bluuebunny/crossref_metadata_2025 huggingface dataset:
A10 Presence and frequency of M184V mutation in the MOBIDIP trial
Authors: Armero A , Chaix M L , Nere M L , Delaporte E , Peeters M , Delaugerre C
Published: August 2019

The MOBIDIP trial evaluated the simplification by protease (PI/r) monotherapy for HIV infection versus dual therapy and boosted protease inhibitor plus lamivudine (PI/r + 3TC) in controlled patients under second-line regimens. MOBIDIP was interrupted because of a significant number of patients with virological failure (VF) at week 48 (W48) in PI/r (33/133, ∼25%) versus in PI/r + 3TC (4/132, ∼3%). At the time of first-line VF, 96 per cent of patients harbored the M184V mutation. The presence of the M184V mutation was related to a protective effect against VF in the PI/r + 3TC arm. We developed a methodology that allows to determine the frequency of M184V/I mutations in the HIV reverse transcriptase (RT) gene in peripheral blood mononuclear cells (PBMC) obtained before MOBIDIP simplification. Paired-end sequences were obtained from 252 PBMC samples covering the first 855 bp of the RT gene (HXB2: 2485–3405) by MiSeq technology. These sequences were subjected to an in-house Bioinformatics pipeline. The results of our pipeline were compared to the output of PASeq (https://www.paseq.org), an open web-tool for the identification of drug resistance mutations. The M184V mutation was identified at a frequency greater than 1 per cent in 178 individuals (∼71%). The M184I mutation was observed in 34 patients (∼13%), always in the presence of stop codons, and is in agreement with expectations, as this mutation is a known APOBEC-targeted site. Sixty-seven patients (∼27%) had a frequency of the M184V mutation with values greater than 75 per cent. PASeq confirmed the presence of M184V mutation in 173 patients. The frequencies estimated by the PASeq tool and in-house pipeline were correlated up to 99.5 per cent. We found a significant loss of the M184V mutation archived in PBMC between the first-line regimen treatment failure and the beginning of the MOBIDIP trial. In patients under long-term antiretroviral therapy, as in our case, viral sub-populations could be lost, reducing the presence, and frequency of a mutation. In the next step, we will evaluate the association between the presence and frequency of M184V mutation and MOBIDIP results.
A14 Estimating time since HIV infection using next-generation sequencing data: A unique tool to help understand HIV prevention among high-risk young women in Ukraine
Authors: Cholette Francois , Daniuk Christina , Lee Emma , Capina Rupert , Cheuk Eve , Becker Marissa , Mishra Sharmistha , Ma Hui Ting , Balakireva Olga , Pavlova Daria , Sandstrom Paul
Published: August 2019

The transitions study examines HIV risk among adolescent girls and young women through their sexual life course from first sex, to past and current engagement in casual sex, transactional sex, and, for some, formal sex work (FSW). Understanding the timing of HIV infection and the circumstances around early infection in young females is critical to HIV prevention interventions. We inferred time since HIV infection using next-generation sequencing (NGS) of the HIV pol gene isolated from cross-sectional samples among high-risk young women in Dnipro, Ukraine. Dried blood spots were collected on Whatman 903 cards from young women aged 14–24 engaged in casual sex (n = 894), transactional sex (n = 464), and FSW (n = 452). The HIV pol gene was sequenced using an in-house NGS HIV drug resistance mutation genotyping assay. Time since HIV infection was inferred using an online tool as described by Puller et al. (2017) freely available at https://hiv.biozentrum.unibas.ch/ETI/. The mean estimated time since HIV infection (ETI) for participants engaged in casual sex, transactional sex, and FSW is 1.98, 1.84, and 3.01 years, respectively. ETI was used to determine the duration of HIV infection for each participant and compared to the number of sexually active years prior to FSW. Among FSW, 61 per cent of participants were infected with HIV prior to entry into sex work. In general, ETI from NGS data suggests that FSWs were infected with HIV before entry into FSW. Expansion of targeted prevention programs beyond FSW could play an important role in mitigating HIV transmission at the population level.
A17 The effect of intra-host evolution of HIV-2 capsid on disease progression
Authors: Boswell M T , Palm A , Karlson S , Månsson F , Norrgren H , Jansson M , Medstrand P , Rowland-Jones S , Esbjornsson J
Published: August 2019

The human immunodeficiency virus type 2 (HIV-2) is an important cause of acquired immune deficiency syndrome (AIDS) in West Africa. The virus started circulating in humans around 1938 and has spread predominantly within West Africa with an estimated 1–2 million people being infected today. Compared with the pandemic HIV-1, HIV-2 infected people have longer AIDS-free survival times, higher CD4+ counts and lower risk of vertical and horizontal transmission. Approximately 35 per cent of HIV-2 infected individuals are classified as so-called long-term non-progressors with undetectable viral loads and limited disease progression after 10 years of follow-up. It has been shown that HIV-2 is more sensitive to the host restriction factor TRIM5α when compared with HIV-1, and this has been linked to conformational changes in the retroviral capsid. TRIM5α binds at the interface between three capsid hexamers, initiates early uncoating and proteasomal degradation. TRIM5 genotype has shown only modest effects on HIV-1 disease outcomes. HIV-2 capsid sequences bearing a specific poly-proline motif have been associated with lower viral loads and presentation of protective HLA I-restricted epitopes. The major aims of this study were to (1) determine HIV-2 capsid intra-host evolutionary rates and (2) identify residues that are affected by positive selection and that can be linked to HIV-2 viral load and disease progression in conjunction with TRIM5 genotype. The Guinea-Bissau Police cohort is unique, with decades of relatively frequent follow-up. One hundred and sixty-five patients were included for genotyping of TRIM5, 62 females and 103 males. Median age at enrolment was 52.6 years (range 30–87) and 7.9 per cent of patients had a CD4 percentage < 15 per cent at enrolment. Six of these individuals were included for amplification of HIV-2 capsid from longitudinally collected samples. Viral RNA was extracted from stored blood plasma samples and capsid of the circulating viral quasispecies was amplified, cloned, and sequenced, as previously described. Bayesian analysis will be used to determine intra-host evolutionary rates, dN/dS ratios and how these parameters associate with disease progression and TRIM5 genotype.
A29 Genetic heterogeneity of influenza A (H3N2) viruses in the United Kingdom, 2016–8
Authors: Galiano M , Miah S , Akinbami O , Gonzalez Gonoggia S , Ellis J , Zambon M
Published: August 2019

For the last four influenza seasons in the UK, genetic characterization of seasonal influenza viruses has shifted from single hemagglutinin (HA) and neuraminidase (NA) genes to whole genome (WG) analysis, allowing for better insight into the evolutionary dynamics of this virus. Sequences (WG or HA/NA) were obtained from >900A (H3N2) viruses sampled in the UK during influenza seasons 2016/7 and 2017/8 and the inter-seasonal period. Viral RNA was extracted from clinical samples and amplified using a multi-segment RT-PCR. Amplicons were sequenced using Nextera library preparation for Illumina MiSeq sequencing. Sequence data ????were processed using BAM-SAM tools and PHE in-house scripts. Phylogenetic analysis of the HA gene indicates that they belong to genetic group 3C.2a, which has circulated since 2014. Season 2016/7 was characterized by the emergence of cluster 3C.2a.1; further genetic heterogeneity was seen with 6 new subclusters within 3C.2a and 3C.2a.1, with predominance of those characterized by amino acid changes N121K and S144K (3C.2a) and N121K, N171K, I406K, G484E (3C.2a.1). The NA genes clustered with a similar topology to the HA. Season 2017/8 was characterized by persistence of some clades from previous season with further diversification. Three of the 3C.2a clusters continued to circulate, with predominance of clade showing T131K, R142K, and R261Q (clade 3C.2a.2). The majority of HA sequences in 3C.2a1 fall into a new subcluster which has become predominant within this subgroup, with amino acid changes E62G, K92R, and T135K (3C.2a.1b). The topology of NA and internal gene trees showed evidence of reassortment events occurring at some point between the two seasons, with group 3C.2a2 acquiring NA and some internal genes from 3C.2a1 lineage viruses. The predominance of this group during 2017–8 might be due to fitness advantage related to the new genetic constellation. Emerging viruses from group 3C.3a also have acquired genes from lineage 3C.2a1, which could be the reason for their increased frequency to 20 per cent by the end of season 2017–8. Molecular epidemiology indicates emerging genetic diversity in A(H3N2) viruses during the period of study, leading to co-circulation of variants. The frequency of circulating HA genetic groups was quite variable, with rapidly changing patterns of predominance. Evidence of reassortment events was observed which could be responsible for the rise and predominance of some clades, and might predict the emergence of other variants.
A35 The first laboratory confirmation of chikungunya outbreak in Ethiopia
Authors: Mengesha Tsegaye Mesfin , Tayachew Aadamu , Belay Desalegn , Alemu Abebe , Beyene Berhane
Published: August 2019

Chikungunya is a viral disease (genus Alphavirus) which is transmitted to humans by infected mosquitoes—including Aedes aegypti and A. albopictus. An outbreak of febrile illness, suspected to have been caused by chikungunya, was reported in June 2016 from Dolloado district, Suuf Kebele, in the Somalia regional state of Ethiopia that borders the Mandera county of Kenya where a confirmed chikungunya outbreak was ongoing. Laboratory investigation was carried out to confirm if the outbreak in Ethiopia was caused by Chikungunya virus. Ten serum samples were collected from suspected patients visiting a health center in Suuf Kebel, who were then sent to the Nation laboratory in Ethiopian Public Health Institute. RNA was extracted from the serum samples using QIAgene RNA Mini kit, and PCR detection of dengue, chikungunya, and Zika virus nucleic acid was done using Trioplex Real-time RT-PCR Assay following the protocol from the Center for Disease Control (CDC). The Trioplex Real-time RT-PCR assay, for detection and differentiation of RNA from dengue, Chikungunya and Zika, was provided by CDC as part of the zika emergency preparedness effort. Of the nine samples tested, eight (88.88%) were found to be positive for chikungunya virus nucleic acid but negative for dengue and Zika virus nucleic acids. The median age of the affected sampled patients was 40 years, and males appear to be more affected (66.6% of sampled patients). The laboratory investigation confirmed that the outbreak was caused by chikungunya virus. Even though further molecular characterization of the positive isolates will provide more information as to the circulating genotypes and elucidate the origin of the outbreak virus, it is also possible to assume that the outbreak was an extension of the outbreak in neighboring countries in Kenya and, therefore, warrants that cross-border integration efforts to control chikungunya should be implemented by the concerned countries.
A39 Reconstruction of Ebola chains of transmission using sequence and epidemiological data
Authors: Robert A , Edmunds J , Eggo R , Henao-Restrepo A -M , Gsell P -S , Watson C H , Longini I M , Rambaut A , Camacho A , Hué S
Published: August 2019

Transmission trees can be established through detailed contact histories, statistical inference, phylogenetic inference, or a combination of methods. Each method has its limitations, and the extent to which they succeed in revealing a ‘true’ transmission history remains unclear. Moreover, the net value of pathogen sequencing in transmission tree reconstruction is yet to be assessed. We explored the accuracy and sensitivity to biases of a range of methods for transmission chain inference. We studied eight transmission chains determined by contact tracing, each one having more than a third of its cases sequenced (87 samples over 199 cases in total). We compared three inference methods on the selected transmission chains: (i) phylogenetic inference: the Ebola virus (EBOV) sequences derived from patients were mapped onto a dated EBOV phylogeny tree including 398 EBOV sequences sampled in Guinea between March 2014 and October 2015; (ii) statistical inference: we used the maximum likelihood framework developed by Wallinga and Teunis to infer the most likely transmitter-recipient relationships from the onset dates; (iii) combined method: we inferred probabilistic transmission events using both pathogen sequences and collection dates with the R package Outbreaker2. The cases coming from each transmission chain were mostly clustered together in the phylogenetic tree. The few misclassified cases were most likely allocated to the wrong chains of transmission because of the timing of their symptom onsets. Probabilistic transmission tree using only onset dates broadly matched the contact tracing data, but multiple potential infectors were identified for each case. The combined method showed that an a priori knowledge of the number of independent imports had an important impact on the outcome. Although cases were allocated to the correct transmission chains, discrepancies were found in identifying direct case linkage and transmission generations within a chain. Phylogenetic, epidemiological, and combined approaches for transmission chain reconstructions globally concurred in their output. Sequence data proved useful (if not necessary) to place the sampled cases in a wider context, identify transmission clusters, and misclassified cases when epidemiological chains are inferred from date of symptom onset only, and to identify links between supposedly independent chains of transmission.
A42 Next-generation sequencing to analyze multiple-strain infections, genotype distribution, and antiviral resistance in hematopoietic stem cell transplantation recipients with human cytomegalovirus infection
Authors: Dhingra A , Suárez N , Varanasi P , Zischke J , Heim A , Mischak-Weissinger E , Schulz T , Davison A , Kay-Fedorov P , Ganzenmueller T
Published: August 2019

Next-generation sequencing (NGS) produces comprehensive insights across the entire genome of the human cytomegalovirus (HCMV), which is an important opportunistic pathogen following hematopoietic stem cell transplantation (HSCT). To assess the clinical impact of HCMV diversity, genotype distribution, and resistance mutations, we performed NGS directly on plasma specimens from HSCT recipients with HCMV reactivation. Twenty-nine HCMV-positive plasma samples (median viral load 1.7 × 103 IU/ml) collected from a prospective allogenic HSCT recipient cohort (n = 16) between 21 and 80 days after transplantation were sequenced on an Illumina MiSeq after preparation of target-enriched sequencing libraries. Consensus HCMV genome sequences were assembled for 24 samples. The presence of multiple-strain infections and antiviral resistance mutations in genes UL54 and UL97 was determined by variant analysis. Genotype distribution was determined by specific marker analysis of several hypervariable genes (RL5A, RL6, RL12, RL13, UL1, UL9, UL11, UL73, UL74, UL120, UL146, and UL139). Associations between genomic and clinical features (e.g. graft-versus-host disease (GvHD), donor/recipient HCMV serostatus, dynamics of HCMV antigenemia, survival) were explored. Multiple infections involving up to 3 HCMV strains were detected in seven out of sixteen patients, with one patient analyzed at > 2 time points, showing a switch of the dominant HCMV population. No known antiviral resistance mutations were detected, which may be expected due to sample collection early after HSCT from patients without antiviral prophylaxis. Multiple-strain infection was associated with an earlier peak of HCMV-antigenemia (P = 0.054), but not with duration of viremia, antigenemia peak values, donor/recipient HCMV serostatus, T-cell depletion, acute or chronic GvHD, disease relapse, or reduced survival. Genotype distribution analysis revealed a potential link of one genotype of the immunomodulatory gene UL11 with GvHD incidence after HCMV reactivation. NGS of HCMV diversity directly from plasma samples, even with low viral loads, enables the acquisition of data of potential clinical interest. To identify reliable associations between clinical features and HCMV diversity, further patient cohorts with suitable sample sizes are required.
A57 An evolutionary framework to guide the hunt for human dsDNA viruses
Authors: Aghebatrafat A , Merkel K , Leendertz F , Krüger D H , Calvignac-Spencer S
Published: August 2019

It is becoming increasingly obvious that we only know a fraction of the human virome. The development of next-generation sequencing (NGS) technologies has dramatically increased our ability to hunt viruses. Yet, the small genomes and low copy numbers characteristic of most viruses make undirected (shotgun) hunts a relatively inefficient strategy. Here, we propose to speed-up the rate of double-stranded DNA (dsDNA) virus discovery by combining NGS with evolutionary thinking. dsDNA viruses are thought to have co-diverged with their hosts. As this applies to the hominine lineages (gorillas, humans, chimpanzees, and bonobos), it is theoretically possible to estimate the phylogenetic position of cryptic human viruses by identifying co-divergent viral lineages infecting non-human hominines. Where these lineages do not comprise a human-infecting counterpart, a yet-unknown human virus may be hiding. The first phase of this project will consist in the high-throughput characterization of dsDNA viruses (herpesviruses, papillomaviruses, and polyomaviruses) infecting wild gorillas, chimpanzees, and bonobos. For this, we will use an exhaustive collection of fecal samples (in terms of hominine species/sub-species diversity) and apply a discovery strategy combining in-solution capture and NGS. This strategy has been developed in the ancient DNA field but has a very broad applicability; it will constitute a nice addendum to the institute technical portfolio. Thanks to the massive amount of information collected, we will be able to reconstruct the evolutionary history of many dsDNA virus lineages and to identify those where a human virus would be expected but is still unknown. This will pave the way to the second phase of the project which will consist in a pre-oriented dsDNA human virus hunt based on the use of specific PCR systems implemented in multiplex. We expect that this project will generate an unprecedented amount of data on the processes at play along dsDNA virus evolution (co-divergence versus cross-species transmission), help determine the directionality, frequency, and timing of cross-species transmission events between hominines and unveil the existence of yet-to-be-discovered human viruses.
A61 Large RNA genomes: Is RNA polymerase fidelity enough?
Authors: Ferron F , Canard B
Published: August 2019

Large-genome Nidoviruses and Nidovirus-like viruses reside at the current boundary of largest RNA genome sizes. They code for an unusually large number of gene products matching that of small DNA viruses (e.g. DNA bacteriophages). The order of appearance and distribution of enzyme genes along various virus families (e.g. helicase and ExoN) may be seen as an evolutionary marker in these large RNA genomes lying at the genome size boundary. A positive correlation exists between (+)RNA virus genome sizes and the presence of the RNA helicase and the ExoN domains. Although the mechanistic basis of the presence of the helicase is still unclear, the role of the ExoN activity has been linked to the existence of an RNA synthesis proofreading system. In large Nidovirales, ExoN is bound to a processive replicative RNA-dependent RNA polymerase (RdRp) and corrects mismatched bases during viral RNA synthesis. Over the last decade, a view of the overall process has been refined in Coronaviruses, and in particular in our lab (Ferron et al., PNAS, 2018). We have identified genetic markers of large RNA genomes that we wish to use to data-mine currently existing metagenomic datasets. We have also initiated a collaboration to sequence and explore new viromes that will be searched according to these criteria. Likewise, we have a collection of purified viral RdRps that are currently being used to generate RNA synthesis products that will be compared to existing NGS datasets of cognate viruses. We will be able to have an idea about how much genetic diversity is possibly achievable by viral RdRp (‘tunable fidelity’) versus the detectable diversity (i.e. after selection in the infected cell) that is actually produced.
A65 Characterization of endolysin gene of bacteriophages infecting Listeria spp. isolated from dairy industry wastewater
Authors: Fernández Blanco , Barrios M E , Cammarata R V , Torres C , Mbayed V A
Published: August 2019

Bacteriophages and their endolysins, enzymes that degrade the cell walls of bacteria, are emerging as alternative tools to detect and inhibit growth of pathogen bacteria. Listeria monocytogenes is a foodborne pathogen that causes listeriosis, a serious invasive disease that affects both humans and a wide range of animals. Listeria spp. are ubiquitous in the dairy farm environment and could be present in dairy-processing plants and wastewater. All Listeria-specific bacteriophages found to date are members of the Caudovirales, of the Siphoviridae or Myoviridae families. Myophages infecting Listeria have been recently classified by the ICTV in the Spounavirinae subfamily, as well as in the P100 virus genus. The aim of this work was to isolate Listeria spp. bacteriophages and their endolysin codifying genes from wastewater of a dairy industry. Wastewater with and without treatment was sampled during the course of a year, and isolation of bacteriophages was performed after an enrichment step using as hosts L. innocua, L. ivanovii, and L. monocytogenes serotypes 1/2a, 1/2b, and 4b. Bacteriophages infecting L. innocua and L. ivanovii were isolated (n = 24) from 3 out of 12 samples. Bacteriophages were purified, and the host range was determined using spot test and EOP against five collection strains and several field isolates of Listeria spp. Two bacteriophages of narrow and broad host range, vB_Lino_VEfB7, and vB_Liva_VAfA18, were selected for further characterization. High titer stocks of bacteriophages were purified by centrifugation with ammonium acetate, and morphological information on the purified bacteriophages was obtained by negative staining and transmission electronic microscopy. Their morphology, size, and contractile tails indicated that these bacteriophages belonged to the Myoviridae family. Bacteriophage genomes were extracted using phenol-chloroform, followed by ethanol precipitation, and tested by digestion with RNAsa A and DNAse I. RFLP was performed, digesting genomes with restriction enzymes HindIII and NcoI. Consistent with the morphological findings, bacteriophages contained dsDNA genomes but showed different RFLP patterns. A PCR designed to amplify conserved domains of endolysins—PGRP and CwlA—was applied to characterize this gene. Another PCR was designed to amplify the complete endolysin gene, and the complete sequence of this gene was obtained and analyzed. Substitution model selection and a maximum likelihood phylogenetic tree of the endolysin gene was carried out using IQ-Tree software. The sequences of the endolysin gene indicated that the codified enzyme is an N-acetyl-muramoyl-L-alanine amidase, related to A511 and P100 species of the recently described P100virus genus. Further evolutionary analyses are needed to evaluate their belonging to this species or their taxonomy within this genus.
Is Treetop Skidding Effective in Reducing Fuel Loading?
Authors: Tesch Steven D. , Lysne David H.
Published: August 2019

In an attempt to reduce fuel loading during commercial thinning in a mixed-conifer forest, treetops were left attached to logs that were skidded to a landing for bucking and top disposal. Designated skidtrails were used to minimize residual stand damage and soil compaction. In a comparison with conventional logging procedures, treetop skidding did not decrease skidding productivity or increase damage to residual crop trees, but neither did it significantly reduce fuels. Whole-tree skidding, which would remove lower limbs, may be necessary to reduce unacceptable fire hazard. West. J. Appl. For. 1:13-15, Jan. 1986
Potential for Expansion of the Special Forest Products Industry in the Northern Rockies
Authors: Schlosser William E. , Blatner Keith A. , Schuster Ervin G. , Carroll Matthew S.
Published: August 2019

The special forest products industry has the potential of making substantial contributions to the troubled forest-based economies of the Northern Rockies. Comprised of floral greens, Christmas ornamentals, wild edible mushrooms, other edibles and medicinals, and Pacific yew segments, the industry has the potential to provide both full-time and part-time employment on a nearly year-round basis. The region's natural resource base and available labor supply seem well-suited to developing special forest products firms. The existing transportation system and business environment is also well suited to expansion of this industry. West. J. Appl. For. 10(4):138-143.
The Role of Uneven-Aged Silviculture in the Context of Ecosystem Management
Authors: Guldin James M.
Published: August 2019

The role of uneven-aged silviculture in an ecosystem management context is established using three elements. A review of succession and disturbance theory establishes an ecological basis for the method. The economic and social basis for the method is derived from comparisons of yields and economics, and discussion of social aspects. The adaptive management context is developed by reviewing four classic case studies, drawing on past successes and failures of the method. Overall the case is made that widespread application of uneven-aged silviculture under ecosystem management carries both potential and risk, and that the trade-offs expand rather than limit future silvicultural options. West. J. Appl. For. 11(1):4-12.
Stem Characteristics on the Lower Log of 35-Year-Old Western Redcedar Grown at Several Spacings
Authors: DeBell Jeffrey D. , Gartner Barbara L.
Published: August 2019

Information on stem characteristics of western redcedar (Thuja plicata) grown in managed stands is quite limited. Stem characteristics are important because they influence the quality of logs and lumber produced. We measured branch diameter, number of branches, taper, and fluting severity on the first 5m log of stems grown at spacings of 1.8 to 4.6 m in a 35-yr-old spacing trial on the University of British Columbia Research Forest. Average branch diameter increased from 15 mm to 25 mm as tree spacing increased from 1.8 m to 4.6 m. Number of branches per unit of stem length was unaffected by spacing. Trees at wider spacings tended to be more tapered and have more butt swell than those at narrower spacings. At wider spacings, more trees showed fluting, and that fluting was more severe than at narrower spacings. However, most trees had no fluting or only mild fluting even at the 4.6 m spacing. Branch diameter, taper, and fluting were all related to stem diameter. Smaller diameter stems tended to have smaller branches, less taper, and were less likely to have severe fluting than large diameter stems. Branch diameter was larger at wider spacings even for trees of the same stem diameter. West. J. Appl. For. 12(1):9-14.
Response of Pacific Yew (Taxus brevifolia) to Partial Removal of the Overstory
Authors: Bailey J. D. , Liegel L. H.
Published: August 2019

Growth response of Pacific yew (Taxus brevifolia) to canopy disturbance or partial removal is undocumented. Ten year radial increment growth was determined from cores of yew stems in adjacent intact and partially harvested stands of Douglas-fir (Pseudotsuga menziesii) in the central Oregon Cascades. The harvested stand had approximately half of its overstory trees removed in 1978. In the intact stand, 10 yr growth increment after 1978 averaged 0.9 mm less than the pre-1978 increment; in the partially harvested stand, the post-1978 10 yr increment averaged 4.7 mm more than the earlier one. This case study in the response of Pacific yew growth rate to partial overstory removal suggests that managers can preferentially retain these trees in select areas to encourage older forest characteristics or supplies for medicinal products. West. J. Appl. For. 12(2):41-43.
Bunny Hops or Vegetable Tunnels? Perceptions and Preferences of Mountain Bike Riders on the San Jacinto Ranger District
Authors: Chavez Deborah J.
Published: August 2019

To investigate mountain bike use on the San Jacinto Ranger District in southern California, mountain bike riders were queried using a mailed survey process. The objectives were to develop a socio-demographic profile of mountain bike riders; profile their activity patterns; and describe user perceptions related to mountain bike use in general and specifically to the region. This information was to be used in developing a regional mountain biking plan. Most respondents were male, about 34 years of age, and had some college education. They were active recreationists yet were committed to the sport of mountain bike riding. Trails were thought to have acceptable numbers of users and amounts of physical impacts. The respondents believed that they should share trails with other users and follow rules of etiquette. The regional biking plan should include little by way of site amenities. Few differences existed between more and less experienced riders. West. J. Appl. For. 12(2):44-48.
Use of Artificially Created Douglas-Fir Snags by Cavity-Nesting Birds
Authors: Chambers Carol L. , Carrigan Tara , Sabin Thomas E. , Tappeiner John , McComb William C.
Published: August 2019

In western Oregon, we created snags by sawing tops off live Douglas-fir (Pseudotsuga menziesii) (n = 821) trees and monitored their condition and use by cavity-nesting birds. We created snags in three silvicultural treatments: modified clearcut stands, two-story stands, and small-patchgroup-selection stands. We used two snag patterns: clumped and scattered. Created snags averaged 3.8/ha in density, 17 m in height, and 75 cm in diameter. Chainsaw-topped snags were used by cavity nesters within 5 yr of creation. Abundance of excavated cavities increased in all silvicultural treatments (P = 0.0001) and was higher in two-story and clearcut stands than in small-patch stands (P ≤ 0.0004). We did not, however, find that snag pattern (clumped v. scattered) affected use by cavity-nesting birds based on abundance of excavated cavities (P > 0.6). We observed excavated cavities in five hardwood species indicating that hardwoods represented an important resource for cavity-nesting birds. Creating conifer snags by topping and retaining hardwoods may retain or increase populations of cavity nesters in areas with low natural snag density. West. J. Appl. For. 12(3):93-97.
Minimizing the Rounding Error from Point Sample Estimates of Tree Frequencies
Authors: Ritchie Martin W.
Published: August 2019

Three solutions are presented for estimating stems per acre when trees are tallied by diameter class with horizontal point sampling. The first solution is based on the arithmetic mean of the diameter-class limits. The second is based on the geometric mean of the diameter-class limits and is unbiased for uniform within-class diameter distributions. The third is a harmonic mean solution; it is derived from the ratio of the geometric mean squared and the arithmetic mean. If the within-class distribution is linear, then the solution based on the geometric mean is preferable. Any of these solutions may be adequate provided diameter-class widths are minimized, particularly for small trees. The geometric-mean solution is the recommended solution in instances where uniformity can be assumed within diameter classes. Observed frequencies in two stands, however, provided inconsistent results.

In estimating tree frequency, errors resulting from grouping become smaller as tree diameter increases. For large trees, estimation of frequency can be obtained with much wider diameter limits than with small trees for a fixed level of grouping error. Rather than fixing diameter-class width, it may be advantageous to consider a narrower class width or exact measurement for trees in smaller diameter classes. West. J. Appl. For. 12(4):108-114.
Evaluating the Association Among Alternative Measures of Cumulative Watershed Effects on a Forested Watershed in Eastern Oregon
Authors: Bettinger Peter , Johnson K. Norman , Sessions John
Published: August 2019

The national forests must address cumulative effects in planning, including cumulative effects on streams and watersheds. This analysis compares predictions of a commonly used index of landscape use [equivalent clearcut acres (ECA)] with predictions of two indices of aquatic habitat quality (stream sediment and stream temperature) and estimated timber harvest levels to test the degree of association over a 100 yr planning horizon. We found significant negative association between predicted ECA and stream temperature index levels. No significant association was observed among all other combinations of predicted variables. All four indices (stream sediment, stream temperature, ECA, timber harvest levels) were evaluated using a different set of spatial and nonspatial data, thus variation in one index did not necessarily imply that a corresponding positive (or negative) variation in another would occur. We concluded that different relationships among these indices may be observed, depending on how a planning problem is formulated. Therefore, predicted ECA levels may not be a good proxy for predicted stream sediment and temperature levels (or vice versa). Finally, we cannot say that the stream sediment index (or temperature index) used here is a good proxy for actual sediment delivery or transport levels (or temperature levels), because the relationship between predicted values and actual field measurements was not investigated. West. J. Appl. For. 13(1):15-22.
Pruning Western White Pine in British Columbia to Reduce White Pine Blister Rust Losses: 10-Year Results
Authors: Hunt R. S.
Published: August 2019

Survey lines were located in areas that had been pruned to control blister rust (Cronartium ribicola) 10 yr previously and adjacent control (unpruned) areas in 10 stands of western white pine. Stands were classified as densely stocked, moderately stocked, or open. Cankers were tallied and their position noted. The success of pruning varied from stand to stand. Since the stands had not been pruned at an early age, there was only a 4 and 5% reduction in threatening cankers and stem cankers respectively, as few new cankers were initiated. Stands with the greatest increase in cankering had Ribes spp., were open grown, or possessed a high component of small white pine. Repruning these specific stands may be worthwhile, but in general, entering stands again to do either pruning or scribing would produce few additional healthy trees. Doing both treatments, however, may significantly enhance the number of healthy stems. To optimize the benefits of pruning, stands should be entered early and pruning should continue until a sufficient number of stems are pruned to a height of 3 m to ensure full stocking. Other species may be impediments to spore movement within stands, and thus they should not be pruned. Dense stands initially had less rust than open stands and could be entered later, but once spaced, they also need to be pruned to 3 m to minimize rust infection. West. J. Appl. For: 13(2):60-63.
Creating Snags and Wildlife Trees in Commercial Forest Landscapes
Authors: Lewis Jeffrey C.
Published: August 2019

Conversion of original older forests to second-growth stands has resulted in the loss of snag and wildlife tree habitat in the Pacific Northwest. Because many species require these habitat features, habitat managers have attempted to create snags and wildlife trees. From written contracts and contractor interviews, I summarized information about currently used snag and wildlife tree creation techniques including operation specifications, cost-effectiveness, safety considerations, and numbers of trees created. Removing the top of a tree with a chainsaw (~$35 per tree) or explosives (~$45 per tree) was commonly used to create snags and wildlife trees. Girdling in or near the base of the crown ($20-30 per tree) has also been used extensively. Cavity creation ($34-50 per tree), fungal inoculation ($23-33 per tree), and limbing (~$32 per tree) have been used to create or enhance snags and wildlife trees and cost less when used in conjunction with topping or girdling. These techniques have shown some success at providing suitable habitat for cavity- and snag-using wildlife; however, they have been used with the assumption that they will be successful. More in-depth research and monitoring are required to assess their effectiveness at meeting wildlife-habitat and forestry objectives. West. J. Appl. For. 13(3):97-101.
Effect of Plot Size on Estimates of Top Height in Douglas-Fir
Authors: Magnussen Steen
Published: August 2019

Top height is frequently used to estimate site quality and growth potential of forest stands. Top height estimates are quantile estimators and thus sensitive to scaling. If top height is defined as the height of the largest dbh tree per 0.01 ha of area, then it follows that any estimate based on ntop trees in a ntop · 0.01 plot will be a function of ntop, the distribution of dbh values, and the height-diameter relationship of the stand. This study quantifies for second-growth Douglas-fir (Pseudotsuga menziesii) stands along the west coast of British Columbia top height estimates derived from plots of size 0.01, 0.03, 0.05, and 1.0 ha. A pool of 635 permanent and remeasured sample plots allowed the estimation of expected stand-level diameter distributions (Weibull) and height-diameter relationships. Simulated sampling from these distributions quantified the impact of plot size. Top height, derived from plots of 0.01 ha, 0.03 ha and 0.05 ha were 5.6%, 3.0%, and 2.5% lower, respectively, than the estimates based on 1.0 ha plots. Yield predictions based on top heights from 0.01 ha plots were, on average, 8% lower than predictions from 1.0 ha plots. Three of four top height predictions based on 0.01 ha plots were significantly (P < 0.05) lower than predictions from a 1.0 ha plot. West. J. Appl. For. 14(1):17-27.
A Decision System for Assessing Stand Differentiation Potential and Prioritizing Precommercial Thinning Treatments
Authors: O'Hara Kevin L. , Oliver Chadwick D.
Published: August 2019

A decision support system was developed to prioritize diverse young stands for precommercial thinning treatments. This system utilizes variables to characterize stand structure and assess the potential for stand differentiation. Stands with greater differentiation potential are considered a low priority for precommercial thinning because of their lower susceptibility to insects and diseases, greater windfirmness, options for future treatments, and faster stand growth rates as compared to stands with less differentiation potential. Key variables include mixed-species stratification patterns, live-crown ratio, variability in heights of crop trees, and number of trees/ac. These variables were organized in a decision key to provide a logical and efficient system to assist land managers in making precommercial thinning decisions. The decision key prioritizes stands for precommercial thinning over a wide range of environmental conditions on a common scale. West. J. Appl. For. 14(1):7-13.
Estimating Extent of Mortality Associated with the Douglas-fir Beetle in the Central and Northern Rockies
Authors: Negron Jose F. , Schaupp Willis C. , Gibson Kenneth E. , Anhold John , Hansen Dawn , Their Ralph , Mocettini Phil
Published: August 2019

Data collected from Douglas-fir (Pseudotsuga menziesii) stands infested by the Douglas-fir beetle (Dendroctonus pseudotsugae) in Wyoming, Montana, Idaho, and Utah, were used to develop models to estimate amount of mortality in terms of basal area killed. Models were built using stepwise linear regression and regression tree approaches. Linear regression models using initial Douglas-fir basal area were built for all study sites but produce low precision estimates. Regression tree models using initial Douglas-fir basal area or stand density index or both were also built for all sites. Regression tree models provide a more realistic approach to estimate potential mortality by creating more homogenous mortality classes with reduced variance. The models developed provide land managers with a basis for determining the potential mortality should a Douglas-fir beetle outbreak develop. West. J. Appl. For. 14(3):121-127.
Rapid Assessment of Risk Using Stand Density Indices
Authors: Ducey Mark J. , Larson Bruce C.
Published: August 2019

When management decisions are based on a stand density measure, there is always a risk that sampling error will result in an incorrect management choice. Estimating confidence limits and associated probabilities for many popular stand density measures is computationally difficult, and can require information that is difficult to obtain in practice. Here, we present an alternative method for rapid assessment of risk that is applicable to Reineke's stand density index, Wilson's relative spacing, Drew and Fiewelling's relative density index, and Curtis's relative density. The method requires an independent estimate of stand density, for example, from a growth and yield model or from a subjective assessment before actual measurement. The results, while inexact, are both easier to obtain and more conservative than those obtained by exact methods. West. J. Appl. For. 14(3):149-152.
Reverse Technology Transfer: Obtaining Feedback from Managers
Authors: Carey Andrew B. , Calhoun John M. , Dick Bob , O'Halloran Kathy , Young Leonard S. , Bigley Richard E. , Chan Sam , Harrington Constance A. , Hayes John P. , Marzluff John
Published: August 2019

Forestry policy, planning, and practice have changed rapidly with implementation of ecosystem management by federal, state, tribal, and private organizations. Implementation entails new concepts, terminology, and management approaches. Yet there seems to have been little organized effort to obtain feedback from on-the-ground managers on the practicality of implementing ecosystem management. We convened a colloquium in Forks, WA, in 1997 to assess the state of ecosystem management. We used a recent interagency modeling exercise to formulate six concepts and questions to present to small working groups of practitioners and listening groups of a scientist, regulator, and conservation group member. Concepts and practices varied in a degree of development and sophistication; practitioners varied in sophistication and comfort with concepts. Many expressed dissatisfaction with new terminology they perceived as abstract and not operational. Research and technology transfer needs were identified. Organizational culture, structure, and centralization of decision making appeared to have influenced the creativity, systems thinking, and professional development of managers. Some practitioners, however, demonstrated narrow focus apparently arising from traditional disciplinary allegiances. Implications for organizations are discussed. West. J. Appl. For. 14(3):153-163.
Technical Note: White Pine Blister Rust, Root Disease, and Bears
Authors: Hunt Richard S.
Published: August 2019

Prior to harvest, nine root disease sites lacked any Ribes spp., but after harvest six supported Ribes spp. Surveys indicated that Ribes spp. and other berry plants were in greater abundance in root disease areas than in adjacently harvested areas. Seed deposition by bears and periodic flourishing in root disease areas are likely contributors to forest seed banks. On one site the blister rust incidence in white pines was 98% in the root disease area and 27% in the adjacent nonroot diseased area. The presence of root disease should be used to rank an area for high hazard potential to blister rust. West. J. Appl. For. 15(1)38-39.
A Comparison of the Economic Efficiency of Living and Artificial Snowfence Designs for Road Protection
Authors: Daigneault William , Betters David R.
Published: August 2019

Both artificial and living snowfences are used to protect roads from blowing and drifting snow. This article evaluates and compares the economic performance of three snowfence designs--the Wyoming and double-row slatted artificial snowfences and a three-row living snowfence. The economic analysis evaluates the snowfences by applying four economic performance indicators: total net benefits, present net value, benefit/cost ratio, and annual breakeven benefits. The study uses snow removal savings and accident reduction benefit information from a case study in the state of Wyoming. The case study results show all the designs are economically efficient when used for road protection. However, the living snowfence outperformed the other designs in three of the four economic performance indicator categories. The largest proportion of total costs of the Wyoming and living snowfence are establishment costs whereas the bulk of total cost of the double-row slatted snowfence is for maintenance. The economic performance of all the snowfences is most sensitive to changes in their useful or effective lives. The procedures and general conclusions of the study can be applied to similar cases elsewhere. West. J. Appl. For. 15(2):70-74.
Kozak's Variable-Exponent Taper Equation Regionalized for White Spruce in Alberta
Authors: Huang Shongming , Price Daryl , Morgan Dave , Peck Karl
Published: August 2019

Kozak's (1988) variable-exponent taper equation was estimated for white spruce by ecoregion of Alberta to reflect stem form variability among different ecoregions. Inspection of fit statistics and residual plots showed that the taper equation fitted the data quite well. Since the relative height constraint p had little impact on the overall performance of the taper equation, the optimum p value was estimated as a part of the nonlinear least squares procedures. Regional differences of the taper equation were examined and tested using the nonlinear extra sum of squares method. Ecoregions of similar taper relationships were combined to provide a composite equation. Performance of the taper equation in predicting diameter inside bark, total volume, and merchantable height was evaluated. Results indicated that the biases in predictions were small, both across different parts of the stem and for various tree sizes. West. J. Appl. For. 15(2):75-85.
Juvenile Height Development in Interior Spruce Stands of British Columbia
Authors: Nigh Gordon D. , Love Bobby A.
Published: August 2019

Good estimates of juvenile heights are important for silviculture and timber supply decision-making. These height estimates are particularly important for estimating the number of years it takes a stand to reach green-up and breast height. Thirty-nine 0.04 ha plots were established in managed juvenile stands of interior spruce in the Prince Rupert Forest Region. Four sample trees in each plot were split longitudinally and height-age data were obtained from the exposed pith nodes or branch whorls. The height-age data were fit to a combined exponential and power function to create a juvenile height model for interior spruce. This model is a function of age and site index. Years to breast height and green-up age models were developed with data generated from the juvenile height model. Forecasts from these models indicate that the time to reach breast height and green-up age is less than previously expected. The juvenile height model, years to breast height model, and green-up age model should be used for site indices above 14.2 m. In addition, the height model should only be used up to total age 20. West. J. Appl. For. 15(3):117-121.