bluuebunny/crossref_metadata_2025 huggingface dataset:
Alcohol Use Disorder Is Differently Associated With Psychotic Symptoms According To Underlying Psychiatric Disorders: A General Population Study
Authors: Pignon Baptiste , Sescousse Guillaume , Amad Ali , Benradia Imane , Vaiva Guillaume , Thomas Pierre , Geoffroy Pierre A , Roelandt Jean-Luc , Rolland Benjamin
Published: August 2019

Aims

Psychotic symptoms can occur in the general population, and alcohol use disorder (AUD) is an identified vulnerability factor. However, it remains unclear how AUD is associated with psychotic symptoms, depending on the underlying psychiatric condition.

We aimed to compare the prevalence of psychotic symptoms among subjects with different types of psychiatric disorders, i.e. unipolar or bipolar disorders, anxiety disorders, psychotic disorders or no psychiatric disorder, depending on whether or not there was an underlying AUD.

Methods

In a 38,694-subject general population study, we compared the likelihood of occurrence of seven types of psychotic symptoms, depending on the AUD status and the underlying psychiatric disorders, after adjustment for age, sex, marital status, education and income levels.

Results

In unipolar depression and anxiety disorders, almost all types of psychotic symptoms were found associated with AUD (odds ratios (ORs) between 1.98 and 2.19). In contrast, in bipolar disorder, only auditory hallucinations were associated with AUD (OR = 2.50). In psychotic disorders, only thought broadcasting was more frequent among subjects with AUD (OR = 1.78).

Conclusion

Our findings in depression and anxiety disorders are in line with the ‘dual diagnosis’ concept, which posits that comorbid psychiatric/addictive disorders form distinctive entities that are more frequently associated with non-specific severity factors, here psychotic symptoms. The co-occurrence of AUD in bipolar/psychotic disorders was not associated with a generalized increased occurrence of psychotic symptoms but altered their manifestations with an increased risk of auditory hallucinations for bipolar disorder and thought broadcasting for psychotic disorders.
Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery
Authors: Hong Jiajun , Luo Yongchao , Mou Minjie , Fu Jianbo , Zhang Yang , Xue Weiwei , Xie Tian , Tao Lin , Lou Yan , Zhu Feng
Published: August 2019

The type IV bacterial secretion system (SS) is reported to be one of the most ubiquitous SSs in nature and can induce serious conditions by secreting type IV SS effectors (T4SEs) into the host cells. Recent studies mainly focus on annotating new T4SE from the huge amount of sequencing data, and various computational tools are therefore developed to accelerate T4SE annotation. However, these tools are reported as heavily dependent on the selected methods and their annotation performance need to be further enhanced. Herein, a convolution neural network (CNN) technique was used to annotate T4SEs by integrating multiple protein encoding strategies. First, the annotation accuracies of nine encoding strategies integrated with CNN were assessed and compared with that of the popular T4SE annotation tools based on independent benchmark. Second, false discovery rates of various models were systematically evaluated by (1) scanning the genome of Legionella pneumophila subsp. ATCC 33152 and (2) predicting the real-world non-T4SEs validated using published experiments. Based on the above analyses, the encoding strategies, (a) position-specific scoring matrix (PSSM), (b) protein secondary structure & solvent accessibility (PSSSA) and (c) one-hot encoding scheme (Onehot), were identified as well-performing when integrated with CNN. Finally, a novel strategy that collectively considers the three well-performing models (CNN-PSSM, CNN-PSSSA and CNN-Onehot) was proposed, and a new tool (CNN-T4SE, https://idrblab.org/cnnt4se/) was constructed to facilitate T4SE annotation. All in all, this study conducted a comprehensive analysis on the performance of a collection of encoding strategies when integrated with CNN, which could facilitate the suppression of T4SS in infection and limit the spread of antimicrobial resistance.
Prestimulus Activity in the Cingulo-Opercular Network Predicts Memory for Naturalistic Episodic Experience
Authors: Cohen Noga , Ben-Yakov Aya , Weber Jochen , Edelson Micah G , Paz Rony , Dudai Yadin
Published: August 2019

Human memory is strongly influenced by brain states occurring before an event, yet we know little about the underlying mechanisms. We found that activity in the cingulo-opercular network (including bilateral anterior insula [aI] and anterior prefrontal cortex [aPFC]) seconds before an event begins can predict whether this event will subsequently be remembered. We then tested how activity in the cingulo-opercular network shapes memory performance. Our findings indicate that prestimulus cingulo-opercular activity affects memory performance by opposingly modulating subsequent activity in two sets of regions previously linked to encoding and retrieval of episodic information. Specifically, higher prestimulus cingulo-opercular activity was associated with a subsequent increase in activity in temporal regions previously linked to encoding and with a subsequent reduction in activity within a set of regions thought to play a role in retrieval and self-referential processing. Together, these findings suggest that prestimulus attentional states modulate memory for real-life events by enhancing encoding and possibly by dampening interference from competing memory substrates.
Posterior Alpha and Gamma Oscillations Index Divergent and Superadditive Effects of Cognitive Interference
Authors: Wiesman Alex I , Wilson Tony W
Published: August 2019

Conflicts at various stages of cognition can cause interference effects on behavior. Two well-studied forms of cognitive interference are stimulus–stimulus (e.g., Flanker), where the conflict arises from incongruence between the task-relevant stimulus and simultaneously presented irrelevant stimulus information, and stimulus-response (e.g., Simon), where interference is the result of an incompatibility between the spatial location of the task-relevant stimulus and a prepotent motor mapping of the expected response. Despite substantial interest in the neural and behavioral underpinnings of cognitive interference, it remains uncertain how differing sources of cognitive conflict might interact, and the spectrally specific neural dynamics that index this phenomenon are poorly understood. Herein, we used an adapted version of the multisource interference task and magnetoencephalography to investigate the spectral, temporal, and spatial dynamics of conflict processing in healthy adults (N = 23). We found a double-dissociation such that, in isolation, stimulus–stimulus interference was indexed by alpha (8–14 Hz), but not gamma-frequency (64–76 Hz) oscillations in the lateral occipital regions, while stimulus–response interference was indexed by gamma oscillations in nearby cortices, but not by alpha oscillations. Surprisingly, we also observed a superadditive effect of simultaneously presented interference types (multisource) on task performance and gamma oscillations in superior parietal cortex.
Comparison of Caregiver Engagement in Telepractice and In-person Family-Centered Early Intervention
Authors: McCarthy Melissa , Leigh Greg , Arthur-Kelly Michael
Published: August 2019

Telepractice—specifically, the use of high-speed internet and interactive videoconferencing technology to deliver real-time audio and video communications between the family and the practitioner—is gaining acceptance as an alternative means of providing family-centered early intervention to families of children who are deaf and hard of hearing. This study examined whether caregivers’ reported perceptions of self-efficacy and involvement differed when early intervention was delivered in-person and through telepractice. The Scale of Parental Involvement and Self-Efficacy (SPISE) was used to evaluate perceptions of two groups of caregivers: one that received early intervention in-person (n = 100) and a group who received services through telepractice (n = 41). Results indicated that mode of delivery of services was not related to caregivers’ perceptions of their self-efficacy or involvement. Further analysis revealed that although certain caregiver or child characteristics did influence some aspects of caregivers’ beliefs about their self-efficacy or involvement, the effect of those variables was similar across both modes of delivery.
Estrogen receptor 1 expression and methylation of Esr1 promoter in mouse fetal prostate mesenchymal cells induced by gestational exposure to bisphenol A or ethinylestradiol
Authors: Bhandari Ramji K , Taylor Julia A , Sommerfeld-Sager Jennifer , Tillitt Donald E , Ricke William A , vom Saal Frederick S
Published: August 2019

Fetal/neonatal environmental estrogen exposures alter developmental programing of the prostate gland causing onset of diseases later in life. We have previously shown in vitro that exposures to 17β-estradiol (E2) and the endocrine disrupting chemical bisphenol A, at concentrations relevant to human exposure, cause an elevation of estrogen receptor α (Esr1) mRNA in primary cultures of fetal mouse prostate mesenchymal cells; a similar result was observed in the fetal rat urogenital sinus. Effects of these chemicals on prostate mesenchyme in vivo are not well understood. Here we show effects in mice of fetal exposure to the estrogenic drug in mixed oral contraceptives, 17α-ethinylestradiol (EE2), at a concentration of EE2 encountered by human embryos/fetuses whose mothers become pregnant while on EE2-containing oral contraceptives, or bisphenol A at a concentration relevant to exposures observed in human fetuses in vivo. Expression of Esr1 was elevated by bisphenol A or EE2 exposures, which decreased the global expression of DNA methyltransferase 3A (Dnmt3a), while methylation of Esr1 promoter was significantly increased. These results show that exposures to the environmental estrogen bisphenol A and drug EE2 cause transcriptional and epigenetic alterations to expression of estrogen receptors in developing prostate mesenchyme in vivo.
Native T1 time of right ventricular insertion points by cardiac magnetic resonance: relation with invasive haemodynamics and outcome in heart failure with preserved ejection fraction
Authors: Nitsche Christian , Kammerlander Andreas A , Binder Christina , Duca Franz , Aschauer Stefan , Koschutnik Matthias , Snidat Amir , Beitzke Dietrich , Loewe Christian , Bonderman Diana , Hengstenberg Christian , Mascherbauer Julia
Published: August 2019

Aims

Increased afterload to the right ventricle (RV) has been shown to induce myocardial fibrosis at the RV insertion points (RVIPs). Such changes can be discrete but potentially detected by cardiac magnetic resonance (CMR) T1-mapping. Whether RVIP fibrosis is associated with prognosis in heart failure with preserved ejection fraction (HFpEF) is unknown.

Methods and results

We prospectively investigated 167 consecutive HFpEF patients, a population frequently suffering from post-capillary pulmonary hypertension, who underwent CMR including T1-mapping. About 92.8% also underwent right heart catheterization for haemodynamic assessment.

Native T1 times were 995 ± 73 ms at the anterior and 1040 ± 90 ms at the inferior RVIP. By Spearman’s rank order testing, RVIP T1 times were significantly correlated with pulmonary artery pressure (mean PAP, r = 0.313 and 0.311 for anterior and inferior RVIP), pulmonary artery wedge pressure (r = 0.301 and 0.251) and right atrial pressure (r = 0.245 and 0.185; P for all <0.05). During a mean follow-up of 43.2 ± 22.6 months, 30 (18.0%) subjects died. By multivariable Cox regression, NTproBNP [Hazard ratio (HR) 2.105, 95% confidence interval (CI) 1.332–3.328; P = 0.001], systolic PAP (HR 1.618, 95% CI 1.175–2.230; P = 0.003), and native T1 time of the anterior RVIP (HR 1.659, 95% CI 1.125–2.445; P = 0.011) were significantly associated with outcome. Also, by Kaplan–Meier analysis, T1 times at the anterior RVIPs had a significant effect on survival (log-rank, P = 0.002).

Conclusion

Interstitial expansion of the anterior RVIP as detected by CMR T1-mapping reflects haemodynamic alterations, and is independently related with prognosis in HFpEF.
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)
Authors: Wang Lu , Wu Jinwei , Liu Xiaomei , Di Dandan , Liang Yuhong , Feng Yifei , Zhang Suyun , Li Baoguo , Qi Xiao-Guang
Published: August 2019

Background

The golden snub-nosed monkey (Rhinopithecus roxellana) is an endangered colobine species endemic to China, which has several distinct traits including a unique social structure. Although a genome assembly for R. roxellana is available, it is incomplete and fragmented because it was constructed using short-read sequencing technology. Thus, important information such as genome structural variation and repeat sequences may be absent.

Findings

To obtain a high-quality chromosomal assembly for R. roxellana qinlingensis, we used 5 methods: Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, BioNano optical maps, 10X Genomics link-reads, and high-throughput chromosome conformation capture. The assembled genome was ~3.04 Gb, with a contig N50 of 5.72 Mb and a scaffold N50 of 144.56 Mb. This represented a 100-fold improvement over the previously published genome. In the new genome, 22,497 protein-coding genes were predicted, of which 22,053 were functionally annotated. Gene family analysis showed that 993 and 2,745 gene families were expanded and contracted, respectively. The reconstructed phylogeny recovered a close relationship between R. rollexana and Macaca mulatta, and these 2 species diverged ~13.4 million years ago.

Conclusion

We constructed a high-quality genome assembly of the Qinling golden snub-nosed monkey; it had superior continuity and accuracy, which might be useful for future genetic studies in this species and as a new standard reference genome for colobine primates. In addition, the updated genome assembly might improve our understanding of this species and could assist conservation efforts.
A chromosome-level draft genome of the grain aphid Sitobion miscanthi
Authors: Jiang Xin , Zhang Qian , Qin Yaoguo , Yin Hang , Zhang Siyu , Li Qian , Zhang Yong , Fan Jia , Chen Julian
Published: August 2019

Background

Sitobion miscanthi is an ideal model for studying host plant specificity, parthenogenesis-based phenotypic plasticity, and interactions between insects and other species of various trophic levels, such as viruses, bacteria, plants, and natural enemies. However, the genome information for this species has not yet to be sequenced and published. Here, we analyzed the entire genome of a parthenogenetic female aphid colony using Pacific Biosciences long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly.

Results

The final draft genome assembly from 33.88 Gb of raw data was ~397.90 Mb in size, with a 2.05 Mb contig N50. Nine chromosomes were further assembled based on Hi-C data to a 377.19 Mb final size with a 36.26 Mb scaffold N50. The identified repeat sequences accounted for 26.41% of the genome, and 16,006 protein-coding genes were annotated. According to the phylogenetic analysis, S. miscanthi is closely related to Acyrthosiphon pisum, with S. miscanthi diverging from their common ancestor ~25.0–44.9 million years ago.

Conclusions

We generated a high-quality draft of the S. miscanthi genome. This genome assembly should help promote research on the lifestyle and feeding specificity of aphids and their interactions with each other and species at other trophic levels. It can serve as a resource for accelerating genome-assisted improvements in insecticide-resistant management and environmentally safe aphid management.
Validity of polygenic risk scores: are we measuring what we think we are?
Authors: Janssens A Cecile J W
Published: August 2019

Polygenic risk scores (PRSs) have become the standard for quantifying genetic liability in the prediction of disease risks. PRSs are generally constructed as weighted sum scores of risk alleles using effect sizes from genome-wide association studies as their weights. The construction of PRSs is being improved with more appropriate selection of independent single-nucleotide polymorphisms (SNPs) and optimized estimation of their weights but is rarely reflected upon from a theoretical perspective, focusing on the validity of the risk score. Borrowing from psychometrics, this paper discusses the validity of PRSs and introduces the three main types of validity that are considered in the evaluation of tests and measurements: construct, content, and criterion validity. This introduction is followed by a discussion of three topics that challenge the validity of PRS, namely, their claimed independence of clinical risk factors, the consequences of relaxing SNP inclusion thresholds and the selection of SNP weights. This discussion of the validity of PRS reminds us that we need to keep questioning if weighted sums of risk alleles are measuring what we think they are in the various scenarios in which PRSs are used and that we need to keep exploring alternative modeling strategies that might better reflect the underlying biological pathways.
Estimating matching affinity matrices under low-rank constraints
Authors: Dupuy Arnaud , Galichon Alfred , Sun Yifei
Published: August 2019

In this paper, we address the problem of estimating transport surplus (a.k.a. matching affinity) in high-dimensional optimal transport problems. Classical optimal transport theory specifies the matching affinity and determines the optimal joint distribution. In contrast, we study the inverse problem of estimating matching affinity based on the observation of the joint distribution, using an entropic regularization of the problem. To accommodate high dimensionality of the data, we propose a novel method that incorporates a nuclear norm regularization that effectively enforces a rank constraint on the affinity matrix. The low-rank matrix estimated in this way reveals the main factors that are relevant for matching.
A Risk Classification Model to Predict Mortality Among Laboratory-Confirmed Avian Influenza A H7N9 Patients: A Population-Based Observational Cohort Study
Authors: Martinez Leonardo , Cheng Wei , Wang Xiaoxiao , Ling Feng , Mu Lan , Li Changwei , Huo Xiang , Ebell Mark H , Huang Haodi , Zhu Limei , Li Chao , Chen Enfu , Handel Andreas , Shen Ye
Published: August 2019

Background

Avian influenza A H7N9 (A/H7N9) is characterized by rapid progressive pneumonia and respiratory failure. Mortality among laboratory-confirmed cases is above 30%; however, the clinical course of disease is variable and patients at high risk for death are not well characterized.

Methods

We obtained demographic, clinical, and laboratory information on all A/H7N9 patients in Zhejiang province from China Centers for Disease Control and Prevention electronic databases. Risk factors for death were identified using logistic regression and a risk score was created using regression coefficients from multivariable models. We externally validated this score in an independent cohort from Jiangsu province.

Results

Among 305 A/H7N9 patients, 115 (37.7%) died. Four independent predictors of death were identified: older age, diabetes, bilateral lung infection, and neutrophil percentage. We constructed a score with 0–13 points. Mortality rates in low- (0–3), medium- (4–6), and high-risk (7–13) groups were 4.6%, 32.1%, and 62.7% (Ptrend < .0001). In a validation cohort of 111 A/H7N9 patients, 61 (55%) died. Mortality rates in low-, medium-, and high-risk groups were 35.5%, 55.8, and 67.4% (Ptrend = .0063).

Conclusions

We developed and validated a simple-to-use, predictive risk score for clinical use, identifying patients at high mortality risk.
Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation
Authors: Seymour Danelle K , Gaut Brandon S
Published: August 2019

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

Mitochondrial 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

We 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.
Forestland Transfers in Vermont
Authors: Case Kevin M. , Lindsay John J.
Published: August 2019

The sale and subdivision of private woodlands for development cause the fragmentation of forest resources in the rapidly urbanizing Northeast. The objective of this study was to determine how active Vermont's forestland market was for parcel transfers of 100 ac and larger. Following 20 yr of constant price increases, the number and average price per acre of transfers decreased during the last 3 yr of the study. If forestland sales are linked to expanding economies, the next growth cycle will bring a resurgence in transfer activity, which is often the precursor of conversion. We recommend that the state, and perhaps the northeast region, develop a system to monitor NIPF conversion rates. Such a system would assist in developing new policies to sustain this important natural resource. North. J. Appl. For. 13(4):175-179.
White Ash Decline Hazard Assessment and Management Strategies in Massachusetts Stands
Authors: Woodcock Hilary , Davies Karl M. , Patterson William A.
Published: August 2019

White ash decline is characterized by diminished growth rates and vigor, and premature mortality. Reducing its impact should be a primary management objective in stands with a white ash component. Two methods to identify Massachusetts sites with high hazard of decline were developed using continuous forest inventory (CFI) data. Method 1 uses a vegetation-based estimate of relative soil moisture availability and landscape position data to calculate a decline hazard index (DHI) for the site. A DHI > 1.0 indicates a high hazard site. Four of 18 CFI plots with ≥25 % white ash BA had DHI > 1.0. Field observations in 1991 confirmed ash decline on three of the four plots. Trees on the remaining 14 plots were healthy. Method 2 uses site index (SI) and rooting restriction type (from soil maps) to assign sites to one of three classes, and does not require the collection of field data. Class 1 (SI ≥70, deep soils or dense substratum) and class 2 (SI ≤65, all soil types; SI 70, soils with bedrock at 20-40 in.) sites have a low decline hazard. Class 3 (SI 70-75, soils with bedrock at ≤20 in.) sites have a high hazard. Method 2 was tested on a data set of 74 CFI plots with ≥10% ash BA. Differences among site classes in the numbers of plots with decline were significant (P = 0.0016), with decline on 6% of plots in class 1 and 11% in class 2, compared with 42% of plots in class 3. Method 1 should be more accurate since vegetation data are collected onsite, and it integrates the many variables influencing soil moisture available to plants. Method 2 is quicker and easier to apply. Its accuracy could be improved by collecting soil data onsite. North. J. Appl. For. 14(1):10-15.
Pin Cherry Sucker Regeneration After Cutting
Authors: Jobidon Robert
Published: August 2019

Root suckers arising after cutting 10 yr old pin cherry in eastern Quebec were studied. Most suckers emerged during the first 2 yr and only a small proportion emerged after 3 or 4 yr. The number of suckers forming a clone was highly variable and was probably influenced by the degree of interspecific competition affecting this shade-intolerant species. No clonal variations were observed in the diameter of parent roots producing suckers, or in the initiation of new roots around the base of suckers up to 5 yr old. Annual growth of sucker basal diameter differed among clones and also within a clone. The oldest suckers had the greatest rates of basal growth. Results from this study indicate that cutting will not prove effective as a mean for controlling pin cherry during cleaning treatments, but will help to maintain dense pin cherry browse for white-tailed deer or moose. North. J. Appl. For. 14(3):117-119.