bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation
Authors: Seymour Danelle K , Gaut Brandon S 
Published: August 2019

Abstract
A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.
Hypertension-associated mitochondrial DNA 4401A>G mutation caused the aberrant processing of tRNAMet, all 8 tRNAs and ND6 mRNA in the light-strand transcript
Authors: Zhao Xiaoxu , Cui Limei , Xiao Yun , Mao Qin , Aishanjiang Maerhaba , Kong Wanzhong , Liu Yuqi , Chen Hong , Hong Fang , Jia Zidong , Wang Meng , Jiang Pingping , Guan Min-Xin 
Published: August 2019

AbstractMitochondrial tRNA processing defects were associated with human diseases but their pathophysiology remains elusively. The hypertension-associated m.4401A>G mutation resided at a spacer between mitochondrial tRNAMet and tRNAGln genes. An in vitro processing experiment revealed that the m.4401A>G mutation caused 59% and 69% decreases in the 5′ end processing efficiency of tRNAGln and tRNAMet precursors, catalyzed by RNase P, respectively. Using human umbilical vein endothelial cells-derived cybrids, we demonstrated that the m.4401A>G mutation caused the decreases of all 8 tRNAs and ND6 and increases of longer and uncleaved precursors from the Light-strand transcript. Conversely, the m.4401A>G mutation yielded the reduced levels of tRNAMet level but did not change the levels of other 13 tRNAs, 12 mRNAs including ND1, 12S rRNA and 16S rRNA from the Heavy-strand transcript. These implicated the asymmetrical processing mechanisms of H-strand and L-strand polycistronic transcripts. The tRNA processing defects play the determined roles in the impairing mitochondrial translation, respiratory deficiency, diminishing membrane potential, increasing production of reactive oxygen species and altering autophagy. Furthermore, the m.4401A>G mutation altered the angiogenesis, evidenced by aberrant wound regeneration and weaken tube formation in mutant cybrids. Our findings provide new insights into the pathophysiology of hypertension arising from mitochondrial tRNA processing defects.
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
Authors: Buitrago Diana , Codó Laia , Illa Ricard , de Jorge Pau , Battistini Federica , Flores Oscar , Bayarri Genis , Royo Romina , Del Pino Marc , Heath Simon , Hospital Adam , Gelpí Josep Lluís , Heath Isabelle Brun , Orozco Modesto 
Published: August 2019

AbstractWe present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the definition of nucleosome architectures and the detection of changes in nucleosomal organization due to changes in cellular conditions. Results are displayed in the context of genomic information thanks to different visualizers and browsers, allowing the user a holistic, multidimensional view of the genome/transcriptome. The package shows good performance for both locating equilibrium nucleosome architecture and nucleosome dynamics and provides abundant useful information in several test cases, where experimental data on nucleosome position (and for some cases expression level) have been collected for cells under different external conditions (cell cycle phase, yeast metabolic cycle progression, changes in nutrients or difference in MNase digestion level). Nucleosome Dynamics is a free software and is provided under several distribution models.
Multiple cytosolic DNA sensors bind plasmid DNA after transfection
Authors: Semenova Nina , Bosnjak Masa , Markelc Bostjan , Znidar Katarina , Cemazar Maja , Heller Loree 
Published: August 2019

Abstract
Mammalian cells express a variety of nucleic acid sensors as one of the first lines of defense against infection. Despite extensive progress in the study of sensor signaling pathways during the last decade, the detailed mechanisms remain unclear. In our previous studies, we reported increased type I interferon expression and the upregulation of several proposed cytosolic DNA sensors after transfection of several tumor cell types with plasmid DNA (pDNA). In the present study, we sought to reveal the early events in the cytosolic sensing of this nucleic acid in a myoblast cell line. We demonstrated that DNA-dependent activator of interferon regulatory factors/Z-DNA binding protein 1 (DAI/ZBP1) bound plasmid DNA in the cytosol within 15 minutes of transfection and at consistent levels for 4 h. Interferon activated gene 204 protein (p204) and DEAH box helicase 9 (DHX9) also bound pDNA, peaking 15 and 30 min respectively. Plasmid DNA was not detectably bound by DEAD box helicase 60 (DDX60) protein, despite a similar level of mRNA upregulation to DAI/ZBP1, or by cyclic GMP-AMP synthase (cGAS), despite its presence in the cell cytosol. Taken together, these results indicate several DNA sensors may participate and cooperate in the complex process of cytosolic DNA sensing.
Is BAF 10 a Good Choice for Point Sampling?
Authors: Wiant Harry V. , Yandle David O. , Andreas Richard 
Published: August 2019

Abstract
The use of basal-area-factor (BAF)-5 and BAF-10 when point sampling in an Appalachian hardwood forest caused serious underestimation of sawtimber volume BAF's of 20 and 40 gave appropriate volume estimates and smallest mean-square errors. We recommend that BAF's 20 to 40 be used for sawtimber cruises. North. J. Appl. For. 2:23-24, June 1984.
Mechanical Site Preparation and Regeneration Practices in Northern Minnesota
Authors: Butler-Fasteland Marna C. , Alm Alvin A. 
Published: August 2019

Abstract
We surveyed mechanical methods used in 1981 for site preparation in northern Minnesota on 12,500 acres on 330 sites. The results provided data on type of equipment used, time of completion, harvesting system, species planted, type of stock used, and spacing. The results provide baseline data to aid in efforts to integrate harvesting and reforestation. North. J. Appl For. 2:26-29, June 1984.
Early Dominance of Pioneer Hardwood After Clearcutting and Removal of Advanced Regeneration
Authors: Smith David M. , Ashton P. Mark S. 
Published: August 2019

Abstract
Clearcut openings were created in mixed stands of southern New England hardwoods, hemlock, and white pines to observe the development of new stands in which all species started simultaneously. All preexisting woody plants, except beech root-suckers and very small seedlings of red oak and hemlock, were eliminated. Natural seedfall was augmented by direct seeding of some species. The main result, after 2 decades, was replacement of the predominant hardwood species of the old stand by black, paper, and yellow birch. Pin cherry and gray birch were initially prominent, especially near the centers of openings, but had died or become moribund. Hemlocks and white pines from new seed persisted in the bottom strata. Except for the birches and black cherry, the hardwood species of the previous stand showed little or no capacity to develop from seed that germinated after clearcutting and removal of advanced growth. North. J. Appl. For. 10(1):14-19.
Predicting Quaking Aspen Stand Dynamics in Minnesota
Authors: Leary Rolfe A. , Brand Gary J. , Perala Donald A. 
Published: August 2019

Abstract
This paper presents equations for predicting future basal area, number of trees, and total cubic-foot volume of aspen stands in Minnesota. The modeling methodology uses a fully-stocked yield table for quaking aspen as a density standard. A relative density change equation based on observed growth from permanent plots provides the basis for predicting the future relative density and therefore the future basal area, number of trees, and volume. The equations are easy to apply and require only site index, age, and beginning basal area, number of trees, and volume. North. J. Appl. For. 10(1):20-27.
Stem Volume and Site Index Equations for European Larch in Maine
Authors: Gilmore Daniel W. , Briggs Russell D. , Seymour Robert S. 
Published: August 2019

Abstract
Stem analysis data collected from 101 sample trees located in 12 plantations established between 1930 and 1982 throughout central Maine were used to develop total and merchantable stem volume prediction equations, and site index prediction equations for plantation-grown European larch. The inside bark merchantable volume equation (4 in. top dob and 12 ft minimum merchantable bole) using a weighted combined variable was very similar to one for Japanese larch in Pennsylvania. Site index curves from this study were identical to those developed in southern New York and New England below a breast height (bh) age of 20 yr; after bh age 20, our curves predicted increasingly greater height growth and show a 6-12 ft superiority in height at a bh age of 50. North. J. Appl. For. 10(2):70-74.
Evaluation of a Computerized Timber Inventory System for Nonindustrial Private Forest Landowners
Authors: Blinn Charles R. , Vandenberg-Daves John 
Published: August 2019

Abstract
Foresters in many Minnesota counties are interested in gaining access to an automated land use inventory of NIPF lands. The Private Lands Information System (PLIS) was developed to provide field foresters in three Minnesota counties with access to a map-based inventory of NIPF timber stands. An evaluation of that system indicated that most users were pleased with its performance as a tool for targeting areas for management assistance, for working more effectively, and for addressing new issues. PLIS was less expensive to develop initially and to reinventory, on a per land unit basis, than the system which is being applied to state and county lands in Minnesota. However, there is no evidence to suggest which system is more cost effective. Up-front planning is required to develop a system that meets user needs. North. J. Appl. For. 10(3): 123-127.
Potential Use of Quadrivalent Selenium as a Systemic Deer-Browsing Repellent: A Cautionary Note
Authors: Jobidon Robert , Prévost Marcel 
Published: August 2019

Abstract
This study evaluates the potential usefulness and toxicity of applying quadrivalent selenium (selenite ion) to the soil to discourage white-tailed deer from browsing conifer seedlings. After absorption by the root system and internal transport, organoselenium compounds are volatilizedby the foliage, and the characteristic garlic odor is hypothesized to protect coniferous tree seedlings from browsing damage. Results indicate that either 5, 17, or 24 months after treatment, selenized white spruce seedlings did not show significantly different deer-browsing damage from controlseedlings when deer numbers were high. Five and seventeen months after treatment, selenium had not leached but had accumulated in the top soil. Large-scale application of selenium may represent a potential environmental risk, hence we do not recommend use of selenite ion to prevent damagefrom deer-browsing of white spruce seedlings. North. J. Appl. For. 11(2):63-64.
Five-Year Heights of Pitch Pine Progeny at Two New Jersey Plantations
Authors: Kuser John E. 
Published: August 2019

Abstract
Within-species selection was chosen as the method to improve pitch pine for a seed orchard to furnish seedlings for revegetation in southern New Jersey. In a progeny test of 68 families of open-pollinated plus tree seedlings at two plantation sites, after 5 growing seasons the top family among selected pitch pine progeny was as tall as the best pitch x loblolly check stock, and the best five pitch families were in the same range with another pitchlob and two loblolly families. Mean heights were slightly greater on a worked-out sandpit site than on an undisturbed sandy topsoil. North. J. Appl. For. 11(4):146-149.
Short-term Performance of Two Sulfonylurea Herbicides: Efficacy, Seedling Survival, and Growth
Authors: Reynolds Phillip E. , Roden Micheal J. 
Published: August 2019

Abstract
Metsulfuron (ALLY or ESCORT), 36 and 72 g ai/ha (~ 0.5 and 1.0 oz ai/ac), and sulfometuron (OUST), 150, 300, and 450 g ai/ha (~ 2.1, 4.2, and 6.3 oz ai/ac), were applied to a northern New Brunswick clearcut (silty clay loam and silty clay soils) to reduce raspberry competition. Treatment, using skidder-mounted herbicide application equipment, occurred in May and August 1986, with planting of 2+2, bareroot, black spruce seedlings in June 1986 and in June 1987. Seedling survival and growth were measured yearly for 5 growing seasons after planting. By August 1991, raspberry cover was less in some treatments than in controls. Survival of seedlings planted 1 month after spring treatments was less than controls, and no significant stem volume increases were observed. Survival of seedlings planted approximately 1 yr after spring treatments was greater than that of control seedlings. Survival of seedlings planted after some summer treatments also was poor, and no significant stem volume increases were noted for seedlings planted after site preparation with sulfometuron. Optimal stem volume increases over control seedlings were observed for seedlings planted 1 yr after spring sulfometuron treatment. These increases occurred sooner than for seedlings planted 1 yr after spring metsulfuron treatment or after summer metsulfuron treatment. Fifth-year stem volume for these seedlings was correlated with raspberry cover (r² = 0.44), decreasing as raspberry cover increased. We conclude that the use of other less expensive silvicultural herbicides may provide equally effective raspberry control and better black spruce seedling survival and growth. North. J. Appl. For. 12(2):80-85.
An Approach to Assessing Competition in Young Red Pine Plantations
Authors: Johnson James E. , Lindow Scott G. , Rogers Robert 
Published: August 2019

Abstract
Several 5- and 6-yr-old red pine plantations in central Wisconsin were sampled to assess the performance of crop trees and the levels of competing vegetation. A simple tree class system was devised to classify the level of brush competition on a fixed area plot surrounding each sampled crop tree. The tree class was significantly correlated with several measured and derived competition variables, and was also strongly related with three tree performance variables: height, volume, and biomass. Tree Class 1, the lowest competition level, was associated with significantly greater tree heights, volumes, and biomasses for both age groups. Logistic regression equations were developed to derive a quantitative relationship between competition, as measured by tree class, and crop tree performance. Performance was judged to be either adequate or inadequate based on an arbitrary set of standards for both volume and biomass. From the regression equations, probabilities of successful performance were calculated. For volume index and biomass, the Class 1 trees, or the trees with the lowest levels of competition, had success probabilities ranging from 76 to 89%. For the Class 4 trees, or the trees with the highest levels of competition, success probabilities ranged from 3 to 16%. North. J. Appl. For. 12(3):101-108.
A Longitudinal Analysis of Attitudes and Marketing Practices of Non-Industrial Private Forest Landowners
Authors: Rosen Barry N. 
Published: August 2019

Abstract
This paper reports a survey that examined shifts in NIPF owner attitudes and behavior regarding timber marketing over a 9 yr period in a sample of New York NIPF owners. The study found significant deterioration in owners' attitudes toward harvesting over time. Besides pointing out the need for better outreach to owners by foresters and industry, the results suggest caution to those building supply plans which assume substantial increases in NIPF timber harvesting. One of the key deficits in the literature on non-industrial private forest landowners is the absence of longitudinal studies. Such studies are critical in order to properly assess trends and to develop appropriate public policy. The need for these studies is especially great where the economic and social environment for forestry are influx, as at present. This report presents the results of a project designed to examine shifts in Non-industrial private forest landowner (NIPF) management and marketing behavior over time via a longitudinal analysis of data collected on New York owner attitudes before and after a 9 yr period. The report focuses on how landowner decisions have changed regarding how timber is harvested, particularly regarding use of various sources of market information. North. J. Appl. For. 12(4):174-179.
Expansion of Eastern Redcedar in the Lower Midwest
Authors: Schmidt Thomas L. , Leatherberry Earl C. 
Published: August 2019

Abstract
After a steady decline following European settlement, recent forest resource inventories in the Lower Midwest region of the United States—Illinois, Indiana, Iowa, and Missouri—have shown an increase in the area of forestland. Eastern redcedar is one of the primary species involved in this expansion and is projected to continue to increase. This has both positive and negative implications for land management. Landowners and managers can influence the direction and magnitude of the expansion of eastern redcedar. North. J. Appl. For. 12(4):180-183.
Empirical Yield Prediction Equations for Plantation-Grown European Larch in Maine
Authors: Gilmore Daniel W. , Briggs Russell D. 
Published: August 2019

Abstract
Density-free and variable-density empirical yield prediction equations were constructed from stand level data collected from 28 plots established in all of the European latch plantations known to have been successfully established on abandoned farmlands in central Maine prior to 1983. Results can be used directly to predict future plantation yields or incorporated in yield forecasting models. North. J. Appl. For. 13(1):37-40.
Is Eastern Hardwood Sawtimber Becoming Scarcer?
Authors: Luppold William G. , Dempsey Gilbert P. 
Published: August 2019

Abstract
In recent years the hardwood lumber industry has become increasingly concerned about the availability and quality of hardwood sawtimber. However, these concerns seem to contradict USDA Forest Service estimates of increased volume and quality of hardwood sawtimber. This paper examines changes in eastern hardwood sawtimber inventories and the apparent contradiction between the industry's perception of decreasing sawtimber availability and the Forest Service's contention of increasing timber inventories. This study did not find a single explanation for the apparent contradiction. Many of the perceived differences appear to result from the fact that industry draws its conclusions from specific situations confined to finite procurement areas while Forest Survey statistics are based on aggregated data. North. J. Appl For. 13(1):46-49.
Comparison of Formulas for Estimating Volumes of Butt Logs of Appalachian Hardwoods
Authors: Wiant Harry V. , Patterson David W. , Hassler Curt C. , Wood Geoff B. , Rennie John C. 
Published: August 2019

Abstract
A database comprising measurements of over 700 trees and logs of Appalachian hardwoods was used to compare the performance of five formulas (Newton, Huber, Smalian, Bruce, and that of the centroid method)for estimating the volumes of butt logs. In terms of bias and precision, the centroid method was clearly superior to all other methods. Bruce's formula performed better than Smalian's formula and is recommended for use when only the ends of butt logs are accessible for measuring diameter, as in log stacks. North. J. Appl. For. 13(1): 5-7.
The Impact of Federal and State Income Taxes on Timber Income in the Northeast and Midwest Following the 1986 Tax Reform Act
Authors: Siegel William C. , Haney Harry L. , Peters Daniel M. , Bettinger Pete , Callihan Debra S. 
Published: August 2019

Abstract
The structure and provisions of state income taxes are detailed for timber owners in 19 states of the Northeast and Midwest. Using 1994 federal and state income tax rules, the tax liability for a hypothetical married couple with timber sale income was calculated for two federal income tax rate brackets (medium and high income levels) for states in the Northeast and Midwest that impose an income tax. At the medium income level, the state portion of the total income tax liability ranged from 12.7% in Pennsylvania to 25.6% in Delaware. At the high income level, the state portion ranged from 11.1% in Pennsylvania to 24.9% in Minnesota. For both income levels, New Hampshire had the lowest state portion of the total tax liability when considering their business profits tax (12% for the medium and 7% for the high income level). The provision most significantly affecting state income tax liability was the tax rate schedule. Installment sales provide an alternative tax planning strategy for those timber owners who qualify as investors rather than a business and who are in the lowest federal tax bracket. Several states also impose taxes other than an income tax when timber is harvested. For example, Minnesota and New Hampshire both impose a minimum 10% yield tax on the timber's stumpage value. These levies significantly affect the total tax liability on harvest income. North. J. Appl. For. 13(1):8-15.
Registered Michigan Off-Road Vehicle Use and Users: Forest Policy Implications
Authors: Nelson Charles M. 
Published: August 2019

Abstract
From 1975, the number and diversity of off-road vehicles (ORVs) registered in Michigan has grown as have concerns over ORV use and safety. To better understand the situation, the Michigan Department of Natural Resources (MDNR) Forest Management Division commissioned a study of Michigan ORV registrants. The study's objectives were to profile registered ORV users and to identify their use of ORVs in Michigan and their preferences for state policy. A mail questionnaire was sent to a stratified, random sample of 1,200 registrants. Most respondents were male, with higher income and education levels than most Michiganians. Off-road use in Michigan was estimated to be 1.2 million 12 hr recreation days in a 12 month period of 1987-1988. Most use was not on a designated ORV trail, route, or area. Most ORVs were driven by more than the registrant, with many drivers under 16 yr of age. ORV registrants preferred forest roads over other riding situations, and most desired managers to provide more places to ride legally. Following MDNRs public release of this research, the author was invited to testify at legislative hearings reviewing the Michigan ORV statute. Subsequently, the testimony was used as partial basis for revising the ORV law to provide for more designated trails, a "closed unless posted open" rule for state forest ORV use, and restrictions on ORV use by youth. North. J. Appl. For. 13(2):84-88.