bluuebunny/crossref_metadata_2025_split huggingface dataset:
Timing of Longleaf Pine Seedling Release from Overtopping Hardwoods: A Look 30 Years Later
Authors: Boyer William D. 
Published: August 2019

Abstract
Significant differences in longleaf pine (Pinus palustris) growth among early and delayed seedling release treatments were recorded at age 10, but these differences had disappeared upon reexamination at age 31. A study begun in 1949 included six release treatments: complete seedling release from overtopping hardwoods at ages 1, 2, 3, 4, and 8 years, plus an unreleased check. Treatments were randomly applied among six 0.1-acre plots in each of six blocks, which included both poor and average sites. Seedling development was observed through age 10. When pines in five surviving blocks (two poor site, three average site) were remeasured in 1979 at age 31, there were no significant differences among release treatments in average tree heights and diameters or stand basal areas and volumes. The check treatment had significantly lower tree heights, stand densities, and stand volumes than any release treatment.
Hardwood Topkill by Four Herbicides Injected at Wide Spacings
Authors: Campbell T. E. 
Published: August 2019

Abstract
Mixed southern hardwood species ranging from 1 to 12 inches dbh were injected with 2,4-D at 2-inch spacings and with Tordon 101®, Garlon 3A®, and Roundup® at 5-inch spacings. Tordon and Garlon killed 92 and 93% of all stems and were rated as satisfactory. Roundup and 2,4-D killed 82 and 80% of injected stems; although neither was significantly less effective than Tordon and Garlon, both were rated as only marginally satisfactory.
Predicting Axle Loads on Trucks Hauling Tree-Length Logs
Authors: Watson W. F. , Matney T. G. 
Published: August 2019

Abstract
A methodology for predicting legal weight of loads of tree-length stems on tractor-trailer trucks is presented, with examples. The technique uses tree profile equations to predict center of mass and weight of stems. Load distribution on axles is accomplished by simplifying a formula based on the method of moments. One finding shows that with overhang longer than 15 feet, rear axles become overloaded before the maximum gross weight is reached.
Evaluating Landowner Assistance Programs and Other Wood Procurement Options
Authors: Kronrad Gary D. , Franklin E. Carlyle , de Steiguer J. E. 
Published: August 2019

Abstract
A major activity of forest industry is supplying their mills with wood. There are four options for wood procurement: fee land, lease land, landowner assistance programs, and open market. The task of the corporate planner is to allocate the limited budget among these options in such a way that the needed volumes of wood are procured at the least cost. A methodology has been developed to aid in this capital budgeting process and has been incorporated in an easy-to-use computer program.
Southern Forestry and a Modified Flat Tax
Authors: Leuschner William A. , Haney Harry L. 
Published: August 2019

Abstract
We examine the possible impacts of the President's and the Treasury Department's tax reform proposals on forestry investment, using a southern pine plantation model and PNW and IRR investment criteria. Results show reduced returns, particularly for higher-bracket individual taxpayers. Corporate returns are affected less severely than higher-bracket individual taxpayers.
Tree-Volume and Stem-Profile Functions for Baldcypress
Authors: Hotvedt James E. , Cao Quang V. , Parresol Bernard R. 
Published: August 2019

Abstract
No volume tables are available for cypress in the South. A volume and stem-profile prediction system for baldcypress (Taxodium distichum) is presented in this paper. Equations for estimating total and merchantable inside- and outside-bark cubic foot volumes are discussed, as well as a stem-profile equation for estimating diameter at any point on the tree bole. These equations are based on diameters measured at 10 feet above the ground. The prediction system was developed from 157 sample trees measured on 26 locations scattered throughout the south Delta region of Louisiana. Normal diameters ranged from 6 to 24 inches and total heights ranged from 50 to 100 feet.
A2 Phylogenetic investigation of transmitted HIV-1 drug resistance mutations in Denmark, 2009–17
Authors: Fonager J , Fischer T K 
Published: August 2019

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.