bluuebunny/crossref_metadata_2025 huggingface dataset:
A3 Molecular epidemiology of HIV-1 in Nigeria
Authors: Nazziwa J , Faria N , Chaplin B , Rawizza H , Dakum P , Abimiku A , Charurat M , Ndembi N , Esbjörnsson J
Published: August 2019

Nigeria has been reported to have the highest number of AIDS-related deaths in the world. In this study, we aimed to use molecular epidemiology to investigate the HIV-1 diversity and phylodynamics in Nigeria. We analyzed 1,442 HIV-1 pol sequences collected from 1999 to 2014 from seven geopolitical zones in Nigeria. The main circulating strains, CRF02_AG (44.1% of the analyzed sequences), Subtype G (8.3%), and CRF43_02G (16.4%), were introduced to Nigeria in the 1960s, 1970s, and 1980s, respectively. The number of effective infections decreased in Nigeria after the introduction of free antiretroviral treatment in 2006. We also found a significant number of unique recombinant forms (22.7%), the majority of which were recombinants between the two or three of the main circulating strains described above. In addition, phylogeographic analysis indicates multiple occasions of HIV-1 transmission between Lagos and Abuja (two of the main cities in Nigeria). Our results may be relevant for HIV-1 intervention and contribute in making informed decisions in strategies aiming at reducing further spread of HIV-1 in Nigeria.
A7 Co-receptor tropism determined by genotypic assay in HIV-1 non-B subtypes circulating in Cuba: Implications for pathogenesis and Maraviroc resistance
Authors: Méndez M , Kourí V , Pérez L , Alemán Y , Martínez Y , Díaz D , Han R , Pintos Y , Soto Y , Baños Y , Caturla Y , Fonseca C , Pérez J
Published: August 2019

The V3 loop of the HIV-1 envelope (env) gene is involved in binding to the chemokine receptors CCR5 and CXCR4, thus determining viral tropism. With the aim of genetically characterizing the C2V3 env region of HIV-1 samples from Cuban patients, naive to Maraviroc (MVC) therapy, 115 plasma samples were taken in the period of 2014–6 and analyzed by sequencing of the C2V3 region. HIV-1 subtyping was performed using COMET V.2 and Rega subtyping toolV.3 software. Subtypes were confirmed by phylogenetic analyses using Mega-6. Prediction of co-receptor tropism was performed using the geno2pheno algorithm. The viral mutations associated to MVC resistance were analyzed, as well as the association of the subtype with clinical, epidemiological, virological, and immunological variables. The subtypes detected using the C2V3 region were CRF20, 23, 24_BG (35 patients, 30.4%); Subtype B (33 patients, 28.7%); CRF19_cpx (30 patients, 26.1%); CRF18_cpx (10 patients, 8.7%); and others (7 patients, 6.1%). Overall, 60 per cent of the viruses exhibited R5 phenotype, 14.8 per cent were R5X4 and 25.2 per cent were X4. Interestingly, CRF19_cpx virus was associated with having phenotype X4 [46.7%, P = 0.0047, odds ratio (OR): 3.96, 95% confidence interval (95% CI): 1.59–9.84], with infection in young individuals (39.1%, P = 0.025, OR: 3,548; 95% CI: 1,136–11,077) and with higher values of viral load (P ≤ 0.05). The comparison of the amino acid sequences of the V3 loop showed differences between the B and non-B subtypes (P = 0.0001). Mutations reported to be associated with MVC resistance, were detected in 75.7 per cent of the samples, in positions 11 (6.1%), 13 (49.6%), 25 (6.1%), 316 (7.0%), 323 (11.3%), and 319 (3.5%) of Gp120, particularly in the recombinant forms CRF19_cpx and CRF_BGs. HIV variants that use the CXCR4 co-receptor were associated with more than 10 years of diagnosis, with older individuals, in the AIDS stage, with low CD4 counts and higher viral load levels (P < 0.05). The results support the hypothesis previously stated that CRF19_cpx viruses could be more pathogenic and would have limitations for the use of MVC. The high rate of mutations associated to MVC among non-B Cuban subtypes should be further studied.
A20 Sample preparation for whole-genome next-generation sequencing (NGS) of hepatitis C virus (HCV) routine RNA samples
Authors: Hillung Julia , Bracho María Alma , Tamarit Javier Pons , González-Candelas Fernando
Published: August 2019

Next-generation sequencing (NGS) is a technique that can capture the variability of viral populations in transmission studies. The conventional sample preparation for NGS, based on amplicons, is a potential source of errors, derived from the variable affinity of specific primers for different viral variants and from irregular DNA polymerase efficiency. In this context, we propose a more reliable method for viral whole genome sample preparation, starting from nucleic acids obtained and stored with conventional procedures. Our goal was to obtain complete hepatitis C virus (HCV) genome sequences to subsequently perform extensive phylogenetic analyses. Additionally, we aimed to test the effectiveness of nuclease treatment used to remove contaminating host DNA. Nucleic acids were obtained from almost cell-free blood plasma of HCV-infected patients. As a source for Illumina library preparation, double-stranded cDNA was generated using random primers. The HCV genome was not amplified before library preparation, avoiding possible biases derived from unequal copying. To get rid of possible host contaminants in the samples, a DNase treatment step was added. Libraries were paired-end sequenced on the Illumina platform using MiSeq reagent kit v3. After conservative filtering of contaminant human reads by alignment with the human reference genome using Burrows-Wheeler Aligner (BWA), the remaining reads were mapped to the HCV reference genome using BWA. Primary maximum likelihood phylogenetic analyses were performed using ClustalW and IQTREE to infer the phylogenetic relationships of the sequenced samples in the context of complete genome sequences of the same genotype. NGS sample preparation method of HCV from blood plasma was established. Complete genome sequences of HCV could be obtained with variable coverage depending on the viral load of plasma samples. No significant reduction of host DNA proportion in DNase treated samples in comparison to the controls was observed. The new sequences clustered within the Los Alamos National Laboratory database-deposited HCV subtype 4d samples. The method can be used to obtain full-length sequences of HCV from nucleic acid samples not previously planned for NGS. No improvement was observed when DNase pre-treatment of nucleic acids extracted from blood plasma was performed.
A21 Retrospectively describing hepatitis C virus transmission dynamics and tracking HCV transmission networks in real-time for strategic elimination interventions
Authors: Koopsen J , Russell C , van der Valk M , Schinkel J
Published: August 2019

Despite impressive uptake of direct acting antivirals for hepatitis C virus (HCV) in the Netherlands among HIV/HCV co-infected men who have sex with men (MSM), HCV transmission continues, especially among patients previously successfully treated for HCV. The incidence of reinfection occurs at the extremely high rate of 15 per 100 person-years. Clearly, more sophisticated methods are necessary to identify the sources and timing of new HCV infections among MSM. The aim of this research is to phylogenetically characterize HCV transmission dynamics within MSM-specific networks in order to provide a solid base for targeted interventions to monitor, control, and eventually stop the ongoing transmission of HCV among HIV-infected MSM and to prevent further spread of HCV to the community at large. The methodology that will be used is two-fold. Firstly, it concerns setting up a real-time monitoring system to track the HCV epidemic using phylogenetic tools and open-source software from http://nextstrain.org. Secondly, several phylogenetic methods will be used to retrospectively identify transmission clusters in Amsterdam and define epidemiological characteristics, including the directionality of transmission and the size and introduction dates of the clusters. This means that cluster cut-off points will have to be calculated. This research will result in a web-based molecular surveillance tool to monitor the persistence of endemic clades, emergence of new clades, and transmission clusters in ‘real time’, which, combined with clinical and epidemiological data, will be used for targeted interventions. The surveillance tool will be based on the open-source software from nextstrain.org. Secondly, by retrospectively describing the HCV transmission clusters in terms of introduction dates and subsequent dynamics, we may be able to better predict the future dynamics of the different clusters. High-resolution viral sequencing will allow us to identify the source and timing of (new) HCV infections and follow the trajectory of these MSM-specific lineages through the MSM population. Real-time insight in transmission networks using a web-based molecular surveillance tool will identify key targets for rapid interventions, awareness campaigns, and testing strategies. This can be used to prevent further spread to HIV-negative MSM and to control and eventually eliminate HCV from the MSM population.
A26 Molecular epidemiology of hepatitis E virus in Ireland 2016
Authors: Bennett Charlene , Dunford Linda , Coughlan Suzie , De Gascun Cillian , O’Gorman Joanne
Published: August 2019

Foodborne viruses such as hepatitis E virus (HEV) pose an increasing risk to public health and to confidence in Irish food. Hepatitis E has been acknowledged as a significant pathogen of likely zoonotic transmission, with pork products and shellfish being implicated as potential sources. The European Food Safety Authority has recommended that systematic strain typing of viruses in humans, animals, and food commodities is needed to improve understanding of etiological agents and foodborne transmission pathways, in particular for HEV. The dominant autochthonous genotype of HEV in Europe is genotype 3, thought to be associated with consumption of contaminated food, specifically pork products. However, little is known about the epidemiology of HEV in Ireland. In 2016, HEV became a notifiable disease in Ireland. Following this, as part of the Department of Agriculture, Food and the Marine-funded FoVIRA study, the molecular epidemiology of HEV in Irish clinical samples has been characterized for the first time. HEV RNA-positive clinical specimens from 2016 were genetically characterized (n = 14). A 450 nucleotide fragment of the ORF2 region of the HEV genome was amplified, with contiguous sequence assembly performed using DNA Lasergene v14. Sequences were aligned with ClustalW implemented in Bioedit v7.1.9 and compared to reference strains from GenBank. A maximum likelihood phylogenetic tree was constructed using the Hasegawa–Kishino–Yano model and a discrete gamma distribution to model evolutionary rate distances between sites. Evolutionary analyses were conducted in MEGA7. Statistical support was provided by bootstrapping with 1,000 replicates. Fourteen strains belonged to genotype 3 and were classified as the following subtypes: 3c (n = 7), 3e (n = 4), 3f (n = 1), 3 untyped (n = 1), and 1 untyped. Phylogenetic analysis showed the formation of two distinct clusters of genotype 3:3abchij and 3efg, with strong bootstrap support. A genotype 1 was detected and found to be associated with travel. Data generated from this research will contribute to a risk exposure assessment and will be used to identify potential control points and risk mitigation measures for viral foodborne pathogens. This study will provide a unique opportunity to build national capability in the area of food testing within Irish public laboratories.
A27 Whole genome characterization of influenza D viruses detected in cattle herds in northern Italy between 2015 and 2017
Authors: Bianco A , Cavicchio L , Fusaro A , Rizzo G , Milani A , Salviato A , Zamperin G , Beato M S , Schiavon E , Bano L , Monne I
Published: August 2019

Influenza D virus (IDV) is a new viral genus identified within the Orthomyxoviridae family, showing 50 per cent amino acid identity with human influenza C virus. Similar to human influenza viruses of the C genus, IDV also harbors 7 genomic segments and uses 9-O-acetylated sialic acids as cell receptors. This newly emerged virus exhibits a broad host range and is capable of infecting swine, cattle, sheep, goats, ferrets, and guinea pigs. In Italy, IDV was first detected in archived samples collected between 2014 and 2015 from cattle and swine in the Po Valley area. Here, we report the genetic characterization of IDV viruses detected in an extensive area of northern Italy, namely Veneto, Lombardy, and Piedmont, through passive surveillance between September 2015 and October 2017. A total of 482 samples, including nasal swabs, lungs, and bronchoalveolar lavage fluid, collected from 309 cattle farms were tested. Thirty cattle herds turned out to be positive, for a total of 40 samples positive by Real Time RT-PCR targeting the PB2 gene. Representative IDV positive swabs were sequenced on an Illumina Miseq platform, and phylogenetic analyses were performed for each genome segment. The analyses of the seven gene segments demonstrated that the viruses identified in the north of Italy clearly grouped within a genetic cluster of IDV sequences previously described in Italy and in the USA, thus suggesting a common origin for these viruses. Interestingly, the IDVs identified in Italy presented a low similarity (96.1% to 98.8% for the seven gene segments) to the French IDVs, which is the only other European country where this pathogen has been identified and characterized so far. The wide IDV host range and the ability of this virus to reassort are a matter of concern. Results of this study indicate that IDV is extensively circulating among bovine herds in Northern Italy and suggest a potential role of IDV in the bovine respiratory disease complex, highlighting the need to perform surveillance on an ongoing basis to track its spread and evolution.
A41 Deep sequencing of respiratory syncytial virus links viral diversity to disease severity
Authors: Nauwelaers Inne , Talts Tiina , Galiano Monica , Openshaw Peter
Published: August 2019

Respiratory syncytial virus (RSV) is a common virus that can cause bronchiolitis in infants and pneumonia in immunocompromised and elderly people. RSV belongs to the Pneumoviridae family and consists of a genome of 15 kb. Its genome contains ten genes that code for eleven proteins, with M2 coding for two different proteins in overlapping open reading frames. It is unclear why some infected children have severe disease and others have mild or asymptomatic disease. In this project, methods for complete genome sequencing of RSV via Sanger and Illumina MiSeq platforms were optimized. One hundred and twenty-four community samples (59 RSV A and 65 RSV B) from 2014 to 2018 were collected (in collaboration with the Royal College of General Practitioners) and sequenced. Samples were selected based on viral load (e.g. Ct values had to be < 30). The genotype of each sample was determined by constructing phylogenetic trees with reference sequences from all genotypes. Trees were reconstructed using the maximum likelihood method. Furthermore, Illumina sequencing was used to deep sequence seven community samples and four hospital samples that were spatiotemporally matched (obtained via Imperial College NHS Trust hospitals). Variants were studied to investigate if certain variants influence disease severity (e.g. cause mild (community samples) or severe infection (hospital samples)). Analysis so far showed that ON1 (with a seventy-two nucleotide duplication in attachment protein G) is the most common genotype in both community and hospitalized samples (90% and 75% of samples, respectively), with GA2 (without duplication) as the next most common genotype for RSV A subtypes (7% and 25%). Three per cent of community samples were of the GA5 genotype. Samples from the RSV B subgroup all belong to the BA genotypes with a 60-nucleotide duplication in G. Samples that were selected for Illumina sequencing had a Ct value between 19.0 and 29.1, while hospital samples had a Ct value of 18.3 to 29.1. Viral load, therefore, did not explain disease severity in these selected samples. The Shannon entropy from Illumina sequenced samples averaged at 22.78 in community samples (ranges from 15 to 28) and 38.78 in hospitalized samples (ranges from 31 to 57). This indicated that diversity of the virus pool might influence disease severity; however, more samples need to be analyzed. There are no specific variants that could explain disease severity. Diversity of the virus pool could explain the link between higher viral loads and disease severity, which is sometimes found but cannot always be confirmed. Higher viral loads can harbor more diverse viral particles compared to lower viral loads. Future work will focus on more in-depth variation and diversity analysis and on evolutionary analysis of both community and hospital samples. We will also investigate intra-host evolution of RSV in acute infections using consecutive samples and its possible implications on the host response.
A49 Emerging rodent-borne viral pathogens in Italy: Overview of seroprevalence and genomic investigations
Authors: Alfano N , Tagliapietra V , Arnoldi D , Rosso F , Rossi C , Rosà R , Hauffe H C , Rizzoli A
Published: August 2019

Rodents play a key role as reservoirs of many zoonotic pathogens which represent an emerging public health threat worldwide. Among these, Dobrava-Belgrade virus (DOBV) is the most pathogenic hantavirus in Europe with a case-fatality rate of up to 12 per cent, while Lymphocytic choriomeningitis virus (LCMV) has a mortality rate below 1 per cent. Both viruses are predominantly transmitted to humans through the inhalation of infected particles in aerosolized urine, feces, or saliva that are shed in the environment by chronically infected hosts, such as the yellow-necked mouse Apodemus flavicollis. Although no human cases of DOBV or LCMV have been reported in the Province of Trento (northeastern Italy) thus far, in order to evaluate the human hazard for these viruses, the prevalence of antibodies to DOBV and LCMV has been monitored using a specific immunofluorescence assay test in a wild population of A. flavicollis since 2000. These investigations have shown that the two RNA viruses circulate silently in this species in the study area. In particular, a sudden increase (up to 12.5%) in DOBV seroprevalence was observed in this rodent species between 2010 and 2012. Several efforts have been undertaken to isolate these viruses and characterize their genomes, but it has not yet been possible to detect viral RNA from seropositive mice using traditional methods such as RT-PCR. Since RNA viruses are very diverse and often difficult to isolate, innovative molecular methods based on viral targeted enrichment and high-throughput sequencing have been applied. We intend to report on this long-term seroprevalence study and provide an overview of the molecular approaches adopted in the attempt to confirm the presence of these viruses, and identify which variants are circulating in the region, as well as their pathogenicity.
A68 Characterization and comparative genomic analysis of two Bacillus megaterium lytic bacteriophages
Authors: Sharaf A , Oborník M , Hammad A , El-Afifi S , Marei E
Published: August 2019

Next-generation sequencing technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Many Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. Here, we describe biological characteristics and whole-genome sequences and their annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), isolated from Egyptian soil samples and representing two different groups according to their host range and amplified fragment length polymorphism profiles. Both phages have been displaying different thermal inactivation points (82 and 78 °C) and pH tolerance range (5–9.2 and 5–8.4 pH) while having the same longevity in vitro (192 h). Electron microscopy observation has proved that both phages belonged to the Myoviridiae family. Furthermore, growth analyses indicated that phages BM5 and BM10 have a shorter latent period (20 and 25 min) and smaller burst size (103 and 117 PFU) than is typical for Bacillus phages. The genome sizes of phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with a modular organization. Bioinformatic analyses of BM5 and BM10 genomes enabled assignments of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of BM5 and BM10 genome structures with other B. megaterium bacteriophages revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7) within L cluster and display different lifestyles (lysogenic and lytic). Sequenced phages encode proteins associated with Bacillus pathogenesis. BM5 does not contain any tRNA sequences, while BM10 genome codes for 17 tRNAs.
Montana's Mission-Oriented Research Program
Authors: Pfister Robert D. , Fiedler Carl E.
Published: August 2019

The Mission-Oriented Research Program (MORP) was established at the University of Montana in 1981 to work on current second-growth management problems in northern Rocky Mountain forests. Research is focused on the five traditional resources—timber, range, water, wildlife, and recreation—in relation to major program goals of inventory, productivity, and management. The program emphasizes studies of the multiple effects of alternative silvicultural treatments; close liaison with researchers, forest industry, and private landowners; and prompt distribution of information to users. West. J. Appl. For. 1:11-12, Jan. 1986
Snag Management on National Forests in the Pacific Northwest—1984
Authors: Bull Evelyn L. , Thomas Jack Ward , Horn Kirk
Published: August 2019

A questionnaire was sent to each Ranger District in the Pacific North-west Region of the USDA Forest Service to get information on present snag-management programs. Ninety-five percent of the responding Ranger Districts left snags at levels that ranged from 0.15 snags/ha (0 06/ac) to 12-15 snags/ha (5-6/ac) on all forested lands. Live trees were intentionally left as future snags on 93% of the Ranger Districts. Live trees were killed to create snags on 41% of the Ranger Districts. Management recommendations are made as to the kind of snags to leave and methods of maintaining them. West. J. Appl. For. 1:41-43, April 1986
Symptom Expression of Root-Diseased Trees in Mixed Conifer Stands in Central Washington
Authors: Filip Gregory M.
Published: August 2019

Two proposed seed-orchard sites on the Wenatchee and Gifford Pinchot National Forests were examined prior to tree felling and land clearing to evaluate root-disease symptom expression in three species of conifers (Douglas-fir [Pseudotsuga menziesii], grand fir [Abies grandis], and ponderosa pine [Pinus ponderosa]. About half of the trees within infected areas had roots decayed by one of three principal root pathogens, Armillaria ostoyae, Phellinus weirii, and Fomes annosus, as determined from totally excavated root systems.

Trees with above-ground symptoms had significantly moreroot decay than trees without symptoms. Crown symptoms and root-collar symptoms were accurate indicators of 22% of the root-diseased trees. Stain or decay at freshly cut stump surfaces were reliable indicators of 50% of root-diseased trees. Surveys that record crown symptoms and root-collar symptoms in similar stands will give accurate estimates of the number of trees killed by root diseases. However, examination of freshly cut stump surfaces will detect more accurately the total number of root diseased trees, especially if decay associated with butt wounds is absent. West. J. Appl. For. 1:46-48, April 1986
Allowable Cut Effect and Fire-Damage Appraisal
Authors: Montgomery Claire A. , Brodie J. Douglas , Cleaves David A.
Published: August 2019

Analysis of investment in forest fire protection and control first requires appraisal of potential loss. Traditional analysis computes the present net worth of harvest and other benefits lost on a stand-by-stand basis. It assumes harvest scheduling without constraints. Forest planning, on the other hand, requires constraints on harvest scheduling and selection of a preferred alternative schedule. The interaction of timber inventory, age-class distribution, and harvest-scheduling constraints leads to a different allowable cut effect in each combination of forest structure and constraints. Examples of this interaction are provided: the basis of comparison is the present net worth of damage at the stand level when harvest scheduling is unconstrained. West. J. Appl. For. 1:100-103, Oct. 1986.
Survival and Growth of Douglas-Fir Seedlings with Spot-Spraying, Mulching and Root-Dipping
Authors: Tung Chao-Hsiung , Batdorff Jim , DeYoe David R.
Published: August 2019

Two vegetation management methods, paper mulching and spot-spraying with glyphosate, were combined with a root-dipping treatment, Terra Sorb®, to test effects on seedling survival and height growth on a harsh site in Oregon. Survival of Douglas-fir (Pseudotsuga menziesii) seedlings was significantly higher after the third growing season when competing vegetation had been controlled with mulch or glyphosate during the first two growing seasons. Seedlings retreated with paper mulch and glyphosate before the second growing season had 36 and 25% higher survival than those that were not retreated. None of the seedlings was retreated before the third season; after this season, survival of seedlings treated twice with glyphosate was 26, 23, and 21% higher than seedlings receiving one glyphosate treatment and one or two mulch applications, respectively. There were no differences in seedling height growth among treatments. Rootdipping with Terra Sorb® did not influence survival or growth. West. J. Appl. For. 1:108-111 Oct. 86.
Effects of Soil Compaction on Tree Volume in a California Ponderosa Pine Plantation
Authors: Helms John A. , Hipkin C.
Published: August 2019

Soil bulk density was measured around 423 trees (0.48 ha) in a 16-year-old ponderosa pine (Pinus ponderosa) plantation in the Sierra Nevada of California. A landing, skid trail, and areas adjacent to skid trails had soil bulk density increased by 43, 30, and 18% compared to areas with lowest bulk density. Due to differences in mean tree volume and initial survival, volume per unit area in these three locations was reduced by 69, 55, and 13%. Areas between skid trails were relatively unaffected. Assuming full stocking, reduction in productivity by age 40 yr in the most heavily compacted areas is equivalent to about one site index class. Further reduction in projected volume on highly compacted areas could occur due to lower initial survival. Alternative approaches to skid trail management are suggested. West. J. Appl. For. 1:121:124, Oct. 1986.
Do Shade and Shrubs Enhance Natural Regeneration of Douglas-Fir in South-Central Idaho?
Authors: Jones Michael Hunt
Published: August 2019

Shade duration and shrub composition in microsites with naturally regenerated Douglas-fir seedlings (Pseudotsuga menziesii var. glauca) were compared to randomly located control plots without seedlings in hot, dry group selection cuts in the southernmost Boise National Forest. Shade duration was estimated using a sighting device which allowed quantification of the degrees of the sun's arc intercepted by timber, shrubs, or other obstructions. Measurements were standardized for the median date for summer high temperatures. Seedlings received more whole-day (P<0.001) and afternoon (P<0.001) shade than control plots, and seedlings on southern exposures received more shade than those on other aspects. Seedling plots had more shrub cover than control plots (P<0.007). However, of nine shrub species examined, only buckbrush exhibited a significantly positive association with seedlings. Soil surface temperatures under buckbrush were reduced more than under other species, and unshaded surfaces remained above 50°C for extended time periods. These results suggest that natural regeneration of Douglas-fir may be enhanced by harvest practices and site preparation methods which provide shade during critical stages of germination and early seedling establishment. West. J. Appl. For. 10(1):24-28.
Cost of Timber Harvest Under Traditional and "New Forestry" Silvicultural Prescriptions
Authors: Keegan III Charles E. , Fiedler Carl E. , Stewart Fred J.
Published: August 2019

Harvest costs were estimated for New Forestry silvicultural prescriptions designed for application on national forest lands in western Montana. Estimates were derived using an expert opinion format and were compared using constant dollars with actual 1991 costs based on more traditional prescriptions. Costs were developed for three major logging systems(tractor with hand-felling, tractor with mechanical-felling ,and uphill skyline with hand-felling) and four major stand types[lodgepole pine( Pinus contorta), mature ponderosa pine( P. ponderosa)/Douglas-fir(Pseudotsuga menziesii), second-growth pine/fir,and mixed conifer].Average harvest costs for New Forestry prescriptions ranged from no increaset o 48% ($72/mbf)higher.In light of stumpage price increases of >$200/mbf since 1991, these increased costs should be a minor factor in determining the feasibility of future timber harvest.West.J.Appl. For. 10(1): 36•42
Idaho's Timber Harvest Projections by Ownership to 2000: An Issue-Based Survey of Resource Managers
Authors: Hamanishi Craig M. , Wagner Francis G. , O'Laughlin Jay , Gorman Thomas M.
Published: August 2019

Fifty of Idaho's forest resource managers were queried about their outlook for sawtimber harvests and issues impacting future harvest levels. Identical questionnaires were sent to managers representing national forests, other public lands, forest industry, and nonindustrial private lands. Managers were first asked to estimate the impacts of 12 specific issues on past and future harvest levels, and then to provide estimates of future harvest levels for the lands directly under their control or jurisdiction. Managers expected sawtimber harvests in Idaho to decline through the year 2000. Idaho harvest levels between 1994 and 1996 were expected to fall 4.6% from average levels in the base period of 1991-1993, with further declines of 14.6% expected in 1997-2000. Across all ownerships, the most significant issues expected to affect harvest levels in Idaho are threatened, endangered, and sensitive species; cumulative impacts; and new forestry techniques. West. J. Appl. For. 10(3):109-113.
Revenue Sharing and Resource Management in Western States
Authors: Schuster Ervin G.
Published: August 2019

Natural resource management agencies share revenue from sale of commodities with Western States (states north and west of Kansas and New Mexico) through five important programs, including the 25% Fund and PILT. Since 1977, the aggregate value of these payments has increased by about two-thirds, when measured in current dollars; in constant dollars, the aggregate value has decreased by about one-tenth. Revenues shared through the Mineral Lands Leasing Act accounted for the most (49%), and the Taylor Grazing Act accounted for the least (1%). An overview of major revenue-sharing programs is provided. West. J. Appl. For. 11(1):20-24.
Prediction of Pruning Wound Occlusion and Defect Core Size in Ponderosa Pine
Authors: O'Hara Kevin L. , Buckland Paul A.
Published: August 2019

Occlusion following pruning is an important determinant of the size of the inner defect core of a pruned log. A total of 117 branch stubs from 5 ponderosa pine (Pinus ponderosa) logs pruned 32 yr previously were destructively sampled to evaluate occlusion in relation to growth and wound characteristics. Models were developed to predict the size of the occlusion zone and the years to occlusion. The models indicate the size of the occlusion zone is more sensitive to length of the branch stub than stub diameter. Increasing the length of the pruning stub from 1.5 to 3.0 in. increases the predicted size of the occlusion zone from 112-132% depending on stub diameter. Doubling the stub diameter an equal amount increases the size of the occlusion zone by only 3-14%. Minimization of the size of defect core is best achieved by reducing the length of the pruning stub through cutting flush with the bark. These results suggest land managers should not hesitate to prune fast growing ponderosa pine plantations with large branch diameters. West. J. Appl. For. 11(2):40-43.
Relation of Crown and Foliage Traits to Height Growth of Sitka Spruce
Authors: Copes D. L. , Pawuk W. H. , Farr W. A. , Silen R. R.
Published: August 2019

Four crown and foliage traits of a young Sitka spruce (Picea sitchensis) stand were tested with rooted cuttings in greenhouse and field plots for possible thinning selection guidelines. Repeatability estimates of the amount of genetic control over the four traits and the relation of those traits to height growth were evaluated 5 years after rooting. Only the blue-green trait was significantly associated (P < 0.05) with height growth. Average height of cuttings selected for green foliage was 17% greater than cuttings selected for blue foliage. Under greenhouse conditions, repeatability estimates of green or blue foliage were 98% versus 66%, respectively; 72% versus 89% for trees with dense or open crowns, respectively; 65% for the comparison of upright and horizontal branches; and 75% for the comparison of long or short branches. West. J. Appl. For. 11(3):77-80.
A Trial of Plug Transplant Seedling Production in the Southwest
Authors: Tinus Richard W.
Published: August 2019

Plug transplants were developed in the Pacific Northwest as a way to accelerate nursery production and increase root system fibrousness of barefoot seedlings, and the practice has been spreading to other areas. This paper describes a trial of its use in a do: Southwestern area. Ponderosa pine (Pinus ponderosa var. scopulorum Engelm.) seed was sown in February in small containers, transplanted to outdoor nursery beds at Albuquerque NM in May, lifted the following February, and outplanted as plug+1 stock in April. Survival was as good (76 and 71%) and growth better (232 vs. 209 mm) than standard 2+0 stock after 3 yr. A similar regime for Engelmann spruce (Picea engelmannii (Parry) Engelm.) produced seedlings that survived and grew well (survival 86 and 94%, height growth 54 and 56 mm for plug+2 and standard stock, respectively), but they required 2 yr in the nursery bed (plug+2) to reach adequate size for transplanting, which negated the advantage of reduced production time. West. J. Appl. For. 11(3):81-84.
Early Height Growth and Site Index of Lodgepole Pine Under Wet and Dry Soil Moisture Regimes in British Columbia
Authors: Nigh Gordon D.
Published: August 2019

The objective of this study was to determine whether the relationship between site index and early height growth of lodgepole pine (Pinus contorta var. latifolia) is the same on wet and dry sites. If the height growth/site index relationship is the same for different site types, then only one growth intercept model is required to estimate site index. Indicator variables in nonlinear regression were used to incorporate soil moisture availability into a growth intercept model. One set of parameters in a site index/early height growth model was adequate for both wet and dry sites. This result was supported graphically. Therefore, only one growth intercept model is necessary for the sites examined in this study. West. J. Appl. For. 12(1):5-8.
Containerized Jeffrey Pine Growth and Nutrient Uptake in Response to Mycorrhizal Inoculation and Controlled Release Fertilization
Authors: Walker R. F. , Kane L. M.
Published: August 2019

Ectomycorrhizal inoculation with basidiospores of Pisolithus tinctorius and fertilization with two controlled release nutrient formulations, High N 24-4-7 and Sierra 16-6-10 Plus Minors, were evaluated for their effects on containerized Jeffrey pine (Pinus jeffreyi) seedlings. Noninoculated and nonfertilized seedlings and a water soluble fertilizer treatment using Peters 20-10-20 provided for comparisons of mycorrhizal and nutrient amendment effects on growth and mineral nutrition. At 6 months, inoculated seedlings had greater root dry weight while fertilization increased shoot dimensions and weight, with the response to controlled release nutrients exceeding that to water soluble fertilizer. After 12 months, inoculation increased mycorrhizal formation, and inoculated seedlings had greater shoot volume as well as root volume, dry weight, and total length. Controlled release fertilization also promoted greater shoot growth than water soluble nutrients at the final measurement, while root system development was comparable overall among fertilized seedlings regardless of nutrient formulation. Foliar analysis revealed that concentrations of most macro- and micronutrients were sufficient for adequate seedling nutrition in all treatments. However, inoculated seedlings exhibited greater uptake of P, Ca, Mg, S, Fe, Mn, and Zn. Fertilization generally increased foliar concentrations of all of the above elements except Mg and Fe, but also increased N uptake. Overall, these results suggest that inoculation with P. tinctorius and controlled release fertilization with High N 24-4-7 and Sierra 16-6-10 facilitate production of Jeffrey pine container stock suitable for outplanting on harsh sites. West. J. Appl. For. 12(2):33-40.
Thinning Decisions Using Stand Density Indices: The Influence of Uncertainty
Authors: Ducey Mark J. , Larson Bruce C.
Published: August 2019

In practice, stand density indices must be estimated from sample data, leading to uncertainty in both estimates of stand density and resulting thinning decisions. We provide a statistical framework for thinning decisions based on density thresholds. We show how to assess the adequacy of existing cruise data to guide the thinning process, and to design more cost-effective sampling plans. We present this information in a series of graphs which, when used in conjunction with density management diagrams, can improve rational thinning decisions. West. J. Appl. For. 12(3):89-92.
Effectiveness of a Physical Barrier in Deterring Vole and Snowshoe Hare Feeding Damage to Lodgepole Pine Seedlings
Authors: Zimmerling Todd N. , Zimmerling Linda M.
Published: August 2019

We examined the effectiveness of a tubular, polyethylene/polypropylene mesh seedling protection device in reducing overwinter feeding damage by snowshoe hares(Lepus americanus) and meadow voles (Microtus pennsylvanicus) on spring planted, plug stock (1 + 0) lodgepole pine(Pinus contorta). Seedlings fitted with the seedling protection devices (SPD) had significantly lower levels of feeding damage (3 and 9%) than control seedlings (25 and 41%) on two study sites. Most of the feeding damage to treated seedlings was the clipping of the terminal leader or laterals that were not protected by the protection device. In two instances, a vole tunneled under the seedling protection device to damage the stem of the treated seedling; however, this was the exception. This physical barrier can be effective in reducing feeding damage by small mammals on lodgepole pine. West. J. Appl. For. 13(1):12-14.
Technical Commentary: Managing High-Elevation Forests to Produce American Matsutake (Tricholoma magnivelare), High-Quality Timber, and Nontimber Forest Products
Authors: Amaranthus Michael P. , Weigand James F. , Abbott Rick
Published: August 2019

In the Pacific Northwest, nontimber forest products account for more than $200 million in annual revenue yet there is little intentional management to promote the dozens of these harvested species. In the southern Cascade Range in Oregon, management experiments are being installed to develop and refine silvicultural practices that increase financial returns from high-elevation stands. Pretreatment measurements are complete, and harvest treatments will begin in 1998. The harvest treatments will emphasize the most valuable products: high-quality timber, American matsutake mushrooms (Tricholoma magnivelare), and other nontimber forest products such as food-flavoring extracts, decorative boughs, Christmas trees, and pine cones. Management practices will adjust species composition, remove disease and infested trees, prune target species, manage for timber on long rotations, and opportunistically manage and harvest nontimber forest products, especially the highly valued American matsutake. A comprehensive monitoring program will track ecosystem and economic variables at different temporal scales. In this paper we present management scenarios that emphasize forest function and biological diversity while providing an even flow of commercially valuable timber and nontimber forest products. West. J. Appl. For. 13(4):120-128.
A Decision Support System for Incorporating Wildlife Habitat Quality into Forest Planning
Authors: Roloff Gary J. , Carroll Bruce , Scharosch Steve
Published: August 2019

We developed a decision support system to address wildlife habitat quality in the strategic forest planning process. The process involves projecting wildlife habitat attributes using a growth and yield model, combining the attributes into an index of structural habitat quality, generating yield tables of structural habitat quality that can be constrained or optimized in the forest planning model, and relating prescriptions for each forest planning analysis area back to the habitat attributes. The result is a map of habitat components. This mechanism is considered the first step in our wildlife habitat assessment procedure in that it focuses on within-stand or within-analysis area structures. Since many wildlife species depend on multiple stands or analysis areas and the spatial arrangement of habitat components to meet their life requisites, the second step in our habitat assessment procedure is to apply spatially explicit wildlife habitat models to the mapped planning solution. The decision support system offers the capability to evaluate the effects of alternative management strategies on wildlife habitat in the context of a forest planning model solution. West. J. Appl. For 14(2):91-99.
Economics of Living Snow Fences in the Intermountain West
Authors: Kelson Aaron R. , Lilieholm Robert J. , Kuhns Michael R.
Published: August 2019

Past research has found that living snow fences are the most cost-effective option for controlling blowing snow along transportation corridors. Despite this, living snow fences are an underutilized forestry practice throughout much of the Intermountain West, even though these fences can be successfully maintained in the region's harsh climate. Decision-makers may be encouraged to establish more living snow fences in the region when economic efficiency gains can be demonstrated. Efficiency gains from living snow fences, evaluated using the annualized cost approach, demonstrate that the benefits to society outweigh the costs. An example is presented using an average-sized, 1,040-ft-long, 3 row snow fence, and a discount rate of 8%. To offset snow fence costs over a 50 yr expected life, the fence need only reduce traffic accidents by as little as one every 23 yr, or reduce snow plowing by about 6 hr/yr. Other likely but less quantifiable benefits make the benefits of living snow fences even more economical to society. Private expenditures may need to be subsidized if these social benefits are to be provided at optimal levels, however. West. J. Appl. For. 14(3):132-136.
Timber Management Costs in the Northern Region: A Historical Analysis
Authors: Gebert Krista M. , Niccolucci Michael J. , Schuster Ervin G.
Published: August 2019

This study investigates three aspects of timber management (TM) costs in the Northern Region of the USDA Forest Service from 1960 to 1995. Total timber management costs and costs/unit of timber harvested were analyzed to determine: (1) trends in unit costs and their probable causes, (2) whether economies of scale existed in timber management over this period, and (3) the distribution of total cost changes geographically and among expenditure categories. Results indicate the prevailing factor behind the upward trend in unit costs was the decline in timber harvested (especially since 1990). Separation of TM unit costs into seven cost categories shows that from 1960 to 1980, road construction accounted for 50% of overall unit costs. After 1985, however, harvest design and administration expenditures replaced road construction as the dominant expenditure category. By 1995, harvest design and administration accounted for 26% of unit costs, while road construction's share had dropped to 13%. Other analysis found unit costs to decrease as the timber land base increased, indicating economies of scale in timber management. Finally, an examination of total timber management costs shows road construction (including reconstruction) was the largest contributor to both cost increases from 1960 to 1980 and decreases from 1980 to 1995. West. J. Appl. For. 14(4):200-207.
Ten-Year Growth Response of Young Douglas-Fir to Variable Density Varnishleaf Ceanothus and Herb Competition
Authors: Monleon V. J. , Newton M. , Hooper C. , Tappeiner J. C.
Published: August 2019

The effect of different densities of varnishleaf ceanothus (Ceanothus velutinus var. laevigatus) and herbaceous vegetation control on stem diameter, height, and volume of plantation Douglas-fir (Pseudotsuga menziesii vat. menziesii) seedlings was examined during the 10 yr following planting. Initial densities of ceanothus ranged between 0 and 15,000 seedlings/ha and were obtained by interplanting ceanothus germinants or chemical thinning after clearcutting and broadcast-burning. Herbaceous vegetation control was achieved by a single application of glyphosate following planting, with shrub seedlings covered. Ceanothus density in the range of 0 to 6,750 plants/ha did not have an effect on Douglas-fir diameter, height, or volume at age 10; however, Douglas-fir growth was significantly decreased when ceanothus densities reached 15,000 plants/ha. Ten years after planting, Douglas-fir volume in the treatments with 6,750 ceanothus/ha or less was 1.7 times greater than that in the 15,000 ceanothus/ha treatment. On the other hand, removal of herbaceous vegetation after planting significantly increased tree diameter, height, and volume, regardless of ceanothus density. Even 10 yr after the application of the treatment, trees without early herb competition grew faster and had mean dbh, height, and volume that were 1.02 cm, 0.55 m, and 12.98 dm³/tree greater respectively than those with herbs. Thus, a treatment at plantation establishment to control herbaceous vegetation and to reduce ceanothus density to less than 7,000 plants/ha will ensure an increase in growth and stocking for at least 10 yr. West. J. Appl. For. 14(4):208-213.
An Assessment of Cylindrocarpon on Container Western White Pine Seedlings After Outplanting
Authors: Dumroese R. Kasten , James Robert L. , Wenny David L.
Published: August 2019

Cylindrocarpon root disease can destroy root systems of container seedlings. Foresters were concerned that infected nursery stock would perform poorly after outplanting. Root growth potential tests were a poor predictor of disease levels on seedlings that otherwise met standard morphological criteria (height, stem diameter, and firm root plugs) for outplanting. Cylindrocarpon on western white pine persists longer on outplanted stock than Fusarium oxysporum or F. proliferatum on Douglas-fir seedlings on a similar site. Mortality caused by herbivores was as serious a threat to plantation establishment as was mortality caused by all other factors. Our results suggest that western white pine seedlings infected with Cylindrocarpon, but meeting morphological criteria for outplanting, will perform satisfactorily in the field. West. J. Appl. For. 15(1):5-7.