bluuebunny/crossref_metadata_2025_split huggingface dataset:
A27 Whole genome characterization of influenza D viruses detected in cattle herds in northern Italy between 2015 and 2017
Authors: Bianco A , Cavicchio L , Fusaro A , Rizzo G , Milani A , Salviato A , Zamperin G , Beato M S , Schiavon E , Bano L , Monne I 
Published: August 2019

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

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

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

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

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

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

Abstract
Two proposed seed-orchard sites on the Wenatchee and Gifford Pinchot National Forests were examined prior to tree felling and land clearing to evaluate root-disease symptom expression in three species of conifers (Douglas-fir [Pseudotsuga menziesii], grand fir [Abies grandis], and ponderosa pine [Pinus ponderosa]. About half of the trees within infected areas had roots decayed by one of three principal root pathogens, Armillaria ostoyae, Phellinus weirii, and Fomes annosus, as determined from totally excavated root systems.
Trees with above-ground symptoms had significantly moreroot decay than trees without symptoms. Crown symptoms and root-collar symptoms were accurate indicators of 22% of the root-diseased trees. Stain or decay at freshly cut stump surfaces were reliable indicators of 50% of root-diseased trees. Surveys that record crown symptoms and root-collar symptoms in similar stands will give accurate estimates of the number of trees killed by root diseases. However, examination of freshly cut stump surfaces will detect more accurately the total number of root diseased trees, especially if decay associated with butt wounds is absent. West. J. Appl. For. 1:46-48, April 1986
Allowable Cut Effect and Fire-Damage Appraisal
Authors: Montgomery Claire A. , Brodie J. Douglas , Cleaves David A. 
Published: August 2019

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

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

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

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

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

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

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

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

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

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