bluuebunny/crossref_metadata_2025_split huggingface dataset:
A60 Revealing the evolution of virulence in RNA viruses
Authors: Escalera-Zamudio Marina , Gutiérrez Bernardo , Thézé Julien , Pybus Oliver G 
Published: August 2019

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.