bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stem Volume and Taper Functions for Yellow-Poplar in the Southern Appalachians
Authors: Knoebel Bruce R. , Burkhart Harold E. , Beck Donald E. 
Published: August 2019

Abstract
Yellow-poplar (Liriodendron tulipfera L.) is an important commercial species that is marketed as a variety of products. Because merchantability standards change rapidly, it is desirable to have a set of volume estimating equations that are general and flexible for obtaining estimates for any specified portion of tree boles. Data from 336 yellow-poplar trees in the southern Appalachians were used to develop equations for predicting cu.ft. stem volume to any desired top diameter or height limit while insuring that predicted volumes were logically related through the fitting of diameter and height ratio equations. Rearrangement of these ratio equations provides implicit stem taper functions that can be used to estimate height at a given diameter and diameter at a given height.
Estimating Moisture Content in Litter
Authors: Johnson Von J. 
Published: August 2019

Abstract
Moisture in the litter layer of the forest floor varies in time and space in a highly complex manner. Current systems for predicting, or methods for estimating, litter moisture do not account for this inherent variation. A leaf or needle-bending test may have merit for estimating site-specific, real-time litter moisture in preparation for prescribed burning.
Four-Year Growth and Development of Planted Loblolly Pine on Sites with Competition Control
Authors: Knowe Steven A. , Nelson Larry R. , Gjerstad Dean H. , Zutter Bruce R. , Glover Glenn R. , Minogue Patrick J. , Dukes James H. 
Published: August 2019

Abstract
The effects of competition on loblolly pine (Pinus taeda L.) development during the initial 4 years of a plantation were investigated on an Upper Coastal Plain site in east-central Alabama. Height and diameter response to competition control in relation to time following treatment and amount of herbaceous competition were examined. Trees on plots receiving broadcast weed control for 2 years were twice the height and diameter of trees with no weed control after 4 years, while trees receiving banded weed control for 2 years were 1.6 times taller and 1.75 times larger in diameter. Broadcast and banded 1-year treatments were 1.4 times larger in both measures.
Growth of 20-Year-Old Virginia Pine Planted at Three Spacings in Tennessee
Authors: Smalley Glendon W. 
Published: August 2019

Abstract
Average height of dominant and codominant Virginia pines (Pinus virginiana Mill). on a Mid-Cumberland Plateau site was 46 feet at plantation age 20, equivalent to a site index (base age 50) of 75. Trees planted at a spacing of 8 x 8 feet had a merchantable yield (outside bark to a 4.0 inch top for all trees with a dbh of 4.6 inches and larger) of 1,987 ft³ per acre with a basal area of 114 ft² per acre. Comparative statistics on the other spacings tested were: 6 x 6 feet—2,067 ft³ and 123 ft² and 4 x 4 feet—2,155 ft³ and 141 ft². Survival on the plots was: 4 x 4 feet—38%; 6 x 6 feet—58%; and 8 x 8 feet—75%. Height to base of live crown averaged 25 feet, and dead branches remained nearly to the ground on most trees at all spacings.
Soil Properties and Pine Growth Affected by Site Preparation after Clearcutting
Authors: Stransky J. J. , Roese J. H. , Watterston K. G. 
Published: August 2019

Abstract
A pine-hardwood sawtimber stand in southeast Texas was clearcut in September 1972. Random plots were burned, chopped, KG-bladed, or left untreated. In the spring of 1974, 1-0 loblolly pine seedlings (Pinus taeda L.) were handplanted at 8 by 10 foot spacing. Data from soil samples, taken from the 0-5 inch depth before clearcutting and 1, 3, and 5 years after site preparation showed that burning appeared to have changed soil nutrient levels the least. Of the two mechanical treatments, KG-blading altered the chemical composition of the soil most, probably because topsoil organic matter was removed. Planted pines survived and grew best on mechanically prepared areas, producing 1.5 to 3.3 times more cubic-foot volume per acre than either of the other treatments by the end of the eighth year.
Tree Profile and Volume Ratio Equations for Sweetgum and Cherrybark Oak Trees
Authors: Matney Thomas G. , Hodges John D. , Sullivan Alfred D. , Ledbetter Julia R. 
Published: August 2019

Abstract
Equations are presented for predicting the height and cubic foot volume (ib or ob) to any top diameter limit (ib or ob) of sweetgum and cherrybark oak trees. Example applications of the equations are given.
Insecticide Applications During the Pollination Period Do Not Adversely Affect Seed Yields of Loblolly Pine
Authors: DeBarr Gary L. , Matthews Fred R. 
Published: August 2019

Abstract
Three insecticides--Guthion® (azinphosmethyl), Pydrin® (fenvalerate), and Ambush® (permethrin)--were applied to catkins and to ovulate strobili of loblolly pines (Pinus taeda) at the time of maximum ovulate receptivity to determine their effects upon pollen viability, ovulate strobili survival, seed set, seed yields, and seed viability. Concentrations recommended for seed orchard use did not significantly reduce the number of pollen grains/ovule, in vitro or in vivo pollen germination, survival of ovulate strobili, number of developed seeds/cone, number of filled seeds/cone, germination of full seed, or cause an increase in abnormal seed germination. Operational applications of these insecticides to control the webbing coneworm (Dioryctria disclusa) should not cause adverse effects during this sensitive period of seed development in loblolly pine seed orchards.
A4 An amplicon-based approach for universal amplification, sequencing, and assembly of full-length HIV-1 samples from the DRC
Authors: Bletsa M , Vidal N , Vrancken B , Lequime S , Peeters M , Lemey P 
Published: August 2019

Abstract
Phylogenetic studies have contributed to our understanding of the early epidemic onset of HIV-1 in the Democratic Republic of Congo (DRC); however, the factors driving its early emergence and establishment in human populations still remain unresolved. In order to determine the key aspects of its successful epidemic spread, complete genome data are required from samples representative of the viral diversity in the DRC. In this study, we have established a universal PCR-assay that uses seven different panels of primers to produce overlapping amplicons covering the complete HIV genome. To circumvent the limitations of purifying these fragments and sequencing them with traditional approaches, we have developed a massive parallel sequencing method and a protocol for efficiently assembling HIV-1 genomes. A total of thirty-six samples, collected between 1997 and 2001 from different locations across the DRC, have been obtained, and, at this stage, we are focusing on complementing our dataset with more archival samples that can be used as HIV ‘molecular fossils’. By generating complete genome phylogeographic data from the DRC, we aim to create a genomic window into the past evolutionary and epidemiological dynamics of HIV-1 in Central Africa and understand the natural history of this devastating pandemic.
A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission
Authors: Rose R , Redd A D , Lamers S , Porcella S F , Hudelson S E , Piwowar-Manning E , McCauley M , Gamble T , Wilson E A , Kumwenda J , Hosseinipour M C , Hakim J G , Kumarasamy N , Chariyalertsak S , Pilotto J H , Grinsztejn B , Mills L A , Makhema J , Santos B R , Chen Y Q , Quinn T C , Cohen M S , Eshleman S H , Laeyendecker O 
Published: August 2019

Abstract
It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.
A13 Phylodynamic analysis of HIV in Florida
Authors: Richards V , Rich S , Cook R , Prosperi M 
Published: August 2019

Abstract
We are interested in using phylodynamics to better understand molecular clusters of HIV within the state of Florida, USA. To our knowledge, there is currently no study using such methodology to understand the epidemic in Florida. Viral sequences collected from 2007 to 2017 (about 50,000) will be linked with individual-level data (demographics—sex, race/ethnicity—and mode of transmission) accessed through the Patient Reporting Investigating Surveillance Manager (PRISM), and the Enhanced HIV/AIDS Reporting System (eHARS) via the Florida Department of Health (FDOH). Through the use of HIV-TRACE, which analyzes genetic distance matrices, we will create molecular transmission networks including data on mode of transmission, race/ethnicity, and sex. Furthermore, a maximum likelihood phylogenetic tree will be created using software (e.g. IQ-Tree, PhyML, and FastTree2) run on a high-performance cluster. Phylogenetic comparative analysis will be performed to assess the association between phylogenetic clades and demographics (including extended demographics like syphilis and other comorbidities queried from PRISM and eHARS).
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.