bluuebunny/crossref_metadata_2025_split huggingface dataset:
Traits Measured on Seedlings Can Be Used to Select for Later Volume of Loblolly Pine
Authors: Robinson John F. , Van Buijtenen J. P. , Long Ernest M. 
Published: August 2019

Abstract
Seed was collected from individual trees in loblolly pine (Pinus taeda L.) stands in southeast Texas. Although selection on seed characteristics proved ineffective as an indirect selection method for improving five-year volume, selection for seedling characteristics prior to outplanting proved very effective. Families selected in greenhouse and nursery beds averaged 36 percent greater volume after five years in the field than checklots from the same stands. Seed from the southernmost stands produced more volume than seed from more northern stands. Seed weights of selected families were significantly greater than those of appropriate checks.
Loblolly Pine Management and Utilization—State of the Art
Authors: Kellison R. C. , Gingrich Sam 
Published: August 2019

Abstract
The management and utilization of loblolly pine (Pinus taeda L.) were the topics of the Symposium on the Loblolly Pine Ecosystem (East Region) held in Raleigh, North Carolina, on December 8-10, 1982. The East Region is comprised of Virginia, North Carolina, South Carolina, Georgia, and Florida. A second symposium is scheduled for spring 1984 to cover the remaining natural range of loblolly pine. Plantations constitute about 27 percent of the loblolly pine resource of the East Region, with about two-thirds of the area belonging to forest industry. Natural stands can be established for about one-third the cost of plantations, where plans are made for natural regeneration. Optimum value is realized from plantations where site preparation is complete and where pests, competing vegetation, and stocking are controlled. Genetically improved planting stock, fertilization, and thinning are integral parts of plantation forestry. Maintaining site productivity is one of the greatest challenges facing the forest industry.
Sand Pine Survival and Growth on Prepared and Unprepared Sites
Authors: Outcalt Kenneth W. , Brendemuehl Raymond H. 
Published: August 2019

Abstract
Sand pine seedlings were planted on sites prepared by double chopping and on unprepared sites in scrub oak stands in the northwest Florida sandhills. Although survival was lower on unprepared areas, plantations of both Ocala (Pinus clausa var. clausa Ward) and Choctawhatchee sand pine (P. clausa var. immuginata Ward) still had acceptable stocking on unprepared sites at age 10. Thus, both varieties can be successfully established by underplanting among scrub hardwoods. Chopping, however, increased height, diameter, and volume growth. Total stem volume per acre was three to four times greater on chopped sites, and this difference continues to increase. Therefore, chopping prior to planting sand pine on these areas should be economically advantageous.
Minisite Preparation for Summer Planting
Authors: Woods Frank W. , Hay Ronald L. , Irwin Gary H. 
Published: August 2019

Abstract
Virginia pine (Pinus virginiana Mill) and pitch pine (Pinus rigida Mill.) were planted on bare and grassed reclaimed strip-mine areas between 21 June and 5 July 1977. On both sites, tubelings of both species, inoculated with Pisohthus tinctorius [(Pers.) Coker & Couch] were planted in untreated (control) spoil and in holes (minisites) with highly amended spoil. Examinations made 14 months after planting revealed that: (1) minisite preparation improved seedling survival on grassed plots; (2) survival on bare control plots was better than on grassed control plots; and (3) frost heave was a greater problem on control plots than on minisites.
Forage Yields Improved by Site Preparation in Pine Flatwoods of North Florida
Authors: Lewis Clifford E. , Swindel Benee F. , Conde Louis F. , Smith Joel E. 
Published: August 2019

Abstract
In the 3 years following two methods of timber harvest, two intensities of site preparation, and planting of pines, yields of desirable forage plants increased four to sevenfold on flatwoods of north Florida. Vegetation on two watersheds was measured before clearcutting of pine stands and 1, 2, and 3 years after site preparation and planting. Woody competition remained suppressed after 3 years and forage yields averaged 1,400 lb/ac. The fear that site preparation for planting pines depletes forage appears to be unfounded.
A Billion Overtopped White Oak — Assets or Liabilities?
Authors: McGee Charles E. , Bivens Donald L. 
Published: August 2019

Abstract
Many mixed hardwood stands contain pole-sized white oak (Quercus alba L.) trees that are overtopped. A major decision to be made when these stands are regenerated is whether to cut the overtopped white oak or to retain them as crop trees. This study shows that growth and quality of released white oaks can be predicted from stem size, tree age, stem and crown quality, and the degree of release. Overall the study suggests that most overtopped white oaks are not good candidates for crop trees.
Slash Pine Plantation Site Index Curves for West Gulf
Authors: Zarnoch S. J. , Feduccia D. P. 
Published: August 2019

Abstract
New slash pine (Pinus elliottii var. elliottii Engelm.) plantation site index curves have been developed for the West Gulf. The guide curve is mathematically simpler than other available models, tracks the data well, and is more biologically reasonable outside the range of data.
Clearcutting Not Enough for Early Establishment of Desirable Species in Santee River Swamp
Authors: Gresham Charles A. 
Published: August 2019

Abstract
Woody species in a Santee River Swamp area were sampled before and three growing seasons after a summer clearcut. Basal area before harvest was 140 ft², 72% of which was sweetgum (Liquidambar styraciflua), sugarberry (Celtis laevigata), ash (Fraxinus spp.), laurel oak (Quercus laurifolia), and water oak (Q. nigra). Sugarberry dominated the regeneration 3 years after harvest in all but the larger size classes. Reproduction less than 3-feet tall occurred on 39% of the sampled area while 69% of the sampled area contained one or more stems 3 feet or taller. Regeneration species composition and spatial distribution was not considered acceptable and was attributed to the lack of postharvest treatment. Shearing or prescribed fire is recommended to dispose of residual stems and logging slash. Subsequent planting seed or seedlings of cherrybark oak (Q. falcata var. pagodifolia), water oak, or sweetgum should ensure an acceptable species composition.
Double vs. Single-Row Pine Plantations for Wood and Forage Production
Authors: Lewis Clifford E. , Tanner George W. , Terry W. Stephen 
Published: August 2019

Abstract
To find planting patterns for growing high volumes of wood while maintaining forage for cattle and wildlife habitat, slash pine (Pinus elliottii Engelm) was planted in various configurations to increase the open space between rows while holding tree density constant. Thirteen years after planting, there were few significant differences in survival, height, and diameter; basal area and total wood volume were as good or greater in the 4 x 8 foot double-row configuration spaced 40 feet apart. Double-row configurations produced more forage than single-row. This configuration offers a high timber volume and forage mass alternative to the currently favored 8 x 12 foot spacing used for dual resource management.
Growth of Choctawhatchee Sand Pine Plantations in Georgia
Authors: Outcalt Kenneth W. , Brendemuehl Raymond H. 
Published: August 2019

Abstract
Surveys of established plantations of Choctawhatchee sand pine (Pinus clausa var. immuginata Ward) on sandhills in 10 Georgia counties showed that the growth is nearly comparable to that observed on sandhills in Florida within the natural range of this variety. The observed growth is better than could be expected from other pine species on these excessively drained, infertile sites. Significant damage from insects, disease, or cold weather was not evident.
Impact of Feller Bunchers and Plantation Spacing on Thinning
Authors: Watson W. F. , Taylor S. C. , Weaver G. H. , Matthes R. K. 
Published: August 2019

Abstract
There are articulated rubber-tired machines which can selectively thin plantations effectively, if the plantations are established with wide rows with little deviation. The best time to thin to ensure good treatment is planting time. Considering effects of planting on later intermediate thinning treatments provides a greater selection of prescriptions when thinning is undertaken. Machines for selective thinning can best be improved by increasing their maximum angles of left and right articulation. If these angles could be safely increased on existing machines, significantly more marked trees could be removed by articulated feller bunchers in almost all spacings.
Survival and Growth of Loblolly Pine as Influenced By Seedling Grade: 13-Year Results
Authors: South David B. , Boyer James N. , Bosch Leonard 
Published: August 2019

Abstract
Results from a northcentral Louisiana loblolly pine (Pinus taeda) site (site index 94, base age 25) showed that seedling grade affected survival, height, and volume production. Survival of Grade 1 seedlings was significantly greater than cull seedlings and volume production from Grade 1 seedlings was 17.5% greater than that of Grade 2 seedlings. The present value of the additional wood produced at age 13 by Grade 1 seedlings (over that of Grade 2 seedlings) ranged from $50 to $139 per thousand seedlings. Average volume production for Grade 1 seedlings exceeded 30 m3/ha/yr (440 cubic feet per acre per year). To increase volume production, especially on high site land, Grade 1 seedlings should be planted. It is proposed that a portion of the nursery be sown at low densities (ca 200/m2) to provide the field forester with the option of planting a high proportion of Grade 1 seedlings.1
Results of a Tree Species Trial on a Recontoured Surface Mine in Southwestern Virginia
Authors: Torbert J. L. , Burger J. A. , Lien J. N. , Schoenholtz S. H. 
Published: August 2019

Abstract
Fifteen tree species, five pine and ten hardwood, were planted on a reclaimed, return-to-contour, strip-mine site in Wise County, Virginia. A systemic herbicide was sprayed on half of each of four experimental blocks prior to the second growing season. After three growing seasons, this treatment resulted in increased survival of five species. Black locust (Robina pseudoacacia) performed best with 90% survival and a tenfold increase in height. Other hardwoods that showed promise were black alder (Alnus glutinosa), sycamore (Platanus occidentalis), and cottonwood (Populus deltoides). As a group, the pines outperformed the hardwoods. Loblolly (Pinus taeda) and Virginia pine (Pinus Virginiana) were the fastest growing, and survival of each was signifcantly higher on the sprayed plots.
Skidder and Tire Size Effects on Soil Compaction
Authors: Greene W. Dale , Stuart William B. 
Published: August 2019

Abstract
Soil compaction in a Chewacla silt loam was significantly reduced by the use of larger tire sizes when the soil was moist (at its plastic limit). Reducing the skidder size slightly did not reduce soil compaction significantly. More important in determining compaction levels were soil moisture content and the number of trips the machine made across a site. Although larger tires can reduce soil compaction, reducing logging activity in wet soil or confining traffic to skid roads can minimize site damage.
Preharvest Herbicide Treatment Improves Regeneration in Southern Appalachian Hardwoods
Authors: Loftis David L. 
Published: August 2019

Abstract
Preharvest herbicide treatment of undesirable and unmerchantable vegetation was compared to postharvest felling. Ten years after the clearcut harvesting, the preharvest treatment had increased the number and proportion of desirable stems and decreased the number and proportion of undesirable sprouts in the dominant stand. Stands that developed after the preharvest herbicide treatment are dominated by single-stemmed desirable species, and excellent future stocking is assured. Because of the presence of undesirable sprout clumps, plots receiving the postharvest felling have an uncertain future. An effective preharvest treatment that costs about the same as postharvest felling is recommended.
A3 Molecular epidemiology of HIV-1 in Nigeria
Authors: Nazziwa J , Faria N , Chaplin B , Rawizza H , Dakum P , Abimiku A , Charurat M , Ndembi N , Esbjörnsson J 
Published: August 2019

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

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

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

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

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