bluuebunny/crossref_metadata_2025 huggingface dataset:
A15 Archived ART resistance in the latent reservoir of virally suppressed Ugandans
Authors: Capoferri A A , Lynch B A , Prodger J L , Reynolds S J , Kasule J , Serwadda D , Lamers S , Martens C , Quinn T C , Redd A D
Published: August 2019

The increased access of antiretroviral therapy (ART) has drastically improved the health of infected individuals. However, increased levels of ART resistance globally threaten ART effectiveness. Resistance monitoring is currently limited to viremic individuals or prior to ART initiation. The archival nature of the HIV latent reservoir (LR) of virally suppressed patients allows examination for the persistence of ART-resistant latent viral variants. Whole blood samples were collected longitudinally in Rakai, Uganda, from 70 virally suppressed HIV-1 infected individuals. The quantitative viral outgrowth assay was performed to measure the frequency of replication-competent latently infected resting-memory CD4 + (rCD4) T-cells. RNA was extracted from HIV p24-positive outgrowth supernatant, and the reverse transcriptase (RT) region was sequenced using a validated site-specific next-generation sequencing assay (Illumina, San Diego, CA). Consensus sequences containing >2.5 per cent of the total raw amplicons of each outgrowth well were analyzed for ART drug resistance mutations using the Stanford Database. The presence of clonal sequence is expressed as both percent clonality and Shannon Entropy. Replication-competent virus was cultured from 52/70 (74.3%) individuals, of which, RT-pol sequence data were obtained from 49/52 (94.3%) individuals. The presence of ART-resistant virus was found in the LR from one individual on second-line therapy that included a protease inhibitor. There were 20 and 44 total prominent consensus sequences from all wells at years 1 and 3 of follow-up, respectively. ART-resistant mutations for both RT-inhibitor drug classes were found in 30 per cent and 27.3 per cent of the total prominent consensus sequences of this one individual from years 1 and 3, respectively. The major ART resistance profile in this individual included: M184V, Y188L, K191E, and G190A. The percentage of total outgrowth that was clonal (percent clonality) increased from year 1 to year 3 (38.1–81.8%) and Shannon Entropy decreased (0.722–0.576). The presence of archived replication-competent ART-resistant virus in the LR was found in only one individual. There were two ART-resistant prominent consensus sequences isolated at year 3 that were not sampled 2 years earlier. The persistence of resistant, intact replication-competent proviral sequences in the LR of this individual seem to be supported by clonal expansion.
A25 Impact of polymorphism in the hepatitis B surface gene on human leukocyte antigen (HLA) class II
Authors: Choga W -T , Anderson M , Phinius B -B , Mbangiwa T , Bell T -G , Seatla K -K , Musonda R -M , Moyo S , Blackard J -T , Gaseitsiwe S
Published: August 2019

There is still no cure for chronic hepatitis B virus infection (CHBV), a major cause of liver cancers and related malignancies. Elucidating the role of CD4+ T-helper cells in activating immunological responses that clear antigenic peptides during primary HBV infection holds a potential strategy for developing potent vaccines. Since the strength of CD4+ T cell responses is dictated by binding of viral epitopes to class-II human leukocyte antigens (HLAs), we hypothesize that the quality of immunological responses in CHBV patients is influenced by host genetics and HBV genotypes. Here, ninety-two non-recombinant complete HBV surface-gene proteins (PreS1/S) from Botswana were sequenced (genotype A 44(47.8%); D 48(52.2%)) and 15-mer binding epitopes restricted to nine HLA-class II molecules (DRB5/1) were mapped in silico. The HLAs used have high population coverage in Botswana. The total predicted epitopes per HLA were 94-(genotype A) and 105-(genotype D) for PreS1, 42 (A and D) for PreS2, and 105 (A and D) for S. Epitope densities (binding peptides to total epitopes) were 3 per cent and 6 per cent (PreS1A&D), 4 per cent and 2 per cent (PreS2A&D), and 23 per cent and 22 per cent (S1A&D). SA&D proteins had most polytopes: CPGYRWMCLRRFII66-81, PGYRWMCLRRFIIF67-82, GYRWMCLRRFIIFL68-83, and YRWMCLRRFIIFLF69-84 binding to 5 (55.6%) HLAs (DRB1*0101/0701/1101/1501 and DRB5*0101) used. HLA-DRB*0101 bound the most epitopes, and the least were bound by HLA-DRB*0302/0701/0401 for both genotypes. PreS1D polytope: PAFRANTANPDWDFN32-46 binds to DRB1*0101/0401/1302 and PreS2 polytopes: TAFHQALQDPRVRG6-19 and AFHQALQDPRVRGL7-20 bind to DRB1*010/1501 alleles. Non-synonymous mutations impair peptide-HLA binding when assessed as combinations of > 2. The least active HLAs may be associated with CHBV and vice-versa for HBV clearance, thus the algorithm may be used to predict HBV prognosis for different haplotypes. The results favor the use of epitopes from S protein as broad genotype vaccine. This study highlights the need to explore further the mechanisms of PreS1 and its effect on the immune system.
A36 Analysis of CHIKV evolution during the Caribbean outbreak, 2013–5, using complete genome sequences
Authors: Hoornweg T E , Vennema H , Reimerink J H J
Published: August 2019

Chikungunya virus (CHIKV) is a re-emerging, mosquito-borne alphavirus that causes chikungunya fever, a febrile illness characterized by severe acute and persistent arthralgia. At the end of 2013, autochthonous CHIKV transmission was detected for the first time in the Americas, on the Caribbean island of Saint Martin. Subsequently, CHIKV rapidly spread through the Caribbean Islands and onto the American mainland, causing millions of cases of chikungunya fever. During the outbreak, the Dutch National Institute of Health performed diagnostics on patient samples originating from the six Caribbean islands that belong to the Kingdom of the Netherlands. Using a subset of PCR-positive patient samples, we aimed to retrospectively analyze the 2013–5 CHIKV outbreak on the Dutch Caribbean islands using whole-genome sequences. Twenty-five CHIKV-positive sera were selected for next-generation sequencing based on viral load, location, and date of sampling. Sera were subjected to high speed centrifugation, filtration, and nuclease treatment to reduce the amount of background sequences from human and bacterial origin. Total RNA was extracted, primed with random nanomers for reverse transcription, after which dsDNA was produced and purified. Libraries were created using Nextera XT library preparation kit, and samples were run on a MiSeq desktop sequencer. Reads were trimmed and mapped to a reference sequence using the CLC Genomics workbench. To date, eight full-genome sequences were obtained, originating from four different islands and dating from the start of the outbreak (December 2013) to April 2015, when the outbreak was waning. High similarity (>99%) between sequences was found; nevertheless, all genome sequences were unique with a minimum of three SNPs differentiating one sequence from another. Thirty-three unique single nucleotide polymorphisms (SNPs) were identified, of which 29 were located in the coding regions of the genome. Eight SNPs were informative, and ten SNPs led to amino acid changes. Of the amino acid changes, nine were located in the non-structural proteins (1× nsP1, 5× nsP2, and 3× nsP3), and one was located in E2. In conclusion, we report the first whole-genome sequences of CHIKV isolates from the 2013 to 2015 outbreak that originated from the Dutch Caribbean islands. Sequencing of the remaining samples is still in progress.
A38 Genomic epidemiology quantifies gaps in Aedes-borne virus transmission in the Americas
Authors: da Silva Cândido Darlan , Pybus Oliver G , Faria Nuno Rodrigues
Published: August 2019

The rapid spread and severity of pathogens, such as Zika (ZIKV) and Chikungunya (CHIKV) viruses in the Americas, demonstrate the need for a better understanding of when and where outbreaks emerge. Sequence evolution of these viral pathogens occurs simultaneously with geographic spread, which allows phylodynamic processes to be recovered from genomic data. Here, we used time-calibrated phylogeographic analyses implemented in a Bayesian phylogenetic framework to characterize the date of introduction of ZIKV, CHIKV, dengue, and yellow fever viruses in different geographic regions of the Americas. To estimate ‘surveillance gaps’, we compared the estimated dates of introduction of these pathogens to the first confirmations of virus circulation in the region. Datasets included all publicly available geo-referenced and time-stamped genetic data from the Americas. A series of environmental and ecological covariates will be tested to infer what factors are associated with the delayed detection of arbovirus transmission in each geographic region. These results will provide important information on where to concentrate surveillance strengthening measures in order to prevent future mosquito-borne virus epidemics.
A53 MERS-CoV in East African dromedary camels
Authors: Zhou Ziqi , Chu Daniel K W , Ali Abraham , Demissié Getnet F , Peiris Malik
Published: August 2019

Human Middle East respiratory syndrome is a zoonotic respiratory disease caused by Middle East respiratory syndrome coronavirus (MERS-CoV) originating from camels in the Arabian Peninsula. While there are a large number of camels in East Africa, often traded to the Arabian Peninsula, no autochthonous human MERS-CoV case is reported in East Africa. Furthermore, there is limited information of MERS-CoV in East Africa. In this study, MERS-CoV in dromedary camels from Ethiopia was detected using RT-qPCR. Next-generation sequencing was used to obtain the full genome of MERS-CoV. MERS-CoV antibodies were also detected through MERS-spike pseudoparticle neutralization assay. Phylogenetic analysis of full-genome sequences and spike-genome antibodies indicates that MERS-CoV in East Africa is genetically distinct from those in the Arabian Peninsula. The results from this study show that MERS-CoV circulating in dromedary camels in East Africa are genetically distinct from those in the Arabian Peninsula. Further studies are needed to evaluate the risk of zoonotic transmission in East Africa.
A59 A strategy to studying zoonotic infectious diseases
Authors: Anh P , Tam P , Tue N , Rabaa M , Thwaites G , Baker S
Published: August 2019

An increasing number of zoonotic viruses have been detected in animals, especially in poultry species. Understanding the diversity of zoonotic infections and the local behavior helps to characterize the pathogen diversity in human and animals and predict the risk of pathogen spill-over from animals to human. Vietnam is considered, along with other countries in Southeast Asia, as a hotspot for zoonotic viruses. In Vietnam, domestic animals are typically farmed in close proximity to humans, which may increase the risk of transmission of zoonotic pathogens. Our previous studies found the presence of some zoonotic viruses (e.g. rotavirus group A, hepatitis E virus) in domestic pigs. However, the risk of pathogenic transmission from domestic animals to humans has not been determined. Detailed genomic sequence data may help to track the origin and evolution of zoonotic pathogens. To understand the origins and emergence of zoonotic infections in people, who have regular contact with animals, we will investigate the viral diversity in farmers and domestic animals in their farm, using high-throughput sequencing technique. Viral RNA was extracted from pooled fecal samples of 30 farmers and 50 pigs, and used as input for SureSelect target enrichment and Illumina MiSeq sequencing.
A60 Revealing the evolution of virulence in RNA viruses
Authors: Escalera-Zamudio Marina , Gutiérrez Bernardo , Thézé Julien , Pybus Oliver G
Published: August 2019

A combination of high rates of mutation and replication, coupled with strong natural selection, ensures that RNA viruses experience rapid genotypic and phenotypic evolution. Such a ‘fast-forward’ evolution enables viruses to rapidly adapt to new host species, evade host immune responses, and to develop resistance to anti-viral drugs. Similarly, rapid evolution allows viruses to attain new levels of virulence, defined as the ability to cause severe disease in hosts. We hypothesize that distinct viral groups share genetic determinants that modulate virulence that have been acquired through convergent evolution. Thus, common patterns reflecting changing virulence-related specific viral groups could be detected. The main goals for this project are (1) to understand how genetic and phenotypic diversity can be generated among different viral groups by analyzing the variation patterns and determining the selective forces behind them (impact in viral fitness) and (2) to understand how fixed mutations can modulate virulence within different viral groups by performing comparison of strains with differing virulence within a longitudinal timescale. The subject of the study is key emerging and re-emerging virus families of medical importance. Such groups include: Coronaviridae (severe acute respiratory syndrome and Middle East respiratory syndrome-associated coronaviruses), Picornaviridae (Hepatitis A virus), Flaviviridae (Yellow fever, West Nile, Hepatitis C, Dengue, and Zika viruses), Togaviridae (Rubella and Chikungunya virus), Bornaviridae (Borna-disease virus), Filoviridae (Ebola and Marburg viruses), Paramyxoviridae (Measles, Nipah, and Hendra viruses), Rhabdoviridae (Lyssaviruses), Arenaviridae (Lassa virus), Bunyaviridae (Hanta- and Crimean-Congo hemorrhagic fever viruses), and Orthomyxoviridae (Influenza A viruses). Viral genomes collected at different time points, different hosts (human and their most closely related animal reservoirs) and different locations will be compiled. Extensive molecular evolutionary analyses will be carried out to infer gene expansion/contraction within groups, rates of evolution, and changes in selection pressure, including the detection of positive selected genes and sites (adaptive evolution). Positively selected sites will be mapped onto the viral protein structures to reveal their impact on function, and hence the location of potential virulence determinants. Virulence changes among particular viral strains and types will be defined and measured according to definitions based on an increase in: (1) transmissibility, (2) host tropism, (3) immune evasion, (4) morbidity and mortality, (5) drug resistance, and by the incorporation of epidemiological data to determine whether high or low virulence strains within different hosts and localities are spreading most efficiently in nature.
A64 Viral sequence classification using deep learning algorithms
Authors: Nieuwenhuijse David , Munnink Bas Oude , Phan My , Koopmans Marion
Published: August 2019

Sewage samples have a high potential benefit for surveillance of circulating pathogens because they are easy to obtain and reflect population-wide circulation of pathogens. These type of samples typically contain a great diversity of viruses. Therefore, one of the main challenges of metagenomic sequencing of sewage for surveillance is sequence annotation and interpretation. Especially for high-threat viruses, false positive signals can trigger unnecessary alerts, but true positives should not be missed. Annotation thus requires high sensitivity and specificity. To better interpret annotated reads for high-threat viruses, we attempt to determine how classifiable they are in a background of reads of closely related low-threat viruses. As an example, we attempted to distinguish poliovirus reads, a virus of high public health importance, from other enterovirus reads. A sequence-based deep learning algorithm was used to classify reads as either polio or non-polio enterovirus. Short reads were generated from 500 polio and 2,000 non-polio enterovirus genomes as a training set. By training the algorithm on this dataset we try to determine, on a single read level, which short reads can reliably be labeled as poliovirus and which cannot. After training the deep learning algorithm on the generated reads we were able to calculate the probability with which a read can be assigned to a poliovirus genome or a non-poliovirus genome. We show that the algorithm succeeds in classifying the reads with high accuracy. The probability of assigning the read to the correct class was related to the location in the genome to which the read mapped, which conformed with our expectations since some regions of the genome are more conserved than others. Classifying short reads of high-threat viral pathogens seems to be a promising application of sequence-based deep learning algorithms. Also, recent developments in software and hardware have facilitated the development and training of deep learning algorithms. Further plans of this work are to characterize the hard-to-classify regions of the poliovirus genome, build larger training databases, and expand on the current approach to other viruses.
A66 Tracing the evolutionary history of an emerging Salmonella 4,[5],12:i:- clone in the United States
Authors: Elnekave E , Hong S , Taylor A , Boxrud D , Rovira A , Alvarez J
Published: August 2019

Salmonellosis is one of the leading causes of foodborne disease worldwide, with an estimated one million cases a year in the United States. Salmonella 4,[5],12: i:-, a monophasic variant of Salmonella typhimurium, is an emerging serovar that has been associated with multiple foodborne outbreaks throughout the world, mostly attributed to pig and pig products. Recently, we have demonstrated that two distinct groups of Salmonella 4,[5],12:i:- circulate in the USA and Europe, with the majority of isolates recovered during recent years belonging to an emerging multidrug-resistant clade (Elnekave et al. 2018). We applied Bayesian phylodynamic reconstruction to uncover the evolutionary history of this clade. We used a dataset of whole-genome sequences of 1446 4,[5],12:i:- isolates from different sources (livestock, human, food products, and others) from the USA (n = 752) and Europe (n = 694), collected between 2008 and 2017 and belonging to the Multilocus Subtype 34, which was predominant in the emerging clade (Elnekave et al. 2018). A subset (n = 110) of Salmonella 4,[5],12:i: isolates was then randomly selected after stratifying by location and year of isolation in order to achieve balanced sampling. Evidence of temporal signal was confirmed by looking at root-to-tip divergences using TempEst. Evolutionary hypotheses using strict and relaxed-clock models were tested using BEAST for a variety of demographic models and assuming a general time reversible substitution model. Model selection was performed by estimating Bayes Factors using path sampling and stepping-stone sampling. The selected model was then used for applying discrete trait models comparing different scenarios of transmission between locations (i.e. bidirectional symmetric/asymmetric or unidirectional). Our preliminary phylodynamic inference results indicate that the origin of this subtype was in Europe and dates back to 1990 (HPD 95%: 1984–2001). We report an exponential growth rate of 0.362 per year, which corresponds to a doubling time of 1.43 years. Our results suggest that this subtype was introduced to the US in the year 2000 (HPD 95%: 1994–2006). Phylodynamic analysis suggests that the recent increase in isolation of Salmonella 4,[5],12:i:- from different sources in the USA may be due to the exponential expansion of an emerging clone which originated in Europe and then expanded to the USA. The emergence and expansion of this serovar is of great public health importance due to the high prevalence of multidrug resistance traits found in USA isolates from this group and especially due to the presence of plasmid-mediated resistance genes for quinolones and extended spectrum cephalosporins, key antimicrobials used for the treatment of invasive Salmonella infections.
Wildfire Patterns Change in Central Idaho's Ponderosa Pine-Douglas-fir Forest
Authors: Steele Robert , Arno Stephen F. , Geier-Hayes Katheleen
Published: August 2019

Study of long-term fire histories (from fire scars on old trees) helps determine if severe fires were characteristic of the ponderosa pine (Pinus ponderosa) forests in central Idaho before the arrival of Euroamericans. Before 1895, all sample sites had average fire intervals of 10 to 22 years, implying a pattern of light to moderate surface fire. After 1895, fire intervals lengthened considerably, and severe fires became relatively common. Factors apparently influencing this change were a reduction in uncontrolled fires started by American Indians and Euroamericans; heavy livestock grazing that removed fine fuels; establishment of a fire suppression program; accumulation of slash from early logging; and development of dense conifer understories (ladder fuels). Applications of prescribed burning might reduce the risk of severe wildfires. West. J. Appl. For. 1:16-18, Jan, 1986
Snag Requirements of Cavity-Nesting Birds: Are USDA Forest Service Guidelines Being Met?
Authors: Morrison Michael L. , Dedon Mark F. , Raphael Martin G. , Yoder-Williams Michael P.
Published: August 2019

USDA Forest Service guidelines for retention of standing dead trees were analyzed in the eastern Sierra Nevada by surveying snags and recording the use of snags for nesting by birds. Surveys showed the density of large, hard snags to be only about 25% of that required by the guidelines. Birds tended to nest in snags 30 to 40 cm or more dbh. The majority of snags, however, were less than 40 cm dbh. Our results indicate that current guidelines for retention of large snags are appropriate. Because these guidelines are not being met, however, the practice of removing snags for fuelwood or other purposes is questioned. West. J. Appl. For. 1:38-40, April 1986
Naturalization of Russian-Olive in the Western United States
Authors: Olson Thomas E. , Knopf Fritz L.
Published: August 2019

Since its introduction into the United States, Russian-olive (Elaeagnus angustifolia) has escaped cultivation at many locations. This exotic tree is now present in every western state, especially within riparian zones. The species has high value for wildlife, but can interfere with agricultural practices and has the potential to displace native riparian trees. West. J. Appl. For. 1:65-69, July 1986.
Effects of Soil Compaction on Height Growth of a California Ponderosa Pine Plantation
Authors: Helms J. A. , Hipkin C. , Alexander E. B.
Published: August 2019

An analysis was made of the extent to which observed variability in plantation height growth could be explained by variability in soil surface characteristics that are modified by harvesting and site preparation activities. The study was done in a 16-year-old ponderosa pine (Pinus ponderosa) plantation in the Sierra Nevada of California. Annual height growth of all 423 trees within a 0.48 ha area was measured together with soil bulk density, A-Horizon thickness, and shrub competition. Soil organic carbon and mineralizeable nitrogen were measured on a subsample of 72 trees. Trees in areas of highest bulk density grew 43% less at age 1 and 13% less at age 15 than those in areas of lowest bulk density. Annual shoot growth was markedly reduced for 4 consecutive years following 2 years of below-normal precipitation, especially in trees growing in soils of lowest bulk density. Bulk density, A-Horizon thickness, and shrub cover accounted for only 13 to 23% of variability in height growth of the 423-tree sample. These same variables, plus organic carbon and mineralizeable nitrogen, accounted for 31% of variability in height growth of the 72-tree sample. West. J. Appl. For. 1:104-108, Oct. 1986.
Towards Successful Forest Planning Through Locally Based Qualitative Sociology
Authors: Brandenburg Andrea M. , Carroll Matthew S. , Blatner Keith A.
Published: August 2019

Generations of public land managers have understood the political importance of direct contacts with a variety of constituents. This article argues for a more formal, systematic use of face to face interactions and information gathering as a means of achieving more socially acceptable resource management. West. J. Appl. For. 10(3):95-100.
Response Surface Analysis of Control of Red Alder and Vine Maple with Glyphosate-Imazapyr and Triclopyr-Imazapyr
Authors: Knowe Steven A. , Cole Elizabeth C. , Newton Michael
Published: August 2019

Quadratic response functions were demonstrated for predicting crown reduction of red alder (Alnus rubra) and vine maple (Acer circinatum) after application of the herbicides glyphosate and triclopyr in combinations with imazapyr. Relationships between crown reduction and the application dates and rates were explored with data from five experiments previously conducted in Oregon in order to estimate optimal timing and optimal rates for each herbicide. The best crown reduction with glyphosate-imazapyr was achieved in the Cascade Mountain foothills with June or July applications and in the Coast Range with August or September applications. Control of red alder was best with 0.05 to 0.09 lb (ae/ac) imazapyr; the additive effect of glyphosate rate was more important in July than in August applications. The optimum imazapyr rates for vine maple may be outside the range of rates included in the studies, and rainfall shortly after the July application compromised the results for one study. Compared to crown reduction of vine maple with the individual herbicides, the effect with glyphosate-imazapyr varied from none to slightly positive, and that with triclopyr-imazapyr from slightly negative to additive. The response model accounted for 69-88% of the observed variation in crown reduction of vine maple. The model for red alder accounted for 44% of the variation in crown reduction. West. J. Appl. For. 10(4):127-132.
Augering and Fertilization Stimulate Growth of Blue Oak Seedlings Planted from Acorns but not from Containers
Authors: McCreary Douglas D.
Published: August 2019

Blue oak (Quercus douglasii), a widely distributed species in California, is reported to be regenerating poorly in portions of the state. To ensure this species can sustain itself, successful artificial regeneration strategies are needed. Two separate studies evaluated the effects of augering and fertilization on the field performance of direct seeded acorns and P+0 container seedlings. In each study, 30 planting spots were established for each of the 8 combinations of fertilization (none and a 21 g slow release tablet) and augering (0, 30, 60, and 90 cm). Field response was evaluated for 4 yr. Fertilization significantly increased the growth of direct seeded acorns, but not of transplanted seedlings. Augering had a similar, but less pronounced positive effect—but again, only for the acorns. For all treatments, acorns tended to grow better than transplants. These results suggest that blue oak can be successfully established by planting acorns, and that both augering and fertilization can enhance field performance. West. J. Appl. For. 10(4):133-137.
Monitoring Timber Harvest Impacts on Stream Sedimentation: Instream vs. Upslope Methods
Authors: Corner Richard A. , Bassman John H. , Moore Barry C.
Published: August 2019

There is increasing pressure on forest managers and natural resource professionals to measure, monitor, and evaluate stream sediment production from timber harvest activities. However, the great expense of instream sediment monitoring severely limits the number of monitoring projects which can be undertaken and has hindered the development of regulations to maintain water quality. The purpose of this study was to compare instream vs. upslope monitoring on three experimental clearcuts in northeast Washington State.

The up slope monitoring approach tested in this study appeared to circumvent most problems associated with instream monitoring and provided a clear physical linkage between measurements and on-site processes. However, on-site observations indicated that important sedimentation event were unaccounted for by both instream and upslope monitoring. It was concluded that qualitative observations can also be important tools for monitoring the effects of forest management activities on sediment production and delivery. West. J. Appl. For. 11(1):25-32.
Estimating the Number of Filled Seeds per Cone of Western Hemlock from Coastal British Columbia
Authors: Meagher M. D.
Published: August 2019

Unopened western hemlock (Tsuga heterophylla) cones from coastal British Columbia were tested for the relationship between total filled seeds per cone and the number of sound seeds exposed by slicing through the center of the cone's long axis, and with cone length. Predictive linear relationships of total number of filled seeds per cone (TFS), based on number of filled seeds cut on the face through the cone's long axis (CC), were found in a cone sample bulked from a number of trees. The regression based on CC explained about 63% of the variation in TFS. More accurate estimates of TFS were found where cone length, and exponential factors of CC and cone length, were included in the analysis. Analyses of cones from seven parents did not find statistically significant trends of TFS on CC in all cases, and differed in slope in most cases. Sample sizes (cones) to estimate TFS to a predetermined level of precision were much larger than cones needed to accept or reject a tree for study. West. J. Appl. For. (11)2:44-49.
Effects of Cutting Time, Stump Height, Parent Tree Characteristics, and Harvest Variables on Development of Bigleaf Maple Sprout Clumps
Authors: Tappeiner II John C. , Zasada John , Huffman David , Maxwell Bruce D.
Published: August 2019

In order to determine the effects of stump height, year of cutting, parent-tree size, logging damage, and deer browsing on bigleaf maple (Acer macrophyllum) sprout clump development, maple trees were cut to two stump heights at three different times. Stump height had the greatest impact on sprout clump size. Two years after clearcutting, the sprout clump volume for short stumps was significantly less than that for tall stumps. The sprout clump volume, area, and number of sprouts were significantly less for trees cut 1 and 2 yr before harvest than for trees cut at harvest. Sprout clump size was positively correlated with parent tree stem diameter and stump volume, and negatively correlated with the percentage of bark removed during logging. Browsing had no significant impact on average clump size. Uncut trees produced sprout clumps at their base and epicormic branches along the length of their stems; thus their crown volume averaged four to five times that of cut trees. Cutting maple in clearcuts to low stumps may reduce maple competition with Douglas-fir regeneration and still maintain maple in the next stand. West. J. Appl. For. 11(4):120-124.
Height-Diameter Equations for Ten Tree Species in the Inland Northwest
Authors: Moore James A. , Zhang Lianjun , Stuck Dean
Published: August 2019

Individual tree height-diameter equations were developed for ten major species in the inland Northwest. The Wykoff function in the Stand Prognosis Model and the Lundqvist function were fit to data which included many large-sized trees. The two models fit the data equally well for all species. Prediction results using the existing Prognosis equation, the refitted Wykoff function, and the Lundqvist function showed that the three models predicted similar heights for trees of small diameter. However, both the refitted Wykoff function and the Lundqvist function predicted larger tree heights for trees with dbh greater than 20 in. for most species. The estimated heights for tree diameters of 70 or 80 in. from the Lundqvist function were closer to the observed "asymptotic" tree heights than the other two. The Lundqvist function showed lower prediction errors for the validation data for the majority of the tree species, especially for large-sized trees. West. J. Appl. For. 11(4):132-137.
Mortality of Douglas-fir After Operational Semiochemical Baiting for Douglas-fir Beetle (Coleoptera: Scolytidae)
Authors: Thier R. W. , Patterson Steve
Published: August 2019

Effects of an operational application of synthetic Douglas-fir beetle (Dendroctonus pseudotsugae Hopkins) attractants applied to Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco) trees have not been well documented. Baits, containing a 1:1 mixture of frontalin and alpha-pinene, were deployed over 64 acres in an area application at the rate of 2 baits/ac. Baited trees, and unbaited Douglas-firs surrounding the bait centers, were selected for measurements. All baited trees were attacked along with 42.3% of the surrounding unbaited Douglas-firs. Attacked trees were significantly larger than unattacked trees and were closer to the bait centers. The percentage of trees attacked was not influenced by cardinal direction from the bait center. Approximately 97% of the baited trees were either moderately or heavily attacked. Almost 60% of the moderately and heavily attacked unbaited Douglas-firs were within 33 ft of the bait centers. A model to predict probability of infestation of unbaited trees surrounding the bait center was developed. West. J. Appl. For. 12(1):16-20.
Using Aggregation and Antiaggregation Pheromones of the Douglas-Fir Beetle to Produce Snags for Wildlife Habitat
Authors: Ross Darrell W. , Niwa Christine G.
Published: August 2019

Pheromone baits for the Douglas-fir beetle were applied alone and in combination with the antiaggregation pheromone, 3-methylcyclohex-2-en-1-one (MCH), to test potential treatments for creating snags to improve wildlife habitat. All baited trees were attacked by beetles following both treatments. However, more unbaited trees were attacked on plots without MCH than on plots with MCH. One year after treatment, more of the attacked trees were dead on plots without MCH than on plots with MCH. Bark beetle pheromones can be used effectively to create snags for improving wildlife habitat, but to achieve specific objectives treatments must be prescribed based on knowledge of the expected beetle population densities. West. J. Appl. For. 12(2):00-00.
Stand Dynamics of the Spruce-Fir Forest in East-Central Arizona
Authors: Moran-Palma Pedro , McTague John P.
Published: August 2019

New functions are presented for spruce-fir survivor growth, ingrowth, and mortality using a data set of Continuous Forest Inventory plots exclusively from the spruce-fir forest type in east-central Arizona. The individual tree diameter squared growth model is validated at the tree and stand level with an independent data set. Individual tree mortality is modeled for any projection interval with a logistic function. Ingrowth dynamics is modeled at three levels of resolution; the stand level, species level, and the diameter class level. Ingrowth trees are distributed to diameter classes using the Uniform distribution. West. J. Appl. For. 12(2):55-61.
Twenty-Five-Year Growth and Mortality of Planted Ponderosa Pine Repeatedly Thinned to Different Stand Densities in Northern California
Authors: Oliver William W.
Published: August 2019

A 20 yr old ponderosa pine (Pinus ponderosa var. ponderosa) plantation on a productive site on the west slope of the Sierra Nevada in northern California was thinned four times over a 25 yr period. Stand densities tested were Stand Density Indexes (SDI) of 73, 128, 183, 238, and 293 (equivalent to 40,70,100,130, and 160 ft2/ac of basal area), replicated three times in a randomized design. Growth was analyzed for each of five 5 yr periods. Periodic annual increments (PAI) of diameter, net basal area, and net total volume differed significantly among periods and, in the earlier periods, among stocking levels. Mortality from winter storms and bark beetles was largely confined to the higher stand densities and in periods 3 and 4 caused PAIs of net basal area and net total volume to decline below that of lower densities. The sensitivity of mortality to stand density suggests a thinning target of SDI 183 (about 100 ft²/ac of basal area) for similar stands—no higher than that recommended for eastside stands of much lower site productivity. This sensitivity coupled with rapid growth suggests that multiple thinnings will be necessary in similar stands to maintain healthy, vigorous trees. West. J. Appl. For. 12(4):122-130.
Increased Value through Optimal Bucking
Authors: Bowers Steve
Published: August 2019

This study documented and field-tested computerized optimal bucking procedures in second-growth Douglas-fir (Pseudotsuga menziesii), comparing computerized bucking solution to the solution of two timber cutters. The increase in the number of logs was negligible; the computer solution often did not use the entire merchantable tree stem. Log volume and value differed between these two solutions primarily because of the locations of long logs versus short logs in the tree. Volume increased 9.5% and value increased 9.3% for 85 trees in the optimal bucking compared with the cutter's solution. West. J. Appl. For. 13(3):85-89.
Propagating Native Species: Experience at the Wind River Nursery
Authors: Harrington Constance A. , McGrath James M. , Kraft Joseph M.
Published: August 2019

Propagation information developed at the USDA Forest Service Wind River Nursery in Carson, WA, is provided for 9 hardwood tree and 30 shrub species native to the Pacific Northwest. This includes information on: seed collection, extraction, stratification, and storage; timing of collection and propagation techniques for cuttings; and a summary of propagation experience (planting media and container used, specialized methods, and type of stock produced). Most species were propagated from seed, some from stem or root cuttings, and some from both seed and cuttings. Some species were very difficult or impossible to propagate at the nursery. West. J. Appl. For. 14(2):61-64.
Clearwood Quality and Softwood Lumber Prices: What's the Real Premium?
Authors: Waggener Thomas R. , Fight Roger D.
Published: August 2019

Diminishing quantities of appearance grade lumber and rising price premiums for it have accompanied the transition from old-growth to young-growth timber. The price premiums for better grades are an incentive for producers to undertake investments to increase the yield of those higher valued products. Price premiums, however, are also an incentive for users to substitute lower grades, lower priced species, or nonwood materials for these higher priced appearance grades. This possibility may cast doubt on the permanence of the price premiums associated with appearance grade lumber. The real price premiums paid for appearance grades of lumber from January 1989 through October 1995 were substantial and quite stable during a widely fluctuating softwood lumber market. We found little or no evidence to suggest that these premiums are either "temporary" or are in decline. Although care is required in extrapolating these findings over future long time horizons typically required for silvicultural investments in wood quality changes, the results of this study may help forest managers better understand the possible magnitude of real price premiums to use in evaluating those investments. West. J. Appl. For. 14(2):73-79.
Weed Control in Spring and Summer After Fall Application of Sulfometuron
Authors: Ketchum J. Scott , Rose Robin , Kelpsas Bruce
Published: August 2019

This study tested the residual spring and summer efficacy of sulfometuron after fall applications in forest regeneration settings in coastal forests of Oregon. This is the first reporting of results from what is becoming a more widely used silvicultural treatment. Sulfometuron alone (S) and sulfometuron plus imazapyr and glyphosate (SIG) were applied to vegetation on mechanically scarified sites and unscarified sites. The applications were replicated each month through fall 1994. Vegetation cover was assessed in mid-June and mid-August 1995. The SIG treatment controlled the vegetation more than the S treatment did, although cover was significantly lower for both herbicide treatments (9% to 54% for summed cover) compared to the control (64% to 104% for summed cover). On scarified sites, the month of application, early or late fall, did not significantly influence the efficacy of S or SIG treatments. On unscarified sites, however, later applications of the SIG treatment were less effective than earlier treatments were. These results suggest that fall applications of sulfometuron are still effective in spring and may eliminate the need to retreat sites in the spring to achieve effective weed control. West. J. Appl. For. 14(2):80-85.
Evaluation of Physical Barriers to Protect Ponderosa Pine Seedlings from Pocket Gophers
Authors: Pipas Michael J. , Witmer Gary W.
Published: August 2019

A 2 yr study on the Rogue River and Mt. Hood National Forests in Oregon evaluated physical barriers for protection of Pinus ponderosa seedlings against damage by Thomomys talpoides. Seedlings protected with one of three weights of: (1) plastic mesh tubing (Vexar®) or (2) sandpapertubing (Durite®) were evaluated against control seedlings. On the Rogue River sites, Vexar® seedlings had the highest survival (62.6%), followed by the controls (59.1%), then Durite® seedlings (17.9%). Gophers were the primary cause of death for the Vexar® seedlings, versus desiccation for the Durite® seedlings. On the Mt. Hood sites, heavyweight Vexar® seedlings had the highest survival (35.4%), medium-weight Durite® seedlings the lowest (2.7%). Seedling mortality caused by gophers was highest for controls (70.2%), followed by light-weight (62.2%) and heavy-weight (53.9%) Vexar® treatments. Overall survival was low (Rogue River = 42%, Mt. Hood = 19.8%). Growth was greatest for the control seedlings but only significantly greater than growth of Durite® seedlings on the Rogue River sites. Growth of seedlings was not compromised by the Vexar® tubing. Although neither type of tubing was highly protective, Vexar® tubes performed better than Durite® tubes. West. J. Appl. For. 14(3):164-168.
Development of a Shrub-Fern-Ponderosa Pine Community Eleven Years After Site Preparation and Release
Authors: McDonald Philip M. , Abbott Celeste S. , Fiddler Gary O.
Published: August 2019

Vegetation management can direct trends in early plant development and species succession and through various treatments achieve specific combinations of species desired by the ecosystem manager. Density and development of several plant species were studied in an area in northern California that was planted with 1-yr-oldponderosa pine (Pinus ponderosa var. ponderosa) seedlings in 1986 and treated with three herbicides (Velpar L, Garlon 4, Escort) in fall 1986 and spring 1987. Abundant species in the new plantation were bush chinquapin (Chrysolepis sempervirens) that regenerated from root crowns, greenleaf manzanita (Arctostaphylos patula)from seed, and bracken fern (Pteridium aquilinum var. pubescens )from rhizomes. After 11 growing seasons, chinquapin sprouts in the control averaged more than 15,900/ac, manzanita seedlings over 16,400/ac, and bracken fronds 11,400/ac. Mean ponderosa pine diameter (5.1 in.), height (12.9 ft), and crown diameter (7.6 ft) were significantly greater in the Velpar treatment than in the control. Additional information is presented on plant diversity, the onset of statistically significant differences among treatments for pine, and the makeup of the plant community in the near future. West. J. Appl. For. 14(4):194-199.
Damage Characteristics in Young Douglas-Fir Stands from Commercial Thinning with Four Timber Harvesting Systems
Authors: Han Han-Sup , Kellogg Loren D.
Published: August 2019

Damage to residual trees from commercial thinning was characterized and compared among four common harvesting systems in western Oregon: tractor, cut-to-length, skyline, and helicopter. Six young (30- to 50-yr-old) Douglas-fir (Pseudotsuga menziesii) stands with various residual densities were studied: Scarring was the most typical damage to crop trees, accounting for 90% of the total damage in most cases. Damage levels greatly decreased as the minimum scar size that defines damage was increased. Scarring by ground-based systems was more severe: scars were larger, and gouge and root damage were more prevalent than in skyline and helicopter systems. Damaged trees were concentrated within 15 ft of skid trails or skyline corridor centerlines. In the cut-to-length system, the harvester caused more wounding (70%) to crop trees than did the forwarder (30%), but forwarder scars were larger and sustained severe gouging. Recommendations for minimizing stand damage are included. West. J. Appl. For. 15(1):27-33.
Evaluating the Accuracy of Ground-Based Hemlock Dwarf Mistletoe Rating: A Case Study Using the Wind River Canopy Crane
Authors: Shaw David , Freeman Elizabeth A. , Mathiasen Robert L.
Published: August 2019

The accuracy of ground based estimates using the six-class dwarf mistletoe rating system was evaluated in an old-growth Douglas-fir/western hemlock forest by comparing ground ratings by five different observers to an examination of tree crowns from a construction crane at the Wind River Canopy Crane Research Facility, Washington. A total of 139 dominant, codominant, and intermediate western hemlock were evaluated. No consistent pattern emerged to indicate where overall error was made. All but one observer was relatively accurate at identifying noninfected trees (73 to 95% noninfected trees accurately rated by four observers). However, the observers were less accurate at estimating the DMR class of the infected trees (11% to 3 7% of the infected trees accurately rated), including a number of trees incorrectly rated by two or more DMR classes. One observer rated 98% of the trees as having infections, while the crane survey estimated only 53% of the trees as having infections. Each observer divided the individual tree crowns into thirds and estimated infections based on summing lower, middle, and upper canopy levels. There was no pattern to the errors associated with estimates by canopy level. One observer significantly overestimated all canopy levels, one observer estimated all accurately, one observer significantly underestimated all canopy levels, one observer underestimated the mid and upper canopies, and one observer underestimated the lower and upper canopies. The principal reasons for inaccurate dwarf mistletoe ratings were assumed to be difficulty in accurately estimating crown thirds, misidentification of infections because of various stem deformities or accumulation of organic debris resembling infections, and the difficulty in observing infections high above the ground and through dense vegetation. Only one of the five observers accurately represented the spatial pattern of the infection center. The implications of this research vary depending on whether the results are to be used for timber management or for research and modeling applications. West. J. Appl. For. 15(1):8-14.