of snags at rotation length are presented. Whether or not equilibrium was achieved depended on three parameters usually beyond management control: annual mortality rate of live trees; snag fall rate; and transition rate from smaller to larger retention trees. At the time of timber harvest, managers can most easily adjust the density and size-class of live retention trees. I recommend erring on the side of retaining more, rather than fewer live trees to prevent long-term declines in the abundance of large snags. West. J. Appl. For. 15(3):140-146.
Processing Value of Small-Diameter Sawtimber at Conventional Stud Sawmills and Modern High-Speed, Small-Log Sawmills in the Western United States—A Comparison
Authors: Wagner Francis G. , Fiedler Carl E. , Keegan Charles E.
Published: August 2019

Past selective logging of early successional species [e.g., ponderosa pine (Pinus ponderosa)] and effective fire suppression have dramatically altered forest composition and health over millions of acres in the western United States. Implementation of ecological restoration treatments to address these conditions will produce large volumes of small-diameter sawtimber for processing. Since sawmills currently process a majority of sawtimber harvested in the West (more than 80% in some regions), this study concentrated on determining the value of small-diameter sawtimber delivered to sawmills. A conventional stud sawmill and a modern, high-speed, small-log sawmill were profiled. A simulator (MSUSP) was employed to describe these sawmills and to determine breakeven delivered-sawtimber values by dbh class for each sawmill. Data inputs included machinery type, mill layout, machine speeds, volume and grade recovery, product prices, and fixed and variable manufacturing costs. Results showed that sawtimber 9 in. dbh and under could not cover harvest and delivery costs and earn even a modest (10%) return on invested (ROI) capital at the conventional stud sawmill and that sawtimber 7.5 in. dbh and smaller had negative values. However with a 10% ROI capital, the value of all sizes of sawtimber at the modern, high-speed sawmill equaled or exceeded harvest and delivery costs. West. J. Appl. For. 15(4):208–212.
Cost Impacts of Management Alternatives to Achieve Habitat Conservation Goals on State Forestlands in Western Washington
Authors: Bare B. Bruce , Lippke Bruce R. , Xu Weihuan
Published: August 2019

An optimization approach to sustainable forest management that combines proactive habitat conservation practices and financial goals across an unzoned landscape outperforms a conservative, passive approach based on minimum management within large protective zones. The proactive approach simulta-neously solves the land allocation and harvest scheduling problem whereas the passive approach allocates land to restricted uses and then sequentially schedules timber harvests. Proactive management increases asset values, improves intergenerational equity, stabilizes revenue flows, and provides better habitat—especially for species requiring old forest habitat conditions. The magnitude of these differences is very large in the case tested—the development of habitat conservation plans for state trust lands in western Washington. West. J. Appl. For. 15(4) 217-226.
Effects of Swiss Needle Cast on Three Douglas-Fir Seed Sources on a Low-Elevation Site in the Northern Oregon Coast Range: Results after Five Growing Seasons
Authors: Kastner Walter W. , Dutton Steve M. , Roché David M.
Published: August 2019

Douglas-fir (Pseudotsuga menziesii var. menziesii) seedlings grown from three seed sources were evaluated for 5 yr on a high-disease-hazard site for their relative tolerance to Swiss needle cast. The seed sources were: (1) seed collected from trees showing an apparent degree of tolerance to Swiss needle cast in natural stands in the coastal fog belt, (2) open-pollinated seed orchard seed collected from random single-pair crosses of parent trees in natural stands outside of the coastal fog belt, but west of the Oregon Coast Range summit, whose progeny demonstrated an apparent degree of disease tolerance in coastal Douglas-fir progeny test sites, and (3) standard reforestation seed purchased from a commercial vendor. There were no significant differences among seed sources in basal diameter and total height for all five growing seasons. Needle retention varied among seed sources over the 5 yr period, but current-year needle retention did not vary significantly after the fifth growing season, and retention of 1- and 2-yr-old needles was relatively low for all seed sources. The intense disease pressure on this site may have overwhelmed expression of disease tolerance among seed sources. We do not recommend planting Douglas-fir on such high-hazard sites. West J. Appl. For. 16(1):31–34.
Frequency of Resistant Western White Pine Seedlings from Parents of Different Phenotypes
Authors: Hunt R.S. , Jensen G.D.
Published: August 2019

Seedlings from different western white pine (Pinus monticola) parent phenotypes were inoculated with blister rust (Cronartium ribicola) to determine how they compared to the British Columbia standard candidate phenotype (canker-free with all branches retained) in their ability to produce resistant seedlings. Comparisons were separated into two seed zones, coastal and interior, as well as pooled. The phenotypic categories were: (1) standard candidate, (2) standard candidate except lacking lower branches, (3) standard candidate except for bark reactions in the stem, (4) standard candidate except for stem bark reactions and closer than 100 m to a similar candidate (Texada phenotype), (5) standard candidate except for a tolerant reaction to a basal canker, (6) standard candidate except for a single canker high in the crown, (7) normally cankered trees, (8) USDA Forest Service selections for Dorena, OR, and (9) bulked forest run seedlots. Open-pollinated offspring from parents were inoculated each fall from 1987-1995, and infection spots were tallied the following spring. All seedling infection spot values were normalized to seedlings from a control tree, which were included in each inoculation. The progeny from bulk seedlots and the Texada phenotype were significantly more spotted than the other phenotypes. The least spotted families (top 1/6) were predominantly from the standard, cankered, and bark-reaction phenotypes. Resistance of individual seedlings was detected by annual inspection and recording slow-canker-growth responses up to 7 yr post-inoculation. None of the progeny from bulk seedlots or the control exhibited slow canker growth. There was no significant difference among the progeny of the other eight parental phenotypes in the incidence of slow-canker-growth resistance. Of these eight, only normally cankered candidates failed to have any families rank in the top one-sixth for the most slow-canker-growth resistance. However, since the sample size was small for normally cankered, high cankered, and tolerant phenotype, the results are considered preliminarily. Since we consider slow-canker-growth resistance to be most useful, we recommended that future selection programs for parents include relaxed rule bark reaction and no lower branch phenotypes. West. J. Appl. For. 16(4):149-152.
Efficacy of Wolfin to Repel Black-Tailed Deer
Authors: Nolte Dale L. , Shipley Lisa A. , Wagner Kimberly K.
Published: August 2019

Deer and elk provide many desirable recreational opportunities but also can cause severe conflicts with humans. Excluding them from agricultural resources or from roadways is desirable, but fencing is expensive. A chemical barrier would offer a feasible alternative to reduce damage caused by deer. A series of three tests was conducted to assess whether black-tailed deer avoided areas treated with Wolfin, a synthetic predator odor. Wolfin failed to repel deer during any of these trials. We conclude that Wolfin, as applied within this study, is unlikely to reduce problems caused by free-ranging deer. West. J. Appl. For. 16(4):182-186.
Fertilization and Liming Effects on the Growth and Nutrition of Bareroot Jeffrey Pine Outplanted on an Eastern Sierra Nevada Surface Mine
Authors: Walker R.F.
Published: August 2019

Two controlled-release fertilizer formulations, High N 22-4-6 + Minors and Forestry Dry Site 21-6-2 + Minors, and dolomitic lime were evaluated for their capacity to enhance establishment and nutrition of bareroot Jeffrey pine (Pinus jeffreyi) on an eastern Sierra Nevada surface mine. All amendments were applied at outplanting to the backfill of augered planting holes using a low rate of 8 g and a high rate of 16 g for the two fertilizers and a single 26 g rate for lime. Seedlings without fertilizer or lime served as the control treatment. Survival was unaffected by fertilization regardless of formulation and rate, while height, diameter, and volume growth were increased significantly after three growing seasons. The response to High N exceeded that to Dry Site, and the 16 g application was more stimulatory than 8 g. Liming decreased seedling survival and growth throughout the study. Fertilization increased N, P, and K foliar concentrations while depressing the concentrations of several micronutrients and Al. The influence of the lime amendment on seedling nutrition was sporadic and marginal. These results indicate that controlled-release fertilization at outplanting is a viable means of elevating seedling performance on eastern Sierra Nevada surface mines and similar harsh sites, while the liming approach used here was counterproductive to achieving reforestation objectives. West. J. Appl. For. 17(1):23–30.
Stand Responses Following Partial Cutting in Western Montana
Authors: Schwalm Christopher R. , Milner Kelsey S.
Published: August 2019

Forty-five permanent research installations were established on Champion International Corporation ownership throughout western Montana in 1984–1985. Plots were located in stands with recent harvest activity with a range of harvest intensity and site characteristics. Using increment core data and allometric relationships, the growth trajectories of individual trees were reconstructed. Some 15 yr after cutting, growth rates were similar to or greater than yield table estimates for naturally regenerated, even-aged stands on similar sites with similar volumes. The Forest Vegetation Simulator (FVS) (Inland Empire variant, version 6.1) generally underestimated dimensional increment on the study stands. Residuals of dimensional growth were decreased when using FVS's self-calibration feature. West. J. Appl. For. 17(1):37–45.